GROM-RD: Resolving genomic biases to improve read depth detection of copy number variants

Sean D. Smith, Joseph K. Kawash, Andrey Grigoriev

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Amplifications or deletions of genome segments, known as copy number variants (CNVs), have been associated with many diseases. Read depth analysis of next-generation sequencing (NGS) is an essential method of detecting CNVs. However, genome read coverage is frequently distorted by various biases of NGS platforms, which reduce predictive capabilities of existing approaches. Additionally, the use of read depth tools has been somewhat hindered by imprecise breakpoint identification. We developed GROM-RD, an algorithm that analyzesmultiple biases in read coverage to detect CNVs in NGS data. We found non-uniformvariance across distinct GC regions after using existing GC bias correction methods and developed a novel approach to normalize such variance. Although complex and repetitive genome segments complicate CNV detection, GROM-RD adjusts for repeat bias and uses a two-pipeline masking approach to detect CNVs in complex and repetitive segments while improving sensitivity in less complicated regions. To overcome a typical weakness of RD methods, GROM-RD employs a CNV search using size-varying overlapping windows to improve breakpoint resolution. We compared our method to two widely used programs based on read depth methods, CNVnator and RDXplorer, and observed improved CNV detection and breakpoint accuracy for GROM-RD.

Original languageEnglish (US)
Article numbere836
JournalPeerJ
Volume2015
Issue number3
DOIs
StatePublished - 2015

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Keywords

  • Copy number variant
  • Genomic bias
  • Next gen sequencing

Fingerprint Dive into the research topics of 'GROM-RD: Resolving genomic biases to improve read depth detection of copy number variants'. Together they form a unique fingerprint.

Cite this