Call for Abstracts – Human Genome Meeting 2010
The deadline is soon approaching for abstract submissions to the Human Genome Organisation Human Genome Meeting 2010 in Montepellier, France. The meeting will be held from 18 to 21 May 2010 and abstracts should be submitted by 31 January 2010.
ABSTRACT SUBMISSION GUIDELINES
Each registrant may submit one abstract of his or her work for presentation during the meeting. It is expected that the abstract will include original data not previously published in a peer-review journal or the proceedings of a national meeting. Only those abstracts that have been reviewed and selected by the Scientific Program Committee may be presented. Abstract submissions will only be accepted electronically through the abstract submission service; paper abstracts will not be accepted. ALL abstracts must be in ENGLISH. The abstract submission deadline is 31 January 2010.
Please take note that all abstracts will be reviewed by our international panel of reviewers. They will decide on the final acceptance for either oral or poster presentation for each abstract. We accept up to 8 oral presentations for each workshop.
Click here to submit an abstract online.
Scientific consortium maps the range of genetic diversity in Asia, and traces the genetic origins of Asian populations
by Dr. Vikrant Kumar, Genome Institute of Singapore
As an anthropologist, I always wanted to know if Asians, known for their extensive linguistic and ethnic diversity also have a substantial level of genetic variation. In other words, do they have a common or multiple origins? Or whether the ancestors of Negritos from Philippines, Malaysia and Indonesia differ from those of their neighboring Asians? Or what binds us more: language or geography? The recent paper published in Science by the HUGO Pan-Asian SNP Consortium – Mapping Human Genetic Diversity in Asia quintessentially answers these fundamental questions which have been floating around for years.
To the best of my understanding, so far, this is the only paper where 73 populations scattered across 10 Asian countries are studied together through a massive collaborative effort of scientists from 40 institutes mostly from Asia (~2000 samples covering almost entire spectrum of linguistic and ethnic diversity were genotyped for ~50000 single nucleotide polymorphic markers). Some of the key findings of this paper are:
· East and Southeast Asians share a common origin.
· East Asians have mainly originated from South East Asian populations with minor contributions from Central-South Asian groups.
· A common ancestor of the Negrito and non-Negrito populations of Asia entered into the continent. This supports the hypothesis of one wave of migration into Asia as opposed to two waves of migrations from Africa.
· The Taiwan aborigines are derived from Austronesian populations. This stands in contrast to the suggestion that this island served as the ancestral “homeland” for Austronesian speaking populations throughout the Indo-Pacific.
· Genetic ancestry is highly correlated with linguistic affiliations as well as geography.
The paper stands out in its attempt to understand the peopling of Asia and their genetic relationships and in the process it not only presents a fantastic genotype database but also provides vital clues to scientists of diverse fields –from linguistics to archeology to human genetics. For example, it may be an interesting proposition for a human geneticist to examine if East and Southeast Asians share, more than expected, risk alleles associated with diseases. Likewise, it may be time for the linguists to re-look at the “birthplace” of the Austronesian linguistic family. I hope the consortium continues with their amazing endeavor and include a lot more number of important and isolated populations from whole of Asia and move beyond the analysis of Single Nucleotide Polymorphism to other kinds such as structural variations.
Please see below the fold for the official press release.
How Genome-Wide Variation within the Han Chinese Population Affects Study Design
By Brian Z. Ring, PhD, Director of Technology of YiGene Inc., and Principal Investigator of Applied Genomics
A scan of a rack of magazines these days will likely find at least one article discussing the emergence of China onto the world stage, its headline usually following the standard formula of “The (Sleeping/Red) (Dragon/Giant) (Awakes/Rises)”. Yet despite China’s growing importance to the world news, the genetics of the Han people, the dominant ethnic group in China and the largest ethnic group in the world, has been relatively poorly studied. The HAPMAP project, which characterized 45 Han individuals, not surprisingly revealed that this group has distinct variation from other ethnic groups, yet unveiled little about variation within the Han population. Other studies have been of a small scale or followed only maternal and paternal lineages through Y chromosome and mitochondrial studies. These have suggested an interesting variation within the Han population, primarily on a north-south axis, but not much more.
Fortunately two studies recently published in the American Journal of Human Genetics are shedding more light on the genome wide variation within the Han population. The studies, one led by Jin Li of Fudan University, the second by Jianjun Liu of the Genome Institute of Singapore, each independently studied thousands of autosomal snps in samples collected from several regions in China (the studies utilized 160K snps, 1700 individuals, and 350K snps, 6000 individuals, respectively). The studies by and large reveal a similar story: both show that while the Han Chinese population is comparatively uniform, significant variation exists, and the variation largely seems to correspond to the known north-south settlement of China by this ethnic group. This pattern, as measured by the Genome Institute of Singapore’s study, accounts for roughly 0.4% of the genetic variance within this population. Though small, both studies confirm that this variation could affect genome wide association studies if a geographically diverse population is used without proper stratification. This information will help better guide these surveys and help avoid false positive candidates.
Another important result from these studies is the flip side of the observed genetic variance; though of statistical significance, it is nonetheless relatively small. This is encouraging to a variety of efforts underway in China which presume a relatively flat genetic landscape. Drug development has been carried out, for the most part, in Europe and the United States, and thus the clinical populations have been comprised largely of those of European heritage. This leads to concern on the applicability of the direct translation of these results to other populations. To address this bias, as well as to entail lower costs in the increasingly cost conscious pharmaceutical market, an increasing number of clinical trials are being carried out within China. If there existed strong regional differences in the population’s genetic makeup, these studies would have to be carefully constructed to either properly stratify their cohorts or limit them to a genetically uniform region, especially in trials where there is a potentially significant genetic component to the response to the candidate compound.
While these two studies do not reveal that the intra-ethnic variation within the Han population can be ignored in such studies, it appears it’s likely of a small enough scale to not adversely affect current clinical trial strategies. Similarly, efforts to employ known associations between drug response and genetic variation in crafting public health care services are not disrupted by this new information. For example, cytochrome P450 2D6 is responsible for the metabolism of a wide variety of commonly prescribed drugs. However, mutant forms of this enzyme, though rare in the West, have been revealed by the HAPMAP project to affect roughly a third of Han Chinese. This is encouraging efforts to determine if genotyping prior to prescribing affected drugs could lead to improved health care delivery and lower costs. If there was strong variation within the Han population then strategies created with the HAPMAP data as its basis would not be applicable. Instead, these recent results will serve to improve ongoing studies and ensure meaningful results. Additional studies of genome wide variation within the Han population, encompassing more regions of China, will further fill in the picture and allow an even more refined approach to future translational studies.
Dr. Brian Ring received his PhD in Molecular Biology from Cornell University and currently lives and works in Beijing, China.
Yigene is a Beijing based personal genomics service company. Yigene is working with the Chinese CDC and other public institutions to determine the best methods and practices of translating genetic discoveries to the Chinese public health market.
Image: Wellcome Trust, L0004700, “The doctor is feeling the pulse of a woman patient. Her wrist is supported on a small red bolster. The doctor touches the pulse only with his finger-tips, without looking at the woman,” Watercolour By: Zhao Pei Qun
The Looming Problem of Word Limits and Scientific Publication
…or Length Matters
by HUGO President Prof. Edison T Liu
I have been confronted both as an author and a reviewer with the difficulty of explaining a complex story within a 1500 or even a 5000 word limit for a manuscript. The basis of the word limits in many journals have been historical , and often was because of print costs. But as science advances, this publication boundary has not moved with the times. What exactly have been the trends in the biological sciences?
Genomics has been the vanguard of these trends. The datasets are massive, the analyses are complex, and the validation is also extensive. When a high throughput screen for, let’s say, siRNA knock downs, or for synthetic lethality in a genome-wide scale is presented, the appropriate description for just the initial set up and analysis may run into the maximum 5000 words. The biological interrogations and functional validations can rationally require many more words to explain.
In order to compress the presentation, authors have rendered figures with many subpanels and place critical data in supplementary sections that can be many times the size of the original manuscript. In one systems biology paper (Pujana MA, et al. Nat Genet. 39(11):1338-49, 2007), one figure (figure 4) had 4 parts (a-d) but presented 9 panels of high analytical complexity. Our paper recently published in Nature (Fullwood MJ, et al. Nature. 462(7269):58-64, 2009), had a supplement with ~10,000 words for a manuscript that contained less than 5,000 words. The HUGO Pan-Asian SNP Consortium will publish in Science (December 2009) a scientific story in 4000 words which will require a supplementary section of 14,000 words.
It can be said that the supplemental section should be the place to explain the details not necessary for the core story. However, this is becoming less true, especially in genomics, where the massive nature of the data and the analysis requires compartmented analysis each of which are critical to the main story. Operationally, this is leading to a troubling trend. The supplemental data is given marginal analysis by both readers and reviewers. In many ways, this is like presenting each classical novel as a CliffsNotes summary with a supplement that contains the original chapters. One possible outcome is that a distracted public and even expert review panels will miss serious problems in the analysis that is “tucked” away in the supplemental section (as implied in Coombes KR, Wang J & Baggerly KA, Nature Medicine 13, 1276 – 1277, 2007).
Indeed, our schedules are busy and our time is precious, but perhaps we need a publication format that will preserve the needed scholarship and yet respect the limited attention span of busy scientists. For example, why not have an extended abstract of ~400-500 words that tells the core story (even include a figure or two), but allow for the detailed work to be presented in its entirety as a coherent narrative. Given the online nature of journals, this surely cannot be more expensive than the current main-text-with-online-supplement format.
Regardless of whether you are pro or con to this opinion piece, I would encourage the readers to comment and to engage their communities in such a discussion about change in scientific publishing.
The Impact of Next Generation Sequencing on Society, Policy and Law
by Dr. Benjamin Capps, Centre for Biomedical Ethics, National University of Singapore.
Listening to the discussions at the 2009 HUGO Symposium on Genomics and Ethics, Law and Society, held in the City of Geneva, I was drawn to the writings of Jean-Jacques Rousseau, born in Geneva in 1712. In particular, one paragraph of the Discourse on Inequality (1754) came to mind:
The first man who, having fenced in a piece of land, said "This is mine," and found people naive enough to believe him, that man was the true founder of civil society. From how many crimes, wars, and murders, from how many horrors and misfortunes might not any one have saved mankind, by pulling up the stakes, or filling up the ditch, and crying to his fellows: ‘Beware of listening to this impostor; you are undone if you once forget that the fruits of the earth belong to us all, and the earth itself to nobody.‘
Rousseau could not possibly have known that his ideas would have resonance in the debates on genetic ownership, privacy, and exploitation. As biotech companies trawl isolated regions of the world for their biodiversity, sheltered, until now, by situation and circumstance from the melting pot of migration, international organisations have tried to cultivate a sense of awe in a collective global cultural heritage, while simultaneously asserting on behalf of these communities their rights to be compensated. But now, every individual has an opportunity to demark their uniqueness – to own their genetic sequence – as part of what Linda Avey calls ‘democratising DNA’.
Personalised medicine promises to be a defining advance in allowing drugs to be prescribed effectively and safely. But there were also some words of caution at the Symposium. It should not be forgotten that uncovering our uniqueness brings with it certain risks; most notably ‘bioinformational creep’, a process whereby uncensored access to an individual’s genetic sequence is routinely justified in ‘the public interests’. Moreover, genetic polymorphisms do not always result in expected phenotypes, as was demonstrated by the discovery that James Watson’s genome revealed that he had two normally debilitating, but clearly unexpressed, monogenetic disorders.
Some participants at the HUGO Symposium raised these issues as important concerns for sequencing standards and premature use of sequence data to make future health projections – particularly when made available to the public through commercial enterprises. One may also question where the responsibility for the access and use of this information lies – do these companies have any enduring role to their clients’ wellbeing, particularly subsequent to the delivery of the test results; and who are they bound to divulge, or withhold, this information from? Is it merely paternalistic to raise these concerns, or is it a clear warning that vital individual interests are at risk? Answering these issues will be a task taken forward by the HUGO Ethics Committee over the coming year.
Genetic Diversity in Han Chinese
by HUGO Matters Editor Hsien-Hsien Lei, PhD
When I was in high school, a classmate of mine commented on the San Francisco Miss Chinatown competition.
“How can they tell the difference between all the girls?”
Perhaps I should send her a copy of two recent papers published in the American Journal of Human Genetics (AJHG) that found significant genetic and genomic diversity within the Han Chinese population.
The first paper by Jieming Chen et al. from the Genome Institute of Singapore sampled Chinese from ten provinces in addition to Beijing, Shanghai, and Singapore. They examined over 350,000 genome-wide autosomal SNPs and developed a genetic map of the Han Chinese. They found that:
- Within Guangdong province, genetic differentiation correlated with language.
- Genetic patterns correlated with north to south geographic orientations but not east to west. This finding is consistent with historical migration patterns.
- Metropolitan cities in China have experienced strong modern migration and are thus more difficult to tease apart genetically.
- Han Chinese individuals in Singapore are closest genetically with individuals from southern China.
- Spurious associations in genome-wide association studies (GWAS) can occur if population stratification in Chinese populations is not addressed. Geographic matching, however, can serve as a proxy for genetic matching.
"By investigating the genome-wide DNA variation, we can determine whether an anonymous person is a Chinese, what the ancestral origin of this person in China may be, and sometimes which dialect group of the Han Chinese this person may belong to," senior author Liu Jianjun, leader of the GIS Human Genetics Group, said in a statement. "More importantly, our study provides information for a better design of genetic studies in the search for genes that confer susceptibility to various diseases."
A second smaller study also published in in AJHG by Xu Shuhua et al., confirmed the observations of the paper above. The researchers concluded that genetic differentiation between northern, central, and southern Han can lead to false-positive results in association studies.
NB: On a related note, these maps of China are a riot. They were created by people around China and depict their views of the various provinces.
Linda Avey at the HUGO Symposium on Genomics and Ethics, Law and Society
Many thanks to Linda Avey, co-founder and former co-president of 23andMe, for speaking at HUGO GELS 2009. The founder and president of Brainstorm Research Foundation also Twittered live from the event and contributed some valuable highlights. Last week, Linda started a new blog—The Life and Times of Lilly Mendel—in which her inaugural post talked about her experience at HUGO GELS 2009.
…back to Geneva. The usual arrows were flying at the HUGO conference…a few, very vocal scientists seem to be quite threatened by this notion of democratizing DNA. They characterize it as "trivializing", which simply doesn’t make sense. I just don’t agree that providing people with their genetic data, which would be virtually impossible for them to derive on their own, demeans or trivializes it. Rather, I think the research community has taken the notion of "human subject protection" way too far, to the point of unchecked paternalism (for more on this, check out Anne’s post here, http://j.mp/RHIrX). And I do think the lay public is capable of understanding that what is currently known about their DNA is mostly a work-in-progress.
She also mentions HUGO again in a discussion of the need for a database that makes it possible to cross-reference genetic associations and disease risk.
…the job of curating, evaluating and scoring genetic associations would be taken on by representatives of the scientific community.
Who would take on this fairly gargantuan role? During my visit to the HUGO GELS meeting last week, I threw out the suggestion that HUGO could be one possibility. They’re an international body–which, in my humble opinion, is important–and they seem to be looking for a new raison d’etre. The problem, as always, comes down primarily to funding. Where would the monies come from to host such a service? And who would take the leadership role within the organization?
Thanks again, Linda, for giving us so much to think about! As always, Linda has incredible ideas and her blog is definitely one to follow.
Report from HUGO at the 59th Annual Meeting of the American Society of Human Genetics
This is a guest post from Conover Talbot, Jr. of The Johns Hopkins University School of Medicine.
The warm beaches of Waikiki provided a pleasant contrast to last year’s chilly streets of Philadelphia, but on the Hawaii Convention Center floor, the American Society for Human Genetics (ASHG) 59th annual meeting was all business.
HUGO joined forces with the HUGO Gene Nomenclature Committee and met with over 200 interested registrants who were keen to know more about HUGO and its new initiatives, its mission, and pending initiatives. Many sought information on the coming HUGO HGM2010 annual meeting in Montpellier but topics covered a wide range from the Organisation’s mission to specific scientific issues. We were also able to answer numerous specific questions about the naming of human genes and gene variants.
Some, who remembered HUGO largely from its role in the Human Genome Project and concern for ethics, had heard of HUGO’s new projects and sought information on the focus of the new official society journal, The HUGO Journal , and were keen to submit articles online.
ASHG’s lively booth traffic reflected HUGO’s increased visibility and pointed towards an exciting Human Genome meeting next May in France, where we look forward to welcoming many old and new colleagues.
Twitter Highlights from Day 2 of HUGO GELS 2009 Symposium
Day 2 of the 2009 HUGO Symposium on Genomics and Ethics, Law and Society was just as interesting as the first. Here are some highlights from our Twitter stream @humangenomeorg.
@liuedison: #GELS09. Stylianos Antonarakis says Francis Galton showed mid parental height accounts for 40% of predicting height.
@liuedison: #GELS09. GWAS showed 54 genomic variants account 4 only 5% of ht. Shows limits of molecular genetics in phenotype prediction
@liuedison: #GELS09.Function of information is important in considering privacy.Functional creep describes secondary uses of information.
@liuedison: #GELS09.There is also significance creep. what is marginally important gets expanded in perception
@liuedison: #GELS09.Public has mixed feelings re genetic research.86% trust info from doc but 75% distrust insurer, 83% distrust employer
@liuedison: #GELS09.Marjolein Kriek speaks.jokes that she wanted to be sequenced after Watson since her name is Kriek
@liuedison: #GELS09.what did Kriek family say? all family was fine with it. – Twitterati: What do you think your family would say?
@liuedison: #GELS09.HUGO Journal announcing laumch of Research Vignettes. http://bit.ly/jxd0y
@liuedison: #GELS09.Research Vignettes requirements access to raw data so that the analysis can be replicated
@liuedison: Research Vignettes are short reports 500-1000 words. single observation
@liuedison: Research Vignettes:for GWAS no validation set required.
@liuedison: HUGO Journal Research Vignettes:rely on post-publication for “review”
@liuedison: HUGO Journal Research Vignettes:encourage others to validate data
HUGO President Reports from the HUGO Symposium on Genomics and Ethics, Law and Society 2009
This post was contributed by HUGO President Prof. Edison T. Liu.
The opening talks at the HUGO conference on Genomics and Ethics, Law, and Society in Geneva, Switzerland led to lively discussions from the floor of the stately International Conference Center.
In the morning session, the focus was on the technologies. Dr. Ala Awan from the WHO reminded the audience of the new focus on health outcomes in governments worldwide including those who previously considered to be third world. This is in recognition of the increase in the burden of chronic illnesses as nations advance economically.
Both Edison Liu (Singapore) and Mark McCarthy (Oxford) described the new sequencing strategies and the seven orders of magnitude increase in throughput and decrease in cost of sequencing in the last 15-20 years. But the excitement was the outcome of sequencing many genomes or partial genomes of hundreds to thousands of individuals. Over three million SNPs are found in individuals, many that are new resulting in up to 20,000 amino acid substitutions. When complete genome sequences were compared, only ~700,000 are shared amongst 5 individual genomes, whilst the remaining are either unique to the individual or shared with only one or two other. 300,000 heterozygous and >500,000 homozygous indels (as compared to the reference genome). There is plenty of genomic variation in human beings.
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