Benchmarking challenging small variants with linked and long reads

Published

May 11, 2022

Author(s)

Justin Wagner, Nathanael Olson, Lindsay Harris, Marc L. Salit, Fritz Sedlazeck, Chunlin Xiao, Justin Zook

Abstract

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.

Citation

Cell Genomics

Volume

2

Issue

5

Pub Type

Journals

Download Paper

https://doi.org/10.1016/j.xgen.2022.100128

Local Download

Keywords

genomics, human genome, DNA sequencing, benchmark, reference materials

Citation

Wagner, J. , Olson, N. , Harris, L. , Salit, M. , Sedlazeck, F. , Xiao, C. and Zook, J. (2022), Benchmarking challenging small variants with linked and long reads, Cell Genomics, [online], https://doi.org/10.1016/j.xgen.2022.100128, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=930585 (Accessed November 27, 2025)