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Friday, February 26, 2021

Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads

Introduction: Long-read PacBio SMRT Sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw read error rates of 10-15%, it has remained difficult to call small variants from long reads. Recent improvements in library preparation, sequencing chemistry, and instrument yield have increased length, accuracy, and throughput of PacBio Circular Consensus (CCS) reads, resulting in 10-20 kb “HiFi” reads with mean read quality above 99%. Materials and Methods: We sequenced 11 kb size-selected libraries from the Genome in a Bottle (GIAB) human reference samples HG001, HG002, and HG005 to approximately 30-fold coverage on the…

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Friday, February 26, 2021

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

Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent improvements in library preparation and sequencing chemistry have increased length, accuracy, and throughput of PacBio circular consensus sequencing (CCS) reads, resulting in 15-20kb reads with average read quality above 99%. Materials and Methods: We sequenced a library from human reference sample HG002 to 18-fold coverage on the PacBio Sequel II with two SMRT Cells 8M. The CCS algorithm was used to generate highly accurate (average 99.9%)…

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Friday, February 5, 2021

Video Poster: Accurate, comprehensive variant calling in difficult-to-map genes using HiFi reads

Introduction: Around 5% (1,168) of protein-coding genes in the human genome contain an exon that is difficult to map with typical next-generation sequencing (NGS) read lengths due to homologous pseudogenes or segmental duplications. Among the difficult-to-map genes are 193 with known medical relevance, including CYP2D6, GBA, SMN1/2, and VWF. Long-read DNA sequencing provides increased mappability, accessing many of the difficult-to-map regions by connecting the homologous exon to neighboring unique sequence. Until recently, the read-level accuracy of long-read sequencing had made it challenging to accurately call small variants. The recently developed HiFi reads from the PacBio Sequel II System provide both…

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Friday, February 5, 2021

Virtual Global Summit: DeepVariant – Accurate variant calling with PacBio HiFi data

In this PacBio Virtual Global Summit 2020 presentation, Pi-Chuan Chang of Google shares how DeepVariant identifies SNPs and Indels in PacBio HiFi data, starting from the v0.8 release (April 2019). In her talk, Chang details recent accuracy improvements that won the PrecisionFDA Truth Challenge v2, which are now available in the latest release (v1.0 in September 2020).

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