The African Genome Variation Project shapes medical genetics in Africa

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2014-12-11 02:16Z by Steven

The African Genome Variation Project shapes medical genetics in Africa

Nature: International Weekly Journal of Science
Published online: 2014-12-03
15 pages
DOI: 10.1038/nature13997

Deepti Gurdasani
Wellcome Trust Sanger Institute
Genome Campus
Hinxton, Cambridge, United Kingdom

et. al.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

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Addressing Racial/Ethnic Health Disparities Best Practices for Clinical Care and Medical Education in the 21st Century

Posted in Health/Medicine/Genetics, Live Events, Media Archive, United States on 2013-09-14 18:21Z by Steven

Addressing Racial/Ethnic Health Disparities Best Practices for Clinical Care and Medical Education in the 21st Century

University of Texas, Austin
2013-09-23 through 2013-09-24

One of the primary goals of the US Department of Health and Human Services, the National Institutes of Health, and many public health programs is the reduction of health disparities in the United States. However, significant racial/ethnic disparities persist in the prevalence of disease, access to medical care, quality of care, and health outcomes for the most common causes of death (including cardiovascular and lung disease, infectious disease, cancer, diabetes, and accidents). At this conference, nationally-recognized speakers will discuss the causes of such disparities and describe new approaches in clinical care and medical education that improve care, achieve better health outcomes, and reduce racial/ethnic health disparities. We will also discuss how these best practices can be incorporated into medical training at the new Dell Medical School at The University of Texas and at other medical schools around the country. One key goal of this conference is to help design a cutting-edge curriculum that will better prepare medical students to meet the challenges and opportunities of 21st century medicine.

Conference registration is open to anyone interested in attending this event. See the Continuing Medical Education (CME) tab for information regarding continuing education for the September 23rd portion of the conference.

The second day of the conference (September 24) is open to invited participants only. Discussions and working groups on the second day will focus on developing new pedagogical approaches and innovative learning modules for the pre-clinical curriculum at the Dell Medical School, with the goal of more effectively integrating training on human genomic variation, race/ethnicity, health disparities, and social/environmental determinants of health into the medical curriculum.


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Are medical and nonmedical uses of large-scale genomic markers conflating genetics and ‘race’?

Posted in Articles, Health/Medicine/Genetics, Media Archive, Politics/Public Policy on 2012-03-24 03:04Z by Steven

Are medical and nonmedical uses of large-scale genomic markers conflating genetics and ‘race’?

Nature Genetics
Volume 36, Number 11s (2004)
pages S43-S47
DOI: 10.1038/ng1439

Charles N. Rotimi, Director
Center for Research on Genomics and Global Health

“…with each birth and each death we alter the genetic attributes of human populations and drawing a line around an ephemeral entity like a human race is an exercise in futility and idiocy.” —Pat Shipman, The Evolution of Racism

We now have the tools to describe the pattern of genetic variation across the whole genome and its relationship to the history of human origins and the differential distribution of diseases across populations and geography. We can begin to dissect common complex diseases and devise new therapeutic strategies to reduce adverse drug reactions, a key public health problem ranking between the fourth and sixth leading cause of death in the US. At the social level, the new genomic tools can help us to better appreciate the fluidity of social identity, including ‘race’, ‘ethnicity’ and the more complex notion of ancestry. Challenges surrounding the design of large-scale genotyping projects such as the international HapMap initiative and their future applications illustrate the complexities and ambiguities associated with the use of group labels in genomic research. Depending on how we use this information, the potential exists to describe simultaneously our similarities and differences without reaffirming old prejudices…

…Genetic variation and social identity

To reap the full benefits of the Human Genome Project and spin-offs like the HapMap project, we must be willing to move beyond old and simplistic interpretations of differential frequencies of disease variants by poorly defined social proxies of genetic relatedness like ‘race’. We should allow the genome to teach us the extent of our evolutionary history without abbreviating it with preconceived notions of population boundaries and social identities. We must recognize that social identities are formed in various ways—ancestry, ethnic and tribal background, geopolitical boundaries, language, and other social and behavioral activities. Identities change over time and from one context to another. Their use as markers of ‘relatedness’ in genetic research without appreciation for how they were formed is likely to produce misleading information concerning the distribution of genetic variation.

We all have a common birthplace somewhere in Africa and this common origin is the reason why we share most of our genetic information. Our common history also explains why contemporary African populations have more genetic variation than younger human populations that migrated out of Africa 100,000 years ago to populate other parts of the world, carrying with them a subset of the existing genetic information.

Given this shared history, why do we interpret human genetic variation data as though our differences rise to the level of subspecies? Two facts are relevant: (i) as a result of different evolutionary forces, including natural selection, there are geographical patterns of genetic variations that correspond, for the most part, to continental origin; and (ii) observed patterns of geographical differences in genetic information do not correspond to our notion of social identities, including ‘race’ and ‘ethnicity’. In this regard, no matter what categorical framework is applied, we cannot consistently use genetics to define racial groups without classifying some human populations as exceptions. Our evolutionary history is a continuous process of combining the new with the old, and the end result is a mosaic that is modified with each birth and death. This is why the process of using genetics to define ‘race’ is like slicing soup: “You can cut wherever you want, but the soup stays mixed”.

How can we grasp the population structure of our species? I believe this requires universal awareness that genomic information cannot be used either to confirm or to refine old social, political and economic classifications such as ‘race’. In particular, we should understand the following points: (i) individuals in genetics studies may have membership in more than one biogeographical clusters; (ii) the borders of these clusters are not distinct; and (iii) population clusters are influenced by sampling strategies. For example, the inference drawn from a study with one or two African populations will probably be very different from that drawn from a study with 100 African populations sampled from north, east, west, central and south Africa. As Steve Olson observed, “Not only do all people have the same set of genes, but all groups of people also share the major variants of those genes. Geneticists have never found a genetic marker that is of one type in all the members of one large group and of a different type in all the members of another large group”50. Furthermore, because most alleles are widespread, genetic differences among human populations are the result of gradations in allele frequencies rather than distinctive diagnostic genotypes…

Read the entire perspective here.

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