Assessing structural variation in a personal genome—towards a human reference diploid genome

Abstract

BackgroundCharacterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.ResultsWe demonstrate Parliament’s efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.ConclusionsHS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1479-3) contains supplementary material, which is available to authorized users.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

“…New reference-quality sequence sources are needed, because generation of finished sequence from clone libraries is in significant decline due to cost and some remaining assembly gaps occur in regions recalcitrant to cloning. A growing collection of human genomes in INSDC databases, a prerequisite for any sequence that will contribute to the reference assembly, that were sequenced and assembled with new technologies are candidates for use in assembly improvement (Earl et al 2011;Vezzi et al 2012;Bradnam et al 2013;English et al 2015;Pendleton et al 2015;Seo et al 2016;Shi et al 2016;Zook et al 2016). However, WGS assembly sequences have historically not been considered reference quality, raising concerns about their use in reference genome assembly curation.…”

An Incomplete Understanding of Human Genetic Variation

“…Third, combine computational and experimental methods to resolve the physical haplotype structure of human genomes as opposed to relying on inferential methods (English et al 2015;Pendleton et al 2015). This is especially relevant with respect to STRs and mCNVs where the frequency of recurrent mutation is expected to be high and direct observation and resolution of the sequence structure will be key to associating variants with phenotype.…”

Deep sequencing of 10,000 human genomes

“…This generated a reliable representation of human singlenucleotide variation (SNV) and the reporting of clinically relevant SNVs. We confronted, like other groups, the limitations of shortread sequencing for accurate calling of structural and copy-number variation; even with a variety of methods, resolving structural variation in a personal genome remains a challenge (9).…”