In Sequence | Sequencing

In the debate between whole-genome and whole-exome sequencing, the advantages and disadvantages of each method and how each approach can be used in different areas of study often dictate which method researchers gravitate to.

February 01, 2012 / Genome Technology

BGI Develops a Cloud in a Box for Faster Analysis of Genomic Data

Bioinformatics

February 01, 2012 / Genome Technology

New Genome Sequencing Program Aims to Move Discoveries Closer to the Clinic

NHGRI

February 01, 2012 / Genome Technology

In this issue of In Sequence

Video Spotlight

Sponsored Video: Ambry Genetics - "Fully-Automated"

RainDance's ThunderStorm System is a fully-automated and walkaway high-throughput targeted sequencing solution that enables researchers to process 96 samples per day run on a proven platform that generates higher-quality data faster than ever before.

February 07, 2012

Sponsored Video: Sage Science - Pippin DNA Size Selection

Sage Science is pleased to announce the introduction of the BluePippin DNA size selection system, a pulsed-field electrophoresis version of its popular Pippin Prep instrument.

January 31, 2012

ScienceOnline2012

Genome Technology's Tracy Vence interviewed Sandra Porter, president of Digital World Biology, and Kristi Holmes, a bioinformaticist at the Becker Medical Library, Washington University School of Medicine at ScienceOnline2012.

February 02, 2012

Highlights from SC11 Part IV

In this video, we speak with Todd Smith, senior leader of research and applications of PerkinElmer, and researchers from Stockholm University on accelerating the GROMACS molecular dynamics software suite with GPUs and CPUs.

January 13, 2012
Young Investigator Profile

Juan Dong

Assistant Professor
Rutgers University

Probing Polarity

The Dong lab is focused on building a model for plant cell polarity and its regulation in asymmetric cell division. This includes the identification of additional polarized proteins and of mutants that highlight specific subsets of polarity defects. In the future, her lab will continue to use Arabidopsis as a model system, by studying Breaking of Asymmetry in the Stomatal Lineage and the other newly identified factors, to investigate how proteins become polarly localized, how polarity proteins are involved in establishment of cellular asymmetry, and how cell polarity is instructive of cell fate and differentiation in plants.
Blog

J&J Chief (Partially) Steps Down

Johnson & Johnson's William Weldon is retiring as the company's chief executive.

February 22, 2012

This Week in the Journal of Clinical Pathology

In the Journal of Clinical Pathology this week: Rsf-1 overexpression in nasopharyngeal carcinoma, and more.

February 22, 2012

A Beef with Publishers

One researcher says publishers are to blame for "squelching science communication."

February 22, 2012

Science for All

Jordan's Princess Sumaya bint El Hassan says scientific research must be driven by the world's needs.

February 22, 2012
Papers of Note

Chromosome Painting, Gene Mapping of Tasmanian Devil Facial Tumor Disease
Deakin, Bender et al., PLoS Genetics
A team led by investigators at the Australian National University reports its use of "chromosome painting and gene mapping to deconstruct the DFTD [Tasmanian devil facial tumor disease] karyotype and determine the chromosome and gene rearrangements involved in carcinogenesis." Through its analysis, the team produced detailed maps of both the devil and tumor karyotypes, which the researchers say will aid future genomic investigations into the transmissible cancer.

Discovery, Prioritization of Somatic Mutations in DLBCL by Whole-Exome Sequencing
Lohr, Stojanov et al., PNAS
An international team led by investigators at the Broad Institute reports on its "discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma by whole-exome sequencing." Using this technique, the team sequenced 55 primary tumor samples from DLBCL patients and their matched normal tissue, finding recurrent mutations in genes known to be functionally relevant in the disease and somatic mutations in genes for which a functional role in DLBCL was not previously suspected, including MEF2B, MLL2, BTG1, GNA13, ACTB, P2RY8, PCLO, and TNFRSF14.
People on the Move

Randy Scott will lead a new subsidiary at Genomic Health that will focus on integrating genomic data into clinical practice for patients with common and rare genetic conditions. Scott will step down as Genomic Health's executive chairman but will remain a board member, while CEO Kim Popovits will assume the role of chairman.

Scott is a founder of Genomic Health and was previously CEO of the company. He also founded Incyte, where he served in various positions including chief scientific officer; and has served as senior director of research at Invitron.

Genomic Health has also appointed Julian Baker to be lead independent director. Baker has served on the firm's board since 2001 and is a managing partner at Baker Brothers Investments. He is also a director of Incyte, Neurogen, Theravance, and Trimeris.

Life Technologies this week named Alan Sachs as head of global research and development and Ronnie Andrews as president of medical sciences.

Sachs was previously the vice president of exploratory and translational sciences for Merck Research Laboratories, where he spent 10 years in various leadership roles, Life Tech said. Prior to that Sachs served an associate professor of biochemistry and molecular biology at the University of California, Berkeley, and as a Whitehead fellow at the Whitehead Institute for Biomedical Research.

Andrews joins Life Tech from GE Molecular Diagnostics, where he served as a segment leader following GE's 2010 acquisition of Clarient, where Andrews was CEO. Andrews has also held executive positions with Abbott Diagnostics, Roche Diagnostics, and Immucor.
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Science
A research team led by the Wellcome Trust Sanger Institute and Yale University has sifted through data from three 1000 Genomes Project pilot efforts to find a set of authentic loss-of-function variants in the human genome. They estimate that each person, on average, carries roughly 100 loss-of-function variants and has around 20 genes that have been rendered inactive by loss-of-function mutation that affect both copies of the gene.
Business
Illumina said that the US District Court for the Northern District of California had adopted claims constructions that are "favorable" to its case for the key terms in litigation filed against Complete Genomics. Illumina has alleged that Complete Genomics is infringing three of its patents. Complete Genomics, however, said that some of the definitions from the claims construction decision are in its favor, while others favor Illumina.
Funding
Under the Obama Administration's plan to provide flat year-over-year funding of $30.7 billion for the NIH in 2013, NHGRI's funding would be cut $1 million to $511 million, while the new National Center for Advancing Translational Sciences is marked for a boost of $64 million to $639 million. The funding proposal reflects a tight fiscal environment, a dramatic drop in the cost of sequencing, and an increased emphasis on translational science.
Genome Technology Magazine
The whole-genome and whole-exome sequencing clash has been going on for years. Exome sequencing is less expensive than whole-genome sequencing as it takes into account only the coding portion of the genome, but the tradeoff is that it misses non-coding variation and some structural variation. Further, there's bioinformatics aspect — making sense of the millions of data points means trying to make sure that the right data points are being analyzed. The advantages and disadvantages of whole-genome and whole-exome sequencing method and how each approach can be used in different areas of study often dictate which method researchers gravitate to.

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In this issue of In Sequence

Video Spotlight

Young Investigator Profile

Blog

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People on the Move

Upcoming Events

Science

Business

Funding

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