GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing

Background The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair. Results In this study, a new algorithm called genomic scar analysis (GSA) has developed and...

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Vydané v:BMC bioinformatics Ročník 22; číslo 1; s. 562 - 19
Hlavní autori: Chen, Dongju, Shao, Minghui, Meng, Pei, Wang, Chunli, Li, Qi, Cai, Yuhang, Song, Chengcheng, Wang, Xi, Shi, Taiping
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 23.11.2021
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Analysis
Bioinformatics
Biomarkers
Biomedical and Life Sciences
BRCA mutations
BRCA1 protein
Breast cancer
Chromosomes
Clinical trials
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Copy number
Copy number variations
DNA Copy Number Variations
DNA damage
DNA Repair
Epigenetics
FDA approval
Genes
Genomes
Genomic analysis
Genomic instability
Genomic scar analysis
Genomics
Genotypes
Health aspects
High-Throughput Nucleotide Sequencing
Homologous Recombination
Homologous recombination deficiency
Homologous recombination repair
Homology
Humans
Identification and classification
Life Sciences
Mathematical analysis
Methods
Microarrays
Mutation
Neoplasms - genetics
Ovarian cancer
p53 Protein
Ploidies
Ploidy
Purity
Quality control
Scars
Segmentation
Sequences
Software
Tumor purity and ploidy correction
Tumor suppressor genes
Tumors
China
Genomic scar analysis
Segmentation
Copy number variations
Tumor purity and ploidy correction
Homologous recombination deficiency
ISSN:1471-2105, 1471-2105
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Popis
Shrnutí:Background The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair. Results In this study, a new algorithm called genomic scar analysis (GSA) has developed and validated to calculate homologous recombination deficiency (HRD) score. The two critical submodules were tree recursion (TR) segmentation and filtering, and the estimation and correction of the tumor purity and ploidy. Then, this study evaluated the rationality of segmentation and genotype identification by the GSA algorithm and compared with other two algorithms, PureCN and ASCAT, found that the segmentation result of GSA algorithm was more logical. In addition, the results indicated that the GSA algorithm had an excellent predictive effect on tumor purity and ploidy, if the tumor purity was more than 20%. Furtherly, this study evaluated the HRD scores and BRCA1/2 deficiency status of 195 clinical samples, and the results indicated that the accuracy was 0.98 (comparing with Affymetrix OncoScan™ assay) and the sensitivity was 95.2% (comparing with BRCA1/2 deficiency status), both were well-behaved. Finally, HRD scores and 16 genes mutations ( TP53 and 15 HRR pathway genes) were analyzed in 17 cell lines, the results showed that there was higher frequency in HRR pathway genes in high HRD score samples. Conclusions This new algorithm, named as GSA, could effectively and accurately calculate the purity and ploidy of tumor samples through NGS data, and then reflect the degree of genomic instability and large-scale copy number variations of tumor samples.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04487-9