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Saturday, February 20, 2021

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II System, powered by Single Molecule, Real-Time (SMRT) Sequencing technology, you can comprehensively detect variants in a human genome. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

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Friday, February 5, 2021

ASHG Virtual Poster: De novo assembly of a diploid Asian genome

Yunfei Guo, from the University of Southern California, presents his ASHG 2015 poster on a de novo assembly of a diploid Asian genome. The uniform coverage of long-read sequencing helped access regions previously unresolvable due to high GC bias or long repeats. The assembly allowed scientists to fill some 400 gaps in the latest human reference genome, including some as long as 50 kb.

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Friday, February 5, 2021

Podcast: Marc Salit discusses creating the foundation of genomics

Marc Salit is the leader of the Genome Scale Measurement Group at the National Institute of Standards and Technology or NIST. In this Mendelspod podcast, he explains how NIST played a pivotal, foundational role in enabling the ‘Century of Physics.’ Now Marc and NIST are looking for the right set of standards to enable the already-upon-us “Century of Biology.” The human reference genome is an example of a standard that Marc and his team are developing. Currently they are piloting what they call “Genome in a Bottle,” a physical reference standard to which all other human genomes can be measured.…

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Friday, February 5, 2021

Podcast: Reference genome making major strides in ethnic diversity, says Valerie Schneider, NCBI

Valerie Schneider of the National Center for Biotechnology Information discuss how the Genome Reference Consortium (GRC) is bringing more ethnic diversity to the latest human reference assembly (GRCh38) by adding patches and alternate loci scaffolds. Scientists working with population graphs are among the early adopters of these new alternate loci scaffolds. She also discusses work underway at the McDonnell Genome Institute at Washington University to generate a set of high-quality, de novo whole genomes from a wide variety of populations. The new ethnic genomes “are also intended to stand on their own as complements to the reference so users can…

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Friday, February 5, 2021

AGBT Virtual Poster: Generation of local reference genomes using PacBio and BioNano data, and analysis of the “dark matter” of structural variants in 1000 Swedish genomes

In this AGBT 2017 poster, Ulf Gyllensten from Uppsala University presents two local reference genomes generated with PacBio and Bionano Genomics data. These assemblies include structural variation and repetitive regions that have been missed with previous short-read efforts, including some new genes not annotated in the human reference genome.

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Friday, February 5, 2021

Webinar: Assembling high-quality human reference genomes for global populations

This webinar highlights global initiatives currently underway to use Single Molecule, Real-Time (SMRT) Sequencing to de novo assemble genomes of individuals representing multiple ethnic populations, thereby extending the diversity of available human reference genomes. In their presentations, Tina Graves-Lindsay from Washington University and Adam Ameur from Uppsala University spoke about diploid assemblies, discovering novel sequence and improving diversity of the current human reference genome. Finally, Paul Peluso of PacBio presented data from the recent effort to sequence a Puerto Rican genome and shared a SMRT Sequencing technology roadmap showing the next several upgrades for the Sequel System.

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Friday, February 5, 2021

ASHG PacBio Workshop: Characterization of a large, human-specific tandem repeat array associated with bipolar disorder and schizophrenia

In this ASHG workshop presentation, Janet Song of Stanford School of Medicine shared research on resolving a tandem repeat array implicated in bipolar disorder and schizophrenia. These psychiatric diseases share a number of genomic risk variants, she noted, but scientists continue to search for a specific causal variant in the CACNA1C gene suggested by previous genome-wide association studies. SMRT Sequencing of this region in 16 individuals identified a series of 30-mer repeats, containing a total of about 50 variants. Analysis showed that 10 variants were linked to protective or risk haplotypes. Song aims to study the function of these variants…

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Friday, February 5, 2021

User Group Meeting: The trials and tribulations of high quality human genome assembly

In this PacBio User Group Meeting presentation, Tina Graves-Lindsay of the McDonnell Genome Institute and the Genome Reference Consortium speaks about the importance of phasing human reference genomes. Her team is now working on its fifteenth human genome assembly — part of a major effort to improve genomic representation of ethnic diversity — with a pipeline that generates 60-fold PacBio coverage for a de novo assembly, followed by scaffolding with other technologies. They are also using FALCON-Unzip to separate haplotypes, leading to reference-grade diploid assemblies. This approach has already helped resolve errors seen in other genomes and even the gold-standard…

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Tuesday, December 22, 2020

Improving the reference with a diversity panel of sequence-resolved structural variation

Although the accuracy of the human reference genome is critical for basic and clinical research, structural variants (SVs) have been difficult to assess because data capable of resolving them have been limited. To address potential bias, we sequenced a diversity panel of nine human genomes to high depth using long-read, single-molecule, real-time sequencing data. Systematically identifying and merging SVs =50 bp in length for these nine and one public genome yielded 83,909 sequence-resolved insertions, deletions, and inversions. Among these, 2,839 (2.0 Mbp) are shared among all discovery genomes with an additional 13,349 (6.9 Mbp) present in the majority of humans,…

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Tuesday, December 22, 2020

Structural variant detection with long read sequencing reveals driver and passenger mutations in a melanoma cell line

Past large scale cancer genome sequencing efforts, including The Cancer Genome Atlas and the International Cancer Genome Consortium, have utilized short-read sequencing, which is well-suited for detecting single nucleotide variants (SNVs) but far less reliable for detecting variants larger than 20 base pairs, including insertions, deletions, duplications, inversions and translocations. Recent same-sample comparisons of short- and long-read human reference genome data have revealed that short-read resequencing typically uncovers only ~4,000 structural variants (SVs, =50 bp) per genome and is biased towards deletions, whereas sequencing with PacBio long-reads consistently finds ~20,000 SVs, evenly balanced between insertions and deletions. This discovery has…

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Tuesday, December 22, 2020

High-quality human genomes achieved through HiFi sequence data and FALCON-Unzip assembly

De novo assemblies of human genomes from accurate (85-90%), continuous long reads (CLR) now approach the human reference genome in contiguity, but the assembly base pair accuracy is typically below QV40 (99.99%), an order-of-magnitude lower than the standard for finished references. The base pair errors complicate downstream interpretation, particularly false positive indels that lead to false gene loss through frameshifts. PacBio HiFi sequence data, which are both long (>10 kb) and very accurate (>99.9%) at the individual sequence read level, enable a new paradigm in human genome assembly. Haploid human assemblies using HiFi data achieve similar contiguity to those using…

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Tuesday, December 22, 2020

Using whole exome sequencing and bacterial pathogen sequencing to investigate the genetic basis of pulmonary non-tuberculous mycobacterial infections.

Pulmonary non-tuberculous mycobacterial (PNTM) infections occur in patients with chronic lung disease, but also in a distinct group of elderly women without lung defects who share a common body morphology: tall and lean with scoliosis, pectus excavatum, and mitral valve prolapse. In order to characterize the human host susceptibility to PNTM, we performed whole exome sequencing (WES) of 44 individuals in extended families of patients with active PNTM as well as 55 additional unrelated individuals with PNTM. This unique collection of familial cohorts in PNTM represents an important opportunity for a high yield search for genes that regulate mucosal immunity.…

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Tuesday, December 22, 2020

Sequencing and de novo assembly of the 17q21.31 disease associated region using long reads generated by Pacific Biosciences SMRT Sequencing technology.

Assessment of genome-wide variation revealed regions of the genome with complex, structurally diverse haplotypes that are insufficiently represented in the human reference genome. The 17q21.31 region is one of the most dynamic and complex regions of the human genome. Different haplotypes exist, in direct and inverted orientation, showing evidence of positive selection and predisposing to microdeletion associated with mental retardation. Sequencing of different haplotypes is extremely important to characterize the spectrum of structural variation at this locus. However, de novo assembly with second-generation sequencing reads is still problematic. Using PacBio technology we have sequenced and de novo assembled a tiling…

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Tuesday, December 22, 2020

From Sequencing to Chromosomes: New de novo assembly and scaffolding methods improve the goat reference genome

Single-molecule sequencing is now routinely used to assemble complete, high-quality microbial genomes, but these assembly methods have not scaled well to large genomes. To address this problem, we previously introduced the MinHash Alignment Process (MHAP) for overlapping single-molecule reads using probabilistic, locality-sensitive hashing. Integrating MHAP with Celera Assembler (CA) has enabled reference-grade assemblies of model organisms, revealing novel heterochromatic sequences and filling low-complexity gap sequences in the GRCh38 human reference genome. We have applied our methods to assemble the San Clemente goat genome. Combining single-molecule sequencing from Pacific Biosciences and BioNano Genomics generates and assembly that is over 150-fold more…

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