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Thursday, January 7, 2021

Whitepaper: Structural variation in the human genome

Structural variation accounts for much of the variation among human genomes. Structural variants of all types are known to cause Mendelian disease and contribute to complex disease. Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution and genetic diversity.

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Wednesday, January 6, 2021

Movie: The new biology part II – cancer

Part II of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.

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Wednesday, January 6, 2021

Movie: The new biology

This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.

Read More »

Wednesday, January 6, 2021

Movie: The new biology part III – infectious disease

Part III of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.

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Wednesday, January 6, 2021

Labroots Webinar: More comprehensive views of human genetic variation

In this BioConference Live webinar, PacBio CSO Jonas Korlach highlights how multi-kilobase reads from SMRT Sequencing can resolve many of the previously considered ‘difficult-to-sequence’ genomic regions. The long reads also allow phasing of the sequence information along the maternal and paternal alleles, demonstrated by full-length, fully phased HLA class I & II gene sequencing. In addition, characterizing the complex landscape of alternative gene products is currently very difficult with short-read sequencing technologies, and he describes how long-read, full-length mRNA sequencing can be used to describe the diversity of transcript isoforms, with no assembly required. Lastly, in the exciting area of…

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Wednesday, January 6, 2021

PAG Conference: Endless forms: Genomes from the Darwin Tree of Life Project

Mark Blaxter, project lead of the Sanger Institute’s Darwin Tree of Life, shared an update of the ambitious effort to sequence all 60,000 species believed to be on the British Isles over the next 12 years in this presentation at the PAG 2020 Conference. The Sanger team has already generated data for 94 species, including 44 new moth and butterfly (Lepidoptera) PacBio assemblies, which Blaxter describes in this presentation.

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Wednesday, January 6, 2021

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, December 22, 2020

Complete HIV-1 genomes from single molecules: Diversity estimates in two linked transmission pairs using clustering and mutual information.

We sequenced complete HIV-1 genomes from single molecules using Single Molecule, Real- Time (SMRT) Sequencing and derive de novo full-length genome sequences. SMRT sequencing yields long-read sequencing results from individual DNA molecules with a rapid time-to-result. These attributes make it a useful tool for continuous monitoring of viral populations. The single-molecule nature of the sequencing method allows us to estimate variant subspecies and relative abundances by counting methods. We detail mathematical techniques used in viral variant subspecies identification including clustering distance metrics and mutual information. Sequencing was performed in order to better understand the relationships between the specific sequences of…

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Tuesday, December 22, 2020

Rapid sequencing of HIV-1 genomes as single molecules from simple and complex samples.

Background: To better understand the relationships among HIV-1 viruses in linked transmission pairs, we sequenced several samples representing HIV transmission pairs from the Zambia Emory HIV Research Project (Lusaka, Zambia) using Single Molecule, Real-Time (SMRT) Sequencing. Methods: Single molecules were sequenced as full-length (9.6 kb) amplicons directly from PCR products without shearing. This resulted in multiple, fully-phased, complete HIV-1 genomes for each patient. We examined Single Genome Amplification (SGA) prepped samples, as well as samples containing complex mixtures of genomes. We detail mathematical techniques used in viral variant subspecies identification, including clustering distance metrics and mutual information, which were used…

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Tuesday, December 22, 2020

High-throughput analysis of full-length proviral HIV-1 genomes from PBMCs.

Background: HIV-1 proviruses in peripheral blood mononuclear cells (PBMCs) are felt to be an important reservoir of HIV-1 infection. Given that this pool represents an archival library, it can be used to study virus evolution and CD4+ T cell survival. Accurate study of this pool is burdened by difficulties encountered in sequencing a full-length proviral genome, typically accomplished by assembling overlapping pieces and imputing the full genome. Methodology: Cryopreserved PBMCs collected from a total of 8 HIV+ patients from 1997-2001 were used for genomic DNA extraction. Patients had been receiving cART for 2-8 years at the time samples were obtained.…

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Tuesday, December 22, 2020

Harnessing kinetic information in Single-Molecule, Real-Time Sequencing.

Single-Molecule Real-Time (SMRT) DNA sequencing is unique in that nucleotide incorporation events are monitored in real time, leading to a wealth of kinetic information in addition to the extraction of the primary DNA sequence. The dynamics of the DNA polymerase that is observed adds an additional dimension of sequence-dependent information, and can be used to learn more about the molecule under study. First, the primary sequence itself can be determined more accurately. The kinetic data can be used to corroborate or overturn consensus calls and even enable calling bases in problematic sequence contexts. Second, using the kinetic information, we can…

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Tuesday, December 22, 2020

Sequencing complex mixtures of HIV-1 genomes with single-base resolution.

A large number of distinct HIV-1 genomes can be present in a single clinical sample from a patient chronically infected with HIV-1. We examined samples containing complex mixtures of near-full-length HIV-1 genomes. Single molecules were sequenced as near-full-length (9.6 kb) amplicons directly from PCR products without shearing. Mathematical analysis techniques deconvolved the complex mixture of reads into estimates of distinct near-full-length viral genomes with their relative abundances. We correctly estimated the originating genomes to single-base resolution along with their relative abundances for mixtures where the truth was known exactly by independent sequencing methods. Correct estimates were made even when genomes…

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Tuesday, December 22, 2020

Data release for polymorphic genome assembly algorithm development.

Heterozygous and highly polymorphic diploid (2n) and higher polyploidy (n > 2) genomes have proven to be very difficult to assemble. One key to the successful assembly and phasing of polymorphic genomics is the very long read length (9-40 kb) provided by the PacBio RS II system. We recently released software and methods that facilitate the assembly and phasing of genomes with ploidy levels equal to or greater than 2n. In an effort to collaborate and spur on algorithm development for assembly and phasing of heterozygous polymorphic genomes, we have recently released sequencing datasets that can be used to test…

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