32 results about "Homologous Recombination Deficiency" patented technology

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of homologous recombination deficiency (HRD) or an HRD signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an HRD signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

The invention includes compositions and methods for treating or preventing a cancer in a subject. In one aspect the invention provides methods of administering to a subject suffering from a cancer with cells containing an IDH1 or IDH2 mutation, at least one compound comprising a DNA repair inhibitor. The invention also provides methods of treating a cancer with 2 HG, a derivative of 2-HG, any variant and any mixtures thereof. In one aspect the invention provides a pharmaceutical composition comprising an anti-tumor effective mount of at least one compound selected from the group consisting of 2-hydroxyglutarate (2-HG), a derivative of 2-HG, any variant and any mixtures thereof.

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 lowlikelihood 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.

The invention relates to the field of biomedicine, in particular to a method and application for predicting homologous recombination deficiency in ovarian cancer based on biomarkers of genome copy number variation. The biomarker is a CNV based on any of chromosome segment 5q13.2, 8q24.2 or 19q12. The method for predicting the homologous recombination deficiency of ovarian cancer by the biomarkers is as follows: collecting surgical resection samples or tissue biopsy samples of ovarian cancer patients; performing DNA sequencing on the samples to obtain corresponding sequencing files; using GISTIC 2.0 to analyze the DNA sequencing files , to obtain the CNV map of the whole tumor genome; predict the HRD status of ovarian cancer based on the CNV of chromosome fragment 5q13.2, 8q24.2 or 19q12. The present invention provides the application of copy number variation CNV at the subchromosomal and gene levels in predicting homologous recombination defects in ovarian cancer patients, so as to screen potential beneficiaries of targeted therapy and bring more clinical benefits to HRD patients.

The invention relates to a method and a kit for determining genome instability based on a second-generation sequencing technology, and belongs to the technical field of molecular detection. In order to overcome the lack of genome structure variation in the detection of homologous recombination defects in the prior art, the present invention provides a method and kit for determining genome instability based on next-generation sequencing technology. In this method, the gene to be tested is interrupted and A Connectors, after corresponding PCR reactions, use the designed probes for hybridization capture, amplify the captured DNA library, perform library sequencing, and then use software to evaluate the homologous recombination defect status. Compared with the existing technology, this method can comprehensively evaluate the HRD status, the data results are reliable, and it is suitable for promotion.

The invention provides a method for correcting tumor purity in the process of bioinformatics analysis and a method for detecting homologous recombination defects based on an NGS platform. The method of the invention compares the sequencing depth and single nucleotide polymorphism of clinical samples and negative samples in the target region The differences in the allele frequencies of sex loci can be effectively corrected for tumor purity and ploidy, and HRD assessment can be realized.

The invention discloses a method for judging homologous recombination defects based on DNA sequencing data, which obtains characteristic attributes; extracts effective data; Attribute processing efficiency, choosing three different base classifiers H 1 , H 2 , H 3 ; for H 1 , H 2 , H 3 Iterative training is performed to obtain an expanded training set, thereby updating the model and completing the training process; using the trained model to label the unlabeled sample set U, and completing the HRD status determination according to the labeling result. The invention solves the limitation of using a single or a small amount of local features such as genomic instability state to determine the HRD state, overcomes the difficulty that the number of samples with known HRD states is very small in clinical practice, and realizes multi-feature attributes under the existing sample data. It can improve the performance of HRD judgment method.

A single-sample genome-wide method for predicting allele-specific copy number variations, the method comprising: analyzing the sequencing data of a test sample compared to a reference genome, extracting tumor purity information, genome-wide replication information, and total copy number variations information, and then perform classification processing according to the total copy number variation information of each segment of the chromosome, and convert the total copy number variation information into allele-specific copy number variation information, if the total copy number variation information of the chromosome segment is an odd interval or 0 interval, the allele-specific copy number variation information is directly deduced, and if the total copy number variation information of the chromosome segment is a non-zero even interval, the allele-specific copy number variation of the interval is obtained through model prediction information. The invention only needs a single sample and does not need paired normal samples. The required sample to be tested has a low sequencing depth and high detection accuracy, and can detect homologous recombination defects in samples with low tumor purity.

Compositions and methods for prevention of ovarian cancer recurrence and for the treatment of BRCA1 / 2-wild type ovarian cancer are disclosed herein. In some embodiments, the composition comprises an autologous tumor cell vaccine comprising cells genetically modified for furin knockdown and GM-CSF expression. In some embodiments, the method comprises administration of an autologous tumor cell vaccine prior to administration of a combination of the autologous tumor cell vaccine and atezolizumab. Also disclosed herein are methods for treating a cancer in an individual comprising a wild-type BRCA1 gene, a wild-type BRCA2 gene, or a combination thereof, and is identified as homologous recombination deficiency (HRD)-negative.