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Thursday, August 27, 2020

Immunology Brochure: Invaluable insights into immunology

In order to understand the molecular mechanisms governing the outcomes of disease, health and survival, immunologists have to characterize exceptionally complex genomic regions, like major histocompatibility complex (MHC), killer cell immune receptors (KIR), and the B and T-cell immune repertoire. Single Molecule, Real-Time (SMRT) Sequencing delivers the long read lengths, uniform coverage and high accuracy necessary to comprehensively and confidently resolve these immune sub-genomic regions. The granularity of data generated by PacBio® reads provides new access to imputation-free characterization of genes and haplotypes for invaluable genomic insights to advance disease association and evolutionary research.

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Thursday, August 27, 2020

HLA Sequencing Application Brochure: Fully phased, allele-specific HLA sequencing – the perfect pair

Single Molecule Real-Time (SMRT) Sequencing delivers reads that span the lengths of the majority of HLA class I and II genes. Unambiguously phase 4-field HLA types without imputation. With a more accurate and complete picture, gain deeper understanding of immune-related disease causality, graft-versus-host disease in hematopoietic transplantation, and drug hypersensitivity.

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Thursday, August 27, 2020

Application Note: Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies

Target enrichment capture methods allow scientists to rapidly interrogate important genomic regions of interest for variant discovery, including SNPs, gene isoforms, and structural variation. Custom targeted sequencing panels are important for characterizing heterogeneous, complex diseases and uncovering the genetic basis of inherited traits with more uniform coverage when compared to PCR-based strategies. With the increasing availability of high-quality reference genomes, customized gene panels are readily designed with high specificity to capture genomic regions of interest, thus enabling scientists to expand their research scope from a single individual to larger cohort studies or population-wide investigations. Coupled with PacBio long-read sequencing, these…

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Thursday, August 27, 2020

Human Biomedical Research Brochure: The most comprehensive view of the human genome

To understand the genetic factors underlying health and disease and to address hidden heritability, scientists require a more comprehensive view of all the variations in the human genome. Single Molecule, Real-Time (SMRT) Sequencing delivers the read lengths, uniform coverage, and accuracy needed for accessing the complete size spectrum of sequence variant types — from single nucleotides to complex structural variants. PacBio’s long single-molecule reads also provide direct variant phasing information across full-length genes and chromosome haplotype blocks. With SMRT Sequencing, scientists gain new insight into the genetic basis of health and disease.

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Wednesday, May 13, 2020

Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing

Studying microbial genomics and infectious disease? Learn how the PacBio Sequel II System can help advance your research, with first-hand perspectives from scientists who are investigating SARS-CoV-2 and COVID-19. In this webinar, Melissa Laird-Smith (Mt. Sinai School of Medicine) discusses her work evaluating the impact of host immune restriction in health and disease with high resolution HLA typing. She is joined by Corey Watson (University of Louisville School of Medicine) who talks about overcoming complexity to elucidate the role of IGH haplotype diversity in antibody-mediated immunity. Hosted by Meredith Ashby, Director of Microbial Genomics at PacBio. Access additional PacBio resources…

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Tuesday, April 21, 2020

HLA*LA – HLA typing from linearly projected graph alignments.

HLA*LA implements a new graph alignment model for HLA type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data); and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample.HLA*LA is implemented in C?++ and Perl and freely available as a bioconda package or from https://github.com/DiltheyLab/HLA-LA (GPL v3).Supplementary data are available online. © The Author(s) 2019. Published by…

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Tuesday, April 21, 2020

Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands.

Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, -DRB3/4/5, and -DQB1 assignments of 1009 unrelated volunteers for the unrelated donor registry in The Netherlands. The analysis characterizes all HLA exons and introns for class I alleles; at least exons 2 to 3 for HLA-DRB1; and exons 2 to 6 for HLA-DQB1. Of the distinct alleles present, there are 229 class I and 71 class II; 36 of these alleles are novel. The majority (approximately 98%) of the cumulative allele frequency at each locus is contributed by alleles that appear three or more times. Alleles encoding…

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