Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller
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- 作者：Chang Xu ; Mohammad R. Nezami Ranjbar ; Zhong Wu ; John DiCarlo ; Yexun Wang
- 关键词：Variant caller ; Molecular barcode ; Statistical model ; PCR enrichment
- 刊名：BMC Genomics
- 出版年：2017
- 出版时间：December 2017
- 年：2017
- 卷：18
- 期：1
- 全文大小：986KB
- 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
- 卷排序：18
文摘
BackgroundDetection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models.