Advances in Next-Gen Sequencing Speed Evolution of Bioinformatics Tools in 2009

December 18, 2009

A prime example of the progress made in bioinformatics over the last year was the publication this week in Nature of the panda genome, which the Beijing Genomics Institute in Shenzhen sequenced and assembled de novo using only the Illumina Genome Analyzer platform and the SOAPdenovo algorithm for assembly.

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In this issue of BioInform

Video Spotlight

Shashikant Kulkarni at ACMG

BioArray News editor Justin Petrone sat down with Shashikant Kulkarni, an associate professor at Washington University School of Medicine at St. Louis, to discuss chromosomal microarrary analysis in the clinic, SNP arrays versus CGH platforms for post-natal testing, and more.

May 16, 2012

Miragen Therapeutics' Eva van Rooij

Miragen Therapeutics' Eva van Rooij discusses microRNA-based therapeutics, the challenges associated with chronic microRNA knockdown, therapeutic microRNA antagonists, and more.

May 08, 2012

A Conversation with CeGaT's Saskia Biskup

In this video, Julia Karow, Editor of Clinical Sequencing News, interviews Saskia Biskup, CEO of the Center for Genomics and Transcriptomics, or CeGaT, at the company's headquarters in Tübingen, Germany.

May 02, 2012

A Tour of Illumina's CLIA Lab

In this video, Illumina's CLIA laboratory manager Suneer Jain gives InSequence and Clinical Sequencing News Editor Monica Heger a tour of Illumina's CLIA lab at the company's San Diego headquarters.

April 25, 2012
Young Investigator Profile

Vincent Fusaro

Harvard Medical School
Postdoctoral Fellow

Informatics and PGx

Vincent Fusaro is using a Pathways to Independence grant from the National Library of Medicine to develop informatics methods for identifying new uses for existing drugs as well as confirming their benefit using electronic medical records from health-care providers.
Blog

This Week in the Journal of Molecular Diagnostics

In the Journal of Molecular Diagnostics this week: long-range PCR to detect PKD1 and PKD2 mutations, more.

May 18, 2012

An Accreditation Module

The College of American Pathologists teams up with SoftTech Health.

May 18, 2012

Political Science

Sometimes, researchers have to get political, says one writer.

May 18, 2012

In Charge of Research

Geneviève Fioraso is the new French research minister.

May 18, 2012
Papers of Note

KCTD13 a Driver of Neurodevelopmental Phenotypes Associated with the 16p11.2 CNV
Golzio, Willer et al., Nature
An international team led by investigators at Duke University shows that KCTD13 "is a major driver for the neurodevelopmental phenotypes associated with the 16p11.2 CNV [copy-number variant]," a finding that it says substantiates "the idea that one or a small number of transcripts within a CNV can underpin clinical phenotypes, and offer an efficient route to identifying dosage-sensitive loci."

Approach to Reduce Allelic Bias in RNA-seq Read-Mapping
Satya, Zavaljevski, and Reifman, Nucleic Acids Research
Researchers at the US Department of Defense Biotechnology High Performance Computing Software Applications Institute present an approach to reduce allelic bias in RNA-seq read-mapping based on the "construction of an enhanced reference genome that includes the alternative alleles at known polymorphic loci." In this paper, the team shows that "mapping to this enhanced reference reduced the read-mapping biases, leading to more reliable estimates of ASE [allele-specific expression]."
People on the Move

IntegenX has appointed David Smith to serve as its new COO. Smith most recently served as CFO of Thoratec, and previous to that was CFO at Chiron. He currently is chair of the audit committee and a director of OncoGenex Pharmaceuticals and previously was chair of the audit committee and a director of Perlegen Sciences.

Vermillion said this week that President and CEO Gail Page will be leaving the company by September and the firm has begun the process to find her successor. Page also has resigned her seat on the board of directors, and effective immediately Vermillion amended its bylaws to eliminate the vacant seat, reducing its board from seven to six members.

Genomic Health has appointed Richard Tompane as president of its new subsidiary InVitae, which will focus on developing next-generation-based sequencing diagnostics for genetic diseases. Tompane was previously president and CEO of Gemfire and has also served as an independent consultant.
Upcoming Events

Conferences, Meetings & Deadlines

The iMedicine & Mobile Life Sciences World Summit
May 16-17 / Boston
Arrowhead Publishers

New Perspectives on Immunity to Infection
May 19-22 / Heidelberg, Germany
EMBL

TIDES: Oligonucleotides and Peptide Technology & Product Development
Applications of Nucleic Acids Technologies in Molecular Diagnostics, Oligonucleotide Therapeutics Discovery, and Peptide Discovery and Development
May 20-23 / Las Vegas
IBC Life Sciences

Microtubules: Structure, Regulation and Functions
May 23-26 / Heidelberg, Germany
EMBL

Evidence for Clinical Utility of Molecular Diagnostics in Oncology: A Workshop
May 24 / Washington, DC
Institute of Medicine

Abstract & Registration Deadlines

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Science
A study published in Science Translational Medicine suggests high-throughput sequencing is effective for finding post-treatment leukemia cells that can lead to patient relapse. Researchers used sequencing to test matched pre- and post-chemotherapy samples from 43 individuals with T-lineage acute lymphoblastic leukemia. They found that the sequencing method tracked down minimal residual disease in 25 of the cases tested, including several missed by flow cytometry.
Business
Agilent Technologies will spend $2.2 billion to acquire Danish diagnostics firm Dako. The deal marks a major push by Agilent into the diagnostics arena and provides the firm with Dako's portfolio of immunohistochemical cancer diagnostic tools and emerging companion diagnostics alliances as well as an entry into the $2.2 billion anatomic pathology market. Dako is expected to generate $373 million in revenues in fiscal 2013 with a $68 million operating profit.
Funding
The National Institute on Aging will provide up to $6 million in 2013 to support up to three projects undertaking whole exome and/or whole genome sequencing data analysis to identify genomic contributions to both the risk for and protection against Alzheimer's disease. The funding program is part of the Presidential Initiative on Alzheimer's Disease and is expected to fund between one and three awards with up to $2 million direct cost per award for fiscal year 2013.
Genome Technology Magazine
For this month's Q&A, Matthew Dublin speaks with McGill University's John Breitner about a European consortium that aims to develop molecular diagnostics for both Alzheimer's and Parkinson's disease. As part of the program, Breitner is developing standardized ways to describe patient samples as a first step in bringing innovations to the clinic. Breitner says that there are a number of biomarkers than can confirm or deny a presumptive diagnosis, but there is not yet a standard way to run tests based on such markers.

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Advances in Next-Gen Sequencing Speed Evolution of Bioinformatics Tools in 2009

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In this issue of BioInform

Video Spotlight

Young Investigator Profile

Blog

Papers of Note

People on the Move

Upcoming Events

Science

Business

Funding

Genome Technology Magazine

TechGuides Listings

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