105 results about "Tumor Sample" patented technology

Disclosed herein are systems, methods, and compositions for treating a subject diagnosed with, or suffering from cancer. In some embodiments, the method comprises determining whether a tumor sample from the subject includes a cytotoxic gene signature, and treating the subject based on the determination. In some embodiments, the subject has or is suspected of having a loss of heterozygosity in human leukocyte antigen (HLA) class I genes. In some embodiments, the therapy comprises one or more checkpoint inhibitors. In some embodiments, the cancer is colorectal, uterine, stomach, lung, skin, head or neck, or non-small cell lung carcinoma.

The invention discloses a microsatellite instability detection method based on single-sample high-throughput sequencing for microsatellite site micro-offset, and relates to the technical field of bioinformatics, and the microsatellite instability detection method comprises the following steps: processing a sequencing sequence of a to-be-detected sample obtained by a high-throughput sequencing technology to obtain a comparison file; according to the method, selection and quality control of microsatellite sites are strictly controlled, a microsatellite instability detection method based on single-tumor sample high-throughput sequencing can be used for analyzing the repetition times of candidate microsatellite site repetition units without depending on a control sample, and meanwhile, the method has very good sensitivity to a sample with relatively large offset, so that the accuracy of the microsatellite instability detection is greatly improved. The method can also be applied to other cancer species with MSI characteristics, and can adapt to detection requirements of different cancer species by adjusting candidate microsatellite loci no matter whether a micro-migration condition exists or not, provide visualization, assist in seeing the degree of microsatellite migration, facilitate manual recheck and reduce misjudgment.

The present disclosure encompasses methods for molecularly subtyping formalin-fixed paraffin-embedded tumor samples. The disclosure works particularly well for old and degraded (archival) samples for which standard methods are unfeasible. Further, the methods disclosed allow for the correlation of patient outcome data with the molecular subtype of the tumor and provides a wealth of information which will guide treatment decisions and / or selection of therapeutic agents.

Provided are methods for expanding tumor-infiltrating lymphocytes (TILs), which include co-culturing an initial cell population containing TILs with first feeder cells to obtain a first expanded cell population; and then co-culturing the first expanded cell population with second feeder cells to obtain an expanded TIL population. The methods can quickly produce a large number of TILs from a small tumor sample.

The present invention relates to the provision of vaccines which are specific for a patient's tumor and are potentially useful for immunotherapy of the primary tumor as well as tumor metastases. In one aspect, the present invention relates to a method for providing an individualized cancer vaccine comprising the steps: (a) identifying cancer specific somatic mutations in a tumor specimen of a cancer patient to provide a cancer mutation signature of the patient; and (b) providing a vaccine featuring the cancer mutation signature obtained in step (a). In a further aspect, the present invention relates to vaccines which are obtainable by said method.

Described herein are techniques for predicting whether a subject will respond to an immune checkpoint inhibitor (ICI) therapy based on RNA expression data and cytometry data obtained for the subject. In some embodiments, the techniques include: obtaining the RNA expression data, the RNA expression data having been previously obtained from a tumor sample from the subject; selecting, using the RNA expression data, an MF profile type for the tumor sample; obtaining the cytometry data, the cytometry data having been previously obtained from a blood sample from the subject; determining, using the cytometry data, a G2 score for the blood sample, wherein the G2 score is indicative a likelihood that the blood sample is of a Primed (G2) immunoprofile type of multiple immunoprofile types; and predicting, based on the selected MF profile type and the G2 score, whether the subject will respond to the ICI therapy.

The invention provides a fusion transcript recognition method, device and system based on transcriptome multiple comparison data and a medium, and the core of the method is to construct a set of full-chain analysis framework oriented to multiple mapping reads to realize fusion gene detection. Comprising a pairing read segment preliminary screening module based on a loose mapping strategy, a candidate fusion construction module based on an exon graph structure, a remapping module based on an enhanced reference transcriptome, a transcript abundance estimation module based on a probability generation model, and a fusion scoring module based on fusion site specificity support degree. And a false positive inhibition module based on coverage consistency and biological filtration. According to the method, the dependence of a traditional fusion gene detection method on a unique mapping read is broken through, multiple comparative analysis on the fuzzy mapping read abandoned due to sequence homology is proposed for the first time, and high sensitivity and low false positive rate of the fuzzy mapping read are verified in simulated data and real tumor samples; the method has remarkable technical advancement, clinical applicability and expandability.

Methods, systems, and software are provided for determining a homologous recombination pathway status of a cancer in a test subject, e.g., to improve cancer treatment predictions and outcomes. In some embodiments, classifiers using one or more of (i) a heterozygosity status for DNA damage repair genes in a cancerous tissue, (ii) a measure of the loss of heterozygosity across the genome of the cancerous tissue, (iii) a measure of variant alleles detected in a second plurality of DNA damage repair genes in the genome of the cancerous tissue, (iv) a measure of variant alleles detected in the second plurality of DNA damage repair genes in the genome of a non-cancerous tissue, and (v) tumor sample purity are provided.

There is provided a method for quantifying texture features in histological sample from a tumor sample, comprising:receiving a digital image of the histological sample, thendividing the digital image into a plurality of sub-areas, thenusing a trained machine learning model to predict a presence of at least one biological feature for each of the sub-areas, where a probability for the presence of the biological feature is represented by a value, thenforming a data matrix by arranging the values for the probabilities of the biological features in the same way as the sub-areas are arranged in relation to the digital image, thenapplying image analysis to the data matrix for a set of texture features, to produce a quantification of at least one texture feature.

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

The application discloses a kind of detection methods and purposes of SOS1 protein content, belong to biological medicine technical field.The method includes the following steps: sample to be tested enzymolysis, obtain the enzymolysis product comprising the characteristic peptide segment of SOS1 protein, the amino acid sequence of characteristic peptide segment is: FEIPEPEPTEADR and QLTLLESDLYR, stable isotope-labeled SOS1 protein characteristic peptide segment is used as internal standard, the signal value of characteristic peptide segment and internal standard peptide segment is detected using liquid chromatography-tandem mass spectrometry, the relative content of SOS1 protein is calculated by peak area ratio, and the absolute content is obtained by substituting calibration curve linear equation.The method can be used for the quantitative detection of SOS1 protein in tumor sample and other tissues, cells, blood sample, with the advantages of high sensitivity, good accuracy and the like.

This invention discloses a tumor sampling device, comprising: a housing, a sample body, a piston rod, a sealing separation plate, a linkage mechanism, and a reset drive. The sample body is fitted inside the housing to form a receiving space, and its interior has a sampling chamber communicating with the outside. The piston rod movably extends into the sampling chamber and has an operating end, a piston end, and a pushing part, with the piston end slidably connected to the sampling chamber. The sealing separation plate is slidably connected to the sample body and is used to close or open the sampling chamber. The linkage mechanism is located within the receiving space and is driven by the pushing part to drive the sealing separation plate to close the sampling chamber. The reset drive is located within the receiving space and is used to drive the sealing separation plate to open the sampling chamber. This invention provides a tumor sampling device that can achieve integrated sampling and sealing operations.

The invention provides a method of characterising a DNA sample obtained from a tumour, the method including the steps of: determining the presence or absence of a plurality of base substitution signatures, rearrangement signatures and indel signatures in the sample and copy number profiles for the sample; generating, from the presence or absence of said plurality of base substitution signatures, rearrangement signatures and indel signatures and the copy number profile for the sample, a probabilistic score; and based on said probabilistic score, identifying whether said sample has a high or low likelihood of being homologous recombination (HR)-deficient. Identification of a tumour as HR-deficient may be used to inform treatment choices, for example treatment with a PARP inhibitor or platinum therapy or an anthracycline.

A method of detecting loss of HLA allele heterozygosity is provided. The method may include accessing a trained machine learning model, the model being trained using a training dataset, the training dataset including at least the following training datasets: an adjusted B allele frequency, it represents a ratio between a first B allele frequency of a heterozygous allele corresponding to the genomic region in the tumor sample and a second B allele frequency of a heterozygous allele associated with one or more control samples in the genomic region. The method may also include using the machine learning model to generate a result corresponding to a probability of whether a loss of heterozygosity exists in HLA alleles identified in a biological sample of a particular subject by processing sequence data using the machine learning model.

The utility model relates to a kind of postoperative sample storage devices of oncology department. Including shell and inner shell, the top and front of shell are open, the front of inner shell is open, between the bottom wall of both shell and inner shell, between side wall and rear wall, all be equipped with heat preservation layer, detachable upper cover is installed in the top of shell, cooling ice bag is equipped between the top of upper cover and inner shell, shell side opening is equipped in the side of shell and is installed with openable side door, heat preservation layer side opening is equipped in the side of heat preservation layer, inner shell side opening is equipped in the side of inner shell;In inner shell, drawer is inserted and installed, which can be front and rear pull displacement, top is open, drawer side opening is equipped in the side of drawer, drawer front panel is equipped in the front end of drawer, drawer rail is equipped in the side of drawer, inner shell slide is equipped on the inner wall of inner shell.The utility model provides a kind of postoperative sample storage devices of oncology department, flexible to use, can be placed in preservation cabinet as a whole and the sample in inside can be conveniently taken.

The invention discloses an application of a TNFRSF12A inhibitor in preparation of a medicine for treating oral squamous cell carcinoma. Based on single cell transcriptome data, oral squamous cell canceration related tissues are divided into four tissue ecological subtypes, and a tumor sample is divided into two subtypes ET3 and ET4. The ET3 subtype is a lymphocyte infiltration type, and shows CD8 + T cell infiltration, immune activation pathway activity enhancement and high expression of CD3, CD8A and PDCD1; the ET4 subtype is a lymphocyte rejection type, is enriched with COL1A1 + fibroblasts, and is accompanied by high expression of TNFRSF12A, COL1A1 and CD276. According to the application disclosed by the invention, the expression of the TNFRSF12A in the ET4 subtype is obviously improved, in-vivo experiments prove that knockout or blocking of the TNFRSF12A can promote lymphatic T cell infiltration and inhibit tumor growth, and a stronger inhibition effect is shown when the knockout or blocking of the TNFRSF12A is combined with an immune checkpoint inhibitor. The invention provides a system for typing oral squamous cell carcinoma.

The present invention includes methods for treating a FLT3 mutated proliferative disorder comprising: measuring expression of a mutated FLT3 and a one or more driver mutations in a nuclear transport protein that results in a loss of localization of the nuclear transport protein in a sample obtained from a tumor sample obtained from the patient, wherein the presence of the one or more genetic abnormalities indicates that the patient has a poor prognosis; and administering to the patient a therapeutically effective amount of Crenolanib or a pharmaceutically acceptable salt thereof, wherein the Crenolanib increases a chance of survival of the patient having both the mutated FLT3 and mutation in NPM1 or NUP98, wherein the Crenolanib, as shown below, is administered to a subject suffering from said disorder:

Methods for treating non-small cell lung cancer (NSCLC) include the administration of a combination of 2,2'-dithio-bis-ethane sulfonate, carboplatin, and pemetrexed. The methods are based on tumor mutational burden (TMB) assessment, with specific treatment regimens tailored to the mutational profile of the tumor. When a low tumor mutational burden is detected in a tumor sample, the combination therapy of 2,2'-dithio-bis-ethane sulfonate, carboplatin, and pemetrexed is administered, offering enhanced therapeutic efficacy.

The tumor sampling device comprises a positioning assembly and a sampling barrel, the upper end and the lower end of the sampling barrel are open, a detachable guide pipe is installed at the bottom of the sampling barrel, a movable plate is arranged in the sampling barrel in a sliding mode, and an installation plate is fixed to the bottom of the movable plate. A sampling needle is fixed on the side surface of the mounting plate and is arranged in the guide pipe in a sliding manner. According to the tumor sampling device for the pathological diagnosis of the tumor patient, the positioning assembly is additionally arranged, the arranged positioning assembly assists the guide cylinder in use, the situation that the guide cylinder moves or even falls off when the sampling needle is moved is avoided, the sampling needle is conveniently positioned and guided through the guide cylinder, and meanwhile the guide cylinder plays a role in protecting the sampling needle; tumor cells after sampling are prevented from falling off from the sampling needle when the sampling needle is taken out, and the guide cylinder is arranged to assist the sampling needle to move to the tumor, so that the tumor cells are effectively sampled by the sampling needle.

The invention provides a tumor neoantigen screening method and application thereof, and the method comprises the following steps: analyzing WES data of a tumor sample and WES data of a normal sample of a to-be-detected individual to obtain candidate SNV / INDEL data; the method comprises the following steps: analyzing RNA-seq data of a tumor sample to obtain candidate fusion data; the candidate SNV / INDEL data and the candidate fusion data are filtered, mutation with low expression is filtered out, and mutation sites after filtering are obtained; calculating the mutation sites and intercepting sequences containing the mutation sites to obtain candidate mutation polypeptide sequences; and screening the candidate mutant polypeptide sequences according to antigen binding, immune presentation, antigen similarity and self similarity to obtain a target polypeptide sequence, and selecting the neoantigen from the target polypeptide sequence.

Disclosed herein are methods for identifying stable control loci for fluorescence in situ hybridization (FISH) assays and for determining whether a copy number change (e.g., amplification) of a target genomic locus (e.g., a gene, e.g., cyclin E1 (CCNE1)) has occurred in a biological sample (e.g., a non-tumor sample, a precancerous lesion, and / or a tumor). In particular, the present disclosure provides an extended repository of genomic loci that can act as a stable control (e.g., a stable control locus) for a FISH assay intended to determine copy number changes in the target genomic locus.

The invention relates to a method to indicate the clinical outcome of a cancer patient by labelling a cancer sample with labelled molecular probes, assaying the expression of a plurality of biomolecules at the resolution of a single cell and assigning a cellular identity (CI) to each single cell in the sample based on their expression pattern; then assigning a single cell pathology (SCP) patient group according to the proportion of each CI the sample contains.The invention in other aspects relates to methods of treatment of a patient with anticancer drugs according to the patient's assignment to particular SCPs. Alternatively, this aspect may be formulated as the provision of certain drugs for treatment of cancer in patients characterized by tumours assigned to certain SCPs.

Context-specific tumor-only mutation classification is described. A mutation classification module may classify a mutation identified in sequencing data from a tumor sample as germline or somatic based on a likelihood ratio relative to a threshold, the likelihood ratio comparing a germline model likelihood of a germline model of the mutation to a somatic model likelihood of a somatic model of the mutation and the threshold calculated based on a context of the mutation. The mutation classification module may output the classification of the mutation.

The present invention relates to an improved method for diagnosing homologous recombination deficiencies (HRDs) in tumors. The method according to the present invention comprises the steps of: evaluating the number of large genomic alterations (LGAs) in a tumor sample by obtaining a copy number alteration (CNA) profile by shallow coverage whole-genome sequencing (sWGS); and determining an LGA score corresponding to the number of LGAs adjusted for the complexity of the tumor genome and the presence of one or two markers selected from a group of markers consisting of (1) phenotypes associated with mutations in cyclin-dependent kinase 12 (CDK12) with multiple intermediate gains in the CNA profile; (2) amplification of cyclin E1 (CCNE1); (3) amplification of human epidermal growth factor receptor-2 (HER2); and (4) phenotypes of amplification at multiple sites.

Provided herein are methods for making a tumor infiltrating lymphocytes (TILs) product enriched with neoantigen-reactive T cells (NARTs), comprising: generating a plurality of TIL populations by fractioning a tumor sample; selecting one or more TIL populations enriched with NARTs by profiling the plurality of TIL populations using multiplex digital PCR (dPCR); and preferentially expanding the NARTs by co-culturing the one or more TIL populations enriched with NARTs with tumor cells from the tumor sample in a first cell culture medium to generate the TIL product enriched with NARTs. Further provided is a method for assessing tumor reactivity of a population of T cells, comprising measurement of the expression level of a panel of target genes of the population of T cells.

Disclosed are pharmaceutical formulations comprising a compound of formula (I): in which R1, R2, R3, and R4 are as described herein, or a pharmaceutically acceptable salt thereof. Also provided are methods for treating pancreatic adenocarcinoma comprising administration of a compound of formula (I), or a pharmaceutically acceptable salt thereof, and methods of detecting the change in expression levels of one or both of FoxAl and FoxO6 in a pancreatic adenocarcinoma tumor sample from a mammal, wherein the mammal has been administered a compound of formula (I), or a pharmaceutically acceptable salt thereof.

The utility model provides a tumor sampling device which comprises a shell, a hollow puncture needle is arranged at the end of the shell, a sampling opening is formed in the side wall of the puncture needle, a cutting pipe is rotatably and slidably arranged in the puncture needle, a cutting groove is formed in the side wall of the cutting pipe, a cutting knife is arranged on the side edge of the cutting groove, and a locking assembly is arranged on the shell. Sliding of the cutting pipe can be selectively locked or unlocked through the locking assembly, the suction assembly connected with the cutting pipe is arranged in the shell, air in the cutting pipe is sucked through suction, and the cutting pipe can be controlled to rotate. Compared with a traditional mode of sampling by rotating a scraper, the device has the advantages that the tumor cutting area is smaller in the sampling process, so that the injury to a patient is effectively reduced.

The present invention is in the field of molecular subtyping of tumor samples and therapy guidance. The present invention relates to methods, arrays, prognostic assays, systems and uses thereof for prediction of the response or resistance to and / or benefit from a systemic treatment, in particular adjuvant or neoadjuvant chemotherapy, of a subject suffering from a HR+ and HER2− breast cancer, based on the measurement(s) of expression level(s) of three or more markers in tumor samples of said subject. Equally, the present invention relates to methods, arrays, prognostic assays, systems and uses thereof for prediction of the outcome benefit from a systemic treatment, in particular adjuvant or neoadjuvant chemotherapy, of a subject suffering from a HR+ and HER2− breast cancer, based on the measurement(s) of expression level(s) of three or more markers in tumor samples of said subject.

The invention discloses a microsatellite instability detection marker combination screening method based on an NGS technology and application, and belongs to the technical field of gene detection.The method comprises the steps that firstly, MSS normal samples serve as the basis, high-consistency samples are screened through a sliding window algorithm to construct a coverage baseline, MSI-H tumor sample signals are corrected in combination with tumor purity, and the coverage baseline is obtained; calculating a false positive control threshold and a detection rate threshold by adopting binomial distribution and dichotomy, and screening out a specific MSI-H marker; a two-dimensional baseline model is constructed by utilizing an MSS negative tissue sample, an MSIscore / MSSscore scoring system and a dynamic judgment threshold are included, and a standardized detection process of coverage calculation-effective site screening-signal scoring-state judgment is formed. The method solves the problems that a traditional method is poor in site universality, rigid in threshold value and insufficient in low-purity sample adaptability, is widely applied to MSI detection of colorectal cancer, endometrial cancer and other tumors, is suitable for clinical low-tumor-content sample scenes, and has high accuracy, high stability and good clinical applicability.