ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation.

ABSTRACT:

Background

Internal tandem duplications (ITDs) are tandem duplications within coding exons and are important prognostic markers and drug targets for acute myeloid leukemia (AML). Next-generation sequencing has enabled the discovery of ITD at single-nucleotide resolution. ITD allele frequency is used in the risk stratification of patients with AML; higher ITD allele frequency is associated with poorer clinical outcomes. However, the ITD allele frequency data are often unavailable to treating physicians and the detection of ITDs with accurate variant allele frequency (VAF) estimation remains challenging for short-read sequencing.

Results

Here we present the ScanITD approach, which performs a stepwise seed-and-realignment procedure for ITD detection with accurate VAF prediction

SUBMITTER: Wang TY 

PROVIDER: S-EPMC7450668 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature