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News Briefs from the Genomes, Medicine, And the Environment Conference 2007

Danaher Motion to DistributeChurch Lab’s 'Polonator' Sequencer
The Dover business of Danaher Motion, based in Salem, NH, will distribute the Polonator G.007, the new high-throughput sequencer that has been under development in George Church’s group at Harvard (see In Sequence 6/26/2007), Church said during a talk at the conference last week.
The price per instrument, which runs 36 flow-cells with 60 million beads per flow-cell, will range from $124,000 to $136,000, depending on order volume, and includes a computer and a one-year warranty. Service contracts will be available at an additional cost. The instrument has an output of 10 gigabases of raw sequence data per run, based on a read length of 28 bases and 16 percent of the beads giving high quality sequences, according to Church. His group is also working with Enzymatics, an enzyme producer based in Beverly, Mass., to cut the cost of the enzymes required for sequencing by ten-fold.
The cost of sequencing on the new instrument is currently about $2.88 per megabase, or $1,800 to sequence 1 percent of the genome at 20X coverage. Next year, Church predicted, the output efficiency will improve two-fold and the overall costs six-fold. This technology is being used for the Personal Genome Project.
Danaher Motion, which provides machine parts for a variety of industries, is one of “several strategic platforms” that make up Danaher, according to the company website.

JCVI to Complete Venter’s Genome With ABI, 454, Illumina Tools
The J. Craig Venter Institute is planning to use several next-gen sequencing technologies to complete Venter’s genome, in anticipation of its planned large-scale human genome sequencing study (see In Sequence 10/9/2007).
JCVI is currently working with ABI to generate an additional 12X of coverage of Venter’s genome on the SOLiD system, and expects to receive its own instrument shortly, Sam Levy, a senior JCVI scientist, told In Sequence during the conference last week.
Institute scientists are also planning to fill gaps in Venter’s genome by targeted sequencing of fosmids and BAC clones, using a combination of 454’s and Illumina’s sequencing platforms, and to corroborate insertions and deletions using Nimblegen tiling arrays, according to Levy.
Next year, JCVI scientists plan to sequence between 10 and 50 individuals and evaluate a number of next-generation sequencing technologies, which could include tools developed by Applied Biosystems, 454 Life Sciences, Illumina, and George Church’s lab at Harvard, Levy said.
That project will serve as a pilot study for a large-scale human genome sequencing study that aims to map approximately 10,000 genomes within the next decade.
Following the publication of Venter’s genome in PLoS Biology last month, 200 volunteers had offered to have their genomes sequenced, Levy said.
The institute is currently establishing an informed-consent protocol and deciding who will make up the first group of individuals to be sequenced.
The aim is to make this initial batch “as diverse as possible,” Levy said, including men and women, different ethnicities, as well as people with common diseases.
JCVI will design the study with Scripps Genomic Medicine and will obtain clinical samples with help from the Ludwig Institute for Cancer Research.
The institute is also exploring ways to pay for the study, including encouraging volunteers to subsidize two other genomes, to be chosen by JCVI, in addition to their own, according to an institute spokeswoman.

UK Sequencing Startup Signs Up for X Prize for Genomics; Foundation to Start Outreach Next Year
UK-based start-up Base4 Innovation is the first competitor from outside the US to participate in the Archon X Prize for Genomics, the X Prize Foundation said last week.
The Coventry-based company is developing a new DNA sequencing method that combines “well-known techniques such as photon detection and fluorescent labeling with nanostructures and cutting-edge methods of nanofabrication,” according to the foundation. 
Base4 is supported by the University of Warwick and Warwick Ventures, and includes a group of physicists and biologists from the Universities of Oxford, Cambridge, and Warwick.
Four other teams have entered the race, which will pay $10 million to the first team to sequence 100 human genomes in 10 days for less than $10,000 per genome: VisiGen Biotechnologies, 454 Life Sciences, the Foundation for Applied Molecular Evolution, and Reveo.
According to Larry Kedes, senior advisor and scientific director, as well as SAB co-chair for the prize, the foundation recently debated whether to narrow the scope of the task to selective sequencing but decided to stick with the original goal of whole-genome sequencing.
“Without the whole genome sequence, we don’t have all the information,” Kedes said during a talk at last week’s conference. Functionally relevant information may reside in non-coding or repetitive regions, he added.
Next year, the X Prize Foundation will begin an educational and marketing outreach initiative, Kedes said, in order to educate the public about genome sequencing, as well as to “demystify personal genetics and create excitement and support for the competing teams.”
Also, 100 “spokespersons” for the Archon X Prize will have their genomes sequenced, including Larry King, Richard Branson, and Stephen Hawking.
The foundation is holding a meeting in Toronto at the end of November, entitled “The Personal Genome: A Workshop on Emerging ELSI challenges,” during which 40 researchers will discuss ethical issues of human genome sequencing.
Since the prize will probably take “three years, more likely five to seven years” to be won, according to Kedes, the foundation is also considering an annual team “bake-off,” a contest with more limited goals where participating teams can showcase their technologies.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.