Methods and systems for detecting residual disease - Patents.com

Abstract

Described herein are methods, devices, and systems for measuring the level of disease (e.g., cancer), for example, the proportion of nucleic acid molecules (e.g., cell-free DNA) in a sample from an individual related to diseased tissue (e.g., cancer tissue). Methods, devices, and systems for measuring the presence, recurrence, progression, or regression of disease in an individual are also described. Certain methods include using nucleic acid sequencing data related to an individual to compare a signal indicating the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue with a background index indicating the sequencing false-positive error rate or a noise index indicating the sampling variance across the selected loci.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Patent Application No. 62 / 849,414, filed May 17, 2019, and U.S. Provisional Patent Application No. 62 / 971,530, filed February 7, 2020, the contents of each of which are incorporated by reference in their entirety herein.

[0002] Submitting a sequence listing as an ASCII text file The following submission in an ASCII text file is incorporated by reference in its entirety herein: Sequence Listing in Computer Readable Form (CRF) (Filename: 165272000140SEQLIST.TXT, Recorded: May 14, 2020, Size: 1KB).

[0003] FIELD OF THEINVENTION Described herein are methods, systems and devices for using nucleic acid sequencing data to measure the proportion of nucleic acid molecules in a sample that are associated with a disease, such as cancer. Also described are methods, systems and devices for measuring the presence, recurrence, progression or regression level of a disease, such as cancer. [Background technology]

[0004] background Detection and quantification of residual disease before, during and after cancer treatment can be used to monitor the effectiveness of cancer treatment or cancer remission in patients. Targeted nucleic acid sequencing methods have been used to determine the differences (i.e. variants) between disease-free and cancerous tissues. Targeted sequencing methods often look for mutations in known driver genes or known mutation hotspots within the cancer genome or exome, or utilize deep sequencing methods to ensure accurate variant calling at specific target loci.

[0005] The amount of cell-free DNA ("cfDNA") originating from a tumor in an individual (also called "circulating tumor DNA" or "ctDNA") can correlate with the severity of the disease. Except in most advanced disease states, only a small fraction of the DNA in a sample originates from diseased tissue, and the vast majority of the DNA comes from non-diseased tissues in an individual. This makes it particularly difficult to accurately measure the amount of cfDNA originating from diseased tissue. Current methods often require ultrasensitive schemes, such as custom qPCR or custom enrichment, that target relatively rare cancer-specific variants. Summary of the Invention [Means for solving the problem]

[0006] Brief Summary of the Invention Described herein are methods, systems and devices for determining the level of disease (eg, cancer) in an individual, as well as methods for determining the presence, recurrence, progression or regression of disease in an individual.

[0007] In some embodiments, a method for measuring the level of disease in an individual comprises using nucleic acid sequencing data associated with the individual to compare a signal indicative of the rate at which sequenced loci selected from a personalized panel of disease-associated small nucleotide variant (SNV) loci are derived from diseased tissue to a background index indicative of the rate of sequencing false positive errors across the selected loci; and determining the level of disease in the individual based on the comparison of the signal and the background index.

[0008] In some embodiments, a method of measuring disease recurrence in an individual comprises using nucleic acid sequencing data associated with the individual to compare a signal indicative of the rate at which sequenced loci selected from a personalized panel of disease-associated small nucleotide variant (SNV) loci are derived from diseased tissue to a background index indicative of the rate of sequencing false positive errors across the selected loci; and determining a level of disease in the individual based on the comparison of the signal to the background index.

[0009] In some embodiments, a method for measuring disease progression or regression in an individual includes using nucleic acid sequencing data associated with the individual to compare a signal indicating the rate at which sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel are derived from diseased tissue with a background index indicating the rate of sequencing false positive errors across the selected loci; and determining the level of disease in the individual based on a comparison of the signal and the background index; and comparing the measured level of disease to a previously measured level of the disease in the individual. In some embodiments, disease progression or regression is based on a statistically significant change in the measured level of disease.

[0010] In some embodiments of any of the above methods, the level of disease is a proportion of nucleic acid molecules associated with the disease in a sample from the individual. In some embodiments of any of the above methods, the comparing step includes subtracting a background index from the signal.

[0011] In some embodiments of any of the above methods, the method further comprises determining an error for the measurement of the level of the disease. In some embodiments, the error is a confidence interval for the level of the disease. In some embodiments, the error is proportional to the total number of individual small nucleotide variant reads detected at the selected locus. In some embodiments, the level of the disease is a proportion of nucleic acid molecules associated with the disease in a sample from the individual, and the proportion and the error are:

number

[0012] In some embodiments, a method for detecting disease in an individual includes using nucleic acid sequencing data associated with the individual to compare a signal indicating the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue with a noise index indicating sampling variance across the selected loci; and determining whether the individual has disease based on the comparison of the signal to the background index. In some embodiments, if the signal exceeds the noise index by more than a predetermined threshold, the individual is determined to have disease recurrence or a residual level of disease. In some embodiments, if the signal exceeds the noise index by k times or more, the individual is determined to have disease recurrence or a residual level of disease, where k is about 1.5. In some embodiments, k is about 3.0. In some embodiments, k is about 5.0. In some embodiments, k is about 10. In some embodiments, the method includes detecting disease recurrence.

[0013] In some embodiments, a method for detecting recurrence, progression or regression of disease in an individual comprises measuring at least one of: (a) the likelihood that a value indicative of a proportion of nucleic acid molecules in a sample that originates from the individual's diseased tissue, F, is greater than zero, where F greater than zero indicates the presence of disease in the individual; and (b) a statistically significant change in a value indicative of a proportion of nucleic acid molecules in a sample that originates from the individual's diseased tissue, F, where the statistically significant change is greater than or equal to a previously measured proportion, F. prior, where a statistically significant change in F indicates disease progression or regression in an individual, and the proportion F is the total number of single nucleotide variants (SNVs) detected in the cell-free nucleic acid sequencing data, N total wherein the SNVs are selected from a personalized panel of disease-associated SNV loci. total and the number of SNVs selected from the SNV panel, N var , adjusted by the average sequencing depth, D, and further adjusted by the sequencing false positive error rate, E, across the selected SNVs, N var It is determined by comparing with

[0014] In some embodiments of any of the above methods, the method further comprises generating a personalized disease-associated SNV locus panel. In some embodiments, generating a personalized disease-associated SNV locus panel comprises sequencing nucleic acid molecules from a sample of diseased tissue to determine a set of disease-associated SNVs, and filtering the set of disease-associated SNVs to remove germline variants and non-cancer associated somatic variants. In some embodiments, the sample of diseased tissue is a tumor biopsy sample obtained from the individual. In some embodiments, the germline variants or somatic variants, or both, are determined by sequencing nucleic acid molecules from a sample of non-diseased tissue obtained from the individual. In some embodiments, the sample of non-diseased tissue comprises white blood cells. In some embodiments, the sample of non-diseased tissue is a buffy coat. In some embodiments, the method further comprises filtering the set of disease-associated SNVs to remove SNVs that are only supported by one sequencing read. In some embodiments, the method further comprises filtering the set of disease-associated SNVs to remove SNVs that are not supported by complementary sequencing reads. In some embodiments, the method further comprises filtering the set of disease-associated SNVs to remove SNVs that are present in the general population of individuals at allele frequencies higher than a predetermined threshold. In some embodiments, the predetermined threshold is about 0.01. In some embodiments, the method further comprises filtering SNVs in low-complexity genomic regions (i.e., homopolymeric regions, or short tandem repeats (STRs)).In some embodiments, the nucleic acid sequencing data is obtained by sequencing nucleic acid molecules from a fluid sample obtained from the individual using non-terminating nucleotides provided in separate nucleotide flows according to a flow cycle order comprising a plurality of flow positions, the flow positions corresponding to the nucleotide flows; generating the personalized disease-associated SNV loci panel further comprises filtering the set of disease-associated SNVs such that the nucleic acid sequencing data and the reference sequencing data, when sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the flow cycle order, result in nucleic acid sequencing data that differs from the reference sequencing data associated with the reference sequence at more than two flow positions.

[0015] In some embodiments of any of the above methods, the nucleic acid sequencing data is obtained by sequencing nucleic acid molecules from a fluid sample obtained from the individual using non-terminating nucleotides provided in separate nucleotide flows according to a flow cycle order comprising a plurality of flow positions, the flow positions corresponding to the nucleotide flows; the method further comprises generating a personalized disease-associated SNV locus panel comprising sequencing nucleic acid molecules from the sample of diseased tissue to determine a set of disease-associated SNVs; generating the personalized disease-associated SNV locus panel further comprises filtering the set of disease-associated SNVs such that the nucleic acid sequencing data and the reference sequencing data, when sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the flow cycle order, include only SNVs that result in nucleic acid sequencing data that differs from the reference sequencing data associated with the reference sequence at more than two flow positions.

[0016] In some embodiments of any of the above methods, the nucleic acid molecule is a cell-free nucleic acid molecule. In some embodiments, the nucleic acid molecule is a DNA molecule. In some embodiments, the nucleic acid molecule is an RNA molecule.

[0017] In some embodiments of any of the above methods, the nucleic acid sequencing data is derived from nucleic acid molecules in a fluid sample obtained from the individual. In some embodiments, the fluid sample is a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample.

[0018] In some embodiments of any of the above methods, the disease is cancer. In some embodiments, the cancer is metastatic cancer.

[0019] Some embodiments of any of the above methods further include sequencing the nucleic acid molecule to obtain sequencing data.

[0020] In some embodiments of any of the above methods, the nucleic acid sequencing data is obtained by sequencing the nucleic acid molecule according to a predetermined nucleotide sequencing cycle order. In some embodiments, the nucleic acid sequencing data is further obtained by resequencing the nucleic acid molecule according to a different predetermined nucleotide sequencing cycle, the different predetermined nucleotide sequencing cycle resulting in a different false positive variant rate in the subset of sequencing loci compared to the first predetermined nucleotide sequencing cycle order.

[0021] In some embodiments of any of the above methods, the sequencing data is non-targeted sequencing data. In some embodiments, the sequencing data is obtained from a non-targeted whole genome.

[0022] In some embodiments of any of the above methods, the average sequencing depth of the sequencing data is at least 0.01. In some embodiments, the average sequencing depth of the sequencing data is less than about 100. In some embodiments, the average sequencing depth of the sequencing data is less than about 10. In some embodiments, the average sequencing depth of the sequencing data is less than about 1.

[0023] In some embodiments of any of the above methods, the panel of disease-associated SNV loci comprises passenger mutations and / or driver mutations.

[0024] In some embodiments of any of the above methods, the panel of disease-associated SNV loci comprises single nucleotide polymorphism (SNP) loci. In some embodiments, the panel of disease-associated SNV loci comprises indel loci.

[0025] In some embodiments of any of the above methods, the selected loci from the panel of disease-associated SNV loci include about 300 or more loci.

[0026] In some embodiments of any of the above methods, the loci selected from the disease-associated SNV panel are selected based on the false positive rate of each individual locus.

[0027] In some embodiments of any of the above methods, the loci selected from the disease-associated SNV panel are based on unique SNVs associated with a selected subclone of the disease.

[0028] In some embodiments of any of the above methods, the disease-associated SNV panel is determined by comparing sequencing data associated with diseased tissue to sequencing data associated with non-diseased tissue. In some embodiments, the method further comprises sequencing nucleic acid molecules derived from diseased tissue to obtain sequencing data associated with diseased tissue. In some embodiments, the method further comprises sequencing nucleic acid molecules derived from non-diseased tissue to obtain sequencing data associated with non-diseased tissue.

[0029] In some embodiments of any of the above methods, the nucleic acid sequencing data is obtained using surface-based sequencing of the nucleic acid molecules, and the nucleic acid molecules are not amplified prior to attachment of the nucleic acid molecules to the surface.

[0030] In some embodiments of any of the above methods, the nucleic acid sequencing data is obtained without the use of a unique molecular identifier (UMI).

[0031] In some embodiments of any of the above methods, the nucleic acid sequencing data is obtained without the use of a sample identification barcode.

[0032] In some embodiments of any of the above methods, the sequencing false positive error rate is measured using a panel of control loci.

[0033] In some embodiments of any of the above methods, the sequencing data is obtained by sequencing nucleic acid molecules obtained from a plurality of individuals in a pooled sample. In some embodiments, the selected loci are unique to each individual among the plurality of individuals. In some embodiments, at least one locus among the selected loci is common between at least two individuals among the plurality of individuals. In some embodiments, the sequencing depth is determined for each individual, and the signal for each individual is adjusted based on the sequencing depth associated with that individual. In an embodiment of the present invention, for example, the following items are provided: (Item 1) 1. A method for determining the level of a disease in an individual, comprising: Using nucleic acid sequencing data associated with the individual, comparing a signal indicative of the rate at which sequenced loci selected from a personalized panel of disease-associated small nucleotide variant (SNV) loci are derived from diseased tissue to a background index indicative of the rate of sequencing false positive errors across the selected loci; and determining the level of disease in the individual based on the comparison of the signal to the background index. The method includes: (Item 2) 2. The method of claim 1, wherein the level of the disease is a percentage of nucleic acid molecules associated with the disease in a sample from the individual. (Item 3) 3. The method of claim 1 or 2, wherein the comparing step comprises subtracting the background index from the signal. (Item 4) 4. The method according to any one of items 1 to 3, further comprising a step of determining an error in the measurement of said level of said disease. (Item 5) 5. The method of claim 4, wherein the error is a confidence interval for the level of the disease. (Item 6) 6. The method of claim 4 or 5, wherein the error is proportional to the total number of individual small nucleotide variant reads detected at the selected loci. (Item 7) the level of the disease is a proportion of nucleic acid molecules associated with the disease in a sample from the individual, and the proportion and error are

number

[0034] [Figure 1] FIG. 1 shows an exemplary method for determining the proportion of disease-associated nucleic acid molecules in a sample from an individual.

[0035] [Diagram 2] FIG. 2 shows another exemplary method for determining the proportion of disease-associated nucleic acid molecules in a sample from an individual.

[0036] [Diagram 3] FIG. 3 shows an exemplary method for determining the level of disease in an individual.

[0037] [Figure 4] FIG. 4 shows an exemplary method for determining the level of disease in an individual.

[0038] [Diagram 5] FIG. 5 shows an exemplary method for monitoring disease recurrence, progression or regression in an individual.

[0039] [Figure 6] FIG. 6 shows another exemplary method of monitoring disease recurrence, progression or regression in an individual.

[0040] [Figure 7] FIG. 7 illustrates an example of a computing device, according to one embodiment, that can be used to perform the methods described herein.

[0041] [Figure 8A] 8A shows sequencing data obtained by extending a primer with the sequence TATGGTCGTCGA (SEQ ID NO: 1) using a repeated flow cycle sequence of TACG. This sequencing data is representative of the extended primer strand, and the sequence information of the complementary template strand can be easily determined to be effectively equivalent.

[0042] [Figure 8B] FIG. 8B shows the sequencing data shown in FIG. 8A with the most likely sequences selected based on highest likelihood at each flow location and from which the sequencing data was obtained (as indicated by stars).

[0043] [Figure 8C]Figure 8C shows the sequencing data shown in Figure 8A with traces representing two different candidate sequences: TATGGTCATCGA (SEQ ID NO:2) (solid circle) and TATGGTCGTCGA (SEQ ID NO:1) (open circle). The likelihood that the sequencing data matches a given sequence can be determined as the product of the likelihood that each flow position matches a candidate sequence. In some embodiments, the first candidate sequence (SEQ ID NO:2) can be considered a reverse-phase sequence of the exemplary reference sequence, and the second candidate sequence (SEQ ID NO:1) can be considered an SNV-containing sequence.

[0044] [Figure 8D] FIG. 8D shows sequencing data for a nucleic acid molecule containing an SNV (SEQ ID NO:1) obtained using an AGCT sequencing cycle and compared to a reference sequence (SEQ ID NO:2). DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0045] Detailed Description of the Invention The methods, devices and systems described herein relate to the detection and / or measurement of the level of disease in an individual. The level of disease can be related to the proportion of nucleic acid molecules (e.g., cell-free DNA) in a sample that originates from diseased tissue (e.g., cancer tissue). For example, disease can be detected or its level can be measured by measuring a signal that indicates the detection rate of small nucleotide variant (SNV) reads in nucleic acid molecules that originate from diseased tissue at a selected locus, and comparing this signal with a background index that indicates the sequencing false positive error rate, or a noise index that indicates the sampling variance across loci. The detected proportion of nucleic acid molecules in a sample that are associated with diseased tissue provides information on the level of disease in an individual. By detecting the level of disease in an individual, the recurrence of an already existing disease (or a disease that was previously thought to be in remission) can be determined, and the progression or regression of the disease state can also be determined.

[0046] A particular diseased tissue, especially cancer, may contain thousands (or tens of thousands, hundreds of thousands, or more) of mutations throughout the diseased genome compared to the normal healthy genome of an individual. These mutations may be driver mutations that confer a growth advantage (e.g., proliferation or survival) to the cancer, or passenger mutations that can be found throughout the coding or non-coding regions of the genome but are not thought to confer any growth advantage. In some cases, passenger mutations accumulate in cells that become cancerous before they become cancerous, and even healthy tissues have a certain mutation rate. The broad mutations for any given disease in a patient are unique to the patient, and even to a particular diseased tissue clone or subclone, thus resulting in a unique genetic signature for the diseased tissue. By comparing the genome (or a portion thereof) of diseased tissue with the genome (or corresponding genome) of non-diseased tissue of the same patient, a personalized disease-associated small nucleotide variant (SNV) locus panel for the diseased tissue can be established. Optionally, a subset of loci from the panel can be selected for analysis, which can be based, for example, on a lower false positive error rate at a given locus than, for example, other loci. SNV panels can include passenger mutations and / or driver mutations.

[0047] By taking into account the false positive error rate and / or sampling variance when determining the proportion of affected nucleic acid molecules or the level of disease in a patient, the overall sequencing depth can be reduced, thereby saving considerable time and cost. False positive errors can arise due to chemical damage, mis-incorporation of bases, or fluorescent read errors during sequencing, which can erroneously indicate that an SNV is present at a given locus. Sampling variance is related to the number of detected SNV reads, including both false positive errors and true positive calls. To prevent potential false errors at a particular locus, other disease detection methods often require multiple independent SNV calls at a given locus, which can only be obtained by sequencing the locus at a depth inversely proportional to the proportion of affected nucleic acid in the sample. In some cases, other methods include determining a consensus sequence at a locus from multiple sequencing reads. Deep sequencing used by other methods generally requires targeting specific loci or narrow subsets of the genome (e.g., mutation hotspots or whole exome sequencing). In addition, other sequencing methods often require amplification of nucleic acid molecules during library preparation in order to independently sequence multiple copies of the same nucleic acid molecule, and this amplification process carries the risk of introducing additional spurious errors.

[0048] Regardless of the false positive error at any particular locus, the method described herein uses the false positive error rate and / or sampling variance across the loci selected for analysis to measure the proportion of diseased nucleic acid molecules or the level of disease.Once the loci are selected, the false positive at any particular locus does not significantly affect the measurement.Therefore, the loci selected for analysis can be selected using the false positive error rate at each particular locus, but does not take into account the impact of any particular error that may result from sequencing at a given locus. definition

[0049] As used herein, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise.

[0050] Reference herein to "about" a value or parameter includes (and describes) a variation about that value or parameter itself. For example, a reference to "about X" includes the description of "X."

[0051] The term "average," as used herein, refers to either the average or median value, or any value used to estimate the average or median value.

[0052] "Variation" or "variance" as used herein refers to any statistical metric that defines the width of a distribution, which may be, but is not limited to, the standard deviation, variance, or interquartile range.

[0053] The terms "individual," "patient," and "subject" are used synonymously and refer to animals, including humans.

[0054] As used herein, the term "tissue" refers to any cellular material and can include circulating or non-circulating cells.

[0055] It will be understood that the embodiments and variations of the invention described herein include "consisting of" and / or "consisting essentially of" the embodiments and variations.

[0056] When a range of values ​​is provided, it is to be understood that each intervening value between the upper and lower limit of that range, and any other stated or intervening value within that stated range, is encompassed within the scope of the disclosure. When a stated range includes an upper or lower limit, ranges that do not include either of those included limits are also included in the disclosure.

[0057] The section headings used herein are for organizational purposes only and should not be construed as limiting the subject matter described. This description is provided to enable one of ordinary skill in the art to make and use the invention and is provided in the context of a patent application and its requirements. Various modifications of the described embodiments will be readily apparent to those skilled in the art, and the general principles herein may be applied to other embodiments. Thus, the present invention is not intended to be limited to the embodiments shown, but is to be accorded the widest scope consistent with the principles and features described herein.

[0058] 1-8D illustrate various example processes. These example processes may be performed, for example, using one or more electronic devices implementing a software platform. In some examples, one or more of the example processes are performed using a client-server system, and the blocks of the illustrated processes may be divided in any manner between a server device and a client device. In other examples, the blocks of the example processes are divided between a server device and multiple client devices. Thus, while portions of the example processes are described herein as being performed by a particular device of a client-server system, it will be understood that the processes are not so limited. In other examples, one or more of the example processes are performed exclusively using a client device (e.g., a user device) or exclusively using one or more client devices. In these example processes, some blocks are combined as needed, the order of some blocks is changed as needed, and some blocks are omitted as needed. In some examples, additional steps may be performed in combination with the example processes. Thus, the operations as illustrated (and described in more detail below) are exemplary in nature and, therefore, should not be considered limiting.

[0059] The disclosures of all publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety. In the event that any reference incorporated by reference conflicts with the present disclosure, the present disclosure shall control. Personalized locus panels

[0060] A particular disease, e.g., cancer, in an individual can give rise to mutated nucleic acid sequences that confer a signature of that disease. The sequence of nucleic acid molecules associated with diseased tissue (i.e., diseased genome) can be compared to the sequence of nucleic acid molecules associated with non-diseased tissue from the same individual (i.e., healthy or non-diseased genome). The difference between the diseased genome (or a portion thereof) and the non-diseased genome (or a portion thereof) determines the variant of the diseased tissue. Some or all of the small nucleotide variants (e.g., single nucleotide polymorphisms (SNPs) or small indels (generally 1-5 bases in length)) between the genomes (or portions of the genomes) can be used to establish a personalized disease-associated SNV locus panel specific to the individual's disease. The SNV locus panel is in-silico and is not embodied in, e.g., a set of oligonucleotide primers. Thus, the personalized disease-associated SNV locus panel is constructed based on the difference between the relevant nucleic acid sequences from diseased tissue and the relevant nucleic acid sequences from healthy (i.e., non-diseased) tissue. In some embodiments, the sequencing data associated with diseased and / or healthy tissues is targeted sequencing data. In some embodiments, the sequencing data associated with diseased and / or healthy tissues is non-targeted (e.g., genome-wide or whole genome) sequencing data.

[0061] In some embodiments, the SNV locus panel is generated by filtering germline variants and / or non-disease (e.g., non-cancer) associated somatic variants from SNVs associated with diseased (e.g., cancerous) tissue. For example, diseased tissue can be sequenced to determine multiple variants associated with diseased tissue. The resulting sequencing reads can be compared, for example, with a reference genome, and variants can be selected based on the difference between the sequencing reads and the reference genome. The identified variants can include variants that are unique to diseased tissue, as well as variants found in healthy tissues (e.g., variants found in white blood cells or other healthy tissues). For example, variants found in white blood cells can be obtained by sequencing matched buffy coat samples from the same subject and comparing the sequencing data with a reference genome. These variants may include cancerous variants, but a large number of variants may result from clonal hematopoiesis associated with aging. In some embodiments, the variants identified by buffy coat / white blood cell sequencing are treated as an approximate representative population of non-cancer-related somatic variants.Therefore, germline variants and / or non-disease-related somatic variants (with respect to reference genome) can be determined by sequencing healthy tissue and comparing sequencing reads with reference genome.Then, once disease-related SNV locus panel is generated, the SNVs associated with diseased tissue can be filtered to remove germline variants and / or somatic variants.

[0062] In some embodiments, sequence data associated with diseased tissue and / or sequence data associated with healthy tissue are determined in advance (i.e., prior to sequencing and / or analysis of nucleic acid molecules in a fluid sample). For example, any healthy tissue obtained from an individual can be used to determine the sequence of a healthy genome (or a portion thereof). The healthy tissue can be obtained, for example, from a fluid sample (e.g., from acellular nucleic acid molecules (e.g., cfDNA) or healthy blood cells in a fluid sample), from a buccal swab, from a biopsy of healthy tissue, or from any other suitable method. In some embodiments, the healthy tissue includes white blood cells, e.g., white blood cells obtained from a buffy coat. In some embodiments, the healthy tissue includes non-diseased tissue. For example, a tumor biopsy sample (e.g., a solid tumor biopsy sample, e.g., a n FFPE tissue sample) can include both healthy (i.e., non-diseased) tissue and diseased tissue. In some embodiments, the healthy tissue includes a healthy cfDNA sample, for example, an individual may undergo routine health checkups, including whole genome sequencing (WGS) analysis of blood samples, such as plasma and / or white blood cell-containing samples. Such data can be stored in the individual's health record. When an individual subsequently develops a pathological condition, such as cancer, the previously obtained sequencing data can be used to establish a health baseline for the individual. Conversely, for an individual known to have a pathological condition (e.g., liver or breast cancer) that has undergone a treatment (e.g., a surgical procedure), the healthy tissue can include one or more samples taken appropriately after the treatment when the pathological condition can no longer be detected. Such healthy tissue can be used as a baseline sample to which subsequent samples are compared to assess whether the disease has relapsed in the individual. A nucleic acid sequencing library can be prepared from the healthy tissue and sequenced to obtain sequencing data attributable to the genome (or a portion thereof) of the healthy tissue. Although a small amount of diseased tissue may be extracted along with the healthy tissue, the diseased tissue will generally be a minor component that can be ignored in order to obtain sequencing data for the healthy tissue.

[0063] Sequence data of nucleic acid molecules (e.g., genome or a portion thereof) associated with diseased tissue can be determined by obtaining a tissue sample of diseased tissue, e.g., primary or secondary cancer, which can be resected, biopsied or otherwise sampled, and sequencing the nucleic acid molecules in the obtained tissue. In some embodiments, multiple samples are obtained from diseased tissue, which can capture mosaicism within the diseased tissue (e.g., different clones or subclones of the diseased tissue). In some embodiments, sequencing data associated with diseased tissue is obtained by sequencing nucleic acid molecules obtained from a fluid sample (e.g., acellular nucleic acid molecules (e.g., cfDNA) in the fluid sample or from healthy blood cells). Although the fluid sample can also contain nucleic acid molecules associated with healthy tissue, the sequencing data associated with healthy tissue will generally have a fairly high depth count and can be ignored in determining the sequencing data associated with diseased tissue. Diseased tissue can be sampled, for example, before the start of disease treatment (e.g., chemotherapy for cancer treatment) or after the start of disease treatment.

[0064] A personalized disease-associated SNV locus panel includes variants (including loci of variants and mutational changes) of nucleic acid molecules from diseased tissues compared to nucleic acid molecules from non-diseased tissues. The panel cannot include all of the nucleic acid differences between healthy and diseased tissues without missing a single difference, because certain variants may not have been detected due to limitations on sequencing data of healthy and / or diseased tissues, or may occur in regions of the genome that are technically difficult to sequence, such as low-complexity regions or regions where degeneracy is mapped. In some embodiments, the personalized panel includes driver mutations, passenger mutations, or both driver mutations and passenger mutations. In some embodiments, the locus panel includes mutations in coding regions of the genome, non-coding regions of the genome, or both. The number of variants in the personalized panel depends on the affected tissue, including the type of affected tissue, or the severity of the disease. In some embodiments, a personalized panel includes two or more, five or more, ten or more, twenty-five or more, fifty or more, one hundred or more, two hundred or more, three hundred or more, five hundred or more, one thousand or more, two hundred or more, five hundred or more, five thousand or more, ten,000 or more, twenty-five,000 or more, fifty,000 or more, one hundred,000 or more, two-fifth, five-tenth, five-tenth, five-tenth, one-million, five-million ... Screening loci for redundant variant calls limits the number of false positive variant loci introduced into the panel.In some cases, the panel includes only variants that have been verified to differ between diseased and unaffected tissue by consensus nucleic acid sequencing determined with high confidence.

[0065] Not all of the individualized disease-associated SNV loci panels need to be analyzed for the methods described herein. In some embodiments, a portion of the loci in the individualized disease-associated SNV loci panels are selected for analysis. Certain loci or variants may be more prone to false positive errors than other loci or variants. In addition, certain sequencing methodologies may be more prone to false positive errors than other methodologies. In some embodiments, a locus is selected from the individualized loci panel based on the false positive error rate at that locus. For example, a locus can be selected if the false positive error rate at that locus is about 1% or less, about 0.5% or less, about 0.25% or less, about 0.1% or less, about 0.05% or less, about 0.025% or less, about 0.01% or less, about 0.005% or less, about 0.0025% or less, or about 0.0001% or less. By way of example only, certain sequencing methodologies may have a lower false positive error rate for detecting certain mutations (e.g., G→A) than other mutation types (e.g., G→C), and may select variants with lower false positive error rates. In some embodiments, the selected genes include 2 or more, 5 or more, 10 or more, 25 or more, 50 or more, 100 or more, 200 or more, 300 or more, 500 or more, 1000 or more, 2500 or more, 5000 or more, 10,000 or more, 25,000 or more, 50,000 or more, 100,000 or more, 250,000 or more, or 500,000 or more loci. In some embodiments, all loci in the personalized locus panel are selected.

[0066] Filtering germline and non-disease-associated somatic variants from SNVs associated with diseased tissues is one technique that can be used to select loci from (or generate) disease-associated SNV loci panels. cfDNA present in blood can originate from several cellular sources, including cancerous and non-cancerous cells. Hematopoietic stem cells can contain clonal hematopoietic-associated somatic variants that can lead to the expansion of clonal populations of blood cells. These clonal hematopoietic-associated somatic variants are often non-malignant, and the clonal expansion driven by these somatic variants can be referred to as clonal hematopoiesis of indeterminate potential (CHIP). See Steensma et al, Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes, Blood, vol., 126, pp. 9-16 (2015). Several studies have shown that at least 10% of the elderly population older than 70 years old carry CHIP due to oligoclonal expansion of mutated hematopoietic stem cells. See Jaiswal et al., Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes, N. Engl. J. Med., vol. 371, no. 26, pp. 2488-2498 (2014). Thus, these non-disease-related somatic variants may be significantly represented in cfDNA even if they are not associated with disease. See US Patent Application Publication No. 2019 / 0385700A1, US Patent Application Publication No. 2019 / 0355438A1, US Patent Application Publication No. 2020 / 0013484A1, the contents of each of these reference patent documents are incorporated herein by reference for all purposes. Removal of these non-disease-associated somatic variants from SNV locus panels can significantly reduce the background error rate.Non-disease associated somatic variants, such as clonal hematopoietic associated somatic variants, can be identified, for example, by sequencing nucleic acid molecules derived from white blood cells, such as white blood cells in a buffy coat.

[0067] In some embodiments, the SNV locus panel includes SNVs associated with diseased tissue that have been filtered to remove germline and non-disease-associated somatic variants (i.e., somatic variants that are not associated with disease). For example, these non-disease-associated somatic variants can be determined by sequencing nucleic acid molecules derived from healthy tissue (e.g., samples containing white blood cells, such as buffy coats). Removal of germline and non-disease-associated somatic variants detected by sequencing nucleic acid molecules obtained from white blood cells (e.g., from buffy coats) can be particularly useful when the level of disease is measured by sequencing cfDNA. When cfDNA is sequenced for analysis, both disease-associated variants and non-disease-associated somatic variants and germline variants arising from tumors are detected. Removal of germline and non-disease-associated somatic variants from the analysis can reduce erroneous attribution to ctDNA. Thus, removing non-disease-associated somatic variants can reduce the false positive error rate (i.e., SNVs that are erroneously attributed to diseased tissues).

[0068] Other techniques can additionally or alternatively be used to select loci from disease-associated SNV loci panels or to generate disease-associated SNV loci panels. For example, in some embodiments, loci can be selected from disease-associated SNV loci panels (or disease-associated SNV loci panels can be generated to include SNVs) only if the disease-associated variant is supported by two or more (e.g., three, four, five, or more) sequencing reads obtained when sequencing nucleic acid molecules derived from diseased tissue. By requiring two or more sequencing reads to support a variant associated with diseased tissue, the possibility of false positives can be reduced (e.g., by limiting the number of variants called due to sequencing errors or other errors when analyzing diseased tissue). Thus, false positive error rates (i.e., SNVs that are erroneously attributed to diseased tissue) can be reduced by removing SNVs that are not reliably supported by sequencing data obtained by sequencing nucleic acid molecules derived from diseased tissue.

[0069] In some embodiments, loci in a disease-associated SNV locus panel can be selected (or a disease-associated SNV locus panel can be generated) by removing common variant alleles from the general population, e.g., variants that are more frequent than a predetermined frequency threshold. Common variants are likely to be germline mutations and not unique to the affected tissue, and therefore can be removed to reduce errors. In some embodiments, the predetermined frequency threshold is about 0.005 (or greater), about 0.01 or greater, about 0.02 or greater, or about 0.05 or greater. Thus, false positive error rates (i.e., SNVs that are erroneously attributed to affected tissue) can be reduced by removing SNVs that are common in the general population and therefore likely to be due to germline variance.

[0070] In some embodiments, loci in a disease-associated SNV locus panel can be selected (or a disease-associated SNV locus panel can be generated) by eliminating variants detected in nucleic acid sequencing data that have an allele frequency higher than a predefined threshold or higher than a statistical threshold. cfDNA from diseased tissue is generally a minor fraction of cfDNA, and variants with high allele frequency are likely to be due to germline and / or somatic variants unrelated to disease (e.g., non-disease-associated somatic variants, or somatic variants related to a different condition or disease) and can be excluded from the analysis to measure the level of disease. When plotting a histogram of allele frequency, a lower allele frequency cluster, which is generally due to diseased tissue or sequencing noise, and a higher allele frequency cluster, which is generally due to germline and / or somatic variants, can be generally obtained. In some embodiments, a statistical parameter is determined to distinguish between the lower allele frequency cluster and the higher allele frequency cluster, and variants associated with the higher allele frequency cluster can be eliminated. In some embodiments, a predetermined threshold is used to eliminate variants in higher allele frequency clusters. The predetermined threshold can be, for example, about 0.2 or higher, about 0.25 or higher, or about 0.3 or higher.

[0071] In some embodiments, loci in disease-associated SNV panels can be selected by eliminating variants within homopolymeric regions (stretches of consecutive nucleotides with the same base type) (by eliminating such variants, disease-associated SNV loci panels can be generated). In some embodiments, homopolymeric regions contain 3, 4, 5, 6, 7, 8, 9, 10, or more consecutive nucleotides with the same base type. Variants within homopolymeric regions are suspected to be false positive variants and may not accurately reflect diseased tissue. Thus, removing SNVs contained within homopolymeric regions can reduce the false positive error rate (i.e., SNVs that are falsely attributed to diseased tissue).

[0072] In some embodiments, loci in a disease-associated SNV locus panel can be selected by eliminating variants that are not supported by complementary strands among nucleic acid molecules derived from diseased tissues (such variants can be eliminated to generate a disease-associated SNV locus panel). For example, if a variant is called in a sequencing read associated with a first strand, but a complementary variant is not called in a second strand complementary to the first strand, a sequencing error or other artifact can be assumed, and the variant can be eliminated from further analysis. Thus, false positive error rates (i.e., SNVs that are erroneously attributed to diseased tissues) can be reduced by removing SNVs that are not reliably supported by sequencing data obtained by sequencing nucleic acid molecules derived from diseased tissues.

[0073] In some embodiments, loci in a disease-associated SNV locus panel can be selected by including only variants that induce cycle shifts (e.g., flowgram signal shifts by one or more flow cycles compared to a reference based on flow cycle order) and / or result in new zero or new non-zero signals in the sequencing data (a disease-associated SNV locus panel can be generated by including only such variants). See, for example, U.S. Patent Application No. 16 / 864,981 and International Patent Application No. PCT / US2020 / 031147, the contents of each of which are incorporated herein by reference in their entirety for all purposes. Since cycle shift events are unlikely to exist in the absence of true positive events (as further described herein), in some embodiments, loci from a disease-associated SNV locus panel can be selected if a variant at that locus results in a cycle shift event. Thus, by including only SNVs that result in strong signals, false positive error rates (i.e., SNVs that are erroneously attributed to diseased tissue) can be reduced.

[0074] Using the methods described herein, different clones or different subclones of diseased tissue in the same individual can be analyzed simultaneously. Different clones of diseased tissue (e.g., independent cancer clones) generally have unique or nearly unique variant signatures. Subclones of diseased tissue may have some overlapping variants, but generally have a sufficient number of unique variants to select a unique or nearly unique subset of variants. In some embodiments, sequenced loci are selected from the disjunction of variant loci associated with several disease subclones, and the analysis detects a fraction of the sample that contains all disease subclones, and also detects the fraction of disease from each subclone. In some embodiments, the sequenced loci selected for analysis for a given clone or subclone are selected to avoid overlapping variants (i.e., any variants shared by two or more clones or subclones are not selected). Thus, the level of disease for separate clones or subclones, or the proportion of nucleic acid molecules associated with separate clones or subclones, can be determined using the same sample from an individual. In some embodiments, one or more of the clones or subclones are refractory to one or more cancer treatments, and the methods can be used to monitor the progression or regression of the refractor clones or subclones. Patient samples and sequencing

[0075] Fluid samples are a relatively non-invasive method for obtaining samples from individuals. Such fluid samples can include, for example, blood, plasma, saliva, feces or urine samples. In addition, for residual disease, malignant disease, or other diseases without primary or solid diseased tissue (or without significant primary or solid diseased tissue), fluid samples allow obtaining nucleic acid molecules related to diseased tissue without tumor biopsy. Therefore, the method can be particularly useful when the location of diseased tissue is unknown or solid diseased tissue is too small to be sampled.

[0076] A fluid sample taken from an individual with a disease such as cancer generally has cell-free DNA (or "cfDNA"), including nucleic acid molecules derived from cancer tissue and nucleic acid molecules derived from non-diseased tissue. The nucleic acid sample from which sequencing data is obtained can be, but does not have to be, cfDNA. For example, the fluid sample can provide other nucleic acids from which sequencing data can be obtained. For example, if the disease is a blood disease (e.g., blood cancer), blood cells can be obtained from the blood sample, and the nucleic acid molecules from the blood cells can be sequenced to obtain sequencing data. In some embodiments, the nucleic acid molecules are cell-free RNA molecules obtained from the fluid sample.

[0077] Any suitable sequencing method can be used to sequence nucleic acid molecules to obtain sequencing data from nucleic acid molecules.Exemplary sequencing methods can include, but are not limited to, high-throughput sequencing, next-generation sequencing, sequencing by synthesis, flow sequencing, massively parallel sequencing, shotgun sequencing, single molecule sequencing, nanopore sequencing, pyrosequencing, semiconductor sequencing, sequencing-by-ligation, sequencing by hybridization, RNA-Seq, digital gene expression, single molecule sequencing by synthesis (SMSS), clonal single molecule array, sequencing by ligation, and Maxim-Gilbert sequencing. In some embodiments, nucleic acid molecules can be sequenced using high-throughput sequencers, such as Illumina HiSeq2500, Illumina HiSeq3000, Illumina HiSeq4000, Illumina HiSeqX, Roche 454, Life Technologies Ion Proton, or public sequencing platforms such as those described in U.S. Patent No. 10,267,790, the entirety of which is incorporated herein by reference. Other sequencing methods and sequencing systems are also known in the art. In some embodiments, nucleic acid molecules are sequenced using a sequencing-by-synthesis (SBS) method. In some embodiments, nucleic acid molecules are sequenced using a "natural sequencing-by-synthesis" or "non-terminating sequencing-by-synthesis" method (see U.S. Patent No. 8,772,473, the entirety of which is incorporated herein by reference).

[0078] The sequencing method selected can affect the false positive error rate, either uniformly or as applied to a particular variant type. As discussed above, in some embodiments, the loci selected for analysis from the personalized locus panel can be selected based on the false positive error rate for a given variant. In some embodiments, the nucleic acid molecule is sequenced using two or more different sequencing methods. By using two or more different sequencing methods with different false positive error rates for different variants, the false positive error rate can be applied to the different sequencing methods to select a larger number of variants. For example, a particular sequencing method relies on a predetermined nucleotide sequencing cycle (e.g., CTAG, ATCG, TCAG, etc.), and the sequencing error rate of a variant type can depend on the order of the cycle. Thus, in some embodiments, sequencing data is obtained by sequencing a nucleic acid molecule according to a first predetermined nucleotide sequencing cycle, and re-sequencing the nucleic acid molecule according to a different predetermined nucleotide sequencing cycle order. In some embodiments, the sequencing data is obtained using two, three, four or more different nucleotide sequencing cycle sequences.

[0079] In some embodiments, the sequencing data is non-targeted sequencing data. Certain sequencing methodologies rely on targeting specific regions or loci of genomes to limit the breadth of sequencing and / or enrich specific regions. Common targeting methods include hybridization targeting (e.g., using a nucleic acid probe bound to a label or bead is used to selectively target regions of nucleic acid molecules in a sample for targeted sequencing), primer-based targeting (e.g., using a nucleic acid primer to amplify a target nucleic acid region by amplification (e.g., PCR)), array-based capture, and in-solution capture methods. Target regions can be, for example, previously identified variants, genes in genomes that are known drivers of cancer growth, or mutation hotspots in genomes. However, targeted sequencing ignores a significant portion of the information across the affected tissue genome that can be used by the methods described herein.

[0080] The method is carried out using sequencing data obtained by whole genome sequencing (WGS) if necessary. By using whole genome sequencing, a larger number of variant loci can be detected and used for analysis. The detected signal increases at a faster rate than the noise as the number of loci analyzed increases, and by using the whole genome, a larger amount of data can be analyzed with simpler preparation. Thus, in some embodiments, no region of the genome is targeted. In some embodiments, the sequencing data is obtained from untargeted whole genome sequencing.

[0081] The methods described herein can be used with a wide range of sequencing data (e.g., non-targeted or whole genome sequencing data), so the average sequencing depth does not need to be as high as target enrichment methods. For example, in some embodiments, the average sequencing depth of the sequencing data is about 100 or less, about 50 or less, about 25 or less, about 10 or less, about 5 or less, about 1 or less, about 0.5 or less, about 0.25 or less, about 0.1 or less, about 0.05 or less, about 0.025 or less, or about 0.01 or less. In some embodiments, the average sequencing depth is about 0.01 to about 1000, or any depth therebetween.

[0082] In some embodiments, the sequencing data is obtained without amplifying the nucleic acid molecule before establishing the sequencing colony (also called sequencing cluster). Methods for generating sequencing colonies include bridge amplification or emulsion PCR. Shotgun sequencing and methods that rely on calling consensus sequences generally use unique molecular identifiers (UMIs) to label nucleic acid molecules and amplify the nucleic acid molecules to generate a large number of copies of the same nucleic acid molecule that are sequenced independently. The amplified nucleic acid molecules can then be bound to a surface and bridge amplified to generate sequencing clusters that are sequenced independently. The UMIs can then be used to associate the independently sequenced nucleic acid molecules. However, the amplification process can introduce errors into the nucleic acid molecule, for example due to the limited fidelity of DNA polymerase. As discussed above, the methods provided herein can be performed without calling consensus sequences, and therefore this initial amplification process is not required and can be avoided to reduce false positive error rates. In some embodiments, the nucleic acid molecules are not amplified prior to amplification to generate colonies for obtaining sequencing data. In some embodiments, the nucleic acid sequencing data is obtained without the use of unique molecular identifiers (UMIs).

[0083] Pooled sequencing data and individual-related sequencing data can be used to determine the proportion of individual samples in a pool of samples.The genome of an individual has a unique variant signature, and this signature can be used to determine the proportion of nucleic acid molecules that originate from that individual.Therefore, samples from multiple individuals can be pooled, and the portion of nucleic acid molecules in the pooled samples that are associated with an individual can be determined without using sample identification barcodes.

[0084] In some embodiments, the individual has or has previously had a disease. In some embodiments, the disease is cancer. Exemplary cancers encompassed by the methods described herein include acute lymphocytic leukemia, acute myeloid leukemia, adenocarcinoma (e.g., prostate, small intestine, endometrium, cervix, colon, lung, pancreas, esophagus, rectum, uterus, stomach, breast, and ovary), B-cell lymphoma, breast cancer, carcinoma, cervical cancer, chronic myelogenous leukemia, colon cancer, esophageal cancer, glioblastoma, glioma, blood cancer, Hodgkin's lymphoma, leukemia, lymphoma, lung cancer (e.g., non-small cell lung cancer), Cancers that may be treated include, but are not limited to, liver cancer, melanoma (e.g., metastatic malignant melanoma), multiple myeloma, neoplastic malignancies, neuroblastoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic adenocarcinoma, prostate cancer (e.g., hormone-refractory prostate adenocarcinoma), renal cancer (e.g., clear cell carcinoma), squamous cell carcinoma (e.g., cervix, eyelid, conjunctiva, vagina, lung, oral cavity, skin, bladder, tongue, larynx, and esophagus), head and neck squamous cell carcinoma, T-cell lymphoma, and thyroid cancer. In some embodiments, the cancer is ineffective against one or more treatments. In some embodiments, the cancer is in remission or is believed to be in remission. Flow sequencing and cycle shift detection

[0085] An exemplary method of sequencing a nucleic acid molecule may include using a flow sequencing method to sequence the nucleic acid molecule to generate sequencing data. Flow sequencing may allow for the selection of variant loci in disease-related SNV panels with high confidence, for example, by selecting loci or variants with low error rates. For example, in some embodiments, loci in disease-related SNV loci panels can be selected by including only variants that induce cycle shift (i.e., flowgram signal shift by one full cycle (e.g., four flow positions) compared to reference based on flow cycle order) and / or generate new zero or new non-zero signals in sequencing data, as further described herein (only including such variants can generate disease-related SNV loci panels).

[0086] Flow sequencing methods can include extending a primer attached to a template polynucleotide molecule according to a predetermined flow cycle in which a single type of nucleotide can reach the extension primer at any given flow position. In some embodiments, at least a portion of the nucleotides of a particular type include a label, and when the labeled nucleotide is incorporated into the extension primer, the label provides a detectable signal. The sequence obtained by incorporating such a nucleotide into the extended primer should be the reverse complement of the sequence of the template polynucleotide molecule. In some embodiments, for example, sequencing data is generated using a flow sequencing method that includes extending a primer using a labeled nucleotide and detecting the presence or absence of the labeled nucleotide incorporated into the extension primer. Flow sequencing methods are sometimes referred to as "sequencing by natural synthesis" or "non-terminating sequencing by synthesis" methods. Exemplary methods are described in U.S. Patent No. 8,772,473, which is incorporated herein by reference in its entirety. Although the following description is provided with respect to flow sequencing methods, it will be understood that other sequencing methods may be used to sequence all or a portion of the sequenced region. For example, the sequencing data discussed herein may be generated using pyrosequencing methods.

[0087] Flow sequencing involves the use of nucleotides to extend a primer hybridized to a polynucleotide. Nucleotides of a given base type (e.g., A, C, G, T, U, etc.) can be mixed with the hybridized template to extend the primer if a complementary base is present in the template strand. The nucleotide can be, for example, a non-terminating nucleotide. When a nucleotide is a non-terminating nucleotide, more than one consecutive base can be incorporated into the extended primer strand if more than one consecutive complementary base is present in the template strand. A non-terminating nucleotide contrasts with a nucleotide that has a 3' reversible terminator, where the blocking group is generally removed before the consecutive nucleotides are bound. If a complementary base is not present in the template strand, primer extension stops until a nucleotide that is complementary to the next base in the template strand is introduced. At least a portion of the nucleotide can be labeled, so that incorporation can be detected. Most commonly, only a single nucleotide type is introduced at a time (i.e., added individually), although in certain embodiments, two or three different types of nucleotides may be introduced simultaneously. This methodology can be contrasted with sequencing methods that use reversible terminators, in which after every single base extension, primer extension is halted until the terminator is flipped to allow incorporation of the next subsequent base.

[0088] Nucleotides can be introduced in flow order during primer extension, and this process can be further divided into flow cycles. A flow cycle is a repeated nucleotide flow order and can be of any length. Nucleotides are added stepwise, which allows the added nucleotide to be incorporated into the end of the sequencing primer of the complementary base present in the template strand. Simply by way of example, the flow order of the flow cycle can be ATGC, or the flow cycle order can be ATCG. Alternative orders can be easily envisioned by those skilled in the art. The flow cycle order can be of any length, but flow cycles containing four unique base types (A, T, C and G in any order) are the most common. In some embodiments, the flow cycle comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more separate nucleotide flows in a flow cycle order. By way of example only, the flow cycle sequence can be TCACGATGCATGCTAG, where these 16 separately provided nucleotides are provided in this flow cycle sequence over several cycles. Between introductions of different nucleotides, unincorporated nucleotides can be removed, for example, by washing the sequencing platform with a wash solution.

[0089] Polymerase can be used to extend sequencing primer by incorporating one or more nucleotides to the end of primer in a template-dependent manner.In some embodiments, polymerase is a DNA polymerase.Polymerase can be naturally occurring or synthetic (e.g., mutant) polymerase.Polymerase can be added at the first step of primer extension, but supplementary polymerase can be added during sequencing, for example, by using stepwise addition of nucleotides or after several flow cycles, if necessary. Exemplary polymerases include DNA polymerases, RNA polymerases, thermostable polymerases, wild-type polymerases, modified polymerases, Bst DNA polymerase, Bst 2.0 DNA polymerase, Bst 3.0 DNA polymerase, Bsu DNA polymerase, E. coli DNA polymerase I, T7 DNA polymerase, bacteriophage T4 DNA polymerase Φ29 (phi 29) DNA polymerase, Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase, and SeqAmp DNA polymerase.

[0090] When determining the sequence of the template strand, the introduced nucleotide can include a labeled nucleotide, and the presence or absence of the incorporated labeled nucleic acid can be detected to determine the sequence. The label can be, for example, an optically active label (e.g., a fluorescent label) or a radioactive label, and the signal emitted or altered by the label can be detected using a detector. The presence or absence of the labeled nucleotide incorporated into the primer hybridized to the template polynucleotide can be detected, which allows the sequence to be determined (e.g., by generating a flowgram). In some embodiments, the labeled nucleotide is labeled with a fluorescent moiety, a luminescent moiety, or other light-emitting moiety. In some embodiments, the label is attached to the nucleotide via a linker. In some embodiments, the linker is cleavable, for example, by a photochemical or chemical cleavage reaction. For example, the label can be cleaved after detection and before incorporation of the successive nucleotide. In some embodiments, the label (or linker) is attached to the nucleotide base or another site on the nucleotide that does not interfere with the extension of the nascent DNA strand. In some embodiments, the linker comprises a disulfide or PEG-containing moiety.

[0091] In some embodiments, the nucleotide introduced comprises only unlabeled nucleotides, and in some embodiments, the nucleotide comprises a mixture of labeled and unlabeled nucleotides.For example, in some embodiments, the portion of labeled nucleotides compared to the total nucleotides is about 90% or less, about 80% or less, about 70% or less, about 60% or less, about 50% or less, about 40% or less, about 30% or less, about 20% or less, about 10% or less, about 5% or less, about 4% or less, about 3% or less, about 2.5% or less, about 2% or less, about 1.5% or less, about 1% or less, about 0.5% or less, about 0.25% or less, about 0.1% or less, about 0.05% or less, about 0.025% or less, or about 0.01% or less. In some embodiments, the portion of labeled nucleotides compared to total nucleotides is about 100%, about 95% or more, about 90% or more, about 80% or more, about 70% or more, about 60% or more, about 50% or more, about 40% or more, about 30% or more, about 20% or more, about 10% or more, about 5% or more, or or more, about 4% or more, about 3% or more, about 2.5% or more, about 2% or more, about 1.5% or more, about 1% or more, about 0.5% or more, about 0.25% or more, about 0.1% or more, about 0.05% or more, about 0.025% or more, or about 0.01% or more.In some embodiments, the portion of labeled nucleotides compared to total nucleotides is from about 0.01% to about 100%, e.g., from about 0.01% to about 0.025%, from about 0.025% to about 0.05%, from about 0.05% to about 0.1%, from about 0.1% to about 0.25%, from about 0.25% to about 0.5%, from about 0.5% to about 1%, from about 1% to about 1.5%, from about 1.5% to about 2%, from about 2% to about 2.5%, about 2.5% to about 3%, about 3% to about 4%, about 4% to about 5%, about 5% to about 10%, about 10% to about 20%, about 20% to about 30%, about 30% to about 40%, about 40% to about 50%, about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90%, about 90% to less than 100%, or about 90% to about 100%.

[0092] Prior to generating sequencing data, the polynucleotide is hybridized with a sequencing primer to generate a hybridized template. The polynucleotide can be ligated to an adaptor during sequencing library preparation. The adaptor can include a hybridization sequence that hybridizes with the sequencing primer. For example, the hybridization sequence of the adaptor can be a uniform sequence across multiple different polynucleotides, and the sequencing primer can be a uniform sequencing primer. This allows multiplex sequencing of different polynucleotides in a sequencing library.

[0093] Polynucleotides can be attached to a surface (e.g., a solid support) for sequencing. Polynucleotides can be amplified (e.g., by bridge amplification or other amplification techniques) to generate polynucleotide sequencing colonies. The amplified polynucleotides in a cluster are substantially identical or complementary (some errors may be introduced during the amplification process, so that a portion of the polynucleotide may not necessarily be identical to the original polynucleotide). Colony formation allows for signal amplification such that a detector can accurately detect labeled nucleotide incorporation for each colony. In some cases, colonies are formed on beads using emulsion PCR, and the beads are distributed across the sequencing surface. Examples of systems and methods for sequencing can be found in U.S. Patent Application No. 10,344,328, the entirety of which is incorporated herein by reference.

[0094] The primers hybridized to the polynucleotides are extended through the nucleic acid molecule using separate nucleotide flows according to a flow order (which may be periodic according to a flow cycle order), and incorporation of nucleotides can be detected as described above, thereby generating a sequencing data set for the nucleic acid molecule.

[0095] Primer extension using flow sequencing allows long-range sequencing of hundreds or even thousands of bases in length. The number of flow steps or cycles can be increased or decreased to obtain the desired sequencing length. Primer extension can include one or more flow steps for stepwise extension of the primer using nucleotides with one or more different base types. In some embodiments, primer extension includes between 1 and about 1000 flow steps, for example, between 1 and about 10 flow steps, between about 10 and about 20 flow steps, between about 20 and about 50 flow steps, between about 50 and about 100 flow steps, between about 100 and about 250 flow steps, between about 250 and about 500 flow steps, or between about 500 and about 1000 flow steps. The flow steps can be divided into the same or different flow cycles. The number of bases incorporated into the primer depends on the sequence of the region to be sequenced and the flow order used to extend the primer. In some embodiments, the region to be sequenced is from about 1 base to about 4000 bases in length, e.g., from about 1 base to about 10 bases in length, from about 10 bases to about 20 bases in length, from about 20 bases to about 50 bases in length, from about 50 bases to about 100 bases in length, from about 100 bases to about 250 bases in length, from about 250 bases to about 500 bases in length, from about 500 bases to about 1000 bases in length, from about 1000 bases to about 2000 bases in length, or from about 2000 bases to about 4000 bases in length.

[0096] Sequencing data can be generated based on the detection of incorporated nucleotides and the order of nucleotide incorporation. Take the following extended sequences (i.e., each reverse complement of the corresponding template sequence): CTG, CAG, CCG, CGT, and CAT (assuming that neither the preceding nor the following sequences are subjected to the sequencing method), as well as the repeated flow cycles of TACG (i.e., sequential addition of T, A, C, and G nucleotides during the repeated cycles). A particular type of nucleotide at a given flow position will be incorporated into the primer only if the complementary base is present in the template polynucleotide. The resulting exemplary flowgram is shown in Table 1, where 1 indicates that the introduced nucleotide is incorporated and 0 indicates that the introduced nucleotide is not incorporated. The flowgram can be used to derive the sequence of the template strand. For example, the sequencing data (e.g., flowgram) discussed herein represents the extended primer strand and its reverse complement, which can be easily determined to represent the sequence of the template strand. An asterisk (*) in Table 1 indicates that a signal may be present in the sequencing data if additional nucleotides were incorporated into the extended sequencing strand (eg, the longer template strand). [Table 1]

[0097] Flowgrams can be binary or non-binary. Binary flowgrams detect the presence (1) or absence (0) of an incorporated nucleotide. Non-binary flowgrams can more quantitatively determine the number of nucleotides incorporated from each stepwise incorporation. For example, an extended sequence of CCG will contain incorporation of two C bases into the extension primer in the same C flow (e.g., at flow position 3), and the signal emitted by the labeled base will have a higher intensity than the intensity level corresponding to a single base incorporation. This is shown in Table 1. Non-binary flowgrams can also indicate the presence or absence of a base and provide additional information including the number of bases likely to be incorporated into each extension primer at a given flow position. The values ​​do not have to be integers. In some cases, the values ​​may reflect the uncertainty and / or probability of the number of bases incorporated into a given flow position.

[0098] In some embodiments, the sequencing data set includes flow signals representing base counts that indicate the number of bases in the sequenced nucleic acid molecule that are incorporated at each flow position. For example, as shown in Table 1, a primer extended with a CTG sequence using a TACG flow cycle sequence has a value of 1 at position 3, indicating a base count of 1 at that position (the 1 base is a C that is complementary to a G in the sequenced template strand). Also in Table 1, a primer extended with a CCG sequence using a TACG flow cycle sequence has a value of 2 at position 3, indicating a base count of 2 at that position of the extended primer while at this flow position. Here, the 2 bases refer to the first CC sequence of the CCG sequence in the extended primer sequence, which is complementary to the GG sequence in the template strand.

[0099] The flow signals in the sequencing data set may include one or more statistical parameters that indicate the likelihood or confidence interval for one or more base counts at each flow position. In some embodiments, the flow signals are determined from analog signals detected during the sequencing process, such as the fluorescent signal of one or more bases that are incorporated into the sequencing primer during sequencing. In some cases, the analog signals can be processed to generate statistical parameters. For example, machine learning algorithms can be used to correct for the context effect of analog sequencing signals, as described in published international patent application WO2019084158A1, the entirety of which is incorporated herein by reference. Although zero or more integer numbers of bases are incorporated into any given flow position, a given analog signal may not perfectly match that analog signal. Thus, a statistical parameter can be determined that indicates the likelihood of the number of bases that are incorporated into a flow position, given the detected signals. By way of example only, for the CCG sequence in Table 1, the likelihood that the flow signal indicates two bases were incorporated at flow position 3 may be 0.999, and the likelihood that the flow signal indicates one base was incorporated at flow position 3 may be 0.001. If the flow signal includes statistical parameters indicating the likelihood for multiple base counts at each flow position, the sequencing data set can be formatted as a sparse matrix. By way of example only, a primer extended with a sequence of TATGGTCGTCGA (SEQ ID NO: 1) (i.e., sequencing reads the reverse complement) using a repeated flow cycle sequence of TACG may result in the sequencing data set shown in FIG. 8A. The statistical parameters or likelihood values ​​may vary, for example, depending on noise or other artifacts present in the detection of the analog signal during sequencing.In some embodiments, if a statistical parameter or likelihood falls below a predetermined threshold, the parameter may be set to a predetermined non-zero value that is substantially zero (i.e., some very small or negligible value) to aid in statistical analyses, as discussed further herein, where using a true zero value may result in calculation errors or may not adequately distinguish between levels of unlikeliness, e.g., very unlikely (0.0001) from unlikely (0).

[0100] A value indicating the likelihood of a sequencing data set for a given sequence can be determined from the sequencing data set without sequence alignment. For example, the most likely sequence from which data is obtained can be determined by selecting the base count with the highest likelihood at each flow position, as shown by an asterisk in FIG. 8B (using the same data as shown in FIG. 8A). Thus, the sequence of primer extension can be determined according to the most likely base count at each flow position: TATGGTCGTCGA (SEQ ID NO: 1). From this, the reverse complement sequence (i.e., the template strand) can be easily determined. Furthermore, the likelihood of this sequencing data set obtaining the TATGGTCGTCGA (SEQ ID NO: 1) sequence (or the reverse complement sequence) can be determined as the product of the selection likelihoods at each flow position.

[0101] A sequencing dataset associated with a nucleic acid molecule is compared to one or more (e.g., 2, 3, 4, 5, 6 or more) possible candidate sequences. A close match (based on a match score, as discussed below) between a sequencing dataset and a candidate sequence indicates that the sequencing dataset is likely to have arisen from a nucleic acid molecule having the same sequence as the close matched candidate sequence. In some embodiments, the sequence of the sequenced nucleic acid molecule can be mapped to a reference sequence (e.g., using the Burrows-Wheeler Alignment (BWA) algorithm or other suitable alignment algorithm) to determine a locus (or loci or loci) for the sequence. A sequencing dataset in flow space can be easily converted to base space (or vice versa, if the flow order is known), and mapping can be performed in flow space or base space. The locus (or loci) corresponding to the mapped sequence can be associated with one or more variant sequences that can act as candidate sequences (or haplotype sequences) for the analysis methods described herein. One advantage of the method described herein is that it does not require the sequence of sequenced nucleic acid molecules and each candidate sequence to be aligned, which is generally computationally expensive in some cases, using alignment algorithm.Instead, it can use the sequencing data in flow space to determine the match score for each candidate sequence, which is computationally more efficient.

[0102] The match score indicates how well the sequencing data set supports the candidate sequence. For example, the match score, which indicates the likelihood that the sequencing data set matches the candidate sequence, can be determined by selecting a statistical parameter (e.g., likelihood) at each flow position that corresponds to the base count at the flow position where the expected sequencing data for the candidate sequence was obtained. The product of the selected statistical parameters can give the match score. For example, the sequencing data set shown in FIG. 8A for the extended primer, and TATGGTC A Assume a candidate primer extension sequence of TCGA (SEQ ID NO:2). Figure 8C (showing the same sequencing data set in Figure 8A) shows a trace for the candidate sequence (solid circle). For comparison, TATGGTC G The trace of the TCGA (SEQ ID NO:1) sequence (see FIG. 8B) is shown in FIG. 8C using open circles. There is a large difference between the match score indicating the likelihood that the sequencing data corresponds to the first candidate sequence TATGGTCATCGA (SEQ ID NO:2) and the match score indicating the likelihood that the sequencing data matches the second candidate sequence TATGGTCGTCGA (SEQ ID NO:1), even though these sequences only vary by a single base variation. As can be seen in FIG. 8C, the difference between the traces is seen at flow position 12 and propagates over at least nine flow positions (and potentially longer if the sequencing data extends over additional flow positions). This propagation, which continues over one or more flow cycles, is sometimes referred to as a "cycle shift" and is generally a very unlikely event if the sequencing data set matches a candidate sequence.

[0103] An SNV induces cycle shift when the sequencing data associated with a nucleic acid molecule having an SNV is compared with the reference sequence sequencing data associated with a reference sequence (i.e., a sequence having the same sequence as the nucleic acid molecule except that it does not have an SNV) and shifts by one or more flow cycles when the nucleic acid sequencing data and the reference sequencing data are sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the flow cycle order. That is, the sequencing data and the reference sequencing data are different over one or more flow cycles. The reference sequencing data does not have to be obtained by sequencing a reference nucleic acid molecule, but can be generated in silico based on the reference sequence.

[0104] An exemplary cycle shift that induces an SNV is illustrated by Figure 8C. The second candidate sequence shown in Figure 8C is the sequence read reverse complement of the sequence TATGGTC associated with the SNV-containing nucleic acid molecule (and associated with the sequencing data shown in the flowgram at the top of the figure). G TCGA (SEQ ID NO: 1), and the first candidate sequence is the sequencing read reverse complement of the reference sequence TATGGTC A Assume that the sequence of both sequences is TCGA (SEQ ID NO:2). The A→G SNP (at base position 8 of both sequences) induces a cycle shift, which can be observed by a one cycle leftward shift of the sequencing data associated with the SNV-containing nucleic acid molecule compared to the reference sequencing data. For example, the T base at base position 9 is sequenced at flow position 13 according to the sequencing data associated with the SNV-containing nucleic acid molecule, and at position 17 according to the reference sequencing data. Similarly, the CG bases at base positions 10 and 11 are sequenced at flow positions 15 and 16 according to the sequencing data associated with the SNV-containing nucleic acid molecule, and at positions 19 and 20 according to the reference sequencing data.

[0105] Because cycle shift events are unlikely to exist in the absence of true positive events, in some embodiments, a locus from a panel of disease-associated SNV loci may be selected only if a variant at that locus results in a cycle shift event.

[0106] The sensitivity of short genetic variants to induce cycle shifts may depend on the flow cycle order used to sequence the nucleic acid molecule with SNV. The example described in FIG. 8C includes a TACG flow cycle order, but other flow cycle orders can be used to induce cycle shifts in other variants. Any flow order can be used to observe the possibility that SNVs induce cycle shift events by generating new zero signals or new non-zero signals in the sequencing data. Thus, even if the selected flow order does not induce cycle shift events, SNVs can induce cycle shift events using different flow cycle orders. In some embodiments, a locus from a disease-associated SNV locus panel is selected only if the variant at that locus results in different sequencing data and reference sequencing data in terms of sequencing data with new zero signals or new non-zero signals when the nucleic acid sequencing data and the reference sequencing data are sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the flow cycle order. The signal change can be continuous in some embodiments. In some embodiments, a locus from a panel of disease-associated SNV loci is selected only if a variant at that locus results in differing sequencing data and reference sequencing data at two or more flow positions (which may be consecutive) when the nucleic acid sequencing data and the reference sequencing data are sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the flow cycle order.

[0107] Since the nucleic acid molecules are sequenced using different flow cycle orders, the sequencing data sets are different. Figure 8D shows an exemplary sequencing data set for an SNV-containing nucleic acid molecule having the reverse complement sequence of TATGGTCGTCGA (SEQ ID NO: 1) determined using a different flow cycle order (AGCT) (compared to Figure 8C, obtained using TACG flow cycle). Reference sequencing data is mapped onto the sequencing data for the SNV-containing nucleic acid molecule. The SNV produces a new zero signal at position 17 and a new non-zero signal at position 18. Thus, even though the TACG flow cycle induces cycle shift (see Figure 8C), the AGCT flow cycle does not induce it, even though the SNV is the same. Nevertheless, the new zero and new non-zero signals indicate that the SNV may induce cycle shift when using different cycle orders. Variant Signals, False Positive Errors, and Noise

[0108] Nucleic acid molecules in a fluid sample obtained from an individual are sequenced to obtain sequencing data associated with the individual. The sequencing data includes sequencing data associated with non-diseased tissues and sequencing data associated with diseased tissues. However, due to the presence of false positive errors occurring during sequencing, not all differences between the sequencing data associated with non-diseased tissues and the sequencing data associated with diseased tissues can be attributed to mutations in the genome of the diseased tissue. In other words, the total number of individual small nucleotide variant (SNV) reads detected at loci selected from the personalized locus panel in the sequencing data, N total , is the number of detected SNV reads at the selected position from the personalized locus panel resulting from the diseased tissue, N det , and the number of detected SNV reads among the positions selected from the personalized locus panel due to false positive errors (i.e., background), N bkg, which is the sum of N total =N det +N bkg .

[0109] The number of detected SNV reads among the selected loci resulting from diseased tissue, N det , is the number of loci selected from the personalized locus panel, N var , is proportional to the average sequencing depth, D, and the fraction of nucleic acid molecules in the fluid sample that are derived from diseased tissue, F. In some embodiments, N det has a linear relationship with the rate, F. In some embodiments, N det =N var Defender. Similarly, the number of detected SNV reads among the selected loci due to false positive errors, N bkg , is the number of loci selected from the personalized locus panel, N var , is proportional to the average sequencing depth, D, and the error rate, E, across the selected loci. bkg has a linear relationship with the error rate, E. That is, in some embodiments, N bkg =N var DE. Therefore, N total can be determined in some embodiments roughly as follows: N total =N var D(F+E).

[0110] The number of detected SNV reads among the selected loci due to false positive errors, N bkg Since , is proportional to the error rate E, the error rate E can be reduced by eliminating loci that are more likely to produce false positive errors. Exemplary methods for selecting loci with lower false positive errors are described further herein.

[0111] The proportion of nucleic acid molecules in a sample that are associated with disease in an individual is N detIn some embodiments, the determination can be made using

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[0112] The signal-to-noise ratio (SNR) for the number of selected SNVs from among the SNVs selected from the personalized locus panel resulting from diseased tissue can be determined by assuming Poisson sampling noise for the number of false positive errors and for the true detections. Thus, N total The sampling noise of (i.e.,

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[0113] The error on the determined ratio, F, may also be determined based on sampling noise. For example, in some embodiments, the error on F may be

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[0114] The level of disease in an individual can be correlated with the proportion, F, of nucleic acid molecules in a sample derived from diseased tissue. Thus, the presence or level of disease can be measured, for example, by determining this proportion. Disease recurrence, progression or regression can be determined by measuring the level of disease in an individual at multiple time points. In some embodiments, the confidence intervals of two or more measurement proportions are compared and can be used to determine statistically significant differences between the measurement proportions (e.g., to measure disease progression or regression).

[0115] In some embodiments, the signal to noise ratio is used to detect the presence or recurrence of disease, with a higher SNR indicating an increased likelihood that disease is present or has recurred.

[0116] In some embodiments, multiple samples from different individuals are pooled together to obtain pooled nucleic acid sequencing data that includes nucleic acid sequencing data associated with the test individual. Nucleic acid molecules associated with a given individual's diseased tissue have unique or nearly unique variant signatures, which allows many detected variant reads to be assigned to the individual. In some embodiments, the sequenced loci selected for analysis are selected to avoid variant overlap (i.e., any variants shared by two or more individuals are not selected). In other embodiments, variant reads of variants common to two or more individuals are included in the analysis, for example, by counting variant reads for individuals that share the variant, or by weighting the variant read counts across individuals that share the variant (e.g., based on the relative amount of nucleic acid molecules from the individual) or by maximum likelihood analysis of the proportion of samples or diseases relative to the entire sequence pool. The measured proportion of nucleic acid molecules associated with the disease in individuals in a pool of individuals (i.e., using pooled nucleic acid sequencing data) will be determined first as the proportion of nucleic acid molecules in the pool of samples, and can be adjusted based on the proportion of samples in the pool. By way of example only, if the measured proportion of nucleic acid molecules derived from diseased tissue of an individual in a pool of samples is 0.5%, and the sample from that individual represents 5% of the nucleic acid molecules in the pool, then the proportion of nucleic acid molecules derived from diseased tissue in the sample from that individual is 10%.

[0117] Accurate determination of the false positive error rate, E, results in more accurate determination of the proportion, F, and the signal-to-noise ratio, SNR. In some embodiments, the false positive error rate is determined by experiment. In some embodiments, the false positive error rate is determined using sequencing data from one or more other individuals. In some embodiments, the false positive error rate is determined using sequencing data from the same individual, for example in a region outside the personalized locus panel. In some embodiments, the false positive error rate is determined essentially from the sequencing data associated with the individual used to determine the proportion, signal-to-noise ratio, or disease level. For example, in some embodiments, a set of control loci can be selected to determine the false positive error rate. The control loci can be selected loci where variants are unlikely to be highly abundant, for example loci in highly conserved regions of the genome. For example, the control loci can be in the coding region of an essential gene where true variants result in cell death. Thus, true variants in the control loci are unlikely to be highly abundant, and any detected variants can be attributed to false positive errors. The total number of SNV base reads detected in the control loci, N total,con , the total number of control loci, N con , and the average sequencing depth, D, can be used to determine the false positive error rate. That is, in some embodiments,

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[0118] FIG. 1 illustrates an exemplary method 100 for measuring the level of disease (e.g., cancer) in an individual, e.g., the proportion of nucleic acid molecules (e.g., cfDNA molecules) associated with the disease in a sample from the individual. The sample can be a fluid sample, e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample. In step 105, nucleic acid sequencing data associated with the individual is used to compare the signal to a background index. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. The signal indicates the rate at which sequenced loci selected from a personalized disease-associated SNV locus panel are derived from diseased tissue. Optionally, the loci selected from the disease-associated SNV panel are selected based on the false positive rate of the individual loci. In some embodiments, the signal is

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[0119] FIG. 2 illustrates another exemplary method 200 for measuring the level of disease (e.g., cancer) in an individual, e.g., the proportion of nucleic acid molecules (e.g., cfDNA molecules) associated with the disease in a sample from the individual. The sample can be a fluid sample, e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample. At step 205, a personalized disease-associated small nucleotide variant (SNV) locus panel is constructed using sequencing data associated with the diseased tissue and sequencing data associated with the non-diseased tissue. The personalized locus panel is based on the difference between the sequencing data associated with the diseased tissue and the sequencing data associated with the non-diseased tissue. At step 210, loci are selected from the personalized locus panel. In some embodiments, all loci in the personalized locus panel are selected, and in some embodiments, a subset of loci in the personalized locus panel are selected. Loci can be selected from the personalized locus panel, e.g., based on the false positive rate of individual loci. At step 215, sequencing data associated with the sample from the individual is obtained. The sequencing data can be obtained, for example, by sequencing nucleic acid molecules in a sample or by receiving sequencing data from a record. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. At step 220, the nucleic acid sequencing data associated with the individual is used to compare a signal to a background index. The signal indicates the proportion of sequenced loci selected from the personalized disease-associated SNV loci panel that are derived from diseased tissue. In some embodiments, the signal is

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[0120] The methods described herein may be useful for detecting the presence (e.g., recurrence), measuring the level of disease, or measuring or detecting the progression or regression of disease. In some embodiments of the methods described herein, the individual has previously been treated for the disease. In some embodiments, the disease is believed to be in remission, such as complete or partial remission. After treatment of the disease, for example, by chemotherapy or resection of the cancer, the disease may recur, for example, due to incomplete removal or death of all affected tissue. Cancer may, for example, metastasize and migrate to different locations within the individual's body, or may be too small to be detected by known imaging methods (e.g., MRI, PET scan, etc.). Monitoring of the individual for recurrence, regression, or progression of the disease may be performed periodically, so that the individual can be re-treated if the disease recurs or progresses.

[0121] The presence or residual level of a disease, such as cancer, can be detected, for example, by using nucleic acid sequencing data associated with an individual to compare a signal, which indicates the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue, to a noise index, which indicates the sampling variance across the selected loci; and determining whether the individual has the disease based on a comparison of the signal to the background index. In some embodiments, the signal-to-noise ratio is determined, for example, as described herein.

[0122] The statistical significance of detection signal can be determined by comparing the signal with statistical noise (e.g., sampling variance, which may be based at least on the number of true detections and the number of false positive errors).If the signal is greater than statistical noise, for example, when the signal-to-noise ratio (SNR) is greater than about 1.5, about 2, about 3, about 5, about 8, about 10 or greater, disease can be positively detected.On the contrary, in some embodiments, a lower SNR, for example, an SNR of less than about 1.5, less than about 1.4, less than about 1.3, less than about 1.2, or less than about 1.1, indicates non-detection of disease.

[0123] FIG. 3 illustrates an exemplary method 300 for detecting a disease or recurrence of a disease (e.g., cancer) in an individual. In step 305, nucleic acid sequencing data associated with the individual is used to compare the signal to a noise index. The nuclear sequencing data may be derived from nucleic acid molecules in a fluid sample obtained from the individual. For example, in some embodiments, the nucleic acid sequencing data is derived from cell-free DNA in a fluid sample (e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample) from the individual. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. The signal indicates the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue. Optionally, the loci selected from the disease-associated SNV panel are selected based on the false positive rate of each locus. The noise index indicates the sequencing sampling noise across the selected loci. At step 310, a decision is made as to whether the disease exists in the individual based on the comparison of the signal and the noise index. For example, in some embodiments, a statistically significant signal above the noise index indicates that the individual has the disease.

[0124] FIG. 4 illustrates an exemplary method 400 for the presence or recurrence of a disease (e.g., cancer) in an individual. At step 405, a personalized disease-associated small nucleotide variant (SNV) locus panel is constructed using sequencing data associated with diseased tissue and sequencing data associated with non-diseased tissue. The personalized locus panel is based on the difference between the sequencing data associated with diseased tissue and the sequencing data associated with non-diseased tissue. At step 410, loci are selected from the personalized locus panel. In some embodiments, all loci in the personalized locus panel are selected, and in some embodiments, a subset of loci in the personalized locus panel are selected. Loci may be selected from the personalized locus panel, for example, based on the false positive rate of individual loci. At step 415, nucleic acid sequencing data associated with a sample from the individual is obtained. The sequencing data may be obtained, for example, by sequencing nucleic acid molecules in the sample or by receiving sequencing data for the sample from a record. The sample may be a fluid sample obtained from the individual. For example, in some embodiments, the nucleic acid sequencing data is derived from cell-free DNA in a fluid sample (e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample) from the individual. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. At step 420, the nucleic acid sequencing data associated with the individual is used to compare the signal with a noise index. The signal indicates the proportion of sequenced loci selected from the personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue. The noise index indicates the sampling noise across the selected loci. At step 425, a decision is made as to whether a disease is present in the individual based on the comparison of the signal and the noise index.For example, in some embodiments, a statistically significant signal above the noise index indicates that the individual has the disease.

[0125] The presence or persistence of a disease, such as cancer, can also be detected, for example, by measuring the level of disease in an individual. Optionally, the level of disease is indicated by the proportion of nucleic acid molecules in a sample from an individual that originate from diseased tissue. The proportion of nucleic acid molecules, such as cfDNA, in a fluid sample obtained from an individual that originates from diseased tissue correlates with the severity or level of disease in the individual. Thus, the proportion of nucleic acid molecules that originate from diseased tissue can be used as a marker of the residual level or recurrence of disease. For example, the level can be measured by using nucleic acid sequencing data related to an individual to compare a signal that indicates the rate at which sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel originate from diseased tissue with a background index that indicates the sequencing false positive error rate across the selected loci; and determining the level of disease in the individual based on the comparison of the signal and the background index.

[0126] An error for the measured level of the disease (e.g., an error for the measured proportion), such as a confidence interval for the level, is optionally determined. In some embodiments, the error is proportional to the total number of individual small nucleotide variant reads detected at the selected locus. The error for the measured level can be used to determine, for example, whether the measured level is statistically significant. For example, in some embodiments, if the lower limit of the confidence interval for the proportion is above zero, the measured level indicates the presence or recurrence of the disease. The error can also be used to measure the likelihood that the measured proportion is higher than a predetermined value. In some embodiments, the likelihood that a measured proportion of nucleic acid molecules originating from diseased tissue compared to nucleic acid molecules originating from non-diseased tissue is higher than a predetermined threshold (e.g., 0 or higher, about 0.1% or higher, about 0.2% or higher, about 0.5% or higher, about 1% or higher, about 1.5% or higher, about 2% or higher, about 2.5% or higher, about 3% or higher, about 4% or higher, about 5% or higher, about 6% or higher, about 7% or higher, about 8% or higher, about 9% or higher, or about 10% or higher) is measured, with a proportion higher than the predetermined threshold indicating the presence or recurrence of disease in an individual.

[0127] Disease progression or regression can be determined and / or monitored by measuring the level of disease (e.g., the proportion of nucleic acid molecules in an individual's sample that originate from diseased tissue, or a signal indicative of the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that originate from diseased tissue compared to a background index indicative of the sequencing false positive error rate across the selected loci) at two or more time points. Thus, the measured proportion can be compared to the historical proportion, F prior, and compared. These time points may include, for example, a first time point before the start of disease treatment and a second time point after the start of disease treatment. In some embodiments, an increase in the rate or signal (compared to the background index) indicates disease progression, and a decrease in the rate or a decrease in the signal (compared to the background index) indicates disease regression. In some embodiments, a statistically significant increase in the rate or signal (compared to the background index) indicates disease progression, and a statistically significant decrease in the rate or a statistically significant decrease in the signal (compared to the background index) indicates disease regression. The determination error (e.g., confidence interval) of the level for two or more time points can be used to determine whether the change in the measured level is statistically significant.

[0128] FIG. 5 illustrates an exemplary method 500 for monitoring disease (e.g., cancer) recurrence, progression, or regression in an individual. In step 505, nucleic acid sequencing data associated with the individual is used to compare the signal to a background index. The nuclear sequencing data may be derived from nucleic acid molecules in a fluid sample obtained from the individual. For example, in some embodiments, the nucleic acid sequencing data is derived from cell-free DNA in a fluid sample (e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample) from the individual. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. The signal indicates the proportion of sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel that are derived from diseased tissue. Optionally, the loci selected from the disease-associated SNV panel are selected based on the false positive rate of each locus. The background index indicates the sequencing false positive error rate distribution across the selected loci. At step 510, the level of disease in the individual is determined based on a comparison of the signal and the background index. For example, in some embodiments, a statistically significant signal above the background index indicates that the individual has the disease. At step 515, the level of disease in the individual is compared to a previous level of disease in the individual. A statistically significant change in the measured level of disease compared to a previously measured level of disease indicates that the disease has relapsed, progressed, or regressed. For example, a statistically significant increase in the measured level of disease compared to a previously measured level of disease indicates that the disease has progressed. A statistically significant decrease in the measured level of disease compared to a previously measured level of disease indicates that the disease has regressed.

[0129] FIG. 6 illustrates another exemplary method 600 of monitoring disease (e.g., cancer) recurrence, progression, or regression in an individual. In step 605, a personalized disease-associated small nucleotide variant (SNV) locus panel is constructed using sequencing data associated with diseased tissue and sequencing data associated with non-diseased tissue. The personalized locus panel is based on differences between sequencing data associated with diseased tissue and sequencing data associated with non-diseased tissue. In step 610, loci are selected from the personalized locus panel. In some embodiments, all loci in the personalized locus panel are selected, and in some embodiments, a subset of loci in the personalized locus panel are selected. Loci may be selected from the personalized locus panel, for example, based on the false positive rate of individual loci. In step 615, nucleic acid sequencing data associated with a sample from the individual is obtained. The sequencing data may be obtained, for example, by sequencing nucleic acid molecules in the sample or by receiving sequencing data for the sample from a record. The sample may be a fluid sample obtained from an individual. For example, in some embodiments, the nucleic acid sequencing data is derived from cell-free DNA in a fluid sample (e.g., a blood sample, a plasma sample, a saliva sample, a urine sample, or a fecal sample) from the individual. Optionally, the nucleic acid sequencing data is non-targeted and / or non-enriched nucleic acid sequencing data (e.g., whole genome sequencing data). In some embodiments, the sequencing depth of the sequencing data is less than about 100, less than about 10, or less than about 1. In some embodiments, the sequencing depth of the sequencing data is at least 0.01. At step 620, the nucleic acid sequencing data associated with the individual is used to compare the signal to a background index. The signal indicates the rate at which the sequenced loci selected from the personalized disease-associated small nucleotide variant (SNV) locus panel are derived from diseased tissue. The background index indicates the sequencing false positive error rate distribution across the selected loci.At step 625, the level of disease in the individual is determined based on a comparison of the signal to a background index. For example, in some embodiments, a statistically significant signal above the background index indicates that the individual has disease. At step 630, the level of disease in the individual is compared to a previous level of disease in the individual. A statistically significant change in the measured level of disease compared to the previously measured level of disease indicates that the disease has recurred, progressed, or regressed. For example, a statistically significant increase in the measured level of disease compared to the previously measured level of disease indicates that the disease has progressed. A statistically significant decrease in the measured level of disease compared to the previously measured level of disease indicates that the disease has regressed.

[0130] If necessary, the measured rate, measured level, progression, regression and / or recurrence of the disease is recorded, for example, in an electronic medical record (EMR) or patient file. In some embodiments of any of the methods described herein, the individual is informed of the measured rate, measured level, progression, regression and / or recurrence of the disease. In some embodiments of any of the methods described herein, the individual is diagnosed with the disease, disease recurrence or disease progression. In some embodiments of any of the methods described herein, the individual is treated for the disease. Systems and Reports

[0131] The operations described above, including those described in connection with Figures 1-6, are performed, as appropriate, by the components depicted in Figure 7. It will be apparent to one of ordinary skill in the art how other processes, e.g., combinations or subcombinations of all or some of the operations described above, can be performed based on the components depicted in Figure 7. It will also be apparent to one of ordinary skill in the art how the methods, techniques, systems, and devices described herein can be combined with each other, in whole or in part, whether or not those methods, techniques, systems, and / or devices are performed and / or provided by the components depicted in Figure 7.

[0132] FIG. 7 illustrates an example of a computing device according to one embodiment. The device 700 may be a host computer connected to a network. The device 400 may be a client computer or a server. As shown in FIG. 7, the device 700 may be any suitable type of microprocessor-based device, such as a personal computer, a workstation, a server, or a handheld computing device (portable electronic device), such as a phone or tablet. The device may include, for example, one or more of a processor 710, an input device 720, an output device 730, a storage device 740, and a communication device 760. The input device 720 and the output device 730 may generally correspond to those described above and may be either connectable or integral with the computer.

[0133] The input device 720 may be any suitable device for providing input, such as a touch screen, a keyboard or keypad, a mouse, or a voice recognition device. The output device 730 may be any suitable device for providing output, such as a touch panel, a tactile device, or a speaker.

[0134] The storage device 740 may be any suitable device that provides storage, such as electronic, magnetic or optical memory, including RAM, cache memory, a hard drive or a removable storage disk. The communication device 760 may include any suitable device that can send and receive signals using a network, such as a network interface chip or device. The components of a computer may be connected in any suitable manner, such as via a physical bus or wirelessly.

[0135] Software 750, which may be stored in memory 740 and executed by processor 710, may include, for example, programming that embodies functionality of the present disclosure (e.g., as embodied in the devices described above).

[0136] The software 750 may also be stored and / or transported in any non-transitory computer-readable storage medium for use with or in connection with an instruction execution system, apparatus, or device, such as those described above, from which instructions associated with the software can be retrieved and executed. In the context of this disclosure, a computer-readable storage medium may be any medium capable of containing or storing programming, such as storage device 740, for use with or in connection with an instruction execution system, apparatus, or device.

[0137] The software 750 may also be propagated in any transport medium for use with or in connection with an instruction execution system, apparatus, or device, such as those described above, that can retrieve instructions associated with the software from and execute the instructions in the instruction execution system, apparatus, or device. In the context of this disclosure, a transport medium may be any medium that can convey, propagate, or transport programming for use with or in connection with an instruction execution system, apparatus, or device. Transport-readable media may include, but are not limited to, electronic, magnetic, optical, electromagnetic, or infrared wired or wireless propagation media.

[0138] The device 700 can be connected to a network, which can be any suitable type of interconnected communication system. The network can implement any suitable communication protocol and can be protected by any suitable security protocol. The network can include any suitable configuration of network links capable of communicating and receiving network signals, such as wireless network connections, T1 or T3 lines, cable networks, DSL, or telephone lines.

[0139] The device 700 can implement any operating system suitable for operation in a network. The software 750 can be written in any suitable programming language, for example, C, C++, Java, or Python. In various embodiments, application software embodying functionality of the present disclosure can be deployed, for example, in different configurations, for example, in a client / server configuration, or through a web browser as a web-based application or web service.

[0140] The methods described herein may further include, as required, a step of reporting the information determined using the analytical method and / or a step of generating a report that includes the information determined using the analytical method. For example, in some embodiments, the method may further include a step of reporting or generating a report that contains __ regarding the level of disease in an individual. The information reported or in the report may relate, for example, to the proportion of cfDNA in a sample obtained from an individual that is caused by a disease (e.g., cancer), or the presence or absence of a detectable amount of a disease (e.g., cancer). The report may be distributed or the information may be reported to a recipient, for example, a clinician, a subject, or a researcher. EXAMPLES

[0141] The present application can be better understood by reference to the following non-limiting examples, which are provided as exemplary embodiments of the present application. The following examples are presented to more fully explain the embodiments, but should not be construed as limiting the broad scope of the present application in any way. Although certain embodiments of the present application have been shown and described herein, it should be clear that such embodiments are provided merely as examples. Numerous variations, modifications and substitutions that do not depart from the spirit and scope of the present invention will occur to those skilled in the art. It should be understood that various alternatives to the embodiments described herein can be utilized in carrying out the methods described herein. Example 1

[0142] DNA from a cancer tissue biopsy taken from the individual is sequenced by whole genome sequencing to obtain sequencing data associated with the cancer tissue. A blood sample is taken from the individual and DNA from the whole blood is sequenced to obtain sequencing data associated with the healthy tissue. The sequencing data associated with the cancer tissue is compared to the sequencing data associated with the healthy tissue, and the differences are catalogued in a personalized disease-associated SNV locus panel. The variants in the personalized locus panel are filtered based on the variant's false positive error rate, and the variant with the lowest false positive error rate is selected for analysis. N var Select the total number of loci.

[0143] Cell-free DNA is collected from a fluid sample from an individual and the cfDNA is sequenced using non-targeted and non-enriched whole genome sequencing to obtain sequencing data at a mean sequencing depth of D. This sequencing method results in a sequencing false positive error rate of E. The number of sequencing reads with variant calls from the personalized locus panel, N total , and measure the proportion of nucleic acid molecules in the fluid sample that are associated with disease (F prior ) along with its percentage error.

[0144] The individual undergoes treatment for cancer. After treatment, cell-free DNA is harvested from a subsequent fluid sample from the individual, and the cfDNA is sequenced using non-targeted and non-enriched whole genome sequencing to obtain sequencing data at a mean sequencing depth of D, which is the same or different depth as that of the previous sample. This sequencing method results in a sequencing false positive error rate of E, which is the same or different from that of the previous sample. The number of sequencing reads with variant calls from the personalized locus panel, N total , and measure the proportion of nucleic acid molecules in the fluid sample that are associated with disease (F present ) along with its percentage error.

[0145] The proportion associated with the more recent samples (F present ) to the proportion related to past samples (F prior ) to monitor progression or regression of the cancer. A statistically significant increase in the rate indicates that the disease has progressed, and a statistically significant decrease in the rate indicates that the disease has regressed. Example 2

[0146] DNA from a cancer tissue biopsy taken from the individual is sequenced by whole genome sequencing to obtain sequencing data associated with the cancer tissue. A blood sample is taken from the individual and DNA from the whole blood is sequenced to obtain sequencing data associated with the healthy tissue. The sequencing data associated with the cancer tissue is compared to the sequencing data associated with the healthy tissue, and the differences are catalogued in a personalized disease-associated SNV locus panel. The variants in the personalized locus panel are filtered based on the variant's false positive error rate, and the variant with the lowest false positive error rate is selected for analysis. N var Select the total number of loci.

[0147] The individual undergoes treatment for cancer. After treatment, cell-free DNA is harvested from a subsequent fluid sample from the individual, and the cfDNA is sequenced using non-targeted and non-enriched whole genome sequencing to obtain sequencing data at a mean sequencing depth of D, which is the same or different depth as that of the previous sample. This sequencing method results in a sequencing false positive error rate of E, which is the same or different from that of the previous sample. The number of sequencing reads with variant calls from the personalized locus panel, N total , is measured to determine the signal-to-noise ratio (SNR) of the nucleic acid molecules in the fluid sample that are associated with the disease. An SNR ratio above a set threshold (k) indicates that the individual has a residual amount of the disease. Example 3

[0148] Cancer samples were purchased from the Analytical Biological Services (ABS) biobank, where normal and diseased human tissue biospecimens were collected with appropriate informed consent and under strict regulatory compliance requirements for commercial research. Biospecimens include tumor biopsies (archival FFPE) matched to buffy coat and plasma (cfDNA) from cancer donors. This study evaluated the genetic signatures of these samples.

[0149] Samples. FFPE, buffy coat and plasma samples were obtained for Patient 1, a 40-year-old female with metastatic adenocarcinoma of the colon. The FFPE sample contained approximately 80% cancer cells and approximately 10-20% fibroblasts and infiltrating mononuclear cells and necrotic tissue (dead tissue).

[0150] A plasma sample was obtained for Patient 2, a 69-year-old male with metastatic melanoma cancer. The plasma sample from Patient 2 was used as a control to determine the sequencing error rate. The plasma sample was reddish in color, indicative of red and white blood cells in the blood draw. Due to lysed blood cells, there may be a higher than expected background non-tumor cfDNA relative to cancer cfDNA (i.e., ctDNA).

[0151] Nucleic acid extraction and library preparation. Nucleic acid molecules were extracted from 100 μL of buffy coat (Patient 1) using the DNeasy Blood & Tissue Kit or the AllPrep® DNA / RNA Kit. Extracted gDNA from both kits was combined and 1000 ng of extracted gDNA was used for library construction using the Roche KAPA HyperPrep Kit.

[0152] Nucleic acid molecules were extracted from 30 μm sections of FFPE tissue (Patient 1) using the DNeasy Blood & Tissue Kit and xylene or the RecoverAll™ Total Nucleic Acid Isolation Kit. 173 ng of gDNA extracted from FFPE samples using the DNeasy Blood & Tissue Kit with xylene on slides was used for library construction of the first FFPE-based library, and 446 ng of gDNA extracted from FFPE samples using the RecoverAll™ Total Nucleic Acid Isolation Kit (without xylene on slides) was used for library construction of the second FFPE-based library. Libraries were constructed using the Roche KAPA HyperPrep Kit, followed by 7 cycles of PCR with the KAPA HiFi HotStart ReadyMix kit.

[0153] Nucleic acid molecules were extracted from 4 mL of plasma (patient 1 or patient 2) using the MagMAX™ Cell Free Total Nucleic Acid Isolation Kit. 100 ng of cfDNA from patient 1 plasma sample and 25 ng of cfDNA from patient 2 plasma sample were used for library construction using the Roche KAPA HyperPrep Kit, followed by 7 cycles of PCR with the KAPA HiFi HotStart ReadyMix kit.

[0154] Accurate quantification of the adaptor-ligated libraries was performed using the KAPA Library Quantification Kit.

[0155] Whole-genome sequencing. Emulsion PCR and sequencing were performed for each sample at 30–150x coverage using Ultima Genomics equipment and protocols (TACG flow cycle).

[0156] Bioinformatics analysis: 917,319,868 raw reads (library 1, average length 228 bases at median coverage) were obtained for the buffy coat (patient 1) sample library. 2,136,822,000 raw reads (library 2, average length 183 bases) were obtained for the cfDNA (plasma, patient 1) sample library. 553,298,760 raw reads (library 3) and 1,768,786,851 raw reads (library 4) (average length of 186 bases) were obtained for the two different FFPE-based sequencing libraries.

[0157] 211,8786,000 raw reads (average length 187 bases) were obtained for the cfDNA (plasma, patient 2) sample library (library 5).

[0158] Raw reads were aligned to the reference genome (hg38) using BWA (version 0.7.15-r1140) and duplicates were marked using the Picard Tool (version 2.15.0, Broad Institute) for buffy coat and FFPE reads or the SAM Tools rmdup program for cfDNA reads. After alignment and duplicate removal, the median genome coverage was 45x, 84x, 8x, 18x and 56x for libraries 1–5, respectively.

[0159] The HaplotypeCaller program from the GATK4 package (modified to process sequencing data generated by Ultima Genomics instruments and protocols) was used to call variants in the FFPE reads with respect to the hg38 reference genome separately. 4,694,198 variants were called from the first FFPE-based library (library 3) and 6,702,421 variants were called from the second FFPE-based library (library 4). The baseline variants from the two FFPE samples were combined for a list of 7,682,808 unique variants (i.e., "baseline variants") to account for sample processing variance, and for each baseline variant, the number of reads supporting the baseline variant in each of the samples was tabulated. The baseline variants were then filtered to remove germline variants, variants resulting from DNA damage due to sample preparation, and variants resulting from sequencing errors. First, the baseline variants were filtered to include only SNP variants supported by two or more sequencing reads, resulting in 4,179,203 unique variants. These variants were then filtered to remove variants with allele frequency greater than 0.01 (likely to be germline mutations) from a population database (gnomAD v3, available from the Broad Institute), resulting in 1,292,135 unique variants. These variants were then filtered to remove variants of 8 bases or longer in homopolymeric regions, resulting in 1,176,179 unique variants. These variants were then filtered to remove unsupported variants in the complementary strand (suspected to be sequencing errors), resulting in 505,500 unique variants.These variants were then filtered to remove variants detected by reads from buffy coat samples (presumed to be germline and / or non-cancerous somatic mutations), resulting in 67,660 unique variants. From the panel of 67,660 unique variants, 17,073 variants present in both FFPE sample libraries and predicted to induce cycle shifts (i.e., flowgram signal shifts of one full cycle (e.g., four flow positions) or more compared to the reference based on the flow cycle order) were selected for further analysis. As a comparison, 17,509 variants present in both FFPE sample libraries and predicted to induce cycle shifts (i.e., containing new zero or new non-zero flowgram signals) in the case of different flow orders were analyzed, as well as 5,748 variants that could not induce cycle shifts (i.e., containing neither new zero nor new non-zero flowgram signals).

[0160] We performed bioinformatics analyses using patient 1 data and cfDNA from patient 2 to estimate sequencing error rates for the same set of selected variants. The results showed that the estimated fraction of cfDNA associated with cancer in patient 1 was:

number

[0161] By analyzing possible cycle shift variants, the estimated fraction of cancer-associated cfDNA in patient 1 was determined to be 4.34%, and the background level was determined to be approximately 0.44%, thus yielding an error-corrected fraction of 3.9%. See Table 3. [Table 3]

[0162] By analyzing variants that did not induce cycle shifts or potential cycle shifts, the estimated fraction of cancer-associated cfDNA in patient 1 was determined to be 3.92% and the background level was determined to be approximately 0.55%, thus yielding an error-corrected fraction of 3.37%. See Table 4. [Table 4] Example 4

[0163] The genome of DNA sample NA12878 (sample available from the Coriell Institute for Medical Research) was sequenced using non-terminating fluorescently labeled nucleotides following four flow cycles (TACG). The sequencing run generated 415,900,002 reads with an average length of 176 bases. 399,804,925 reads were aligned (with BWA, version 0.7.17-r1188) to the hg38 reference genome.

[0164] After alignment, we selected reads that were either perfectly aligned with the reference genome (178,634,625 reads) or had a single mismatch with the reference genome and aligned with a mapping quality score of 20 or higher (27,265,661 reads). That is, 193,904,639 were not included in further analysis because they had, for example, indels, multiple mismatches, or potentially incorrect (artifactual) alignments with the reference genome. Therefore, we estimated that the 27,265,661 reads included not only true positive NA12878 SNPs, but also any false positive SNPs resulting from sequencing errors. From this pool of 27,265,661 reads, we removed sequencing reads that spanned the mismatch locus more than once, which reduces the effect of true positive NA12878 SNP variants, resulting in a total of 3,413,700 reads with mismatches at depth 1.

[0165] Each of the remaining 3,413,700 reads contained a mismatch that was (1) expected to induce a cycle shift if the flowgram flow signal was shifted one full cycle (e.g., 4 flow positions) relative to the reference based on the flow cycle order, (2) a mismatch that could potentially induce a cycle shift if a different flow cycle was used (e.g., it would generate a new zero or a new nonzero signal in the flowgram), or (3) a mismatch that would not be able to induce a cycle shift regardless of the flow cycle order. Of the 3,413,700 mismatches, 1,184,954 (34%) induced a cycle shift, whereas 1,546,588 (43%) could induce a cycle shift with a different flow order (i.e., "possible cycle shift"). In comparison, theoretical expectations for random mismatches suggested a nominal cycle shift of 42% and a possible cycle shift of 46%. Overall, the mismatch rate inducing a cycle shift was 3.7 × 10 -5 The mismatch rate for inducing a potential cycle shift, in events / base, is 4.8 × 10 -5Table 5 shows the 10 most frequent single mismatches that induce cycle shifts and the relative percentage of occurrence. [Table 5]

[0166] The performance of mismatch-based variant calling in each of the three different classes (i.e., inducing cycle shift, potentially inducing cycle shift, or not inducing cycle shift and not capable of inducing cycle shift) was then evaluated. Reads were aligned to the reference genome using BWA, and variant calling was performed using the HaplotypeCaller tool in GATK (version 4). The resulting mismatch calls were filtered by discarding variant calls in homopolymers longer than 10 bases or within 10 bases adjacent to homopolymers having a length of 10 bases or more.

[0167] Mismatch calls were compared to calls generated for the same NA12878 by the genome-in-the-bottle (GIAB) project to determine the accuracy #TP / (#FP+#FN+#TP) for each class of mismatch. Sequencing data were randomly downsampled to the average genomic depths indicated. Cycle-shift-inducing and potential cycle-shift-inducing mismatches had higher accuracy than non-cycle-shift-inducing mismatches, as demonstrated in Table 6. [Table 6]

Claims

1. 1. A method for providing (a) a likelihood that a value indicative of a proportion of nucleic acid molecules in a sample that originates from diseased tissue of the individual, F, is greater than zero, and / or (b) a change in a value indicative of the proportion of nucleic acid molecules in a sample that originates from diseased tissue of the individual, F, as an indication of the presence, progression or regression of disease in an individual, comprising: (a) the likelihood that the value representing the proportion, F, of nucleic acid molecules in the sample is greater than zero, where F greater than zero is indicative of the presence of the disease in the individual; and (b) a change in the value indicative of the proportion, F, of nucleic acid molecules in the sample, which change is relative to a previously measured proportion, F prior, and wherein the change in F is indicative of progression or regression of the disease in the individual; measuring at least one of The ratio F is determined according to the following formula: [0010] The total number of single nucleotide variants (SNVs) detected in the cell-free nucleic acid sequencing data, N ｔｏｔａｌ wherein the SNV is selected from a personalized disease-associated SNV locus panel. ｔｏｔａｌ and the number of loci associated with SNVs selected from the personalized disease-associated SNV locus panel, N ｖａｒ , adjusted by the average sequencing depth, D, ｖａｒ and adjusting for a sequencing false positive error rate, E, across the locus associated with the selected SNV; The method is determined by:

2. generating said personalized panel of disease-associated SNV loci; sequencing nucleic acid molecules from said sample of diseased tissue to determine a set of disease-associated SNVs; and filtering said set of disease-associated SNVs to remove germline variants and non-disease-associated somatic variants. The method of claim 1 , comprising:

3. The method of claim 1 or 2, further comprising filtering the set of disease-associated SNVs to remove SNVs that are supported by only one sequencing read, SNVs that are not supported by one or more complementary sequencing reads, or SNVs that are present in the general population of individuals at an allele frequency higher than a predetermined threshold.

4. the nucleic acid sequencing data is obtained by sequencing nucleic acid molecules from a fluid sample obtained from the individual using non-terminating nucleotides provided in separate nucleotide flows according to a first flow cycle sequence comprising a plurality of flow positions, the flow positions corresponding to the nucleotide flows; generating the personalized disease-associated SNV loci panel further comprises filtering the set of disease-associated SNVs to include only SNVs that, when the nucleic acid sequencing data and reference sequencing data are sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the first flow cycle order, result in nucleic acid sequencing data that differs from the reference sequencing data associated with a reference sequence at two or more flow sequential positions. A method according to claim 2 or claim 3 when dependent on claim 2.

5. 5. The method of claim 4, wherein generating the personalized panel of disease-associated SNV loci comprises filtering the set of disease-associated SNVs to include only SNVs that result in nucleic acid sequencing data that differs from reference sequencing data associated with a reference sequence at four or more consecutive flow positions when the nucleic acid sequencing data and the reference sequencing data are sequenced using non-terminating nucleotides provided in separate nucleotide flows according to the first flow cycle order.

6. 6. The method of claim 4 or 5, wherein the nucleic acid sequencing data is further obtained by resequencing the nucleic acid molecules according to a second flow cycle order, the second flow cycle order resulting in a different false positive variant rate in a subset of loci in the SNV locus panel compared to the first flow cycle order.

7. 7. The method of claim 1, wherein the nucleic acid sequencing data is non-targeted sequencing data.

8. 8. The method of claim 1, wherein the average sequencing depth of the nucleic acid sequencing data is at least 0.01 and less than 10.

9. 9. The method of any one of claims 1 to 8, wherein the selected SNVs from the personalized disease-associated SNV locus panel are associated with 300 or more loci.

10. 10. The method of any one of claims 1 to 9, wherein the SNVs are selected from the personalized disease-associated SNV gene presence panel based on the false positive rate of individual loci associated with the SNVs.

11. 11. The method of claim 1, wherein the nucleic acid sequencing data is obtained using surface-based sequencing of the nucleic acid molecule, and the nucleic acid molecule is not amplified prior to attachment of the nucleic acid molecule to a surface.

12. 12. The method of any one of claims 1 to 11, wherein the nucleic acid sequencing data is obtained without the use of unique molecular identifiers (UMIs) or sample identification barcodes.

13. 13. The method of any one of claims 1 to 12, wherein the sequencing false positive error rate is measured using a panel of control loci.

14. 14. The method of any one of claims 1 to 13, wherein the nucleic acid sequencing data is obtained by sequencing nucleic acid molecules obtained from multiple individuals in a pooled sample.

15. The method of claim 14, wherein the selected SNVs are unique to each individual of the plurality of individuals.

16. 16. The method of any one of claims 1 to 15, wherein the disease is cancer.

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