Biologia Molecular

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

rodrigobenevides — Mon, 28 Dec 2009 00:29:30 +0000

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.”

The Technology Pilot

rodrigobenevides — Mon, 28 Dec 2009 00:25:24 +0000

If you’ve been wondering how the 1,000 Genomes Project is doing, here’s an account from Dan Koboldt at his MassGenomics blog about last week’s meeting at Baylor where participants discussed the “Pilot 3″ phase of the project. “Unlike pilots 1 and 2, which emphasized whole genome sequencing to low or high coverage, respectively, in Pilot 3, the exons of 1,000 genes (~1.5 Mbp total) were selectively targeted for sequencing by capture technologies,” Koboldt writes. The team is also checking data across platforms and pipelines. “Overall, the Pilot 3 variant calls are looking good – dbSNP concordances in the 70-80% range or higher, and transition/transversion ratios of about 3-3.50 – and consistent across 454 and Solexa data from multiple centers,” he writes.

Breast Cancer Sequencing Study Finds Many Metastatic Mutations are Undetectable in Primary Tumor

rodrigobenevides — Mon, 28 Dec 2009 00:22:13 +0000

This article, originally published Oct.7, has been updated with comments from an author of the study.

By Julia Karow

A primary breast cancer acquired several new mutations in its protein-coding regions as it progressed toward metastasis, according to a new report by Canadian researchers, who argue that studying these mutations might help scientists understand why cancers become treatment resistant.

The research team, of the BC Cancer Agency in Vancouver, sequenced the genome and transcriptome of a metastatic breast cancer at high depth, using the Illumina Genome Analyzer platform, and analyzed the data for somatic coding mutations.

The scientists then determined how many of these mutations they could already detect in the primary tumor of the same patient, which was removed nine years earlier. Only a fraction of them could be found at all, and even fewer were present at a high frequency.

In addition, by analyzing not only genome but also transcriptome data, they uncovered two new RNA-editing events that change the amino acid sequence of two proteins.

The study “offered the opportunity, for the first time as far as we are aware, to look at the evolution of mutational burden across a very long period of time within the same patient,” said Marco Marra, director of the BC Cancer Agency Genome Sciences Centre in Vancouver, and one of the authors of the report, which appeared online in Nature last week.

“Our results show the importance of sequencing samples of tumor cell populations early as well as late in the evolution of tumors, and of estimating allele frequency in tumor genomes,” the authors noted.

Being able to study how a metastatic cancer’s genome differs from that of a primary tumor “is important because it gets at the heart of how treatment shapes the genetic
constitution of a malignancy,” Marra said. “We need to know, with great precision, what the changes are that allow tumors to evade treatment.”

The project, which was completed about six months ago, according to Marra, was just the beginning of a large-scale effort to study treatment-resistant cancer. “We are going to continue with using large-scale high-throughput approaches, such as DNA sequencing, to get at the mutational spectrum of treatment-resistant [cancers],” he said, including breast cancer, hematologic malignancies, childhood cancers, and lung cancer.

For their study, the Canadian researchers chose lobular breast cancer, an estrogen-receptor positive subtype that makes up about 15 percent of all breast cancers.

One of the reasons for focusing on breast cancer as the first example is that the Vancouver researchers plan to study more breast cancer samples as part of the Molecular Taxonomy of Breast Cancer International Consortium, or METABRIC, project, a collaboration between five hospitals and research centers in the UK and Canada, Marra said.

According to the BC Cancer Foundation, the Vancouver team is now sequencing the genomes of several hundred so-called triple negative breast tumors as part of an effort to build “a comprehensive genomic map of breast cancer” from 2,000 samples.

For their published study, the researchers initially sequenced DNA from a metastatic lobular breast cancer sample, generating approximately 2.9 billion paired-end reads with a mean read length of 48 base pairs, or 141 gigabases of sequence data, on the Illumina Genome Analyzer. About 121 gigabases aligned to the human reference genome, equivalent to about 43-fold coverage.

First genome-wide, single-base-resolution maps

rodrigobenevides — Mon, 28 Dec 2009 00:16:34 +0000

Joe Ecker is senior author on a paper that provides the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome. Comparing both human embryonic stem cells and fetal fibroblasts, they found “widespread differences” between the two, including almost one-quarter of all methylation in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation, they write.

Several opinion pieces appear this week. One checks in with experts and their concerns regarding the stimulus grants, another looks at the open-source Polymath Project, while a third by Cameron Neylon examines the potential of Google’s open-sorce collaboration tool, Google Wave.

A special insight section explores the changing landscape of neuroscience research. Says an editorial, “The experimental landscape has changed markedly over the past few years, given the technological advances in molecular genetics, optogenetics and functional imaging.” Articles cover molecular genetics and imaging technologies for circuit-based neuroanatomy, neuroscience and systems biology, and multimodal techniques for diagnosing Alzheimer’s disease.

Research led by Joel Levine, a neuroscientist from the University of Toronto, has determined that Drosophila melanogaster flies use a single chemical to communicate gender and sibling identity in order to pick the right sex partners. By inserting a transgene into the fly’s genome that killed cells that produced these special hydrocarbon signaling chemicals, they report that hydrocarbon-free male flies attempted copulating with each other, says a story at the BBC. Check out the accompanying video, too.

A Conversation With Carol W. Greider On Winning a Nobel Prize in Science

rodrigobenevides — Mon, 28 Dec 2009 00:12:30 +0000

Q. IS IT TRUE THAT YOU WERE DOING LAUNDRY WHEN YOU GOT THAT EARLY MORNING CALL FROM STOCKHOLM?

Matt Roth for The New York Times
WINNER Dr. Carol W. Greider of the Johns Hopkins School of Medicine.
A. Yes. I don’t usually do the laundry so early in the morning, but I was already up, and there was all this laundry staring at me. I was supposed to later meet two women friends to take our morning spin class. People had speculated that sometime in the next five years, something like this might happen. And last year people said, “Maybe, it will be, ” and it wasn’t. Reuters had made this prediction that we might get it this time. But I really didn’t have any idea. Maybe it would never happen. There are important fundamental discoveries that never get prizes. After I got the call, I sent my friend an e-mail: “I’m sorry I can’t spin right now. I’ve won the Nobel Prize.”

Q. DID YOU ALWAYS WANT TO BE A BIOLOGIST?

A. My parents were scientists. But I wasn’t the sort of child who did science fairs. One of the things I was thinking about today is that as a kid I had dyslexia. I had a lot of trouble in school and was put into remedial classes. I thought that I was stupid.

Q. THAT MUST HAVE HURT.

A. Sure. Yes. It was hard to overcome that. I kept thinking of ways to compensate. I learned to memorize things very well because I just couldn’t spell words. So later when I got to take classes like chemistry and anatomy where I had to memorize things, it turned out I was very good at that.

I never planned a career. I had these blinders on that got me through a lot of things that might have been obstacles. I just went forward. It’s a skill that I had early on that must have been adaptive. I enjoyed biology in high school and that brought me to a research lab at U.C. Santa Barbara. I loved doing experiments and I had fun with them. I realized this kind of problem-solving fit my intellectual style. So in order to continue having fun, I decided to go to graduate school at Berkeley. It was there that I went to Liz Blackburn’s lab, where telomeres were being studied.

Q. WHAT ARE TELOMERES?

A. The concept of telomeres was really laid out by H. J. Muller and Barbara McClintock in the 1940s, when they showed that there must be a special unit, a kind of cap at the end of the chromosome that holds it together. In 1978, Elizabeth Blackburn, working with Joe Gall, identified the DNA sequence of telomeres.

Every time a cell divides, it gets shorter. But telomeres usually don’t. So there must be something happening to the telomeres to keep their length in equilibrium. When I went into Liz Blackburn’s lab in 1984 and began working on this, the most exciting question that was being asked there was, “If we know that telomeres get short over time, how can they be relengthened?” I set out to look for evidence that there was such an enzyme as telomerase that would relengthen the telemeres once they shortened.

What I found out on Christmas Day 1984, through biochemical evidence, was that telomeres could be lengthened by the enzyme we called telomerase, which keeps the telomeres from wearing down. After, I found that out, I went home and put on Bruce Springsteen’s “Born in the USA,” which was just out, and I danced and danced and danced.

Q. WHY WAS THAT IMPORTANT?

A. Because broken or shortened telomeres are implicated in a whole group of diseases. Five or six years later, we and other groups discovered that telomere shortening played a role in the inability of cells to divide after a certain number of divisions — as well as in cancer. So the possibility of a biochemical therapy for some of these diseases was now something that could be explored.

Q. IT’S BEEN SAID THAT YOU AND DR. BLACKBURN DIDN’T RECEIVE THE NOBEL PRIZE EARLIER BECAUSE IT HADN’T YET BEEN PROVED THAT TELOMERES AND TELOMERASE WOULD BE VALUABLE IN UNDERSTANDING DISEASE. DOES THE PRIZE THIS YEAR MEAN THAT THERE NOW IS AN ACCEPTANCE OF THEIR VALUE?

A. I certainly hope so. That’s why Nobel Prizes are usually awarded long after the original discovery. It takes time for the medical implications to become clear. I think it’s clear now that the basic science we did is important to understanding cancers, some human genetic diseases and the age associated degenerative diseases. The clinical relevance still needs to be understood in the medical community.

Q. MANY REPORTERS HAVE ASKED WHY TELOMERES RESEARCH SEEMS TO ATTRACT SO MANY FEMALE INVESTIGATORS. WHAT’S YOUR ANSWER?

A. There’s nothing about the topic that attracts women. It’s probably more the founder effect. Women researchers were fostered early on by Joe Gall, and they got jobs around the country and they trained other women. I think there’s a slight bias of women to work for women because there’s still a slight cultural bias for men to help men. The derogatory term is the “old boys network.” It’s not that they are biased against women or want to hurt them. They just don’t think of them. And they often feel more comfortable promoting their male colleagues.

When Lawrence Summers, then the Harvard president, made that statement a few years ago about why there were fewer successful women in science, I thought, “Oh, he couldn’t really mean that.”’ After reading the actual transcript of his statement, it seems he really did say that women can’t think in that sort of scientific fashion. It was ridiculous!

I mean, women do things differently, which is why I think it would be important if more women were at higher levels in academic medicine. I think people might work together more, things might be more collaborative. It would change how science is done and even how institutions are run. That doesn’t mean that women necessarily have a different way of thinking about the mechanics of experiments. I think it’s more a different social way of interacting that would bring results in differently.Q. DO THIS YEAR’S NOBELS MEAN THAT WOMEN HAVE FINALLY BEEN ACCEPTED IN SCIENCE?

A. I certainly hope it’s a sign that things are going to be different in the future. But I’m a scientist, right? This is one event. I’m not going to see one event and say it’s a trend. I hope it is. One of the things I did with the press conference that Johns Hopkins gave was to have my two kids there. In the newspapers, there’s a picture of me and my kids right there. How many men have won the Nobel in the last few years, and they have kids the same age as mine, and their kids aren’t in the picture? That’s a big difference, right? And that makes a statement.

Carol W. Greider of the Johns Hopkins School of Medicine was one of three women who won a science Nobel last week, which puts her in some rare company. Only eight women had won in physiology or medicine, and there has never been a year when three women won Nobels in the sciences. Dr. Greider shared her prize with Elizabeth H. Blackburn and Jack W. Szostak for their research on telomeres.

miRNA Target for Treating Hepatitis C

rodrigobenevides — Sun, 27 Dec 2009 23:26:11 +0000

Scientists from the Southwest Foundation for Biomedical Research, Santaris Pharma, and Aalborg University may have found a miRNA target for treating hepatitis C. In work appearing in Science Express this week, they show that in chimps infected with hepatitis C virus, injecting a locked nucleic acid complementary to miR-122 “leads to long-lasting suppression of HCV viremia with no evidence for viral resistance or side effects in the treated animals.” HCV needs miR-122 in order to accumulate; by turning this miRNA off, according to transcriptome analysis, they saw that genes targeted by miR-122 were turned back on and interferon-regulated genes were down-regulated.

Two studies in this week’s issue look at the structures of proteins involved in translocation and translation. In the first, scientists led by Roland Beckmann at LMU Munich and the University of Massachusetts Medical School’s Elisabet Mandon combined cryo-electron microscopy and biochemical data to find that the Sec61/SecY complex, which serves as a channel for membrane and secretory proteins during protein translation, acts alone as a monomer, and that the growing peptide occupies the complex’s central pore.

In another, Beckmann led a group that used cryo-electron microscopy to visualize the ribosome stalled during translation of the TnaC leader peptide, which is upstream of the E. coli tryptophanase operon. At 5.8 angstroms, the nascent peptide chain had a distinct conformation within the ribosome exit tunnel that led to stalling of translation. A perspective adds insight.

In more structural work, researchers led by Elizabeth Getzoff at the Scripps Institute report the structure of pyrabactin resistance 1 (PYR1), a component of the abscisic acid receptor protein that functions in early ABA signaling. The phytohormone ABA is important in seed dormancy and protecting plants against environmental stresses like drought. “Small-angle x-ray scattering suggests that ABA signals by converting PYR1 to a more compact, symmetric closed-lid dimer,” they write. A related perspective talks more about seeds and their contribution to a plant’s survival.

This week, Science announced the GE Prize Essay winner, Michael Crickmore. His essay touches on how genetic programs determine whether an animal will be big or small. “Although we know that Hox transcription factors specify the identity of individual fingers, toes, and ribs, little is known about how their individual sizes are programmed,” he writes. Crickmore did his graduate work on size at Columbia University and is now doing a postdoc with Leslie Vosshall at Rockefeller University studying how the brain works.

Bring Your Questions for Genetics Entrepreneur Anne Wojcicki

rodrigobenevides — Mon, 07 Sep 2009 23:14:50 +0000

By Stephen J. Dubner
DESCRIPTIONAnne Wojcicki

Anne Wojcicki, a biotech analyst and biologist, is co-founder of the “personal genetics” company 23andMe — which, for a fee, will take a bit of your spit and map out your DNA to learn genealogical details as well as your risk factors for certain diseases. Clients can also join the company’s gene-themed social networks and share their genetic info with others. Sort of like Facebook for your innards.

Wired’s Adam Rogers wonders whether services like 23andMe could lead to “genetic hypochondria,” leaked genetic information, or a spike in preventive measures that some may consider extreme.

Wojcicki’s husband is a moderately well-known tech guy who, thanks to his wife’s work, learned that he has a genetic mutation that makes him more likely to get Parkinson’s disease.

Before starting 23andMe, Wojcicki spent 10 years in healthcare investing with a focus on biotech companies.

She has agreed to take your questions, so fire away in the comments section below. (I wonder what she thinks of a fat tax — that’s a tax on fat food, people, not fat people.) As with all Q&A’s, we will post the answers here shortly.

Addendum: Wojcicki answers your questions here.

George Church and Craig Venter in One Room

rodrigobenevides — Mon, 07 Sep 2009 23:13:12 +0000

August 03, 2009

George Church and Craig Venter got together to discuss synthetic biology during a master class held by the Edge. According to the Tierney Lab’s John Markoff, during “A Short Course on Synthetic Genetics” both Church and Venter “tried to convey how the world will be changed by the ability to routinely read genetic sequences into computing systems and then store, replicate, alter and insert them back into living cells.”

If You’ve Got Questions, Here’s Your Chance

rodrigobenevides — Mon, 07 Sep 2009 23:10:07 +0000

August 03, 2009

The Freakonomics blog at the New York Times is accepting questions for 23andMe’s Anne Wojcicki. Head to the comments thread to post your question, and the answers will be posted there in about a week. Steven Dubner, in introducing the company’s genetic and social networking aspects, says it is “sort of like Facebook for your innards.”

Cancer Stem Cells Make a Splash

rodrigobenevides — Mon, 07 Sep 2009 23:08:26 +0000

August 14, 2009

In Cell, Eric Lander and his colleagues report on an approach to screen for compounds that selectively target cancer stem cells. Using that technique, they found that salinomycin, which has “selective toxicity for breast CSCs”, leads to a greater than 100-fold reduction in the amount of CSC, as compared to paclitaxel, a chemotherapy drug used to treat breast cancer. In the New York Times, Lander adds that this method gives “a potential for a real renaissance in cancer therapeutics.”

In discussing the Broad Institute paper, the Cancer Research UK’s Kat Arney also blogs about the theory and role of cancer stem cells. “The role of stem cells in cancer is still not crystal clear, and although there’s evidence they play a role in many types of cancer, they’re not always implicated,” Arney writes.