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.
Twitter Highlights from Day 1 of HUGO GELS 2009 Symposium
Day 1 of the 2009 HUGO Symposium on Genomics and Ethics, Law and Society has concluded. Aside from the excellent presentations and engaging discussions that followed, we also had an active Twitter feed @humangenomeorg with live tweets from HUGO President Prof. Edison Liu and 23andMe co-founder, healthcare activist Linda Avey. Here are some Twitter highlights from day 1. For more, follow the hashtag #GELS09.
@mrgunn: @kshameer Me too. GELS is fascinating – can genetic data be anonymized & if not how do we share data?
@lindaavey Technological answers to access/privacy issues. Barth Knoppers trusts the public. Amen!
@liuedison: #GELS09. Knoppers – need to regulate malicious data use rather than to regulate databases
@lindaavey: Barth Knoppers Answers to data access/privacy issues best not to come from the political realm
@liuedison: #GELS09.Genetic protection laws except in the absence of universal health care are not a good way to go.
@lindaavey: Privacy barriers coming down as extension of personal autonomy, zone of freedom individually determined #GELS09 Bartha Knoppers
@liuedison: #GELS09.Linda Avey concerned about data standards in DTC reports.Suggests org like HUGO may want to help dev standards
@liuedison: #GELS09. DTC genetics is challenged as too simplistic.Response: companies work to be clear and public wants this information
@liuedison: #GELS09. Open consent is challenged – because it sounds like it is revealing all possibilities.
@liuedison: #GELS09.Lunshof – Is there more privacy through sharing?
@liuedison #GELS09. Privacy is based on context-relative norms.is the information in a medical context or friendship context?
@liuedison: #GELS09. Privacy affected by revelations of 3rd persons. writing in blogs about friends. Genetic info is also about relatives
@liuedison: #GELS09. Challenges to privacy #3: New exhibitionism – physical (tattoos), blogs, twitter,reality TV
@liuedison: #GELS09. Challenges to privacy #2: Side effects of new technologies – mobile phones, GPS, forensic & genetic databases…
@liuedison: #GELS09 Ruth Chadwick tells that there are three challenges to privacy: 1) intentional from corporations and governments….
@liuedison: #GELS09. Dev countries have special challenges that need their own tech solutions-Avoid blind adoption of 1st world protocols
HUGO President Twittering from Geneva
For the first time, HUGO President Edison T. Liu is live twittering from the HUGO Symposium on Genomics and Ethics, Law and Society, which commenced in Geneva, Switzerland this morning. Follow his tweets – @liuedison at http://twitter.com/liuedison!
Do you know of any other presidents of international scientific organisations who’ve live blogged or twittered a meeting, symposium, or conference?
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