This Week at Nature Biotechnology

04/01/2010 às 09:47 (Diagnóstico Molecular, Medicina)

Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

Guangan Hu1,3, Ana Cabrera2,3, Maya Kono2, Sachel Mok1, Balbir K Chaal1, Silvia Haase2, Klemens Engelberg2, Sabna Cheemadan1, Tobias Spielmann2, Peter R Preiser1, Tim-W Gilberger2 & Zbynek Bozdech1

Abstract
Functions have yet to be defined for the majority of genes of Plasmodium falciparum, the agent responsible for the most serious form of human malaria. Here we report changes in P. falciparum gene expression induced by 20 compounds that inhibit growth of the schizont stage of the intraerythrocytic development cycle. In contrast with previous studies, which reported only minimal changes in response to chemically induced perturbations of P. falciparum growth, we find that ~59% of its coding genes display over three-fold changes in expression in response to at least one of the chemicals we tested. We use this compendium for guilt-by-association prediction of protein function using an interaction network constructed from gene co-expression, sequence homology, domain-domain and yeast two-hybrid data. The subcellular localizations of 31 of 42 proteins linked with merozoite invasion is consistent with their role in this process, a key target for malaria control. Our network may facilitate identification of novel antimalarial drugs and vaccines.

Division of Genetics and Genomics, School of Biological Sciences, Nanyang Technological University, Singapore.
Bernhard Nocht Institute for Tropical Medicine, Department of Molecular Parasitology, Hamburg, Germany.
These authors contributed equally to this work.
Correspondence to: Tim-W Gilberger2 e-mail: gilberger@bni.uni-hamburg.de

Correspondence to: Zbynek Bozdech1 e-mail: zbozdech@ntu.edu.sg

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Building a Cancer Model

29/12/2009 às 16:49 (Diagnóstico Molecular, Medicina, Sequenciamento)

Genome Technology

December 2009/January 2010
By Meredith Salisbury
Ali Torkamani
Title: Assistant Faculty, Scripps Translational Sciences Institute
Education: PhD, University of California, San Diego, 2008
Recommended by: Eric Topol

It’s no surprise that someone who had the foresight to switch from biology to chemistry in order to get a more fundamental understanding of the biology he was really interested in would wind up working at a prestigious research institute.

While some might consider the chemistry major at Stanford to have been an indirect path to a career studying biology, the move not only suited Ali Torkamani, but positioned him for a graduate program that would open up tremendous opportunities.

After graduating from Stanford, Torkamani headed to the University of California, San Diego, where he wound up working in mentor Nicholas Schork’s lab. Torkamani had no computational background before joining Schork, a biostatistician, so he taught himself the computer science as he went, he says.

That computational training was key for Torkamani’s main project, which was to look at all the protein kinase families and to catalog common mutations in them. That included both strongly inherited mutations commonly shared in the population as well as somatic changes in the kinases, which are important anti-cancer drug targets. With that information, Torkamani “developed a computational model where you could predict based on the protein kinase … attributes [such as] where in the structure of the catalytic core the mutation fell,” he says. “You could predict whether or not a mutation was going to impact the function of the protein kinase.”

Ultimately, the idea of the project was to get to a model that could “tease out which mutations were the actual drivers versus the passengers,” Torkamani adds.

Before Torkamani completed his PhD in 2008, Schork moved his lab to the Scripps Research Institute. Torkamani also made the move, and, when he was finished with his doctoral work, Scripps offered him a job. At Scripps, he says, his focus has shifted away from protein kinases but has stayed with cancer. “Now I’ve taken more of a systems biology or network type of approach to studying cancer,” Torkamani says. His work centers on looking “at the network of genes and proteins as a whole within cancer and [determining] what sort of groups of genes … tend to be more frequently mutated.”

Looking ahead

While he doesn’t yet have funding for this project, Torkamani would like to model cancer predictions from people’s genomes. “I would really be interested in seeing whether or not you could predict tumor evolution based on predisposing mutations,” he says. That might involve looking at the variants someone has inherited from his or her parents and then using that to determine what type of cancer he or she is likely to develop, as well as what sorts of mutations would be expected with that particular cancer.

Publications of note

Torkamani was lead author on a paper published in Genome Research this past September called “Identification of rare cancer driver mutations by network reconstruction.” In the publication, he and Schork analyzed data from breast, colorectal, and gliobastoma tumors to identify genetic mutations that are implicated in tumor formation. It also demonstrated the ability to separate out driver mutations from passenger ones.

And the Nobel goes to…

Torkamani’s focus on cancer makes it easy for him to imagine just what he’d like to win the Nobel for. “It would be nice to be one of the key people that … really expanded our genetic knowledge of cancer … and predicting that transition from a normal cell to a cancer cell before it occurs,” he says. “If you can make that prediction, then you would either be able to drive the cancer down an evolutionary dead end where it would be easier to combat the disease, or predict where the tumor will eventually be going [and] what sort of characteristics it would take on that would be deadly to the person.”

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Developing Nanopores for Biosensing

29/12/2009 às 14:55 (Medicina, Sequenciamento)

Getting to the Nanoscale
December 2009/January 2010
By Ciara Curtin
Type size: – + Email Printer-friendly version RSS Feed Vincent Tabard-Cossa
Title: Postdoctoral Fellow, Stanford University
Education: PhD, McGill University, 2005
Recommended by: Andre Marziali

Nanopores sound hopelessly small, but Vincent Tabard-Cossa says they will someday be used as diagnostic tools. The tiny, nanometer-sized holes they make in a thin membrane allow researchers to capture and study single molecules, including DNA.

The creativity in developing nanopores for biosensing is in the type of detector used, Tabard-Cossa says. That, he adds, is where nanopores get their sensitivity. While a postdoc at the University of British Columbia in Andre Marziali’s lab, Tabard-Cossa and his colleagues developed a method called nanopore force spectroscopy that has “tremendous specificity” for molecular recognition, he says. He likens it to the hybridization process on a microarray, but adds that it not only reports the binding, but also measures the strength of the bond. “By measuring the time it takes to break the bond between the probe and the target at a particular force, this provides us with information about the dissociation energy of the two molecules,” Tabard-Cossa says. “And the dissociation energy, in turn, provides information about the sequence of the nucleotides.”

This detection, he adds, can then be carried out in parallel. “We can now repeat all these single-molecule experiments with hundreds of nanopores in parallel — or what would be best thousands or hundred of thousands — and get extremely fast measurement times,” he says. “Ultimately [we could] perform SNP detection from unamplified genomic DNA within minutes after collecting a blood sample. We haven’t really gone that far but [we are] working this way.”

Now at Stanford, Tabard-Cossa is focusing on embedding electrical probes into nanopore walls to sense molecules, particularly DNA, electrostatically. “We are using a unique sensing mechanism that is based on this partial suppression of ionic shielding in high electric fields and that’s due to the presence of electrodiffusion and relaxation effects,” he says. “It means that molecules are not shielded anymore by their ionic clouds, so that you can detect them pretty far away.”

Right now, his sensor can reach down to the scale of hundreds of electrons, which translates to a hundred-nucleotide-level sensitivity. Here, he is limited by electronics and the noise they detect. “Right now, we are not fully integrated, meaning our electronics are not as close as possible on our nanopore detector,” Tabard-Cossa says. “If we keep combining our integration, and really make streamlined electronics on our nanopore device, then we can reach tens of electrons, if not single-electron resolution.”

Looking ahead

Tabard-Cossa says there is still a bit of physics to learn, and, depending on how that pans out, accurate nanopore-based sequencing technology could be viable as soon as five years from now or as far away as 10. “There’s a lot of unexplored physics at this scale,” he says. “We still need to make great advances not only in nanopore fabrication … but also to understand how matter interacts. How does DNA interact with synthetic devices?”

Publications of note

Tabard-Cossa was the first author on a 2007 paper appearing in Nanotechnology that discusses noise in solid-state nanopores. He and his colleagues reduced the dielectric noise by curing the nanopore chip with polydimethylsiloxane. This improved the performance and yielded “an unprecedented signal-to-noise ratio when observing dsDNA translocation events and ssDNA probe capture for force spectroscopy applications,” they report in the paper abstract.

And the Nobel goes to…

Tabard-Cossa says that if he were to win the Nobel Prize, he’d have to share it with an army of people. He hopes that the prize would be for developing single-molecule detectors to be used in cheap and fast diagnostics that drive down the cost of healthcare.

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Scientists Start a Genomic Catalog of Earth’s Abundant Microbes

29/12/2009 às 14:37 (Sequenciamento)

The New York Times

Published: December 28, 2009

There are about 5,400 species of mammals on the planet, but just a spoonful of soil may contain twice as many species of microbes. They can dwell in habitats where so-called higher life forms like us would quickly die, including acid-drenched mines and Antarctic deserts. By one rough estimate, there may be, all told, 150 million species of microbes.

“Microbes represent the vast majority of organisms on earth,” said Hans-Peter Klenk, a microbiologist for the German Collection of Micro-organisms and Cell Cultures, a government microbiology research center.

Yet scientists still know very little about our microbial planet. The genomes of only about 1,000 species of microbes have been sequenced. That leaves 99.99999 percent to go. Making matters worse, the genomes scientists have sequenced so far are clustered together in groups of closely related species, leaving vast stretches of the microbial tree of life virtually unexplored. It would be as if all we knew about the animal kingdom were based entirely on a stuffed ferret and a pickled tarantula.

To shed light on this enormous stretch of biological darkness, the Joint Genome Institute at the Energy Department has started what it calls a “genomic encyclopedia.” It is filling the encyclopedia with the genomes of microbes from remote reaches of the tree of life.

In the Dec. 24 issue of Nature, Dr. Klenk and his colleagues present their first analysis of the encyclopedia, based on the first 56 species they have sequenced. Using this new evolution-based approach, the scientists have discovered many kinds of genes, some of which may prove a boon to the biotechnology industry.

“The encyclopedia is guaranteed to yield new things,” said Norman Pace, a University of Colorado microbiologist who was not involved in the study. “We humans haven’t even scratched the surface of natural microbial diversity.”

When scientists first began to pick microbes for genome sequencing in the 1990s, they favored species they had been studying for years, like E. coli. As the technology improved and costs fell, they moved from these microbial lab rats to species that were important to humans for one reason or another, like those causing diseases.

It gradually became clear that this approach neglected most of the diversity of microbes. A number of microbiologists began to argue that a broader survey of the microbial world would bring many new insights. Comparing a gene in many different species can often help scientists figure out what a gene does in the first place, for example.

“It’s been blatantly obvious that this should be done,” said Jonathan Eisen, an evolutionary biologist at the University of California, Davis, and the lead author of the Nature paper.

Taking advantage of the falling cost of DNA sequencing, Dr. Eisen, Dr. Klenk and their colleagues at the Joint Genome Institute established the Genomic Encyclopedia of Bacteria and Archaea. (Bacteria and Archaea are two of the major branches of the tree of life. The third branch contains eukaryotes, which includes animals, fungi, plants and protozoa.) The scientists selected 200 species to analyze. Dr. Klenk and his colleagues in Germany plucked the microbes from their collection and reared them in huge numbers, split open the cells and isolated long fragments of DNA from them.

Once the scientists had sequenced 56 genomes, they decided to see whether their approach was paying off. For part of their analysis, they tallied up how many new genes they had found: tens of thousands. But more importantly, they found 1,768 new gene families — sets of genes that share a common ancestor. “We didn’t remotely expect it to be this striking,” Dr. Eisen said.

Dr. Eisen expects that many of these new genes will lead to important research. One gene, from a microbe that lives in salt flats, encodes an enzyme that can cut up cellulose in the presence of lots of salt. This type of enzyme might be useful for extracting biofuels from plants. “The biotech industry loves these things,” he said.

The encyclopedia is also upending some basic rules of biology. All eukaryotes, ourselves included, have Lego-like skeletons in our cells made from a molecule called actin. “We have this rule that actin is in eukaryotes,” Dr. Eisen said, “and it’s not in bacteria and archaea.” Now he and his colleagues have found a gene for actin in a species of marine bacteria. “It’s wildly cool,” he said.

Dr. Eisen suspects that the actin gene was ferried from eukaryotes to the bacteria long ago. Now the bacteria may inject actin into eukaryotes to disrupt their cells.

The genomic encyclopedia includes not only the raw data on genes, but also predictions about what those genes are actually for. To see if those predictions are right will require a lot more time and labor. The joint genome institute has set up an “Adopt a Genome Program” to enlist the help of college students. Undergraduate microbiology students can pick a species from the encyclopedia and analyze its biology. “We need them,” Dr. Eisen said.

Students at Davidson College in North Carolina have already published a paper on the salt-flat microbe with the cellulose enzyme.

In years to come, Dr. Eisen and his colleagues hope to have many genomes for students to analyze. They are continuing to select species, and they hope, in a few years, to have 1,500 in the encyclopedia.

“We’ve made a dent,” Dr. Eisen said, “but it’s a small dent.”

There are about 5,400 species of mammals on the planet, but just a spoonful of soil may contain twice as many species of microbes. They can dwell in habitats where so-called higher life forms like us would quickly die, including acid-drenched mines and Antarctic deserts. By one rough estimate, there may be, all told, 150 million species of microbes.

“Microbes represent the vast majority of organisms on earth,” said Hans-Peter Klenk, a microbiologist for the German Collection of Micro-organisms and Cell Cultures, a government microbiology research center.

Yet scientists still know very little about our microbial planet. The genomes of only about 1,000 species of microbes have been sequenced. That leaves 99.99999 percent to go. Making matters worse, the genomes scientists have sequenced so far are clustered together in groups of closely related species, leaving vast stretches of the microbial tree of life virtually unexplored. It would be as if all we knew about the animal kingdom were based entirely on a stuffed ferret and a pickled tarantula.

To shed light on this enormous stretch of biological darkness, the Joint Genome Institute at the Energy Department has started what it calls a “genomic encyclopedia.” It is filling the encyclopedia with the genomes of microbes from remote reaches of the tree of life.

In the Dec. 24 issue of Nature, Dr. Klenk and his colleagues present their first analysis of the encyclopedia, based on the first 56 species they have sequenced. Using this new evolution-based approach, the scientists have discovered many kinds of genes, some of which may prove a boon to the biotechnology industry.

“The encyclopedia is guaranteed to yield new things,” said Norman Pace, a University of Colorado microbiologist who was not involved in the study. “We humans haven’t even scratched the surface of natural microbial diversity.”

When scientists first began to pick microbes for genome sequencing in the 1990s, they favored species they had been studying for years, like E. coli. As the technology improved and costs fell, they moved from these microbial lab rats to species that were important to humans for one reason or another, like those causing diseases.

It gradually became clear that this approach neglected most of the diversity of microbes. A number of microbiologists began to argue that a broader survey of the microbial world would bring many new insights. Comparing a gene in many different species can often help scientists figure out what a gene does in the first place, for example.

“It’s been blatantly obvious that this should be done,” said Jonathan Eisen, an evolutionary biologist at the University of California, Davis, and the lead author of the Nature paper.

Taking advantage of the falling cost of DNA sequencing, Dr. Eisen, Dr. Klenk and their colleagues at the Joint Genome Institute established the Genomic Encyclopedia of Bacteria and Archaea. (Bacteria and Archaea are two of the major branches of the tree of life. The third branch contains eukaryotes, which includes animals, fungi, plants and protozoa.) The scientists selected 200 species to analyze. Dr. Klenk and his colleagues in Germany plucked the microbes from their collection and reared them in huge numbers, split open the cells and isolated long fragments of DNA from them.

Once the scientists had sequenced 56 genomes, they decided to see whether their approach was paying off. For part of their analysis, they tallied up how many new genes they had found: tens of thousands. But more importantly, they found 1,768 new gene families — sets of genes that share a common ancestor. “We didn’t remotely expect it to be this striking,” Dr. Eisen said.

Dr. Eisen expects that many of these new genes will lead to important research. One gene, from a microbe that lives in salt flats, encodes an enzyme that can cut up cellulose in the presence of lots of salt. This type of enzyme might be useful for extracting biofuels from plants. “The biotech industry loves these things,” he said.

The encyclopedia is also upending some basic rules of biology. All eukaryotes, ourselves included, have Lego-like skeletons in our cells made from a molecule called actin. “We have this rule that actin is in eukaryotes,” Dr. Eisen said, “and it’s not in bacteria and archaea.” Now he and his colleagues have found a gene for actin in a species of marine bacteria. “It’s wildly cool,” he said.

Dr. Eisen suspects that the actin gene was ferried from eukaryotes to the bacteria long ago. Now the bacteria may inject actin into eukaryotes to disrupt their cells.

The genomic encyclopedia includes not only the raw data on genes, but also predictions about what those genes are actually for. To see if those predictions are right will require a lot more time and labor. The joint genome institute has set up an “Adopt a Genome Program” to enlist the help of college students. Undergraduate microbiology students can pick a species from the encyclopedia and analyze its biology. “We need them,” Dr. Eisen said.

Students at Davidson College in North Carolina have already published a paper on the salt-flat microbe with the cellulose enzyme.

In years to come, Dr. Eisen and his colleagues hope to have many genomes for students to analyze. They are continuing to select species, and they hope, in a few years, to have 1,500 in the encyclopedia.

“We’ve made a dent,” Dr. Eisen said, “but it’s a small dent.”

If you want to appreciate the diversity of life on earth, you will need a microscope.

There are about 5,400 species of mammals on the planet, but just a spoonful of soil may contain twice as many species of microbes. They can dwell in habitats where so-called higher life forms like us would quickly die, including acid-drenched mines and Antarctic deserts. By one rough estimate, there may be, all told, 150 million species of microbes.

“Microbes represent the vast majority of organisms on earth,” said Hans-Peter Klenk, a microbiologist for the German Collection of Micro-organisms and Cell Cultures, a government microbiology research center.

Yet scientists still know very little about our microbial planet. The genomes of only about 1,000 species of microbes have been sequenced. That leaves 99.99999 percent to go. Making matters worse, the genomes scientists have sequenced so far are clustered together in groups of closely related species, leaving vast stretches of the microbial tree of life virtually unexplored. It would be as if all we knew about the animal kingdom were based entirely on a stuffed ferret and a pickled tarantula.

To shed light on this enormous stretch of biological darkness, the Joint Genome Institute at the Energy Department has started what it calls a “genomic encyclopedia.” It is filling the encyclopedia with the genomes of microbes from remote reaches of the tree of life.

In the Dec. 24 issue of Nature, Dr. Klenk and his colleagues present their first analysis of the encyclopedia, based on the first 56 species they have sequenced. Using this new evolution-based approach, the scientists have discovered many kinds of genes, some of which may prove a boon to the biotechnology industry.

“The encyclopedia is guaranteed to yield new things,” said Norman Pace, a University of Colorado microbiologist who was not involved in the study. “We humans haven’t even scratched the surface of natural microbial diversity.”

When scientists first began to pick microbes for genome sequencing in the 1990s, they favored species they had been studying for years, like E. coli. As the technology improved and costs fell, they moved from these microbial lab rats to species that were important to humans for one reason or another, like those causing diseases.

It gradually became clear that this approach neglected most of the diversity of microbes. A number of microbiologists began to argue that a broader survey of the microbial world would bring many new insights. Comparing a gene in many different species can often help scientists figure out what a gene does in the first place, for example.

“It’s been blatantly obvious that this should be done,” said Jonathan Eisen, an evolutionary biologist at the University of California, Davis, and the lead author of the Nature paper.

Taking advantage of the falling cost of DNA sequencing, Dr. Eisen, Dr. Klenk and their colleagues at the Joint Genome Institute established the Genomic Encyclopedia of Bacteria and Archaea. (Bacteria and Archaea are two of the major branches of the tree of life. The third branch contains eukaryotes, which includes animals, fungi, plants and protozoa.) The scientists selected 200 species to analyze. Dr. Klenk and his colleagues in Germany plucked the microbes from their collection and reared them in huge numbers, split open the cells and isolated long fragments of DNA from them.

Once the scientists had sequenced 56 genomes, they decided to see whether their approach was paying off. For part of their analysis, they tallied up how many new genes they had found: tens of thousands. But more importantly, they found 1,768 new gene families — sets of genes that share a common ancestor. “We didn’t remotely expect it to be this striking,” Dr. Eisen said.

Dr. Eisen expects that many of these new genes will lead to important research. One gene, from a microbe that lives in salt flats, encodes an enzyme that can cut up cellulose in the presence of lots of salt. This type of enzyme might be useful for extracting biofuels from plants. “The biotech industry loves these things,” he said.

The encyclopedia is also upending some basic rules of biology. All eukaryotes, ourselves included, have Lego-like skeletons in our cells made from a molecule called actin. “We have this rule that actin is in eukaryotes,” Dr. Eisen said, “and it’s not in bacteria and archaea.” Now he and his colleagues have found a gene for actin in a species of marine bacteria. “It’s wildly cool,” he said.

Dr. Eisen suspects that the actin gene was ferried from eukaryotes to the bacteria long ago. Now the bacteria may inject actin into eukaryotes to disrupt their cells.

The genomic encyclopedia includes not only the raw data on genes, but also predictions about what those genes are actually for. To see if those predictions are right will require a lot more time and labor. The joint genome institute has set up an “Adopt a Genome Program” to enlist the help of college students. Undergraduate microbiology students can pick a species from the encyclopedia and analyze its biology. “We need them,” Dr. Eisen said.

Students at Davidson College in North Carolina have already published a paper on the salt-flat microbe with the cellulose enzyme.

In years to come, Dr. Eisen and his colleagues hope to have many genomes for students to analyze. They are continuing to select species, and they hope, in a few years, to have 1,500 in the encyclopedia.

“We’ve made a dent,” Dr. Eisen said, “but it’s a small dent.”

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Sanger Institute Sequences Two Cancer Genomes on Illumina and SOLiD Platforms

28/12/2009 às 18:27 (Diagnóstico Molecular, Medicina)

Researchers from the Wellcome Trust Sanger Institute in the UK reported last week in Nature that they have sequenced melanoma and lung cancer genomes using Illumina and SOLiD sequencing technology, respectively. In both cases, the techniques identified both known cancer-causing mutations, as well as novel mutations. They also found evidence of ultraviolet damage in the melanoma cancer genome and damage from tobacco carcinogens in the lung cancer genome.

The two papers indicate that whole-genome short-read sequencing is becoming increasingly important for identifying cancer-causing genes that could eventually lead to better diagnosis and treatment, according to the authors.

The studies are part of a growing number of cancer genome sequencing projects, — such as the Sanger Institute’s Cancer Genome Project and the National Cancer Institute’s Cancer Genome Atlas — many of them under the umbrella of the International Cancer Genome Consortium.

The papers “demarcate the new era from the old era,” Peter Campbell, a member of the Wellcome Trust Sanger group that conducted the research, told In Sequence. “They demonstrate quite convincingly that we can find mutations in all classes at a cost that’s rapidly decreasing and a time frame that’s rapidly decreasing.”

The researchers noted that at the time they did the experiments, the sequencing cost around $100,000 on each platform, including both the tumor and normal genomes. They estimated that if they were to do it again today, the price would be around $50,000 on each platform.

The researchers said that they used both the Illumina and SOLiD technologies because they thought it was important to assess the two systems, though they noted that the platforms produced comparable results, and any differences between the technologies would not be relevant today because both platforms have been improved significantly.

“Both were able to deliver high-quality cancer genome sequences in which we could get comprehensive catalogs of somatic mutations,” said Michael Stratton, who heads the Sanger’s Cancer Genome Project and who led the research.

Campbell agreed and said that improving the algorithms would yield more benefits than using one sequencing technology over the other. “You need good informatics to take that data set and pull out what is [a] genuine mutation, what is sequencing error, and what is artifact,” he said.

Both approaches sequenced genomes from the tumor cell line as well as a normal cell line from the same patient and compared the genomes to each other.

To sequence the lung cancer genome, the scientists used the SOLiD platform to generate 25-base pair mate-pair shotgun sequences and achieved about 39-fold coverage of the tumor genome and 31-fold coverage of the normal genome.

In total, they detected 22,910 somatic substitutions, and confirmed an additional 65 indels, 58 genomic rearrangements, and 334 copy number segments.

Of the 29 known base substitutions they found 22. They also tested 79 new coding substitutions and 354 randomly chosen genome-wide variants, and confirmed 97 percent and 94 percent respectively, using capillary sequencing. They also confirmed 25 percent of indels using capillary sequencing.

In addition, they detected mutational patterns previously associated with carcinogens in tobacco smoke. “The complicated mutational processes, all of which can be traced back to carcinogens, indicate that there is a cocktail of carcinogens that work together to produce the mutations that cause cancer,” said Stratton.

To sequence the genome from the malignant melanoma cell line, the scientists used the Illumina Genome Analyzer II and a paired-end sequencing strategy (see In Sequence 9/22/2009). They constructed short libraries of 200 and 400 base pairs and paired mate libraries of 2, 3, and 4 kilobases, generated read lengths of 75 base pairs, and achieved 40-fold coverage of the tumor genome and 32-fold coverage of the normal genome.

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The Top 10 Everything of 2009

28/12/2009 às 17:23 (GWAS, hapmap)

2. The Human Epigenome, Decoded

By EBEN HARRELL Tuesday, Dec. 08, 2009
Visuals Unlimited / Corbis

The decoding of the human genome nearly a decade ago fueled expectations that an understanding of all human hereditary influences was within sight. But the connections between genes and, say, disease turned out to be far more complicated than imagined. What has since emerged is a new frontier in the study of genetic signaling known as epigenetics, which holds that the behavior of genes can be modified by environmental influences and that those changes can be passed down through generations. So people who smoke cigarettes in their youth, for example, sustain certain epigenetic changes, which may then increase the risk that their children’s children will reach puberty early. In October, a team led by Joseph Ecker at the Salk Institute in La Jolla, Calif., studied human skin and stem cells to produce the first detailed map of the human epigenome. By comparing this with the epigenomes of diseased cells, scientists will be able to work out how glitches in the epigenome may lead to cancers and other diseases. The study, which was published in the journal Nature, is a giant leap in geneticists’ quest to better understand the strange witches’ brew of nature and nurture that makes us who we are.

View the full list for “The Top 10 Everything of 2009”

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This Week in PLoS – Genome of a Dental Cavity Bacteria

28/12/2009 às 17:14 (Sequenciamento)

National University of Ireland at Cork’s Douwe van Sinderen and his colleagues sequenced the genome of a dental cavity bacteria called Bifidobacterium dentium Bd1, finding features in it that help explain the bug’s propensity for living in the mouth and causing cavities. “[T]he genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from opportunistic pathogens,” the researchers write. A news story in our sister publication GenomeWeb Daily News has more details.

A California research team took a closer look at genetic variants involved several autoimmune diseases by doing a meta-analysis of genome-wide association studies. They found that certain autoimmune diseases cluster together and that SNPs that increase the risk of some conditions apparently protect against others. And, they say, the approach may be useful for better understanding autoimmune and many other types of disease. “As more GWA data becomes available, our method could be applied across tens or hundreds of diseases yielding the commonalities and differences in genetic architectures across all of human disease,” the team concludes.GenomeWeb Daily News also covered this story here.

An international research group used SNP markers to look at the genetic patterns and estimate linkage disequilibrium in 632 inbred maize lines from public breeding programs around the world in a PLoS ONE paper. After genotyping temperate, tropical, and sub-tropical lines, they applied more than 1,200 informative SNPs to examine everything from genetic diversity and population structure to familial relationships. They also did linkage disequilibrium analyses, showing that the LD distance increases when minor allele frequency increases, when sample size decreases, or in lines with lower genetic diversity (such as those from temperate regions).

French and Swiss researchers used a “Dirty Genome Approach” to find immunogenic proteins in unfinished genome sequences from an emerging human respiratory pathogen called Parachlamydia acanthamoebae using a combination of high-throughput, short-read sequencing and proteomics. Those involved say the proof-of-principle study highlights the potential of unfinished genomes — suggesting they can help guide antigen and DNA-based diagnostic tests for newly discovered pathogens.

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GWAS Meta-Analysis Supports Existence of Autoimmune Disease Clusters

28/12/2009 às 11:13 (Uncategorized)

December 24, 2009

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A new paper in PLoS Genetics today suggests the same genetic variants that increase an individual’s risk for one set of autoimmune diseases may actually make them less susceptible to others.

Researchers from Stanford University and collaborators at a California hospital and clinical center did a meta-analysis of genome-wide association studies on half a dozen autoimmune conditions, including type 1 diabetes and rheumatoid arthritis. They found a pattern in which specific diseases grouped together based on SNP data, with variants that increased the risk of some conditions protecting against others.

Based on these findings, the team suggests it may be useful to classify autoimmune diseases according to their shared genetic factors rather than considering them a single group.

“Maybe we should stop considering all autoimmune diseases in one lumped category,” senior author Atul Butte, a pediatric and bioinformatics researcher at Stanford University and director of the Lucile Packard Children’s Hospital’s Center for Pediatric Bioinformatics, said in a statement. “It looks as if there may be at least two different kinds.”

Although autoimmune diseases share some common disease mechanisms, Butte and his team noted, certain autoimmune diseases have more in common than others. For example, past research suggests that individuals with type 1 diabetes are at increased risk for autoimmune diseases such as autoimmune thyroid disease, multiple sclerosis, and celiac disease.

And, they added, at least one SNP has already been shown to have opposing effects in different autoimmune conditions: the G allele of that SNP, called rs2076530, is more common in individuals with type 1 diabetes or rheumatoid arthritis whereas the A allele is more common in those with systematic lupus erythematosus.

That led Butte and his colleagues to speculate about how genetic factors relate to autoimmune disease clusters. In the current paper, the team did a meta-analysis involving 573 SNPs assessed in several GWAS of six autoimmune diseases — type 1 diabetes, rheumatoid arthritis, Crohn’s disease, multiple sclerosis, autoimmune thyroid disease, and ankylosing spondylitis — and five non-autoimmune diseases.

By assessing alleles associated with each disease and the strength of these associations, the team came up with a so-called “genetic variation score” to evaluate ties between specific alleles and diseases across different genotyping platforms.

Of the nearly 600 SNPs evaluated, the team found nine SNPs for which one allele appears to increase an individual’s risk of multiple sclerosis and autoimmune thyroid disease but decrease his or her risk of rheumatoid arthritis and ankylosing spondylitis. The alternative alleles for these SNPs, meanwhile, have the opposite effect.

“What was surprising was our finding that at nine locations generally associated with autoimmunity risk, where a particular chemical unit conferred a heightened risk of certain autoimmune diseases, but reduced risk of getting certain others,” lead author Marina Sirota, a graduate student in Butte’s Stanford University lab, said in a statement.

Based on their analyses, the researchers suggest autoimmune diseases fall into at least two different groups: one containing rheumatoid arthritis and ankylosing spondylitis and another containing multiple sclerosis and autoimmune thyroid disease.

Meanwhile, they reported, type 1 diabetes resembled both of the groups to a certain extent, sharing characteristics with autoimmune thyroid disease but not multiple sclerosis. Crohn’s disease, on the other hand, did not cluster with either group.

In the future, the team hopes that the findings contribute not only to a better understanding of the biological pathways involved in these autoimmune diseases, but also give researchers a better sense of how to apply existing therapies — and come up with new ones.

“Several of these nine interesting SNPs we’ve found are located in or near genes that code for molecules found on cell surfaces,” Butte said, “which makes them potentially easier targets for the drugs pharmaceutical researchers are best at producing.”

And, Butte and his co-workers explained, the repertoire of SNPs involved will likely increase as additional autoimmune disease GWAS turn up new genetic variants involved in these — and other — diseases.

“As more genomic information becomes available on increasingly advanced platforms, this sort of analysis can be done on more diseases, possibly hundreds of them,” Sirota said.

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This Week in Nature

28/12/2009 às 11:06 (Diagnóstico Molecular, Medicina, Sequenciamento)

December 24, 2009

In Nature this week, an international group of researchers led by the Wellcome Trust Sanger Institute’s Mike Stratton followed up on their recent publication of lung and melanoma genomes with a paper looking at rearrangements in breast cancer. Using paired-end sequencing, the team found more than 2,000 chromosomal rearrangements in 24 breast cancers — more than expected in breast cancer. As the Times Online reported, the new study also highlights the diversity within breast cancer, suggesting it can be classified as five or more conditions, each with distinct treatment options and prognoses. For example, the team noted, a sub-group of breast cancers tested that were rife with tandem duplications. For more information, check out yesterday’s feature story in our sister publication In Sequence.

In another cancer-related paper in Nature‘s advance, online edition, a Columbia University-led research team used bioinformatics to home in on two transcription factors acting in cahoots to promote the formation and invasion of an aggressive type of glioblastoma multiforme brain tumor that has a so-called mesenchymal gene expression signature. The researchers found that the transcription factors STAT3 and C/EBPbeta spur this transformation, which is linked to poor outcomes for patients. Without the two transcription factors, though, the signature disappears — as does tumor aggressiveness. “These results show that the activation of a small regulatory module is necessary and sufficient to initiate and maintain an aberrant phenotypic state in cancer cells,” they write.

Microbes were the focus of a paper by researchers with the Genomic Encyclopedia of Bacteria and Archaea, who reported on the first 56 microbial genomes to be sequenced through that project. The group has already found new proteins and protein families and say their results support the validity of phylogeny-based sequencing — not only learning more about how microbes and microbial communities function, but also for informing future biofuel and other research. “[T]argeting microorganisms for genome sequencing solely on the basis of phylogenetic considerations offers significant far-reaching benefits in diverse areas,” senior author Jonathan Eisen and his co-workers write. Our sister publication GenomeWeb Daily News has more here.

A news feature profiles the journal’s “Newsmaker of the Year” Steven Chu, a Nobel laureate and US Secretary of Energy. Meanwhile, The Guardian picked up a letter in the correspondence section in which German chemist Thomas Koop takes exception to the flagrant use of “incorrect ‘designer’ snowflakes” in advertisements and elsewhere. Scientifically accurate snowflakes have six fold symmetry, not eight, Koop explained, owing to “water molecules’ hexagonal crystal lattice, held together by a hydrogen-bonding network and the structural form of lowest energy under the ambient cold conditions.”

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Personal Genome Project Sees Whole-Genome Sequencing as ‘Increasingly a Viable Option’

27/12/2009 às 21:29 (GWAS, hapmap)

Personal Genome Project

By Julia Karow

This article was originally published Oct. 14.

Organizers of Harvard Medical School’s Personal Genome Project said that as the cost of DNA sequencing declines, they are considering whole-genome sequencing rather than exome sequencing for the second phase of the study, PGP-100.

The project has already added results from the genome of its founder and principal investigator, George Church, to its website, whose genome was recently sequenced by Complete Genomics.

Launched in 2007 with 10 participants, the PGP aims to sequence the genomes of 100,000 people and to correlate their genotypes with trait information. In April, the project said that it plans to scale up to 100 participants for its second phase (see In Sequence 5/5/2009).

In a newsletter e-mailed last week to individuals interested in the study, PGP organizers said that they have been closely monitoring the decrease in cost of whole human genome sequencing “because it will impact our sequencing strategy for the PGP-100.”

The cost has already fallen to less than $50,000 per genome, PGP said, “with some speculating that the arrival of $5,000 genomes is imminent,” a reference to Complete Genomics’ $5,000 human genome sequencing service, which is scheduled to launch in January.

The project’s initial strategy, according to the organizers, was to focus on the exome, since it is “information rich” and seemed “a more economical alternative” to whole-genome sequencing.

“However, the cost of exome sequencing has not fallen as rapidly as whole-genome sequencing,” they noted, and as a result, for the PGP-100, “the decision to pursue whole genome is increasingly a viable option.”

It will depend, though, on factors such as the project’s ability to raise funding as well as “the willingness of sequencing companies to publicly showcase their technologies through sponsorship of PGP-100 genomes.”

According to its website, the PGP is funded by donations from individuals, Google, Orbimed, the COUQ Foundation, a grant from the Broad Institute, technology development grants from the Department of Energy and NIH, and in-kind support from various organizations. PersonalGenomes.org, a 501(c)3 charitable organization, seeks to raise $1.5 million in donations for the project this year from foundations, private companies, and individuals.

The project has already posted results from an analysis of Church’s genome, which was recently sequenced by Complete Genomics. Church told In Sequence last month that the company has committed to sequencing nine additional PGP genomes, though it was unclear whether it will charge the PGP for its services (see In Sequence 9/15/2009).

For the interpretation of the genomic information, the PGP is using Trait-o-matic, an open-source tool developed in house, which automatically identifies, filters, and annotates genetic variants. The project plans to use the software to generate research reports that contain variants “that may be of potential significance” and has already generated prototypes of such reports for its first 10 participants, based for nine of them on partial exome sequence data.

Future releases of Trait-o-matic will “enable a community of volunteers to annotate and interpret integrated genomic and trait datasets from the PGP.”

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