A multi-platform reference for somatic structural variation detection

Abstract

Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality gold standard datasets that enable the benchmarking of experimental approaches and bioinformatic analysis pipelines for comprehensive somatic SV detection. Here, we approached this challenge by genome-wide somatic SV analysis of the paired melanoma and normal lymphoblastoid COLO829 cell lines using four different technologies: Illumina HiSeq, Oxford Nanopore, Pacific Biosciences and 10x Genomics. Based on the evidence from multiple technologies combined with extensive experimental validation, including Bionano optical mapping data and targeted detection of candidate breakpoint junctions, we compiled a comprehensive set of true somatic SVs, comprising all SV types. We demonstrate the utility of this resource by determining the SV detection performance of each technology as a function of tumor purity and sequence depth, highlighting the importance of assessing these parameters in cancer genomics projects and data analysis tool evaluation. The reference truth somatic SV dataset as well as the underlying raw multi-platform sequencing data are freely available and are an important resource for community somatic benchmarking efforts.

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers

“…We performed an additional investigation on UNet’s generalization ability on tumor WGS data. We used WGS data of COLO829 tumor cell line provided by Valle-Inclan et al [ 21 ]. SVs were validated with orthogonal technologies, including Illumina Hiseq, Oxford nanopore, Pacific biosciences, and 10x genomics for the sample.…”

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

“…To estimate precision and sensitivity of GRIDSS2, we used a recently generated “gold standard” somatic SV truth set for the COLO829 melanoma cell line and the COLO829BL cell line, which was derived from a normal cell from the same individual, using a combination of Illumina, PacBio, Oxford Nanopore, 10X Genomics linked reads, and optical mapping followed by targeted capture and PCR-based validations and manual curation 18 . To test sensitivity and reproducibility, we ran GRIDSS2, Manta 11 , svaba 19 , and novobreak 20 on 3 independent sequencing replicates of the COLO829T/COLO829BL matched tumour-normal cell lines sequenced to a depth of 100x tumour and 40x normal coverage.…”

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

“…The reference set was curated using a paired melanoma and normal lymphoblastoid COLO829 cell lines using four different technologies (Illumina HiSeq, Oxford Nanopore, Pacific Biosciences and 10x Genomics), along with extensive external validation. 46 Using the reference set, we proceeded to investigate the presence and nature of false positives from the initial callsets. (Note that we focused on WGS for this hackathon, but a similar approach could be applied to other assays such as WES.)…”