15 human genomes each week

The Wellcome Trust Sanger Institute has sequenced the equivalent of 300 human genomes in just over six months. The Institute has just reached the staggering total of 1,000,000,000,000 letters of genetic code that will be read by researchers worldwide, helping them to understand the role of genes in health and disease. Scientists will be able to answer questions unthinkable even a few years ago and human medical genetics will be transformed.

The amount of data is remarkable: every two minutes, the Institute produces as much sequence as was deposited in the first five years of the international DNA sequence databases, which started in 1982. It is a global milestone.

"I am delighted that our rapid adoption of next-generation sequencing technologies has been so successful in driving forward our biomedical research," says Dr Harold Swerdlow, Head of Sequencing Technology at the Wellcome Trust Sanger Institute. "Our internal projects, our work with external collaborators and our participation in major international programmes are all benefiting from our success. "

The Institute has major roles in projects such as The 1000 Genomes Project, The International Cancer Genome Consortium and the second round of the Wellcome Trust Case Control Consortium, all of which will depend on DNA sequence to uncover genetics variants that are important for human disease. Next-generation sequencing is also enabling the Institute's own research portfolio.

"The Sanger Institute is positioned to take on challenges and to answer questions that are daunting to most," says Professor Allan Bradley, Director. "We can explore important biomedical questions in a way that few can match, and next-generation sequencing is a vital part of that quest."

The 1000 Genomes Project, launched in January 2008, will produce a map of DNA sequence variants of unparalleled accuracy. Expected to take three years, the Project is currently in a pilot phase. The Sanger Institute is ahead of schedule and has deposited more than 300 billion bases to date, more than half of the global total so far.

"The 1000 Genomes Project is exploring the genome at a resolution nobody has attempted before," says Dr Richard Durbin, who co-heads the Project. "Our goals are ambitious and all of us are still learning, but we can already see that, through the efforts of the Sanger Institute and our partners in the consortium, the results will have a major impact on our understanding of human genetics and disease."

Next-generation sequencing platforms can uncover a wide range of variants in genomes, from single-base changes (called single nucleotide polymorphisms, or SNPs) to larger regions that can be absent from some people or duplicated in others (called copy number variants, or CNVs). Before the Human Genome and HapMap Projects - in which the Sanger Institute played a leading role - the extent of CNVs in human biology was not appreciated. With those tools to hand, scientists could begin to map CNVs across the genome and understand their role in common disease.

It is not only inherited variants that the scientists can tackle using next-generation sequencing platforms. The Sanger Institute's Cancer Genome Project team, co-led by Professor Mike Stratton and Dr Andy Futreal, has searched for genes that are mutated in common cancers for eight years. Until now, that has meant a piecemeal approach, focussing either on a few samples or only a few hundred regions from the genome. While this is a hugely successful method, next-generation sequencing means that all genes and gene regions in many cancer samples can be looked at simultaneously.

"We have already published results from a study of lung cancer samples that illustrate the complexity and diversity of cancer genomes and have obtained more data in six months than in the previous five years," explains Professor Stratton. "The advent of the next-generation sequencing technologies allows us now to search for all the types of somatic change in cancer genomes and to begin complete resequencing of whole cancer genomes, acquiring full catalogues of somatic changes, ultimately in thousands of cancers as a leading player in the International Cancer Genome Consortium."

The Pathogen Sequencing teams, who used conventional sequencing methods to decode the genomes of MRSA, Cdiff and the parasites that cause diseases such as malaria and sleeping sickness, are gathering a rich harvest of data.

"To tackle pathogens we need to understand how they vary, how they acquire new abilities to cause infection and how they spread through populations," says Professor Julian Parkhill, Head of Sequencing and the Pathogen teams. "Together with colleagues in Vietnam and Kathmandu, we are using this new technology to uncover the fine variation that will enable us to understand the transmission of typhoid fever in South-East Asia, and with colleagues in the UK we will be able to investigate how MRSA and Cdiff spread in our hospitals."

Source: Wellcome Trust Sanger Institute

Related stories:

Sequencing thousand and one genomes
(PhysOrg.com) -- Researchers at the Max Planck Institute for Developmental Biology in Tuebingen, Germany, reported the completion of the first genomes of wild strains of the flowering plant Arabidopsis thaliana. The entire genomes of two individuals of this species, one from Ireland, the other from Japan, have now been compared in great detail. They were found to be astonishingly different from each other, as Detlef Weigel and his colleagues write in Genome Research.
Researchers develop new self-training gene prediction program for fungi
Researchers at the Georgia Institute of Technology have developed a computer program that trains itself to predict genes in the DNA sequences of fungi.
After the first decade of metagenomics -- adolescent growth spurt anticipated
Mostly hidden from the scrutiny of the naked eye, microbes have been said to run the world. The challenge is how best to characterize them given that less than one percent of the estimated hundreds of millions of microbial species can be cultured in the laboratory. The answer is metagenomics—an increasingly popular approach for extracting the genomes of uncultured microorganisms and discerning their specific metabolic capabilities directly from environmental samples. Now, some ten years after the term was coined, metagenomics is going mainstream and already paying provocative dividends according to a "Q&A," News and Views by the U.S. Department of Energy Joint Genome Institute (DOE JGI) microbial ecology program head Philip Hugenholtz and MIT researcher Gene Tyson, published in the 25 September edition of the journal Nature.
Benchmark cyanobacterium sequenced could be cheap renewable energy source
(PhysOrg.com) -- A team of researchers headed by biologists at Washington University in St. Louis has sequenced the genome of a unique bacterium that manages two disparate operations — photosynthesis and nitrogen fixation — in one little cell during two distinct cycles daily.
Genome sequence deepens mystery of inconspicuous sea creature
(PhysOrg.com) -- Resembling a smudge more than an animal, a mysterious life form known as a placozoan has now joined other obscure and primitive creatures whose genomes are providing insight into how animals first arose more than 650 million years ago.
Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities
As Aesop said, appearances are deceiving—even in life's tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye. The findings, reported in the August 21 online edition of the journal Nature, establish a group of organisms as a branching point of animal evolution and identify sets of genes, or a "parts list," employed by organisms that have evolved along particular branches.
Scientists show how DNA repairs may reshape the genome
Researchers at Duke University Medical Center and at the National Institute of Environmental Health Sciences (NIEHS) have shown how broken sections of chromosomes can recombine to change genomes and spawn new species.
DOE JGI Director highlights the genomics of plant-based biofuels in the journal Nature
Genomics is accelerating improvements for converting plant biomass into biofuel—as an alternative to fossil fuel for the nation's transportation needs, reports Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), in the August 14 edition of the journal Nature. In "Genomics of cellulosic biofuels," Rubin lays out a path forward for how emerging genomic technologies will contribute to a substantially different biofuels future as compared to the present corn-based ethanol industry—and in part mitigate the food-versus-fuel debate.

News discussion:

Medicine & Health news