Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9.

Abstract

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benchmarking*
  • Breast Neoplasms / genetics*
  • Cell Line, Tumor
  • DNA Mutational Analysis / standards*
  • Datasets as Topic
  • Germ Cells
  • High-Throughput Nucleotide Sequencing / standards*
  • Humans
  • Mutation
  • Reference Standards
  • Reproducibility of Results
  • Whole Genome Sequencing / standards*