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Short Reads: Feb 3, 2009

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Broad Institute Cuts 24 from Sequencing Staff

The Broad Institute is cutting 24 employees from its genome sequencing platform because new sequencing technologies have made some staff unnecessary.

“The rapid evolution of DNA sequencing technologies has required the Broad Institute to transition its genome sequencing efforts from performing high-throughput work on the traditional technologies to actively developing and optimizing the use of next-generation high-throughput sequencing technologies. These new technologies require substantially different capabilities and resources on a different scale than the traditional technologies they are replacing,” Broad said in an e-mail statement to reporters this week.

The decision to trim the staff is not linked to the economic downturn. Rather, the staff cuts are “entirely a reflection of the changes in DNA sequencing technologies, which require us to invest our sequencing resources in different ways,” according to the statement.

Broad also said it has planned “comprehensive outplacement services” for those who are being let go.

The genome sequencing platform conducts or contributes to large-scale genome sequencing projects, including the Human Genome Project, mammals, fish, insects, fungi, bacteria, and viruses. Its major activities include high-throughput genome sequencing, genome finishing, and sequencing informatics.


Expression Analysis to Return Helicos Sequencing System

Helicos BioSciences said in a filing with the US Securities and Exchange Commission last week that Expression Analysis, the first customer of its Helicos Genetic Analysis single-molecule sequencing system, has decided to return the instrument.

According to the filing, the system, which Expression Analysis installed in March 2008 (see In Sequence 3/11/2008), was an early version of Helicos' commercial system and "did not consistently achieve current commercial specifications levels" at EA.

Helicos said that later versions of its sequencing systems "have been consistently achieving this specification." Once EA has returned its instrument, Helicos said it plans to bring it "up to the latest commercial configuration and performance levels."

In the meantime, Helicos and EA "have temporarily suspended their commercial relationship," according to the document.


Univ. of Texas-Austin Acquires SOLiD Sequencer

Researchers at the University of Texas at Austin have acquired an Applied Biosystems SOLiD sequencing system for the university’s genome sequencing and analysis facility, ABI said last week.

Scientists at the school will use the system in medical diagnostics research, animal adaptation studies, biofuels programs, and behavioral genomics research.

The high-throughput sequencing capacity will enable UT to catalog large genomes, conduct transcriptome analyses, and engage in targeted resequencing research, the Life Technologies business said.

One research team will use the system in comparative genomics studies of coral reefs to identify genetic differences between various species, with the goal of identifying the molecular mechanisms involved in how certain species acclimate and adapt to global climate change.

"We are currently moving on to gene expression analysis and whole-genome genotyping, using novel protocols based on next-generation sequencing technologies," said Mikhail Matz, an assistant professor of integrative biology who is involved in the coral project.

Another group will use the system to study the genetics of various species of algae that could be used to produce biofuels. These researchers will look for useful SNPs and CNVs in the algae genomes, as well as for translocations, insertions, and deletions, in order to learn how to convert biomass into biofuels.

Yet another team will conduct targeted resequencing studies in candidate genes in disease pathways.


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Researchers Sequence Sorghum Genome

In a paper appearing online in Nature last week, an international research team reported that they have sequenced the 730 million-base genome of Sorghum bicolor, an African grass grown for human and animal food that also holds promise as a biofuel crop.

Sorghum is commonly grown as a food crop in parts of Africa where its drought tolerance is particularly advantageous. It is also grown in the southern US, mainly for animal feed or biofuel. Ethanol produced from the sorghum grain requires about a third of the water used to produce corn ethanol. And because it can grow eight to 15 feet tall in one growing season, sorghum is a candidate for cellulosic biofuel production, which relies on the non-edible parts of plants.

The international research team that sequenced the genome was led by researchers at the US Department of Energy's Joint Genome Institute and Stanford University's Human Genome Center. They used Sanger sequencing to do paired-end shotgun sequencing of plasmid, fosmid, and BAC libraries of the 730 megabase genome — including the repeat sequences that make up about 61 percent of the genome.

Repetitive DNA is often considered "a horror" for whole-genome shotgun sequencing, lead author Andrew Paterson, director of the University of Georgia's Plant Genome Mapping Laboratory, told In Sequence’s sister publication GenomeWeb Daily News. But he said the method worked well for sequencing sorghum because very good genetic maps were available for the plant and because researchers could refer to sequences from the rice genome.

Conversely, the sorghum genome is helping researchers better understand the rice genome, Paterson noted. "With each [genome], we develop greater confidence in what the common ancestor looked like," he said. "We're much more confident if we get the same answer in sorghum and rice."

For example, the comparison uncovered more than 10,000 proposed rice genes that actually seem to be gene fragments. As for the sorghum genome, the researchers detected some 27,640 protein-coding genes, more than 5,000 gene models, and 727 pseudogenes. They also found 67 known and 82 new sorghum microRNAs.

"One thing that was particularly striking was that there was a high degree of similarity between sorghum and rice," Paterson said. "That suggests their genomes will be predictive, to a large degree, for the remainder of the cereals."

Although the plants diverged roughly 50 million years ago, the results suggest sorghum's genome actually has more in common with the rice genome than with the genome of maize, its closer relative. While this may be somewhat surprising in light of the plants' evolutionary history, Paterson explained, it makes sense in terms of the whole-genome duplication event in maize.

Though the sorghum genome is roughly 75 percent larger than the rice genome, the genomes have similar gene counts and gene structure. In addition, the two plants seem to contain comparable numbers of gene families and gene families of similar sizes. Based on their assessment of the sorghum and rice genomes, the researchers suggested that there are nearly 20,000 conserved grass gene families.

Even so, the similarities between the sorghum and rice genomes were not uniformly distributed. While the euchromatic, gene-coding regions of the genomes were very similar, the sorghum genome contained much more heterochromatin than rice.

Paterson said it will also be interesting to compare the S. bicolor genome with that of Brachypodium distachyon, or purple false brome grass, since its sequence is closely related to wheat and barley but hasn't been through whole-genome duplication.

Researchers hope that by having the S. bicolor genome sequence in hand they will be able to develop tools and markers for increasing sorghum yield and disease resistance. The genome may also offer an opportunity to tweak the biofuel potential of sorghum and gain a better understanding of biofuel crops with more complex, polyploid genomes, Paterson said.

In addition, getting a handle on sorghum's drought tolerance could not only aid sorghum development but also lead to other crop improvements as well, Paterson explained. He said several sorghum re-sequencing projects using various high-throughput sequencing methods are underway at the University of Georgia and elsewhere.

By Andrea Anderson; originally published on GenomeWeb Daily News


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Survey Seeks Information on Next-Gen Sequencing Implementation for ABRF Presentation

A survey conducted by a researcher at the University of Utah seeks information on how core laboratories have implemented next-generation sequencing platforms.

Results from the survey, which is primarily geared at not-for-profit core labs that provide fee-based sequencing services within their institution, will be presented during a workshop on Feb. 9 at the annual meeting of the Association of Biomolecular Resource Facilities in Memphis, Tenn.


Genomatix Joins Illumina-Connect Program

Genomatix Software said last week that it has joined the Illumina-Connect program, an Illumina initiative to work with hardware and software firms to develop new tools and applications for genomic data generated by Illumina's platforms.

Munich, Germany-based Genomatix sells the Genomatic Mining Station and Genomatix Genome Analyzer for analyzing next-generation sequencing data.

"Working with Illumina-generated NGS data has helped us greatly in our ongoing effort to refine and further expand our analysis capabilities in this very demanding market," said Peter Grant, CEO of Genomatix Software's US operations in Ann Arbor, Mich., in a statement. "Being a part of the Illumina-Connect program should help us to better focus those efforts as well as help us keep up with the rapidly expanding portfolio of Illumina NGS applications."


Mondobiotech, 23andMe Team on Rare Disease Research

23andMe and Swiss company Mondobiotech will collaborate to offer researchers information about certain rare genetic diseases, the California consumer genomics firm said last week.

The collaboration will use genetic information from individuals who suffer from diseases such as pulmonary arterial hypertension, sarcoidoisis, and pulmonary fibrosis. Mondobiotech will identify these patients and sponsor their enrollment in 23andMe's Personal Genome Service.

23andMe said that it will coordinate genome-wide association studies for Mondobiotech affiliates using its research infrastructure and bioinformatics expertise.

Mondobiotech CEO Fabio Cavalli said in a statement that this collaboration "could go a long way towards understanding the causes of the diseases we have been researching."

Financial terms of the agreement were not released.


Kapa Biosystems Discloses Customers for DNA Polymerase Platform

Kapa Biosystems said last month that several biotech companies and research centers are using its Kapa2G Fast HotStart DNA polymerase for resequencing and SNP detection studies.

The company said the Kapa2G, which the company developed using its molecular evolution platform, has been adopted by Agencourt Bioscience, Ceres, Memorial Sloan Kettering Cancer Center, and the National Institutes of Health's Intramural Sequencing Center.

The company said the polymerase is aimed at researchers using high-throughput fast PCR, and that it is capable of synthesizing DNA with a one-second-per-kilobase extension time without an impact on performance.

The Scan

Push Toward Approval

The Wall Street Journal reports the US Food and Drug Administration is under pressure to grant full approval to SARS-CoV-2 vaccines.

Deer Exposure

About 40 percent of deer in a handful of US states carry antibodies to SARS-CoV-2, according to Nature News.

Millions But Not Enough

NPR reports the US is set to send 110 million SARS-CoV-2 vaccine doses abroad, but that billions are needed.

PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.