11/4/2022 0 Comments Duplicate detector sims 2However, removal of duplicate reads could result in genotyping errors in libraries constructed from only a small amount of input material because of the inherently imbalanced nature of the sequencing coverage 9. As a quality-control measure for next-generation sequencing (NGS) data, duplicate reads are usually discarded to allow computational ease of downstream analyses and to mitigate PCR amplification biases. To overcome this issue, high-depth sequencing is frequently used to detect rare variants 6, 7, 8. In addition, the heterogeneity of mutations within populations of rare cells in liquid biopsy samples, such as plasma 4 or saliva 5, make it difficult to distinguish between sequencing-related errors and true somatic mutations originating from tumors. It is a major challenge to distinguish true variants from background noise for rare variant discovery 2, 3, because the error rate ranges from 1 to 10%, which prohibits deconvolution of the clonal structure of tumor genomes. Cost could be a substantial concern in large-scale projects, however, because great sequencing depth must be achieved to reliably detect rare alleles in ctDNA samples. Currently, the non-invasive detection of circulating tumor DNA (ctDNA) has great potential to be the ‘holy grail’ of early cancer detection. The cost of sequencing has decreased rapidly 1 since 2005, which has enabled researchers to explore many basic questions in natural science. The advent of massively parallel DNA sequencing has revolutionized the field of genomics and transformed human medical research.
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