June 1, 2021  |  

Copy-number variant detection with PacBio long reads

Long-read sequencing of diverse humans has revealed more than 20,000 insertion, deletion, and inversion structural variants spanning more than 12 Mb in a healthy human genome. Most of these variants are too large to detect with short reads and too small for array comparative genome hybridization (aCGH). While the standard approaches to calling structural variants with long reads thrive in the 50 bp to 10 kb size range, they tend to miss exactly the large (>50 kb) copy-number variants that are called more readily with aCGH. Standard algorithms rely on reference-based mapping of reads that fully span a variant or on de novo assembly; and copy-number variants are often too large to be spanned by a single read and frequently involve segmentally duplicated sequence that is not yet included in most de novo assemblies. To comprehensively detect large variants in human genomes, we extended pbsv – a structural variant caller for long reads – to call copy-number variants (CNVs) from read-clipping and read-depth signatures. In human germline benchmark samples, we detect more than 300 CNVs spanning around 10 Mb, and we call hundreds of additional events in re-arranged cancer samples. Together with insertion, deletion, inversion, duplication, and translocation calling from spanning reads, this allows pbsv to comprehensively detect large variants from a single data type.

June 1, 2021  |  

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has revealed more than 20,000 structural variants spanning over 12 Mb in a healthy human genome. Short-read sequencing fails to detect most structural variants but has remained the more effective approach for small variants, due to 10-15% error rates in long reads, and copy-number variants (CNVs), due to lack of effective long-read variant callers. The development of PacBio highly accurate long reads (HiFi reads) with read lengths of 10-25 kb and quality >99% presents the opportunity to capture all classes of variation with one approach.Methods: We sequence the Genome in a Bottle benchmark sample HG002 and an individual with a presumed Mendelian disease with HiFi reads. We call SNVs and indels with DeepVariant and extend the structural variant caller pbsv to call CNVs using read depth and clipping signatures. Results: For 18-fold coverage with 13 kb HiFi reads, variant calling in HG002 achieves an F1 score of 99.7% for SNVs, 96.6% for indels, and 96.4% for structural variants. Additionally, we detect more than 300 CNVs spanning around 10 Mb. For the Mendelian disease case, HiFi reads reveal thousands of variants that were overlooked by short-read sequencing, including a candidate causative structural variant. Conclusions: These results illustrate the ability of HiFi reads to comprehensively detect variants, including those associated with human disease.

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