41 results about "Fetal dna" patented technology

Compositions, methods, kits, systems, and software are provided for non-invasive prenatal testing for autosomal recessive diseases. Next generation sequencing is used to sequence maternal and fetal DNA isolated from maternal plasma by probe capture. The fetal fraction of the sequencing reads for DNA isolated from maternal plasma is estimated by counting single nucleotide polymorphisms (SNPs) for which an allele is detected that is present in the paternal haplotype but absent in the maternal haplotype, based on the assumption that SNPs having a paternal allele belong to the fetal DNA. The fetal fraction is bioinformatically enriched by excluding sequencing reads over a specified length via in-silico size selection, which increases fetal genotype prediction accuracy. Parental haplotype information together with the read ratios observed at the linked SNPs is used to predict the fetal genotype at a site of a mutation linked to the autosomal recessive disease.

The disclosure relates to methods, compositions, and kits for the early determination of the sex of a fetus. The disclosure also provides methods, compositions, and kits for detecting fetal nucleic acids in biological samples (e.g., cell-free fetal DNA).

The proposed method utilizes telomere length as a marker for estimating the proportion of different components present in a DNA mixture with broad applications in genetic testing. It can be used as an independent or complementary technique to existing methods to increase the precision and reliability of results. In the context of non-invasive prenatal testing (NIRT), the method can provide valuable information about the proportion of fetal DNA present in a maternal blood sample, allowing for the accurate identification of genetic disorders and abnormalities. The method is also applicable in the detection and characterization of ongoing oncological disease, where anomalies in telomere length can indicate the presence of tumor DNA fragments in blood plasma samples.

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The invention provides methods for assessment of fetal DNA samples using target-enriched multiplexed parallel analysis. The methods of the invention utilize TArget Capture Sequences (TACS) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The methods can be used with fetal or embryonic DNA samples, for example for detection of the presence of genetic abnormalities, e.g., for purposes of IVF Pre-implantation Genetic Screening (PGS) and Diagnosis (PGD). Kits for carrying out the methods of the invention are also provided.

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).

The present disclosure provides for a method of treating fetal growth restriction in a fetus comprising obtaining a blood sample from a pregnant subject; isolating cell-free fetal DNA from the blood sample; testing the cell-free fetal DNA for a first DNA methylation level of 0.5800 or less in a group of genes, wherein the group of genes comprises the genes of any one of Tables 19-21, wherein the first DNA methylation level is calculated via an average of all differentially methylated islands of cytosine and guanine dinucleotides separated by only one phosphate in the 5' to 3' direction (5'-C-phosphate-G-3') (CpGIs) in differentially methylated regions (DMRs); and when the first DNA methylation level is 0.5800 or less, selecting a treatment from the following: monitoring the fetus during pregnancy of the pregnant subject, tracking movements of the fetus, admitting the pregnant subject to a hospital prior to going into labor, inducing early delivery of the fetus, performing an emergency Cesarean section on the pregnant subject, administering corticosteroids to the pregnant subject, or administering corticosteroids to the fetus upon birth. Other related methods are disclosed herein.

The invention discloses a method for evaluating fetal DNA concentration (cffDNA) in free blood of a pregnant female parent through a polymorphic site linkage region block. The method comprises the following steps: acquiring low-depth WGS sequencing data of a sample; obtaining a mapping relation between the point location and the linkage polymorphic relation; and according to the low-depth WGS sequencing data and the mapping relationship between the point locations and the linkage polymorphic relationship, performing concentration calculation by taking a plurality of sites forming the linkage polymorphic relationship as units. Wherein the mapping relation between the point location and the linkage polymorphism can be obtained by processing public genome WGS data, processing public linkage polymorphism region block data or processing a large amount of high-depth WGS measured data. Based on the low-depth WGS data, the cffDNA concentration in the free blood of the pregnant female parent can be directly calculated through the heterozygosity of the linkage SNP region blocks, the method is not affected by the gender of a fetus in NIPT practical application, a father sample and an additional experiment are not needed, the stability is high, the performance is high, and the cost is low.

The present application relates to the field of paternity determination, and provides a non-invasive prenatal paternity relationship determination method and system and electronic equipment, the method comprising: obtaining a paternal DNA sample and a pregnant woman's plasma free DNA sample, the pregnant woman's plasma free DNA sample including a fetal DNA sample; performing genomic sequencing on the paternal DNA sample and the pregnant woman's plasma free DNA sample; after genotype filling, determining the paternal genotype and the fetal genotype; calculating the kinship coefficient of the paternal genotype and the fetal genotype; based on the kinship coefficient of the paternal genotype and the fetal genotype and a pre-constructed corresponding relationship between the kinship coefficient and the paternity relationship, determining the paternity relationship between the father and the fetus. The present application solves the defects of low detection efficiency and high technical cost in the related art, and is convenient to operate, completely non-invasive, and does not cause any physiological interference to the pregnant woman and the fetus; the detection can be carried out from the seventh week of pregnancy, and is suitable for precise identification of the biological father of the fetus and unrelated individuals.

The present invention discloses a method and application for evaluating fetal DNA concentration using maternal cell-free DNA and maternal DNA, belonging to the field of bioinformatics technology. The method comprises the following steps: S101: sequencing the dimorphic sites of the maternal leukocyte DNA sample and the maternal cell-free DNA sample to obtain DNA data M and S respectively; S102: obtaining the site set X' that meets the predetermined requirements in S; S103: calculating the probability P of a certain site on the site set X' according to formula I; S104: using the maximum likelihood value method to obtain p when the cumulative probability h of the point set X' is the largest; max ; S105: the concentration N of fetal DNA = 2p max . This method can evaluate the fetal DNA concentration. During paternity testing, it can be determined whether it is necessary to detect the maternal leukocytes and whether it is necessary to resubmit the sample according to the evaluation value; thereby improving the accuracy of paternity testing.

A chromosomal aneuploidy analysis method and a use. The method comprises: using sequencing data of a sample to be tested and an alignment result thereof to calculate the fetal DNA concentration in said sample and the window depth of said sample within a set window; and calculating the average relative depth of all samples in a selected reference set within the set window as a correction baseline, using the correction baseline to correct the window depth of said sample, calculating a Z value of said sample on the basis of the corrected window depth, and on the basis of the Z value, determining whether an aneuploidy abnormality has occurred to a fetal chromosome of said sample. Using the selected reference set to calculate the correction baseline for correcting said sample enables more stable and accurate detection of the chromosomal aneuploidy abnormality in said sample under the condition that there are no samples in a same batch as references, thereby reducing inter-batch variability in testing.

A method of detecting fetal cell-free fetal DNA (cffDNA) in the breath of the pregnant woman is provided. The method includes condensation of the breath sample to liquefy; selection of the target genome region locus; selection of primers that amplify the selected locus; selection of probes that attach to the replicated locus; introducing the targeted site primers and the breath sample into the PCR cycle and amplifying the targeted locus, if present in the sample; binding the probes specific to the amplified region; detecting the fluorescent radiation with the PCR reader and presenting it as data, if there is a targeted region in the breath sample.

This application discloses a method, apparatus, and storage medium for detecting fetal chromosomal aneuploidy. The method for detecting fetal chromosomal aneuploidy includes calculating a new Z-value for the sample based on the fetal DNA concentration, Z-value, and chimerism of the cell-free DNA in the pregnant woman's blood; the new Z-value is used to determine whether fetal chromosomal aneuploidy has occurred. Chimerism is the ratio of abnormal fetal cells to all fetal cells. This application is the first to incorporate chimerism into the detection of fetal chromosomal aneuploidy, comprehensively considering three variables—fetal DNA concentration, chimerism, and Z-value—to calculate a new Z-value, which improves the accuracy of NIPT detection, provides excellent differentiation between true positive and false positive samples, and reduces false positives. The new Z-value conforms to a normal distribution, meeting current regulatory and clinical requirements, reducing data distribution volatility, thereby reducing the gray area rate, reducing the retest rate, and improving the stability of the test results.

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The invention belongs to the technical field of fetal chromosome aneuploid detection, and particularly relates to a DNA library construction method in fetal chromosome aneuploid detection, and the method comprises the following steps: S1, carrying out terminal repair and 3'A addition on DNA; s2, connecting a sequencing joint and a tag; s3, purifying the DNA; s4, carrying out amplification on the purified DNA; according to the method, a PCR reinforcing agent is added in the amplification process to improve the amplification efficiency, a fragment screening step is added in library construction, fragment purification is carried out according to the concentration of magnetic beads, the concentration of fetal DNA can be effectively increased, the content of fetal DNA in peripheral blood is increased, impurity residues are reduced, and the detection sensitivity is improved. Moreover, the enzyme activity is not influenced, and the uniformity and quality of sequencing data are improved.

Provided are a method and apparatus for determining a concentration of fetal DNA. The method for determining the concentration of fetal DNA includes: acquiring multiple sequencing reads of a cell-free DNA (cfDNA) sample under test; aligning the multiple sequencing reads with a reference genome to obtain alignment results; and determining the concentration of fetal DNA based on the alignment results. The concentration of fetal DNA can be determined based on the alignment results between the sequencing reads and the reference genome so that applications to various sequencing platforms including a single-molecule sequencing platform can be satisfied, and the accuracy of determination of the concentration of fetal DNA can be improved.

Systems, apparatuses, and method are provided for determining the contributions of different tissues to a biological sample that includes a mixture of cell-free DNA molecules from various tissues types, e.g., as occurs in plasma or serum and other body fluids. Embodiments can analyze the methylation patterns of the DNA mixture (e.g., methylation levels at particular loci) for a particular haplotype and determine fractional contributions of various tissue types to the DNA mixture, e.g., of fetal tissue types or tissue types of specific organs that might have a tumor. Such fractional contributions determined for a haplotype can be used in a variety of ways.

The invention discloses a chromosome aneuploid analysis method and application, and the method comprises the following steps: calculating the fetal DNA concentration in a to-be-detected sample and the window depth of the to-be-detected sample in a set window by adopting the sequencing data of the to-be-detected sample and the comparison result of the to-be-detected sample; and calculating the average value of the relative depths of all the samples in the selected reference set in the set window as a correction baseline, correcting the window depth of the to-be-detected sample by adopting the correction baseline, calculating the Z value of the to-be-detected sample according to the corrected window depth, and judging whether the aneuploid abnormality occurs in the fetal chromosome of the to-be-detected sample according to the Z value. According to the method, the to-be-detected sample is corrected by calculating the correction baseline by selecting the reference set, so that the chromosome aneuploid abnormality of the to-be-detected sample can be more stably and accurately detected under the condition that no sample in the same batch is taken as a reference, and the batch fluctuation of detection is reduced.

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists in a biological sample. One or more cutoff values ​​are selected to determine an imbalance, for example, the ratio of two sequences (or sets of sequences). The cutoff value can be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, that contains a background of maternal nucleic acid sequences. 1 [ cutoff value can be determined based on an average concentration of a sequence per reaction. In one aspect, the cutoff value is determined by a proportion of informative wells that are estimated to contain a particular nucleic acid sequence, wherein the proportion is determined based on the aforementioned percentage and / or average concentration. The cutoff value can be determined using many different types of methods, such as sequential likelihood ratio testing (SPRT).

This invention relates to a method for non-invasive prenatal screening using cell-free DNA extraction. Specifically, the invention provides a method and system for extracting cell-free DNA from liquid biological samples. The method can be used for determining fetal DNA fractions and for non-invasive prenatal screening of fetal aneuploidy and analysis of other types of cell-free DNA.

A method for evaluating fetal DNA concentration (cffDNA) in maternal blood during pregnancy through polymorphic locus linkage block, comprising: obtaining low-depth WGS sequencing data of the sample; obtaining a mapping relationship between the locus and the linkage polymorphism; and calculating the concentration according to the low-depth WGS sequencing data and the mapping relationship between the locus and the linkage polymorphism and taking a plurality of loci constituting the linkage polymorphism as a unit. Wherein, the mapping relationship between the locus and the linkage polymorphism can be obtained by processing public genome WGS data, processing public linkage polymorphism block data or processing a large amount of high-depth WGS measured data. The present application is based on low-depth WGS data, and the heterozygosity of the linkage SNP block can be used to calculate the cffDNA concentration in the maternal blood during pregnancy, which is not affected by the fetal gender in the actual application of NIPT, does not require the father's sample and does not require additional experiments, has high stability, high performance and low cost.

Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

The present invention discloses a method and application for evaluating fetal DNA concentration using the DNA of the biological father and the mother, belonging to the field of bioinformatics technology. The method comprises the following steps: S101: Sequencing the dimorphic sites of the biological father DNA sample and the pregnant woman's cell-free DNA sample respectively to obtain DNA data F and S; S102: Obtaining the site set X' in S that meets the predetermined requirements; S103: Calculating the probability P of a certain site on the site set X' according to formula I; S104: Using the maximum likelihood value method to obtain p when the cumulative probability h of the point set X' is the largest; S105: The concentration N of fetal DNA = 2p max ; S105: The concentration N of fetal DNA = 2p max . This method can evaluate the fetal DNA concentration. During paternity testing, it can be determined whether it is necessary to detect the white blood cells of the pregnant woman and whether it is necessary to resubmit the sample according to the evaluation value; thereby improving the accuracy of paternity testing.

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, 5 microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality 10 in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The present application discloses a method and apparatus for detecting fetal chromosomal aneuploidy, and a storage medium. The method for detecting fetal chromosomal aneuploidy of the present application comprises: according to the concentration of fetal DNA in the cell-free DNA in the blood of a pregnant woman to be tested, a Z value, and chimerism, calculating a new Z value of the sample to be tested, and according to the new Z value, determining whether an aneuploidy abnormality has occurred in fetal chromosomes, the chimerism being the ratio of abnormal fetal cells to all fetal cells. In the present application, chimerism is inventively applied to fetal chromosomal aneuploidy detection, and three variables, i.e., the fetal DNA concentration, the chimerism, and the Z value, are taken into consideration to calculate the new Z value, such that NIPT accuracy can be improved, and true positive and false positive samples can be distinguished well, thereby reducing false positive samples; and the new Z value conforms to a normal distribution, such that the current supervision and clinical use requirements can be met, and data distribution fluctuations are reduced, thereby reducing the gray scale rate and the retest rate, and improving the stability of the test result.

Methods, systems, and devices are provided for determining whether a nucleic acid sequence imbalance is present in a biological sample.SOLUTION: One or more cutoff values for determining imbalance are selected, e.g., a ratio of two sequences (or sets of sequences). This cutoff value can be determined based, at least in part, on the percentage of fetal DNA in the sample that contains a background of maternal nucleic acid sequences, such as maternal plasma. The cutoff value can also be determined based on the average concentration of sequences per reaction. In one aspect, this cutoff value is determined from the proportion of informative wells that are likely to contain a particular nucleic acid sequence, where the proportion is determined based on the percentages and / or average concentrations described above. This cutoff value can be determined using many different types of methods, such as a sequential probability ratio test (SPRT).SELECTED DRAWING: Figure 1

Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

Methods, apparatuses, and system are provided for analyzing a maternal sample to determine whether a male fetus of a pregnant female has inherited an X-linked mutation from the mother. A percentage of fetal DNA in the sample is obtained, and cutoff values for the two possibilities (fetus inherits mutant or normal allele) are determined. A proportion of mutant alleles relative to a normal allele on the X-chromosome can then be compared to the cutoff values to make a classification of which allele is inherited. Alternatively, a number of alleles from a target region on the X-chromosome can be compared to a number of alleles from a reference region on the X-chromosome to identify a deletion or amplification. The fetal DNA percentage can be computed by counting reactions with a fetal-specific allele, and correcting the number to account for a statistical distribution among the reactions.