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Monday, September 21, 2020

Checkmate, Chromosome 8: The First End-to-End Sequence of a Human Autosome

Even in the field of genomics where new breakthroughs occur every few months, completion of the first-ever fully sequenced human autosome is a momentous achievement. Highly accurate, no gaps, no mis-joins — just chromosome 8 in all its glory. It’s a remarkable feat and we are honored that PacBio HiFi reads played a pivotal role in helping to achieve it. The complete centromere sequence of chromosome 8 shows a diversity of satellite repeats and other abundant genomic repeats, now with near perfect base-level resolution from end to end. Logsdon, G et al. (2020) This work is described in a preprint…

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Thursday, April 30, 2020

Sequencing 101: Looking Beyond the Single Reference Genome to a Pangenome for Every Species

What is a Pangenome? A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. Unless you have an identical twin, no other person has a genome that is identical to yours. The same is true for other animal, plant, and microbial species that reproduce sexually: the genomes of individuals are unique. Less well known, but equally true, is that individual members of a species do not always share even the exact same genes. Nevertheless, scientists mostly use a single reference genome to represent an entire species: one human genome, one…

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Friday, January 3, 2020

Novel Workflow Produces Fully Phased Human Genome Assemblies Without Trio Sequencing

A new preprint from lead authors David Porubsky and Peter Ebert, senior authors Evan Eichler and Tobias Marschall (@tobiasmarschal), and collaborators reports a method for generating fully phased, de novo human genome assemblies without parental data. The approach combines PacBio HiFi reads (>99% accuracy, 10-20 kb) with the short-read, single-cell Strand-seq technique.  The authors provide a proof-of-principle through assembling the genome of a Puerto Rican female from the 1000 Genomes Project. The work extends a recent publication from many of the same authors in which HiFi reads were used to produce an accurate and contiguous assembly of the human haploid…

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Friday, October 18, 2019

Adaptive Selection of CNVs: UW Team Applies SMRT Sequencing to the Melanesian Genome

PingHsun Hsieh presents his findings at ASHG. In a new Science publication, researchers from the University of Washington and other institutions report detailed analyses revealing the adaptive importance of copy number variants (CNVs) acquired from Denisovan and Neanderthal ancestors, the closest relatives of modern humans, in the modern-day Melanesian population. The team used PacBio long-read sequencing to study these complex stretches of DNA and the Iso-Seq method to generate full-length transcript data. “Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes” comes from lead author PingHsun Hsieh (@phhBenson), senior author Evan Eichler, and collaborators.…

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Monday, October 14, 2019

In New Tibetan Genome Assembly, Variants for Living at Altitude and the Imprint of Archaic DNA

The high-altitude Tibetan Plateau. Photo by McKay Savage via Wikimedia Commons A recent bioRxiv preprint reports efforts to sequence the genome of a Tibetan individual and detect the genetic underpinning of adaptive traits associated with tolerating high altitude. The authors used SMRT Sequencing to achieve extremely high contiguity and accuracy, and incorporated scaffolding and other complementary technologies to build a robust assembly. The results are reported in the preprint, “De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation.” Lead author Ouzhuluobu, senior author Bing Su, and collaborators discuss their evaluation of the…

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Thursday, January 24, 2019

Scientists Produce Valuable New Human Structural Variation Resource Using SMRT Sequencing

In an effort to produce a comprehensive list of structural variants in the human genome, scientists from the University of Washington, the University of Chicago, Washington University, and Ohio State University sequenced 15 human genomes and have now released the results of their in-depth analysis. The Cell publication, “Characterizing the Major Structural Variant Alleles of the Human Genome,” comes from lead authors Peter Audano and Arvis Sulovari, senior author Evan Eichler, and collaborators. The data generated by this work “provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity,” the…

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Monday, October 8, 2018

Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date

We’re proud to announce the release of the most contiguous diploid human genome assembly of a single individual to date, representing the nearly complete DNA sequence from all 46 chromosomes inherited from both parents. The sample used was derived from a Puerto Rican female who has been included in population genetics studies such as the 1000 Genomes Project. The phased diploid assembly will give unprecedented views of population-specific variation through the long-range resolution of maternal and paternal haplotypes. This work is part of a larger effort in the field of personalized medicine and human genomics to add ethnic diversity to…

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Wednesday, March 28, 2018

Bio-IT World: Genomic Data Standards Are a ‘Necessity’

Aaron Wenger, Ph.D Genomic data standards will be essential for continuing the growth of genomics and ensuring its smooth transition into the clinic, according to a new Bio-IT World article written by PacBio scientist Aaron Wenger. The piece nicely sums up recent efforts from the Genome in a Bottle Consortium, the Genome Reference Consortium, and the Global Alliance for Genomics and Health to paint a picture of the state of genomic data standard development today. “The more we learn about the human genome, the more needs we identify for data standards,” Wenger reports. “For example, early efforts focused on ensuring…

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Thursday, October 12, 2017

HGSV Consortium Study Identifies Sevenfold Increase in Structural Variation

UPDATE (April 16, 2019): The paper has now been published in Nature Communications. ORIGINAL POST (October 12, 2017): The Human Genome Structural Variation Consortium, a successor to the 1000 Genomes Project Consortium, recently released a preprint describing an in-depth study of structural variant (SV) detection in human genomes. The scientists found that PacBio long-read sequencing and complementary technologies dramatically improve sensitivity for these important genomic elements when compared to standard short-read sequencing. “Multi-platform discovery of haplotype-resolved structural variation in human genomes” comes from lead authors Mark Chaisson, Ashley Sanders, and Xuefang Zhao; along with corresponding authors Charles Lee, Evan Eichler,…

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Monday, September 11, 2017

At PMLS Meeting, a Focus on Boosting Genomic Representation of Ethnic Diversity

A panel session at the recent Precision Medicine Leaders Summit, held in San Diego last month, offered great perspectives on the need to better represent global ethnic diversity in order to make the most of genomic advances for all patients. Panelists included Robert Sebra from the Icahn School of Medicine at Mount Sinai; NCBI’s Valerie Schneider; Benedict Paten from the University of California, Santa Cruz – representing the Global Alliance for Genomics and Health; and Justin Zook, co-leader of the NIST Genome in a Bottle (GIAB) Consortium. The discussion was moderated by our own Luke Hickey. The session kicked off…

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Thursday, June 22, 2017

Stanford Scientists Report First Use of PacBio Whole Genome Sequencing to Identify a Disease-Causing Mutation

An article published today in Genetics in Medicine from Jason Merker, Euan Ashley, and colleagues at Stanford University reports the first successful application of PacBio whole genome sequencing to identify a disease-causing mutation. (Check out Stanford’s news release here.) The authors describe an individual who presented over 20 years with a series of benign tumors in his heart and glands. The individual satisfied the clinical criteria for Carney complex, but after eight years of genetic evaluation, including whole genome short-read sequencing, experts were still unable to pinpoint the underlying genetic mutation and confirm a diagnosis. Ultimately, the authors turned to the…

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Wednesday, May 24, 2017

Genome Assembly Advances Featured in Genome Research Special Issue

The May issue of Genome Research is a special edition focusing on advances in sequencing technologies and genome assembly techniques. The research papers selected for this special issue cover reference-grade genome assemblies, structural variant detection, diploid assemblies, and other features enabled by new high-quality sequencing tools. The issue kicks off with a perspective from NHGRI’s Adam Phillippy, who reflects on the history of sequencing and assembly. Dusting off publications from as early as 1979, he illustrates the remarkable pace of advances in this field for the past four decades. Phillippy has worked with just about every kind of sequence data,…

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Thursday, February 2, 2017

Toward a Gold Standard for Human Structural Variation

Scientists from the University of Washington and McDonnell Genome Institute recently reported in Genome Research the results of an in-depth assessment of structural variation in the human genome using SMRT Sequencing technology. They found far more variation than expected and suggest using this approach to establish a comprehensive database of structural variants that would aid future studies. “Discovery and genotyping of structural variation from long-read haploid genome sequence data” comes from lead author John Huddleston, senior author Evan Eichler, and collaborators. The team fully sequenced two haploid human cell lines (CHM1 and CHM13) with SMRT Sequencing to greater than 60-fold…

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Wednesday, November 9, 2016

More than Halfway There: Richard Gibbs Talks Clinical Genetics with Mendelspod

Many scientists who participated in the original Human Genome Project shared a grand vision that individual genomes would one day be part of routine medical care. Genomics veteran Richard Gibbs, founder and Director of the Genome Sequencing Center at Baylor College of Medicine, tells Mendelspod host Theral Timpson in a new podcast interview that “we are more than halfway [there].” In the podcast, Gibbs shares his perspective on the complementary roles that genomics and genetics approaches have in driving our understanding of human biology.  He noted that long before the Human Genome Project gained momentum, the discovery of human single…

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Wednesday, July 6, 2016

In Chinese Genome Assembly, SMRT Sequencing Finds Novel Genes and Recovers Missing Sequence

A paper just out in Nature Communications reports the de novo genome assembly and transcriptome of a Chinese individual, generated from long-read SMRT Sequencing and other technologies. The effort revealed nearly 13 Mb of sequence not included in the GRCh38 reference genome as well as novel gene and alternative splicing content not annotated in GENCODE. “Long-read sequencing and de novo assembly of a Chinese genome” comes from lead author Lingling Shi at Jinan University and senior author Kai Wang from the University of Southern California, as well as many other collaborators in China and the US. The team was particularly interested in…

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