Carlos Silva: How Flights, Tech Speeds Up Scientific Discovery
"I think it #39;s great we #39;re now able to amass the power of so many different people all over the world to reach a common goal." Carlos Silva talks about the wa...
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Where Did We All Come From? Tracing Human Migration Using Genetic Markers
Presented by Professor Moses Schanfield. Of all species on the face of the earth, humans are the most disperse, in that they occupy the most diverse eco-syst...
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Ethics of Pharmacogenomics
Wylie Burke, M.D., PhD. is chair of the Department of Bioethics and Humanities at the University of Washington and an adjunct professor of medicine and epide...
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Newswise LOUISVILLE, Ky. Excess abdominal fat can be a precursor to diseases such as cardiovascular disease, type 2 diabetes and cancer. A persons measure of belly fat is reflected in the ratio of waist circumference to hip circumference, and it is estimated that genetics account for about 30-60 percent of waist-to-hip ratio (WHR).
Kira Taylor, Ph.D., M.S., assistant professor, University of Louisville School of Public Health and Information Sciences, and her research team have identified five new genes associated with increased WHR, potentially moving science a step closer to developing a medication to treat obesity or obesity-related diseases.
The researchers recently published their findings in Human Molecular Genetics. The team conducted an analysis of more than 57,000 people of European descent, and searched for genes that increase risk of high waist-to-hip ratio, independent of overall obesity. They investigated over 50,000 genetic variants in 2,000 genes thought to be involved in cardiovascular or metabolic traits.
Their analysis identified three new genes associated with increased WHR in both men and women, and discovered two new genes that appear to affect WHR in women only. Of the latter, one gene, SHC1, appears to interact with 17 other proteins known to have involvement in obesity, and is highly expressed in fat tissue. In addition, the genetic variant the team discovered in SHC1 is linked to another variant that causes an amino acid change in the protein, possibly changing the function or expression of the protein.
This is the first time SHC1 has been associated with abdominal fat, Taylor said. We believe this discovery holds great opportunity for medicinal chemistry and eventually, personalized medicine. If scientists can find a way to fine-tune the expression of this gene, we could potentially reduce the risk of excessive fat in the mid-section and its consequences, such as cardiovascular disease.
Prior research has found that mice lacking the SHC1 protein are leaner, suggesting this molecule may have a role in metabolic imbalance and premature cell deterioration by supplying too much nutrition for normal growth and development.
Additional evidence finds SHC1 activates the insulin receptor, triggering multiple signaling events that affect fat cell growth.
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PUBLIC RELEASE DATE:
22-Jan-2014
Contact: Kathy Ridgely Beal kbeal@acmg.net 301-238-4582 American College of Medical Genetics
Do you cover genetics, genomics, healthcare or medicine? The media are invited to register now for the American College of Medical Genetics and Genomics Annual Clinical Genetics Meeting, March 25-29, 2014 at the Nashville Convention Center.
From Incidental Findings to Whole Genome/Exome Sequencing to Cancer Genetics, the focus of the ACMG Meeting is on the actual practice of genetics and genomics in healthcare, showcasing the latest breakthroughs in genetics research and its practical applications to medical practice. The ACMG Annual Meeting attracts medical and scientific leaders from around the world working to apply research in the human genome to the diagnosis, management, treatment and prevention of genetic conditions and rare and common diseases.
Reporters will hear about the latest medical genetics research; have the opportunity to interact with doctors, laboratory professionals and genetic counselors about what is happening right now in genetics and genomics; and view the latest products available in the extensive exhibit hall.
Topics range from common conditions to rare diseases. Sessions include information of interest to the general public, to health professionals and to the industry/trade.
The ACMG Meeting is the genetics meeting most focused on the practical applications of genetic discoveries in the clinical setting. And the 2014 Meeting is already shattering records with a record number of abstracts submitted and attendee registration to date is at an all-time high.
Two Genetics Short Courses on Tuesday, March 25:
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Complimentary press registration now open for ACMG 2014 Annual Clinical Genetics Meeting
In the study of rare disorders, four general patterns of inheritance are distinguishable by pedigree analysis: autosomal recessive, autosomal dominant, X-linked recessive, and X-linked dominant.
The affected phenotype of an autosomal recessive disorder is determined by a recessive allele, and the corresponding unaffected phenotype is determined by a dominant allele. For example, the human disease phenylketonuria is inherited in a simple Mendelian manner as a recessive phenotype, with PKU determined by the allele p and the normal condition by P . Therefore, sufferers from this disease are of genotype p /p , and people who do not have the disease are either P /P or P /p . What patterns in a pedigree would reveal such an inheritance? The two key points are that (1) generally the disease appears in the progeny of unaffected parents and (2) the affected progeny include both males and females. When we know that both male and female progeny are affected, we can assume that we are dealing with simple Mendelian inheritance, not sex-linked inheritance. The following typical pedigree illustrates the key point that affected children are born to unaffected parents:
From this pattern, we can immediately deduce simple Mendelian inheritance of the recessive allele responsible for the exceptional phenotype (indicated in black). Furthermore, we can deduce that the parents are both heterozygotes, say A /a ; both must have an a allele because each contributed an a allele to each affected child, and both must have an A allele because they are phenotypically normal. We can identify the genotypes of the children (in the order shown) as A /, a /a , a /a , and A /. Hence, the pedigree can be rewritten as follows:
Note that this pedigree does not support the hypothesis of X-linked recessive inheritance, because, under that hypothesis, an affected daughter must have a heterozygous mother (possible) and a hemizygous father, which is clearly impossible, because he would have expressed the phenotype of the disorder.
Notice another interesting feature of pedigree analysis: even though Mendelian rules are at work, Mendelian ratios are rarely observed in families, because the sample size is too small. In the preceding example, we see a 1:1 phenotypic ratio in the progeny of a monohybrid cross. If the couple were to have, say, 20 children, the ratio would be something like 15 unaffected children and 5 with PKU (a 3:1 ratio); but, in a sample of 4 children, any ratio is possible, and all ratios are commonly found.
The pedigrees of autosomal recessive disorders tend to look rather bare, with few black symbols. A recessive condition shows up in groups of affected siblings, and the people in earlier and later generations tend not to be affected. To understand why this is so, it is important to have some understanding of the genetic structure of populations underlying such rare conditions. By definition, if the condition is rare, most people do not carry the abnormal allele. Furthermore, most of those people who do carry the abnormal allele are heterozygous for it rather than homozygous. The basic reason that heterozygotes are much more common than recessive homozygotes is that, to be a recessive homozygote, both parents must have had the a allele, but, to be a heterozygote, only one parent must carry the a allele.
Geneticists have a quantitative way of connecting the rareness of an allele with the commonness or rarity of heterozygotes and homozygotes in a population. They obtain the relative frequencies of genotypes in a population by assuming that the population is in Hardy-Weinberg equilibrium, to be fully discussed in Chapter 24 . Under this simplifying assumption, if the relative proportions of two alleles A and a in a population are p and q , respectively, then the frequencies of the three possible genotypes are given by p 2 for A /A , 2pq for A /a , and q 2 for a /a . A numerical example illustrates this concept. If we assume that the frequency q of a recessive, disease-causing allele is 1/50, then p is 49/50, the frequency of homozygotes with the disease is q 2 =(1/50)2 =1/250, and the frequency of heterozygotes is 2pq =249/501/50 , or approximately 1/25. Hence, for this example, we see that heterozygotes are 100 times as frequent as disease sufferers, and, as this ratio increases, the rarer the allele becomes. The relation between heterozygotes and homozygotes recessive for a rare allele is shown in the following illustration. Note that the allele frequencies p and q can be used as the gamete frequencies in both sexes.
The formation of an affected person usually depends on the chance union of unrelated heterozygotes. However, inbreeding (mating between relatives) increases the chance that a mating will be between two heterozygotes. An example of a marriage between cousins is shown in . Individuals III-5 and III-6 are first cousins and produce two homozygotes for the rare allele. You can see from that an ancestor who is a heterozygote may produce many descendants who also are heterozygotes. Hence two cousins can carry the same rare recessive allele inherited from a common ancestor. For two unrelated persons to be heterozygous, they would have to inherit the rare allele from both their families. Thus matings between relatives generally run a higher risk of producing abnormal phenotypes caused by homozygosity for recessive alleles than do matings between nonrelatives. For this reason, first-cousin marriages contribute a large proportion of the sufferers of recessive diseases in the population.
Pedigree of a rare recessive phenotype determined by a recessive allele a . Gene symbols are normally not included in pedigree charts, but genotypes are inserted here for reference. Note that individuals II-1 and II-5 marry into the family; they are assumed (more...)
What are some examples of human recessive disorders? PKU has already served as an example of pedigree analysis, but what kind of phenotype is it? PKU is a disease of processing of the amino acid phenylalanine, a component of all proteins in the food that we eat. Phenylalanine is normally converted into tyrosine by the enzyme phenylalanine hydroxylase:
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Human genetics - An Introduction to Genetic Analysis - NCBI ...
Hertz Fellow David Galas - Chairman of the Board Hertz Foundation
David J. Galas, Hertz Fellow and Chairman of the Fannie and John Hertz Foundation Board of Directors, is Principal Scientist for the Pacific Northwest Diabet...
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Hertz Fellow David Galas - Chairman of the Board Hertz Foundation - Video
Analysis of oldest sequence from a human ancestor reveals close link with Denisovans
Image: Javier Trueba/Madrid Scientific Films
Another ancient genome, another mystery. DNA gleaned from a 400,000-year-old femur from Spain has revealed an unexpected link between Europes hominin inhabitants of the time and a cryptic population, the Denisovans, who are known to have lived much more recently in southwestern Siberia.
The DNA, which represents the oldest hominin sequence yet published, has left researchers baffled because most of them believed that the bones would be more closely linked to Neanderthals than to Denisovans. Thats not what I would have expected; thats not what anyone would have expected, says Chris Stringer, a paleoanthropologist at Londons Natural History Museum who was not involved in sequencing the femur DNA.
The fossil was excavated in the 1990s from a deep cave in a well-studied site in northern Spain called Sima de los Huesos (pit of bones). This femur and the remains of more than two dozen other hominins found at the site have previously been attributed either to early forms of Neanderthals, who lived in Europe until about 30,000 years ago, or to Homo heidelbergensis, a loosely defined hominin population that gave rise to Neanderthals in Europe and possibly humans in Africa.
But a closer link to Neanderthals than to Denisovans was not what was discovered by the team led by Svante Pbo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
The team sequenced most of the femurs mitochondrial genome, which is made up of DNA from the cells energy-producing structures and passed down the maternal line. The resulting phylogenetic analysis which shows branches in evolutionary history placed the DNA closer to that of Denisovans than to Neanderthals or modern humans. This really raises more questions than it answers, Pbo says.
The teams finding, published online in Nature this week (M. Meyer et al. Nature http://dx.doi.org/10.1038/nature12788; 2013), does not necessarily mean that the Sima de los Huesos hominins are more closely related to the Denisovans, a population that lived thousands of kilometres away and hundreds of thousands of years later, than to nearby Neanderthals. This is because the mitochondrial genome tells the history of just an individuals mother, and her mother, and so on.
Courtesy of Nature Magazine
Nuclear DNA, by contrast, contains material from both parents (and all of their ancestors) and typically provides a more accurate overview of a populations history. But this was not available from the femur.
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Earliest Human DNA Shows Unforeseen Mixing with Mystery Population
Angelina Jolie: I feel great, I feel wonderful, and I'm very, very grateful for all the support, it's meant a lot to me. I've been very happy just to see the discussion about women's health expanded and that means the world to me, and after losing my mom to these issues I'm very grateful for it, and I've been very moved by the kind support from people, really very grateful for it.
Joel Werner: Hi, and welcome to the Health Report. I'm Joel Werner. And that was Angelina Jolie. It's been almost a month since she announced via a New York Times op-ed that she'd chosen to have a preventative double mastectomy, a decision reached after learning she carried a mutation on the BRCA1, or Braca-one gene. It was a revelation that resonated around the globe.
Clara Gaff: I thought it was very courageous of her to make public what for many people is a very private decision, and to let people know what was possible and to encourage people in similar situations to her to find out what their situation is and make their own choices.
Joel Werner: Associate Professor Clara Gaff is a genetic counsellor. She's also manager of genomic medicine at the Walter and Eliza Hall Institute for Medical Research. While Clara's reaction to Jolie's Times article epitomised that of many, her colleague Professor Geoff Lindeman wasn't quite so absolute in his praise.
Geoff Lindeman: I think it was somewhat of a mixed blessing. It's always good to have appropriate publicity in this area so that people can be aware, but similarly I think many women must have felt that they had the sword of Damocles hanging over their heads, and that's not necessarily the case for the vast majority of women and even for women who have mutations in the BRCA1 or 2 genes.
Joel Werner: Today on the Health Report it's part two in our special on breast cancer in Australia, and this week we're examining the role genetics plays in the diagnosis and treatment of the disease.
Over the past month, BRCA1 and 2 have been the most heavily publicised genes in the world; celebrity alleles of the human genome. But have you stopped to ask yourself what they actually are? Or how they influence the development of cancer?
Geoff Lindeman is head of the familial cancer centre at Melbourne Hospital, and joint head of breast cancer research at the Walter and Eliza Hall Institute.
Geoff Lindeman: So these were genes that were discovered in the mid-1990s that were identified through women who had a very high risk of breast or ovarian cancer running in their families. The discovery of these genes really helped us to understand their role in helping keep cancer in check. They are basically suppressor genes which help repair DNA in our genome that has become damaged. And for reasons that we still don't fully understand, breast and ovarian cancer are quite prominent amongst the things that can go wrong when there is a fault in these genes.
Joel Werner: And that's the thing, it's when you have mutations in these genes that things go wrong.
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EndoPredict is a second-generation, multigene prognostic test kit for patientsdiagnosed with breast cancer. Under the agreement, Myriad will receive comprehensive marketing rights todistribute and sell EndoPredict, including in high-growth markets in Europe.The agreement will leverage Myriad's 45-person international commercial teamand will significantly increase the number of medical specialists and salesprofessionals supporting EndoPredict. Specific terms of the deal were notdisclosed. EndoPredict provides physicians with information to devise personalizedtreatment plans for their breast cancer patients. The EndoPredict test kitformat is an ideal platform for use by clinical pathologists, who desire toconduct testing within their own laboratories. In contrast to older multi-genetests, EndoPredict detects the likelihood of late metastases (i.e., metastasisformation after more than five years) and can thus guide treatment decisionsfor chemotherapy as well as extended anti-hormonal therapy. Accordingly,therapy decisions backed by EndoPredict confer a high level of diagnosticsafety. EndoPredict was shown to accurately predict cancer-specific diseaseprogression and metastasis in multiple clinical outcome studies with more than2,200 patients. 'Myriad has a significant opportunity to leverage our international presence,and we are pleased to be partnering with Sividon to make EndoPredict even morewidely available to patients in Europe and worldwide,' said Gary King,Executive Vice President, International Operations, Myriad Genetics. 'We arecommitted to contributing to the health of people in Europe through a strongsales and marketing organization that provides enhanced access to life-savingproducts for patients and cost effective solutions for healthcare providers.Myriad's team of field specialists will support EndoPredict's current customersin liaison with Sividon's medical expert team, thus providing additional levelsof support and contact.' 'Sividon's EndoPredict, backed by compelling evidence from clinical studieswith thousands of patients combined with Myriad's strong commercial capabilityand coverage in many key countries creates an outstanding partnership,' saidDr. Christoph Petry, CEO of Sividon Diagnostics. 'Breast cancer affects thelife of more than 388,000 women per year in Europe, and EndoPredict will helpto significantly improve their cancer treatment. We are delighted to partnerwith Myriad to help save and improve the lives of more women with breastcancer.' About Myriad Genetics GmbHMyriad Genetics GmbH is based in Zurich, Switzerland and is the internationalsubsidiary of Myriad Genetics Inc., a leading molecular diagnostic companydedicated to making a difference in patients' lives through the discovery andcommercialization of transformative tests to assess a person's risk ofdeveloping disease, guide treatment decisions and assess risk of diseaseprogression and recurrence. Myriad's molecular diagnostic tests are based on anunderstanding of the role genes play in human disease and were developed with acommitment to improving an individual's decision making process for monitoringand treating disease. Myriad is focused on strategic directives to introducenew products, including companion diagnostics, as well as expandinginternationally. For more information on how Myriad Genetics GmbH is making adifference, please visit the Company's website: http://www.myriad.ch. Myriad and theMyriad logo are trademarks or registered trademarks of Myriad Genetics, Inc. inthe United States and worldwide. MYGN-F, MYGN-G About SividonSividon Diagnostics GmbH was founded in 2010 as a management buyout fromSiemens Healthcare Diagnostics in Cologne, Germany. Sividon is dedicated todevelop modern methods for the molecular pathology laboratory to help improvethe quality of care for cancer patients. Sividon's first product, EndoPredict,has been introduced into the market in 2011 and allows for a moreindividualized therapy management in breast cancer. For more information onSividon please visit the Sividon's website at http://www.sividon.com. Sividon, theSividon logo and EndoPredict are registered trademarks of Sividon DiagnosticsGmbH in Germany and other countries. Safe Harbor StatementThis press release contains 'forward-looking statements' within the meaning ofthe Private Securities Litigation Reform Act of 1995, including statementsrelating to the EndoPredict test and Myriad's partnering with Sividon to marketthe EndoPredict test in Europe and worldwide; and the Company's strategicdirectives under the caption 'About Myriad Genetics.' These 'forward-lookingstatements' are management's present expectations of future events and aresubject to a number of risks and uncertainties that could cause actual resultsto differ materially and adversely from those described in the forward-lookingstatements. These risks include, but are not limited to: the risk that salesand profit margins of our existing molecular diagnostic tests and companiondiagnostic services may decline or will not continue to increase at historicalrates; risks related to changes in the governmental or private insurersreimbursement levels for our tests; the risk that we may be unable to developor achieve commercial success for additional molecular diagnostic tests andcompanion diagnostic services in a timely manner, or at all; the risk that wemay not successfully develop new markets for our molecular diagnostic tests andcompanion diagnostic services, including our ability to successfully generaterevenue outside the United States; the risk that licenses to the technologyunderlying our molecular diagnostic tests and companion diagnostic servicestests and any future tests are terminated or cannot be maintained onsatisfactory terms; risks related to delays or other problems with opeRatingour laboratory testing facilities; risks related to public concern over ourgenetic testing in general or our tests in particular; risks related toregulatory requirements or enforcement in the United States and foreigncountries and changes in the structure of the healthcare system or healthcarepayment systems; risks related to our ability to obtain new corporatecollaborations or licenses and acquire new technologies or businesses onsatisfactory terms, if at all; risks related to our ability to successfullyintegrate and derive benefits from any technologies or businesses that welicense or acquire; risks related to increased competition and the developmentof new competing tests and services; the risk that we or our licensors may beunable to protect or that third parties will infringe the proprietarytechnologies underlying our tests; the risk of patent-infringement claims orchallenges to the validity of our patents; risks related to changes inintellectual property laws covering our molecular diagnostic tests andcompanion diagnostic services and patents or enforcement in the United Statesand foreign countries, such as the Supreme Court decision in the lawsuitbrought against us by the Association for Molecular Pathology et al; risks ofnew, changing and competitive technologies and regulations in the United Statesand internationally; and other factors discussed under the heading 'RiskFactors' contained in Item 1A of our most recent Annual Report on Form 10-Kfiled with the Securities and Exchange Commission, as well as any updates tothose risk factors filed from time to time in our Quarterly Reports on Form10-Q or Current Reports on Form 8-K. All information in this press release isas of the date of the release, and Myriad undertakes no duty to update thisinformation unless required by law. CONTACT: Media Contacts:Ron Rogers(801) 584-3065rrogers@myriad.comEstherLinnenberg+49-221-66956170linnenberg@sividon.comInvestor Contact:ScottGleason(801) 584-1143sgleason@myriad.comNews Source: NASDAQ OMXEnd of Corporate News---------------------------------20.01.2014 Dissemination of a Corporate News, transmitted by DGAP - acompany of EQS Group AG.The issuer is solely responsible for the content of this announcement.DGAP's Distribution Services include Regulatory Announcements,Financial/Corporate News and Press Releases.Media archive at http://www.dgap-medientreff.de and http://www.dgap.de---------------------------------Language: English Company: Myriad Genetics, Inc. United States ISIN: US62855J1043 End of News DGAP News-Service --------------------------------- 248572 20.01.2014
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Human Genetics Truth - Lloyd Pye
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By: AwakeningTruth
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The Journal of Human Genetics is the official journal of the Japan Society of Human Genetics, publishing high-quality original research articles, short communications, reviews, correspondences and editorials on all aspects of human genetics and genomics. It is the leading genetics journal based in the Asia-Pacific region.
*** Announcing Open ***
Journal of Human Genetics now offers authors the option to publish their articles with immediate open access upon publication. Open access articles will also be deposited on PubMed Central at the time of publication and will be freely available immediately. Find out more from the FAQs page.
Special section on Epigenomics
The special section on epigenomics in the July 2013 issue of Journal of Human Genetics features review and original articles by top-level epigenetic researchers covers various topics of epigenetic research, both basic and clinical.
Pharmacogenomics: Recent advances and future directions
The Journal of Human Genetics is pleased to present its first "special section" in the June issue of the journal. These special sections are designed to bring together collections of papers on specific topics of interest; guest editors curate the section, inviting contributions from leading researchers in the field. The topic of the first special section is pharmacogenomics, featuring eight articles on the current state of pharmacogenomics research and its implementation in the clinic.
Biomedical Genomics Series Web Focus - Cancer
The Journal of Human Genetics is delighted to present the latest from the Series on Biomedical Genomics, a Web Focus on Cancer. The Focus includes reports covering genetic research into identifying risk and associations with Breast Cancer, lung squamous cell carcinoma, adenocarcinoma, and cervical cancer in different populations, such as Korean, Chinese, Japanese and Amerindian.
Biomedical Genomics Series Web Focus - Neuropsychiatric Disease
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Jan. 15 (UPI) -- San Diego-based genetic technology company Illumina has announced a machine that can sequence a human genome for $1,000.
The new product, called HiSeq X Ten Sequencing System, was launched at the annual JP Morgan Healthcare Conference in San Francisco. The $1 million sequencer comes in a set of 10 units and can generate 1.8 Tb of sequencing data in 3 days and up to 600 Gb in a single day at no more than $1,000 per genome.
"Breaking the sound barrier of human genetics not only pushes us through a psychological milestone, it enables projects of unprecedented scale," said Illumina CEO Jay Flatley.
This cost includes typical instrument depreciation, DNA extraction, library preparation, and estimated labor. A number of companies have placed orders for the product, including the Broad Institute, an independent biomedical research center affiliated with MIT and Harvard.
"Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine, said Broad Institute founding Director Eric Lander.
The term "$1,000 genome" comes from the Archon X-prize that challenged teams to build machines that could sequence 100 genomes in 30 days or less, with minimal errors and at a cost of $1,000 per genome.
[Illumina]
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Human Genetics: Final Project
This video is on perfect pitch and the genetics of it. Also, this video talks about valproate and how it can help you get perfect pitch.
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Illumina announces a new high-end sequencer made for factory-scale sequencing of human genomes.
Humans only: A new high-throughput sequencing machine from Illumina is optimized to sequence thousands of human genomes in a year.
The $1,000 genome has been a catchphrase of the sequencing industry for years, but despite bold promises from different companies, this benchmark hasnt been met. Now, thanks to a new sequencing machine from Illumina, it may finally be within reach.
At the J.P. Morgan Healthcare Conference on Tuesday, Illumina CEO Jay Flatley announced a new high-end sequencing machine that could accurately sequence whole human genomes at a cost of less than $1,000 each. Competitor Ion Torrent (later bought by Life Technologies) announced in 2012 that it had developed a machine capable of doing so (see Device Brings $1,000 Genome Within Reach), but capability has yet to materialize. Illuminas new machine is scheduled to reach its first customers in March. Faster chemistry and better opticsIlluminas machines read DNA sequences by analyzing patterns of fluorescent nucleotideshave allowed costs to come down.
The $1,000 price tag is often seen as vital to making whole-genome sequencing cost-effective for medical testing and personalized medicine. At this price, it might become reasonable for well-off patients to have their genomes sequenced for potential medical information.
Still, Illuminas new machines will be out of reach for most labs. The ultrahigh-throughput sequencers will be sold in systems of at least 10 machines each, at a starting price of $10 million. According to Flatley, the $1,000 price tag does take into account the cost of the machines, chemicals to do each run of sequencing, sample prep, and more. But these are machines intended to sequence tens of thousands of genomes each year.
Illumina emphasizes that the new machines will speed population-level genome sequencing for large projects aimed at understanding human disease and natural genetic variation. In his presentation, Flatley predicted an explosion of demand for factory-scale sequencing of human genomes. He pointed to a few large-scale projects already in the works, including the U.S. Veterans Affairs project to sequence the genomes of thousands of former soldiers and the U.K.s 100K Genomes project, which will sequence the genomes of National Health Service patients to help guide their care and to study genetic disease (see Why the U.K. Wants a Genomic National Health Service).
Researchers still struggle to understand how changes in DNA sequence cause disease and influence health. Large-scale sequencing projects can help reveal associations between a particular DNA variant and a disease or a healthy outcome. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine, said Eric Lander, founding director of the MIT and Harvard genomics center the Broad Institute, in a released statement.
The Illumina machine was built specifically for human genomes, says Flatley, and it can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor, another high-end Illumina machine. While other machines may sequence human genomes more quickly, they cannot produce the same quality of sequence data at that speed, says Joel Fellis, a senior manager of product marketing at Illumina.
Flatley says the new machine can partially sequence five human genomes in a day. A complete run takes three days, during which time it can produce 16 human genomes at a quality level widely accepted by the sequencing community.
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A colour map shows gradients of myelin in a human brain, red and yellow indicating high myelin and darker colours indicating low myelin. | credits: New York Times Service
Deanna Barch talks fast, as if she doesnt want to waste any time getting to the task at hand, which is substantial. She is one of the researchers here at Washington University working on the first interactive wiring diagram of the living, working human brain.
To build this diagram she and her colleagues are doing brain scans and cognitive, psychological, physical and genetic assessments of 1,200 volunteers. They are more than a third of the way through collecting information. Then comes the processing of data, incorporating it into a three-dimensional, interactive map of the healthy human brain showing structure and function, with detail to 1.5 cubic millimeters, or less than 0.0001 cubic inches.
Barch is explaining the dimensions of the task, and the reasons for undertaking it, as she stands in a small room, where multiple monitors are set in front of a window that looks onto an adjoining room with an MRI machine, in the psychology building. She asks a research assistant to bring up an image.
Its all there, she says, reassuring a reporter who has just emerged from the machine, and whose brain is on display.And so it is, as far as the parts are concerned: cortex, amygdala, hippocampus and all the other regions and subregions, where memories, fear, speech and calculation occur. But this is just a first go-round. It is a static image, in black and white.
There are hours of scans and tests yet to do, though the reporter is doing only a demonstration and not completing the full routine.
Each of the 1,200 subjects whose brain data will form the final database will spend a good 10 hours over two days being scanned and doing other tests. The scientists and technicians will then spend at least another 10 hours analyzing and storing each persons data to build something that neuroscience does not yet have: a baseline database for structure and activity in a healthy brain that can be cross-referenced with personality traits, cognitive skills and genetics. And it will be online, in an interactive map available to all.
Dr. Helen Mayberg, a doctor and researcher at the Emory University School of Medicine, who has used MRI research to guide her development of a treatment for depression with deep brain stimulation, a technique that involves surgery to implant a pacemaker-like device in the brain, is one of the many scientists who could use this sort of database to guide her research.
With it, she said, she can ask, how is this really critical node connected to other parts of the brain, information that will inform future research and surgery.
The database and brain map are a part of the Human Connectome Project, a roughly $40m five-year effort supported by the National Institutes of Health. It consists of two consortiums: a collaboration among Harvard, Massachusetts General Hospital and UCLA to improve MRI technology and the $30m project Barch is part of, involving Washington University, the University of Minnesota and the University of Oxford.
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Jan. 13, 2014 Geneticists from Ohio, California and Japan joined forces in a quest to correct a faulty chromosome through cellular reprogramming. Their study, published online today in Nature, used stem cells to correct a defective "ring chromosome" with a normal chromosome. Such therapy has the promise to correct chromosome abnormalities that give rise to birth defects, mental disabilities and growth limitations.
"In the future, it may be possible to use this approach to take cells from a patient that has a defective chromosome with multiple missing or duplicated genes and rescue those cells by removing the defective chromosome and replacing it with a normal chromosome," said senior author Anthony Wynshaw-Boris, MD, PhD, James H. Jewell MD '34 Professor of Genetics and chair of Case Western Reserve School of Medicine Department of Genetics and Genome Sciences and University Hospitals Case Medical Center.
Wynshaw-Boris led this research while a professor in pediatrics, the Institute for Human Genetics and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UC, San Francisco (UCSF) before joining the faculty at Case Western Reserve in June 2013.
Individuals with ring chromosomes may display a variety of birth defects, but nearly all persons with ring chromosomes at least display short stature due to problems with cell division. A normal chromosome is linear, with its ends protected, but with ring chromosomes, the two ends of the chromosome fuse together, forming a circle. This fusion can be associated with large terminal deletions, a process where portions of the chromosome or DNA sequences are missing. These deletions can result in disabling genetic disorders if the genes in the deletion are necessary for normal cellular functions.
The prospect for effective counter measures has evaded scientists -- until now. The international research team discovered the potential for substituting the malfunctioning ring chromosome with an appropriately functioning one during reprogramming of patient cells into induced pluripotent stem cells (iPSCs). iPSC reprogramming is a technique that was developed by Shinya Yamanaka, MD, PhD, a co-corresponding author on the Nature paper. Yamanaka is a senior investigator at the UCSF-affiliated Gladstone Institutes, a professor of anatomy at UCSF, and the director of the Center for iPS Cell Research and Application (CiRA) at the Institute for Integrated Cell-Material Sciences (iCeMS) in Kyoto University. He won the Nobel Prize in Medicine in 2012 for developing the reprogramming technique.
Marina Bershteyn, PhD, a postdoctoral fellow in the Wynshaw-Boris lab at UCSF, along with Yohei Hayashi, PhD, a postdoctoral fellow in the Yamanaka lab at the Gladstone Institutes, reprogrammed skin cells from three patients with abnormal brain development due to a rare disorder called Miller Dieker Syndrome, which results from large terminal deletions in one arm of chromosome 17. One patient had a ring chromosome 17 with the deletion and the other two patients had large terminal deletions in one of their chromosome 17, but not a ring. Additionally, each of these patients had one normal chromosome 17.
The researchers observed that, after reprogramming, the ring chromosome 17 that had the deletion vanished entirely and was replaced by a duplicated copy of the normal chromosome 17. However, the terminal deletions in the other two patients remained after reprogramming. To make sure this phenomenon was not unique to ring chromosome 17, they reprogrammed cells from two different patients that each had ring chromosomes 13. These reprogrammed cells also lost the ring chromosome, and contained a duplicated copy of the normal chromosome 13.
"It appears that ring chromosomes are lost during rapid and continuous cell divisions during reprogramming," said Yamanaka. "The duplication of the normal chromosome then corrects for that lost chromosome."
"Ring loss and duplication of whole chromosomes occur with a certain frequency in stem cells," explained Bershteyn. "When chromosome duplication compensates for the loss of the corresponding ring chromosome with a deletion, this provides a possible avenue to correct large-scale problems in a chromosome that have no chance of being corrected by any other means."
"It is likely that our findings apply to other ring chromosomes, since the loss of the ring chromosome occurred in cells reprogrammed from three different patients," said Hayashi.
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Study discovers chromosome therapy to correct severe chromosome defect
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Nature Publishing Group Announces OA Journal
Human Genome Variation, the sixth journal collaboration between NPG and JSHG, is a sister title of JSHGs Journal of Human Genetics. Katsushi Tokunaga, a professor at the University of Tokyo, will serve as editor-in-chief. The journal will feature original research articles, summaries, reviews, and data reports. Its audience is human genetics researchers and clinical geneticists.
The journal will provide a forum for scientists working in human genetics, variation and mutation to publish their discoveries, results, analysis and insights, says Dugald McGlashan, publisher of NPGs Asia-Pacific academic journals.
Authors may choose which Creative Commons license to apply to their research articles, which will be OA on publication.
NPG and JSHG will also develop a searchable database sourced from the journals data reports that includes content on genomic variation and variability.
Source: Nature Publishing Group
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PUBLIC RELEASE DATE:
9-Jan-2014
Contact: Aileen Sheehy press.office@sanger.ac.uk 44-012-234-92368 Wellcome Trust Sanger Institute
Contrary to a common belief, researchers have shown that genetic regions associated with increased risk of type 2 diabetes were unlikely to have been beneficial to people at stages through human evolution.
Type 2 diabetes is responsible for more than three million deaths each year and this number is increasing steadily. The harmful genetic variants associated with this common disease have not yet been eliminated by natural selection.
To try to explain why this is, geneticists have previously hypothesised that during times of 'feast or famine' throughout human evolution, people who had advantageous or 'thrifty' genes processed food more efficiently. But in the modern developed world with too much food, these same people would be more susceptible to type 2 diabetes.
"This thrifty gene theory is an attractive hypothesis to explain why natural selection hasn't protected us against these harmful variants," says Dr. Yali Xue, lead author of the study from the Wellcome Trust Sanger Institute. "But we find little or no evidence to corroborate this theory."
The team tested this theory by examining 65 genetic regions that were known to increase type 2 diabetes risk, the most detailed study of its kind.
If these harmful variants were beneficial in the past, the team would expect to see a genetic imprint of this in the DNA around the affected regions. Despite major developments in tests for positive selection and a four-fold increase in the number of genetic variants associated with diabetes to work with, they found no such imprint.
"We found evidence for positive selection in only few of the 65 variants and selection favoured the protective and risk alleles for type 2 diabetes in similar proportions," notes Dr. Qasim Ayub, first author from The Wellcome Trust Sanger Institute, "This is no more than what we would expect to find for a random set of genomic variants."
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PUBLIC RELEASE DATE:
9-Jan-2014
Contact: Melissa A. Wilson Sayres mwilsonsayres@berkeley.edu Public Library of Science
Is the male Y chromosome at risk of being lost? Recent work by Dr Wilson Sayres and colleagues at UC Berkeley, published in PLOS Genetics, demonstrates that the genes on the Y chromosome are important: they have probably been maintained by selection. This implies that despite its dwindling size, the Y chromosome will be sticking around.
The human Y chromosome contains 27 unique genes, compared to thousands on other chromosomes. Some mammals have already lost their Y chromosome (despite still having males, females and normal reproduction); this has led some researchers to speculate that the Y chromosome is superfluous.
As the X and Y chromosomes evolved, male-specific genes became fixed on the Y chromosome. Some of these genes were detrimental to females, so the X and Y chromosomes stopped swapping genes. This meant the Y chromosome was no longer able to correct mistakes efficiently and has thus degraded over time.
There is low genetic diversity in the human Y chromosome, and Dr Wilson Sayres and colleagues were able to precisely measure this by comparing variation on a person's Y chromosome with variation on that person's other 22 chromosomes, the X chromosome and the mitochondrial DNA. The researchers then showed that this low genetic diversity cannot be explained solely by a reduction in the number of males passing on their Y chromosome (successfully fathering male offspring). Instead, the low diversity must also result from natural selection, in this case purifying selection (the selective removal of deleterious alleles).
The movements of human populations around the world are tracked by variations in the Y chromosome. The increased understanding provided by this research will improve estimates of humans' evolutionary history.
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