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BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes
Andrey Kechin1, Evgeniy Khrapov2, Uljana Boyarskikh2
1Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
BRCA-analyzer is a new tool for processing next-generation sequencing (NGS) data from BRCA1/2 genes. It accurately identifies pathogenic variants, outperforming other workflows in detecting mutations for improved genetic diagnostics.
Area of Science:
- Molecular Genetics
- Bioinformatics
- Genomic Data Analysis
Background:
- Next-generation sequencing (NGS) generates vast amounts of data, necessitating efficient and reliable analysis tools for molecular and medical genetics.
- Accurate identification of pathogenic variants in genes like BRCA1 and BRCA2 is crucial for diagnosing genetic diseases and guiding treatment.
Purpose of the Study:
- To develop and validate BRCA-analyzer, an automatic, multithreaded workflow for processing NGS data specifically for BRCA1 and BRCA2 genes.
- To compare the performance of BRCA-analyzer against existing workflows using real-world patient data.
Main Methods:
- Developed BRCA-analyzer, an automatic workflow optimized for processing NGS data from BRCA1/2 gene panels.
- Tested BRCA-analyzer on sequencing data from 899 samples (693 patients), including libraries prepared with Qiagen GeneRead BRCA panel and an in-house method.
- Validated pathogenic variants identified by BRCA-analyzer using Sanger sequencing and compared its performance against Qiagen's workflow and the Canary workflow.
Main Results:
- BRCA-analyzer successfully identified all 27 pathogenic variants in 106 samples (blood and FFPE) confirmed by Sanger sequencing, outperforming Qiagen's workflow which missed 5 variants.
- In comparison with the Canary workflow on 793 samples, BRCA-analyzer identified 135 out of 137 pathogenic variations, while Canary identified 123.
- BRCA-analyzer demonstrated potential for use with hybrid capture panels, though further testing is recommended.
Conclusions:
- BRCA-analyzer is a reliable and efficient automatic workflow for processing amplicon-based targeted NGS data of BRCA1/2 genes, capable of identifying germline and somatic mutations.
- The workflow offers improved accuracy in variant detection compared to existing tools, aiding in more precise genetic diagnostics.
- BRCA-analyzer is freely available, promoting wider adoption and advancement in genetic analysis.
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