Cancer Sequencing with High Coverage on Two Platforms Improves Mutation Detection, Baylor Team Says

July 06, 2010

The Baylor researchers propose to sequence tumor-normal pairs with 60-fold coverage or more on two different sequencing platforms "to get a real handle on false positive and false negative rates that occur in cancer sequencing."

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In this issue of In Sequence

Video Spotlight

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 ScieneOnline2012.

February 02, 2012 / GenomeWeb Video

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 / Sponsored Videos

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 / Informatics Iron

Mass Spec at NYU

We visited the NYU Protein Analysis Facility at the Skirball Institute of Biomolecular Medicine in New York City and discussed the facility's gear and its development with director, Thomas Neubert.

January 01, 2012 / GenomeWeb Video
Young Investigator Profile

Long Cai

Assistant Professor
California Institute of Technology

Single Systems

The Cai lab has recently discovered that, in single cells, signaling, and gene expression events occur in a surprisingly burst-like fashion. They are using quantitative single cell time-lapse fluorescence microscopy to uncover a previously unknown frequency-modulated (FM) mode of control in signaling where signaling proteins are coherently phosphorylated and de-phosphorylated in pulses within a single cell, as well as the frequency and duration of pulses are modulated by external signal.
Blog

Higher Fees, Faster Service

The US Food and Drug Administration and medical device companies reach a deal to speed up the review process.

February 03, 2012 / The Sample

Fighting Disease with iPhones and Big Data

An iPhone app developer is working on tracking skin cancer to facilitate personalized medicine.

February 03, 2012 / Informatics Iron

This Week in the Journal of Molecular Diagnostics

In the Journal of Molecular Diagnostics this week: next-gen sequencing to detect HPV, marker stability for neuroblastoma, and more.

February 03, 2012 / The Sample

A 'Science Groupie' Sings

Bjork's new album, Biophilia, pays homage to concepts of science and nature.

February 03, 2012 / The Daily Scan
Papers of Note

Chromosome-Scale Selective Sweeps and Genomic Diversity in C. elegans
Andersen, Gerke et al., Nature Genetics
Researchers at Princeton University and elsewhere discuss the effects of chromosome-scale selective sweeps on genomic diversity in Caenorhabditis elegans. Taking a high-throughput selective sequencing approach on a collection of 200 wild C. elegans strains, the team found that the nematode's "genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases." Further, the team reports on its population genetic modeling experiments, which showed that "this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years," it writes.

Dissecting the Regulatory Architecture of Gene Expression Quantitative Trait Loci
Gaffney, Veyrieras et al., Genome Biology
A team led by investigators at the University of Chicago this week report their use of a "Bayesian hierarchical model to estimate the enrichment of eQTLs [expression quantitative trait loci] in a wide variety of regulatory annotations" derived from 1,000 Genomes Project data. "We find that [approximately] 40 percent of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions," the authors write.
People on the Move

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.

Stephen O'Brien has left the National Cancer Institute's Laboratory of Genomic Diversity after 25 years to help launch a genome bioinformatics program at St. Petersburg University in Russia. O'Brien received a $5 million grant from the Russian Ministry of Education and Science last year under a program that aims to lure big-name researchers to Russia. Over the coming three years, O'Brien will spend at least four months per year in Russia working at the center, which is scheduled to open in May.

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.
Upcoming Events

Conferences, Meetings & Deadlines

The World Cancer Immunotherapy Conference: Challenges & Opportunities in Clinical Development, Clinical Trial Design & Commercialization
Jan 25-26 / San Diego
Arrowhead Publishers

3rd Annual Health Outcomes and Pharmacoeconomics Research Conference
Jan 30-31 / Philadelphia
Marcus Evans

2012 Genitourinary Cancers Symposium
Feb 2-4 / San Francisco
ASCO

An Introduction to Genomics: Breast Cancer Diagnosis and Treatment
Feb 3 / Bethesda, Md.
NHGRI

SLAS 2012: 1st Annual Conference and Exhibition
Feb 4-8 / San Diego
SLAS

Abstract & Registration Deadlines

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Science
Using genetic data on up to 70,000 women with breast cancer and roughly the same number of controls, an international team of researchers has identified three previously undetected variants influencing risk of the disease. Two of the loci were on chromosome 12: one near the TBX3 gene and another near a gene called PTHLH that has been implicated in breast cancer metastasis to bone. A third locus fell on chromosome 21 in the vicinity of the NRIP1 gene.
Business
Roche has launched a $5.7 billion hostile takeover bid for Illumina. Though the $44.50 per share offer represents a 61 percent premium over the one-month historical average of Illumina's share price, it is far below Illumina's 52-week high of $79.40 reached in early July, and some analysts have suggested Roche will need to up its offer. Illumina said its board will review Roche's offer and then make a recommendation to its stockholders.
Funding
Canada launched a new program that will pump C$67.5 million (US$67.3 million) into projects that will use genomics-based research to advance personalized healthcare. The 2012 Large-Scale Applied Research Project Competition in Genomics and Personalized Health is funded with C$40 million from Genome Canada, C$22.5 million from the Canadian Institute of Health Research, and C$5 million from the Cancer Stem Cell Consortium.
Genome Technology Magazine
The National Center for Biotechnology Information's Teresa Przytycka and her team have developed a pathway-centric computational approach, which is based on eQTL analysis, graph theoretical techniques, and combinatorial algorithms, to identify causative genes for complex diseases. In a paper, her team applied the approach to glioblastoma multiforme, and they identified not only putative causal genes, but also potential nodes and pathways linking those genes.

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Cancer Sequencing with High Coverage on Two Platforms Improves Mutation Detection, Baylor Team Says

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