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02/02/2018

Interested in getting your sequencing project funded? Submit a 250-word proposal for a SMRT Grant, offered by Pacbio certified service provider GENEWIZ. The deadline is March 25, 2018.

Enter by 03/25/18 for the PacBio Grant with GENEWIZ, Learn more and enter here>>

01/02/2018

The Mexican salamander, or the axolotl were sequenced 110 million long reads (32× coverage, N50 read length 14.2 kb) using Pacific Biosciences instruments to avoid the read sampling bias that is often found when using other technologies and to span repeat-rich genomic regions that cause breaks in short-read assemblies.The long reads also allowed to overcome several assembly challenges, such as 18.6 Gb of repetitive sequences (65.6% of the contig assembly) and distinct long terminal repeat (LTR) retroelement classes and endogenous retroviruses with elements more than 10 kb long.

PacBio is the leader in long-read sequencing, providing high-quality genomes to advance scientific discovery. Learn how SMRT Sequencing powers genomic insights in humans, plants, animals and microbes.

30/01/2018

By the third-generation long-read single molecule real-time (SMRT) sequencing (Pacific Biosciences), the precise breakpoints of the deletion were delineated to a 72.8 kb region in the proband and carrier parents. The long-read SMRT sequencing of the deletion breakpoints also determined that the aberration included the neighboring RP9 gene implicated in retinitis pigmentosa. This highlights the utility of long-read SMRT sequencing to map nucleotide breakpoints of clinically relevant structural variants is highly important.

Case Report

30/01/2018

Pacific Biosciences long read sequencing and assembly with the MARVEL algorithm generated 32.4 billion base axolotl genome assembly for an A. mexicanum strain. Another study on planarian flatworm Schmidtea mediterranea, PacBio long read sequencing and MARVEL assembly in combination with Dovetail Chicago HiRise scaffolding generated 782 million base de novo genome assembly with genomic DNA from an in**ed S. mediterranea strain.

Researchers hope the genomes of the Mexican axolotl and the Schmidtea mediterranea worms will facilitate further studies on the processes behind regeneration.

30/01/2018

SOLVE-RD aims to improve the diagnosis and treatment of rare diseases, which in total affect millions of Europeans. The program is applying novel diagnostic tools to around 19,000 cases unsolved by prior short-read exome sequencing. PacBio long-read genome sequencing have shown that each human genome has upwards of 20,000 structural variants (differences ≥50 bp), which affect more base pairs than single nucleotide variants and small insertions and deletions together. Short-read sequencing fails to detect most of these structural variants, which often lie in repetitive regions of the genome or are larger than short reads can span.

PacBio is the leader in long-read sequencing, providing high-quality genomes to advance scientific discovery. Learn how SMRT Sequencing powers genomic insights in humans, plants, animals and microbes.

30/01/2018

The genome-sequencing project of desert Dingo named Sandy won last year's SMRT Grant program. PacBio long read sequencing was used for de novo sequencing of the genome and the resulting reads, including more than 150 billion bases of raw sequence. With bioinformatics and Scaffolding technologies, the dingo genome resulted in 2.4 billion bases long and spans 98 percent of the CanFam3.1 domestic dog reference genome, which was used for preliminary analyses of the new dingo sequence.

An Australian team used Pacific Biosciences long reads, 10X Genomics linked reads, and Bionano Genomics mapping to assemble a desert dingo genome de novo.

16/01/2018

One single genome is not enough to represent the huge amount of variation in genomes. Hence, Pacbio full-Length Isoform sequencing of samples from different environmental conditions, would enable accurate whole plant transcriptome analysis. This would help the community to achieve a greater understanding of the impacts of structural variation on plant genomes which will result in crop improvement.

Maize is amazingly diverse. A study comparing genome segments from two in**ed lines, for instance, revealed that half of the …

10/01/2018

Scientists sequenced Utricularia gibba genome using SMRT Sequencing. The genome was previously sequenced with short-read technology, producing an 82 Mb assembly. With PacBio long-read technology, the team was able to significantly improve on the original assembly. The de novo genome project resulted in an assembly with a contig N50 of nearly 3.5 Mb. The total size was about 100 Mb, adding more than 18 Mb missed by the short-read assembly. Twenty-four contigs included telomeres achieved, with four of those representing complete chromosomes.

Scientists from the University at Buffalo, Nanyang Technological University, and other institutions published results from an effort to elucidate the …

10/01/2018

Join Pacbio January 13-17 at PAG XXVI in San Diego, California and find out how Single Molecule, Real-Time (SMRT) Sequencing can help advance your research.

Here is the registration link:
https://lnkd.in/ffFYHiz

PACBIO WORKSHOP: MONDAY, JANUARY 15, 12:50-3:00 P.M. PST
Location: Town and Country Hotel, Golden West Ballroom

Speakers:

· SMRT Sequencing Highlights: Building Better Genomes and Transcriptomes
Marty Badgett, Senior Director, Product Management, PacBio

· Domestication: Through the Canines of a Dingo
Bill Ballard, Professor, Biotechnology and Biomolecular Sciences, University of New South Wales, Australia

· Long-Read Sequencing Reveals Complex Genomic Architecture in Independent Carnivorous Plant Lineages
Tanya Renner, Assistant Professor, Entomology, Pennsylvania State University

· Using Cattle Subspecies Crosses to Explore Chromosome of Origin Expression through Iso-Seq Analysis
John Williams, Professor, School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide

08/01/2018

Precision Medicine World Conference (PMWC), a three-day (January 22-24) Silicon Valley event focused on exploring challenges and opportunities in personalized medicine. Lori Aro, Pacbio senior director of clinical genomics, will be speaking at PMWC in the Genomic Profiling Showcase on January 24th at 11:15 am. Her presentation will update attendees on how long-read PacBio sequencing can be a good fit for clinical assay development since it provides the longest average reads, highest consensus accuracy, and most uniform coverage of any sequencing technology available today.

There’s still time to register for PMWC 2018 and they’re offering a 10% discount until January 11.

One of our favorite January traditions is taking part in the Precision Medicine World Conference (PMWC), a three-day Silicon Valley …

04/01/2018

Pacbio SMRT Sequencing to characterize transcript isoforms of the FMR1 gene in tissue samples. The Iso-Seq analysis yielded up to 28,000 full-length transcript reads from the premutation carrier tissue samples. In total, 49 unique FMR1 isoforms identified, including 16 previously characterized isoforms and a number of novel ones. Out of the 49 FMR1 isoforms, 30 of them were exclusively detected in premutation carriers. Characterizing the FMR1 isoforms expression levels helps understand the FMR1 gene regulation and also elucidate one of the mechanisms of FMR1-associated disorders.

In a recent publication, scientists from the University of California, Davis, and PacBio reported results from an investigation of alternative …

29/12/2017

The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. De novo genome assembly from Pacbio single-molecule, long-read sequencing data consisting of 135 P. pacificus contigs achieved with 99% of the assembly ordered and oriented into six chromosomes. This allowed chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P. pacificus characterizations with one major translocation from an autosome to the s*x chromosome in the lineage leading to C. elegans identified.

Nematodes are both simple and complex, making them one of the most attractive animal taxa to study basic biological processes, …