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Helicos, Illumina, Washington University, Medical Solutions, NIDCR, 454

Helicos Receives First Order for HeliScope Sequencer
Helicos BioSciences said last week that it has received the first order for its Helicos Genetic Analysis System from an undisclosed customer.
The system consists of the HeliScope sequencer, the HeliScope analysis engine, and the HeliScope sample loader.
Helicos President and COO Steve Lombardi told In Sequence last week that the company plans to name the customer when the instrument is being shipped. He did not provide a timeline for the shipment.

Illumina Sequences HapMap Individual Using Paired Reads
Illumina said last week that it has sequenced the genome of a HapMap individual of African origin by generating paired-end reads on its Genome Analyzer.
Using paired reads, mostly from 200 base pair insert size libraries but also from 2,000 base pair insert size libraries, Illumina scientists generated more than 75 gigabases of sequence data in 27 instrument runs.
They found more than 3.7 million putative SNPs, including more than a million potentially novel ones. The researchers are currently using both long- and short-insert read pairs to characterize structural variation in this genome.

Wash U Buys Five More GS FLX Systems, Gains Early Access to Tech Upgrades
Washington University School of Medicine’s Genome Sequencing Center plans to install five Genome Sequencer FLX systems and will participate in Roche Diagnostics’ early-access program for technology improvements for the platform, Roche said last week.
Roche said that improvements to the 454 Life Sciences sequencing system will include an increase in sequence read length to "beyond 400 base pairs," from a current level of around 250 base pairs, and a "dramatic increase" in the number of reads per instrument run.
The GSC’s purchase of five additional GS FLX systems brings the total number of instruments it owns to eight.
As part of the early-access program, researchers at the center plan to resequence several strains of the nematode Caenorhabditis elegans. The center also intends to use the technology for projects studying the human microbiome, and to augment its current work on tumor transcriptome analysis.

UK Sequencing Service Provider Buys Illumina Platforms
Medical Solutions, a Nottingham, UK-based provider of DNA sequencing and genotyping services, announced last week that it has purchased Illumina’s Genome Analyzer as well as the company’s genotyping BeadStation.
According to the firm, it is the first commercial service provider of those platforms in the UK.
“Customers have already expressed significant interest in applications run on the Genome Analyzer and BeadStation platforms, and it is our intention to develop strategic partnerships with these early adopters,” Tom Weaver, commercial director of Medical Solutions, said in a statement.

NIDCR to Fund Metagenomic Studies of Mouth Microbiome
The National Institute of Dental and Craniofacial Research said last week that it will provide an undisclosed amount of funding for research into the role of microbes in human oral health and disease using metagenomic approaches.
The funding announcement is a reissue of an existing program, which was previously released in December 2006.
NIDCR said it is interested in research “on the total oral microbial community … using metagenomic approaches built upon recent developments in DNA sequencing, gene assembly, and bioinformatics.” The goal is to completely characterize all microbes and their genes in the oral environment. 
The institute is looking for projects “that will analyze the genomes of both cultivatable and uncultivable bacteria, archaea, viruses, fungi, and parasites.”
Applicants “will be expected to work with state-of-the-science genomic sequencing centers and bioinformatics groups to sequence and annotate all microbes in the oral cavity under conditions of health and disease.”
The size and duration of each award will vary, and the total amount awarded and the number of awards will depend upon the numbers, quality, duration, and costs of the applications received, according to NIDCR.
More information is available here.

Scientists Identify New Killer Transplant Virus Using 454 Sequencing Platform
American and Australian scientists reported last week that they have used 454 sequencing to identify the virus behind the deaths of three Australian transplant recipients.
The three women died from a mysterious virus last April after receiving organs from the same donor. Now, researchers from Columbia University’s Mailman School of Public Health, the US Centers for Disease Control and Prevention, the Victorian Infectious Diseases Reference Laboratory in Melbourne, and Roche’s 454 Life Sciences have fingered the culprit: a novel arenavirus. Their findings appeared online last week in the New England Journal of Medicine.
“We would not have found it at all but for the high-throughput sequencing,” senior author Ian Lipkin, an epidemiologist at Columbia University, told In Sequence’s sister publication GenomeWeb Daily News.
Using RNA from liver and kidney tissues from two of the deceased transplant recipients, Lipkin and his team applied 454’s sequencing technology, combined with bioinformatics algorithms developed at Columbia, to cluster suspicious sequences.
This helped them narrow down their search from the 103,632 sequences they had started with to just 14 arenavirus sequences. Their subsequent work, including tissue culture studies, electron microscopy, and immunohistochemical and serological tests, confirmed the identity of the new arenavirus as well as its specificity and pathogenicity.

Researchers Sequence Rare Photosynthetic Microorganism Using 454’s GS 20
Japanese, Australian, and American researchers have sequenced the genome of a rare photosynthetic microorganism that thrives on long-wave, far-red light, rather than the mundane red and blue light most of its contemporaries use.
The team, which reported its findings in the early online edition of the Proceedings of the National Academy of Sciences last week, sequenced the genome of Acaryochloris marina, an unusual cyanobacterium that employs a pigment called chlorophyll d — rather than the more common chlorophyll a — for photosynthesis.
In an effort to characterize both A. marina and its unusual chlorophyll d photosystem, the researchers sequenced the organism, whose genome consists of one circular chromosome and nine plasmids, using 454 Life Sciences’ GS 20 instrument.
The 8.3 million base pair genome — one of the largest bacterial genomes ever sequenced — seems to have expanded to provide the organism with new ways to adapt within the broader bacterial and algal community.

The Scan

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.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.