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Monday, June 29, 2015

Nature Methods Paper Uses Long-Read Data for Highly Contiguous Diploid Human Genome

A new publication in Nature Methods describes a new single-molecule assembly approach that resulted in “the most contiguous clone-free human genome assembly to date,” according to lead authors Matthew Pendleton, Robert Sebra, Andy Pang, and Ajay Ummat. The paper, “Assembly and Diploid Architecture of an Individual Human Genome via Single Molecule Technologies,” comes from a large team of collaborators at the Icahn School of Medicine at Mount Sinai, Cornell, Cold Spring Harbor Laboratory, and other institutions. Their new approach leverages the best aspects of each single-molecule data type by combining long-read sequencing for de novo assembly with single-molecule genome maps…

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Thursday, June 25, 2015

SMRT Data Delivers for Next-Generation HLA Typing at Anthony Nolan Research Institute

A new publication in PLoS One from authors at Anthony Nolan’s Research Institute describes a feasibility study for HLA typing using SMRT® Sequencing. The research institute, where the world’s first bone marrow registry started in 1973, is part of the UK-based charity dedicated to improving the outcomes of bone marrow transplantation. Scientists at Anthony Nolan are leaders in HLA typing, which is an important step in matching a bone marrow or stem cell donor to a patient in need. The Anthony Nolan team adopted the PacBio® system last year, and this publication reflects its efforts to test and establish the…

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Monday, June 15, 2015

Scientists Publish New Methylation Analysis Protocols Using SMRT Sequencing

Scientists from the Icahn School of Medicine at Mount Sinai and the University of Saskatchewan teamed up to develop an innovative approach to methylation analysis using Single Molecule, Real-Time (SMRT®) Sequencing. The resulting method was just published in BMC Genomics. Lead author Yao Yang and colleagues note in the paper [“Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)”] that existing methods for methylation analysis are limited by cost and throughput in the case of Sanger sequencing, or short read lengths with NGS technologies. Their goal was to develop a method combining long reads, high accuracy,…

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Thursday, June 11, 2015

Updated! Data Release: Human MCF-7 Transcriptome

UPDATE: Our R&D team has added a new dataset for the MCF-7 human breast cancer transcriptome, originally released in 2013. The new results were produced using 28 SMRT® Cells with 4-hour movies and P5-C3 chemistry. Sizing was performed with the SageELF™ platform (fractions collected: 1-2 kb, 2-3 kb, 3-5 kb, and 5-10 kb). Sequencing of the larger fractions with our newer sequencing chemistry that generates longer reads added longer transcripts (up to 10 kb) to the MCF-7 dataset, which previously had only transcripts up to 4 kb. New FASTA and GFF files are available, representing the new combined dataset. Raw…

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Tuesday, June 9, 2015

Attend Our Worldwide User Meetings & SMRT Informatics Developers Conference

If you’d like to hear about the latest applications of SMRT® Sequencing from users, we have several events coming up. Our worldwide user group meetings and workshops feature PacBio users sharing their latest research, tips, and protocols, as well as our staff providing training and updates on products and methods to optimize your research. We’re always humbled by the quality and variety of science presented at these meetings. And for the bioinformatics crowd, we have a new event in August focused on developing new analytical tools for PacBio® data. Here’s more detail on each event, including registration details: Americas East…

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Tuesday, June 2, 2015

In Assembler Evaluation, Scientists Recommend Non-hybrid Approach to Bacterial Genomes

A new publication in Nature Scientific Reports recommends using only the PacBio® system to sequence bacterial genomes for the best chance of generating an accurate and finished assembly. The paper, “Completing bacterial genome assemblies: strategy and performance comparisons,” reviews several different long-read assembly methods for bacterial genomes. Authors Yu-Chieh Liao, Shu-Hung Lin, and Hsin-Hung Lin from the Institute of Population Health Sciences in Taiwan note that while several methods exist, efforts to evaluate and compare them have been insufficient. They set out to thoroughly assess these methods, which include hybrid assembly protocols as well as long-read-only protocols. Long-read technology appealed…

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