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Halcyon Molecular, Caliper Life Sciences, NHGRI, RainDance Technologies, National Center for Genome Resources, SAS, JMP, NHLBI, Human Variome Project

Halcyon Molecular Developing EM-Based Sequencing Tech
Startup firm Halcyon Molecular is working on an electron microscopy-based DNA sequencing technology, In Sequence has learned.
The company is continuing the work of AQI Sciences, an Arizona-based startup that was founded in 2003. Michael Andregg, a company co-founder, told In Sequence’s sister publication GenomeWeb Daily News three years ago that the technology would provide megabase-length reads. At the time, AQI was working on a proof-of-principle project (see GWDN 12/19/2005).
Halcyon’s technology is independent of that developed by ZS Genetics, which is also working on an EM-based sequencing method (see In Sequence 5/27/2008).
Halcyon’s CEO, Will Andregg, told In Sequence that the company plans to reveal more about itself in a few months. “At this time, we’re heavily focused on our research and development, and are not yet ready to discuss our work publicly,” he said in an e-mail message.

Caliper to Develop Sample Prep Instrument for Next-Gen Sequencing
Caliper Life Sciences revealed this week that it is developing a sample prep instrument for next-generation sequencing.
“We think this is going to rapidly expand our market,” said Caliper President and CEO Kevin Hrusovsky during the firm’s third-quarter earnings call. He added that the company hopes to roll out the product in 2010.
Hopkinton, Mass.-based Caliper generated $34 million in revenues for the three-month period ended Sept. 30, compared to revenues of $36.7 million for the third quarter of 2007.
Its R&D costs decreased 12 percent to $5 million from $5.7 million, while its SG&A spending fell 23 percent to $10.3 million from $13.4 million.
Caliper’s net loss more than doubled year over year to $5.4 million, or $.11 per share, from $2.4 million, or $.05 per share.
Hrusovsky said during the call that the firm would continue to look to shed non-core businesses, as it focuses on its core imaging, microfluidics, and discovery services businesses.
Caliper finished the quarter with $8.9 million in cash, cash equivalents, and marketable securities. However, Hrusovsky noted during the call that around $18 million was wired into Caliper’s bank account on last week for divested businesses. He said the firm estimates it will have more than $30 million in cash as of Jan. 1.

NHGRI to Spend $14M on 1000 Genomes Project Data Processing, Analysis
The National Human Genome Research Institute plans to spend up to $8 million over two years to fund research to analyze data from the 1000 Genomes Project, and up to $6 million over the same period to fund the development of new methods to process and manage the data.
Examples of the kind of studies NHGRI will support under the data processing program include the development of methods for monitoring data quality; methods for validating gene variants of different frequencies and types by genotyping; methods for combining data across many samples; methods for integrating data on SNPs and structural variants into one map and placing them on one set of haplotypes; and tools to visualize, simulate, and summarize data. More information about that program, which expects to make between four and six awards in July 2009, can be found here.
Researchers seeking to apply for data analysis grants should plan to develop methods that could be used to characterize the full dataset from the program, methods to perform global analyses of the full dataset, and tools to allow several types of data the program will generate to be used by researchers. They should also work on methods needed for providing derived datasets based on the 1000 Genomes data, and evaluate the strategies the researchers in the program used. Researchers could analyze genomic coverage, the frequency of variants, or haplotypes, and the potential value of combining data across samples. More information about this funding program, which intends to make between eight and 10 awards in April 2010, can be found here.
Sequencing for the pilot projects of the 1000 Genomes Project began earlier this year, and sequencing for the full-scale project is expected to being this fall and last through 2010, when the entire dataset is expected to be around 20 terabases.

RainDance Ships Early-Access Instrument to Wash U Genome Center
RainDance Technologies said last week that the Genome Center at Washington University School of Medicine in St. Louis has become the second early-access customer for the firm’s RDT 1000 instrument and its sequence enrichment application, which are based on RainDance's RainStorm droplet-based technology platform.
RainDance will provide the instrument and customized PCR primer libraries to selectively amplify loci of interest for the center’s research initiatives. Researchers there will apply the technology to large-scale targeted sequencing studies.
“If the technology delivers as promised, RainDance Technology stands to significantly advance the art of targeted sequencing,” Wash U Genome Center co-director Elaine Mardis said in a statement.
Washington U is the second early-access customer for the technology, besides the J. Craig Venter Institute. RainDance said that it intends to commercially launch the platform in the first quarter of 2009.

NCGR Using JMP's Visualization Software for Next-Gen Sequencing
The National Center for Genome Resources and SAS business unit JMP will co-develop software tools for next-generation sequencing data analysis, SAS said last week.
NCGR researchers have been using the JMP Genomics software suite to analyze sequence data and have been offering advice about how to enhance it, said Russ Wolfinger, director of scientific discovery and genomics at SAS, in a statement.
Santa Fe, NM-based NCGR, which currently has six Illumina Genome Analyzer II instruments, said that its scientists are using JMP Genomics in its research programs, including studies of schizophrenia and soybeans, under a license signed a year ago.

NHLBI to Award $20M for Lung Microbiome HIV Studies
The National Heart, Lung and Blood Institute will give $20 million over the next five years to fund four sequencing centers and one data center that will study the microbes that reside in human lungs and air passages, including nasal and throat cavities, in individuals infected with HIV and in controls who are not infected.
These studies will aim to identify bacteria and other organisms such as viruses, protozoa, fungi, and organisms without cell walls.
NHLBI expects to fund four clinical sequencing centers and a data collection center with up to $525,000 per year in direct costs for up to five years.
Investigators seeking to apply for funding should use high-throughput technology platforms to create data sets “of sufficient quality and depth” to allow for analysis of the microbes involved in the progression of HIV and in its complications, NHLBI said. The technologies that investigators use could include 167SrRNA gene sequencing and metagenomic shotgun sequencing.
These collected data will be used to study the impact of changes in the respiratory microbiome in the progression of HIV disease, HIV-related respiratory complications, and the effects of anti-HIV therapies.
The Clinical/Sequencing Centers will conduct individual projects, including harvesting and conducting analyses of the lung microbiome, and each must agree to share data and biospecimens and to cooperate with other centers and with the DCC.
The data collection center will support individual projects at each of the other sites, where it will help to develop and implement common protocols. It must be able to store and manipulate large data sets and to support quality control for collaborative protocols.
More information about the funding program is available here.

Human Variome Project Developing Strategies for Cataloguing Disease-Related Genetic Variation
The Australian-led Human Variome Project is taking strides toward creating a resource housing information on genetic polymorphisms known or suspected of influencing disease risk, according to a policy paper published in Science last week.
The Human Variome Project was officially established in 2006. Now, the project is coming into its own, with pilot projects, a new scheme for funding part of the effort, and planning committees aimed at creating information pipelines.
The project was conceived because of a need to catalogue information on variation or changes across the human genome and to make it accessible clinically, co-author Finlay Macrae, a cancer researcher at the Royal Melbourne Hospital, told GenomeWeb Daily News.
In the absence of such a resource for compiling data on mutations and their known or suspected links to specific phenotypes, Cotton said, physicians are often left scratching their heads and trawling numerous databases trying to determine whether a genetic mutation they see in a patient has been previously tied to a disease or not.
To address this, variome participants are working to encourage the development and adoption of standards, define and reach consensus on ethical guidelines, develop automated data submission systems, support curation, promote participation in developing countries, and more.
Ultimately, Macrae explained, the team hopes to be able to “develop systems whereby diagnostic lab DNA information is fed into the Human Variome Project to provide a much more comprehensive database.” That requires methods for capturing both legacy data — disease-related mutations that have been published or are sitting in lab books — and new data from the literature and diagnostic labs, he said.
Several pilot projects are also being organized or are underway, the authors noted. For instance, the International Society for Gastrointestinal Hereditary Tumours, or InSIGHT, started a project in early 2007 to create a database of mutations associated with colon cancer. That project involves creating a pipeline for collecting new and old data and compiling it on the Leiden Open Variation Database. An InSIGHT pilot project is also aimed at compiling worldwide information on mutations in four genes of interest and their relationship to colon cancer.
On a broader scale, those spearheading the Human Variome Project are currently developing strategies and resources to help researchers set up variome projects around the world.
In addition, the team has come up with a new scheme to help pay for such massive collection and curation efforts. The “Adopt-a-Gene Program” is intended to give industry and patient support groups the opportunity to sponsor data collection on mutations in specific genes of interest.
The researchers noted that they see the variome project as complementary to resequencing projects such as the 1000 Genomes Project.
— By Andrea Anderson; originally published on GenomeWeb Daily News

Genomic Research, Personal Genomics Require New Ethical and Regulatory Guidelines, Experts Say
Informed consent and regulation need re-thinking in the genomic research context, according to two policy papers published last week in Nature.
In the first of these, Patrick Taylor, deputy general counsel at the Children’s Hospital Boston and lecturer at Harvard Medical School, argued that mandating informed consent for genomic research is not necessarily the best way to protect individuals' privacy. And, he said, traditional informed consent measures may hamper genetic and genomic research and its translation into healthcare settings.
“Mandating consent increases the burden and biases research,” Taylor wrote, citing a Taiwan study suggesting that several populations, including the elderly, low income individuals, and Taiwan aborigines, were likely to refuse consent for research. “Even if large cohorts muffle consent bias, consent issues will endanger research into rare diseases, including those that cause childhood death,” he wrote.
Researchers need to connect genetic information with medical information in order to improve healthcare, Taylor noted. But requiring patient consent for use of electronic medical records would be a mistake, he argued, adding that Microsoft, patient activists, and others are currently lobbying Congress for such legislation based on a need for individual autonomy.
“For sound reasons, some research, particularly that involving interventions on the body, requires consent altruistically given,” Taylor wrote. “But other research rightly proceeds on different ethical grounds. For good cause, where the primary potential harm is loss of privacy, ethics permits waiving consent given reasonable privacy protection.”
Taylor also argued that consent cannot ensure privacy and suggested that autonomy is just a small part of a much larger picture. He suggested that some ethical principles call for individuals to participate in low-risk research in order to benefit society as a whole. And, he added, beneficence and justice should also be taken into consideration when considering healthcare and genomic research.
“Protection of privacy is critical,” Taylor concluded, “but consent alone is the wrong means to protect it. Working with the public, we must preserve and explore ethical alternatives.”
In a second commentary paper in Nature, an international team of researchers from the UK, US, Australia, Austria, and the Netherlands argued that direct-to-consumer whole-genome tests, such as those offered by 23andMe, Decode Genetics, and Navigenics, should not necessarily be evaluated under the same regulatory frameworks used for traditional genetics.
“We believe that anticipatory governance is premature without a better understanding of how SNP-based whole-genome information is used by, and what it means to, a wide range of users,” lead authors Barbara Prainsack, a biomedicine and society researcher at King’s College London, and Jenny Reardon, a sociologist at the University of California at Santa Cruz, wrote.
Although they did not advocate an unregulated genomics market, the authors urged regulators to wait until information is available on the effects of such tests before introducing regulation. For instance, the team noted that personal genomics is “pushing the individualization of responsibility for health one step further,” without necessarily providing clear information about how genetics ties into health and individual choices.
“Regulation will be effective only if it is informed by the results of a systematic examination of these issues,” they wrote. “We recommend that public authorities make it a priority to fund empirical research exploring what individuals expect from personal genomics, and in what way genetic-susceptibility information is likely to affect practices and lifestyle choices.”
On that front, the authors lauded efforts by New Jersey's Coriell Institute for Medical Research and California’s Scripps Translational Research Institute, Navigenics, and Microsoft for undertaking research to determine how personal genetic tests affect individuals.
The researchers also noted that genomics is blurring the lines between medical tests and genealogical or recreational information — particularly since consumers often play a larger role in interpreting the information than physicians.
“Effective responses to this situation require clarification of the novel issues created by the convergence of information about health, consumer and lifestyle choices, and genealogy; novel relationships between geneticists, patients, consumers and corporate executives; and the continued intensification of collaboration, on both the research and the patient/consumer sides,” the authors wrote.

Sequencing Study Suggests Bacterial Diversity Higher on Women's Hands than Men's
Humans, particularly women, have far more bacterial diversity on the palms of their hands than previously realized, new research suggests.
In a paper appearing online in the Proceedings of the National Academy of Sciences last week, University of Colorado researchers used barcoding and pyrosequencing to assess bacterial communities on the right and left palms of more than 50 volunteers, identifying nearly 5,000 bacterial species. Their results suggest that bacterial species composition on the hands varies widely from person to person and even from hand to hand in the same individual, with women having significantly more diverse bacterial communities than men.
“The sheer number of bacteria detected on the hands of the study participants was a big surprise, and so was the greater diversity of bacteria we found on the hands of women,” lead author Noah Fierer, an ecology and evolutionary biology researcher at the University of Colorado, said in a statement.
By understanding which bacterial species are normally on and in the human body, researchers hope to gain insights into changes in the microbial community that are associated with human disease. For example, efforts such as the Human Microbiome Project and the International Human Microbiome Consortium are attempting to catalogue the diverse microbial communities associated with the human body.
Although the current study was not done as part of the Human Microbiome Project, Fierer told GenomeWeb Daily News that he believes the work has implications for this effort as well. For example, because there seems to be so much variation in the bacterial communities on the skin of healthy individuals, he noted, it may be difficult to establish a baseline and determine which changes are associated with disease.
For this study, Fierer and his colleagues used a sterile swab to sample the bacterial communities on the right and left hands of each of the 51 undergraduate volunteers. They then used the Roche 454 sequencing platform to sequence 16S rRNA genes, which allowed them to look at the bacterial diversity and communities in sample.
From the 332,000 informative sequences they obtained, the researchers found barcodes representing 4,742 different bacterial phylotypes. On average, each palm was home to more than 150 unique bacterial species. Of these, just five were found on the hands of all the participants.
Based on these results, the bacterial diversity on the hands appears to be about three times as diverse as that found in studies of forearm or elbow skin and more closely resembles the level of bacterial richness in the mouth, esophagus, or lower intestine.
Overall, species from the Propionibacterium, Streptococcus, Staphylococcus, Corynebacterium, and Lactobacillus genera were the most prevalent on human hands. But the species composition and diversity varied widely from one individual to the next and even within the same individual.
For example, the researchers found that the bacterial diversity was about 40 percent higher on women’s hands than on men’s hands, Fierer said. The researchers speculated that these may be due to differences in skin environment between men and women caused by factors such as sweat and oil gland production, hormone production, skin thickness, or differences in skin acidity.
In the same individual, just 17 percent of the species were shared between the dominant and non-dominant hand, on average. Meanwhile, an average of 13 percent of bacterial phylotypes were shared between different individuals. The team also saw differences in bacterial species composition on individuals’ palms depending on their handedness and time since hand washing.
When they followed up in a smaller study of four men and four women, the researchers again found sex differences between the bacterial communities. In addition, that experiment suggested that bacterial species composition changed immediately following hand washing, with overall species diversity increasing — potentially due to the removal of the dominant species, Fierer said. The original species composition seems to become re-established just two to four hours after hand washing, he added.

At present, Fierer and his team are doing experiments to try to determine whether the high levels of diversity are a characteristic of microbial communities on or in all parts of the body or whether microbial communities in other parts of the body are more consistent from one individual to the next.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.