population genomics
razib | March 4, 2010A new paper in PLoS, Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples:
Many association studies have been published looking for genetic variants contributing to a variety of human traits such as obesity, diabetes, and height. Because the frequency of genetic variants can differ across populations, it is important to have estimates of genetic ancestry in the individuals being studied. In this study, we were able to measure genetic ancestry in populations of mixed ancestry by genotyping pooled, rather than individual, DNA samples…
razib | December 9, 2009According to search engine traffic one of the most popular posts on this weblog has to do with the genetic background of Ashkenazi Jews. That is, those Jews whose ancestors derive from Central & Eastern Europe, and the overwhelming number of Jews in the United States. The genetic origins of this group are fraught with politics naturally. With the rise of biological science the characteristics of Jews were used as a way to differentiate them as a nation apart in more than a cultural and religious sense. After World War II other researchers attempted to show that Jews were not genetically…
razib | December 5, 2009About six months ago I had a post up on the Cape Coloureds of South Africa. As a reminder, the Cape Coloureds are a mixed-race population who are the plural majority in the southwestern Cape region of South Africa. Like the white Boers they are a mostly Afrikaans speaking population who are adherents of Reformed Christianity. After the collapse of white racial supremacy many white Afrikaners have argued that it is natural and logical to form a cultural alliance with the Cape Coloureds because of the affinity of language and faith (Afrikaans speaking Coloureds outnumber Afrikaans speaking…
razib | November 25, 2009The state of China has 1/5 of humanity within its borders, so it's genetic structure is of interest. It is obviously important for medical reasons to clarify issues of population structure so that disease susceptibility among the Han is well characterized, in particular with the heightened medical needs of an aging population in the coming generation. And of course, there are the nationalistic concerns. About 20 years ago L. L. Cavalli-Sforza reported that his South Chinese samples were genetically closer to Southeast Asians than North Chinese in The History and Geography of Human Genes.…
razib | October 13, 2009I'm talking about coeliac disease:
Coeliac disease is caused by a reaction to gliadin, a gluten protein found in wheat (and similar proteins of the tribe Triticeae, which includes other cultivars such as barley and rye). Upon exposure to gliadin, the enzyme tissue transglutaminase modifies the protein, and the immune system cross-reacts with the small-bowel tissue, causing an inflammatory reaction. That leads to a truncating of the villi lining the small intestine (called villous atrophy). This interferes with the absorption of nutrients, because the intestinal villi are responsible for…
razib | August 29, 2009Dienekes points me to a new paper, European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups. You've seen this song & dance before:
Population substructure in Japan
Population substructure of Mexican Mestizos
European population substructure
Genetic Map of East Asia
The genetics of Fenno-Scandinavia
Finns as European outliers
Uyghurs are hybrids
Genetic structure of Eastern European populations
Genetic map of Europe; genes vary as a function of distance
More genetic maps of Europe
Human population…
razib | July 30, 2009An ancestry informative marker set for determining continental origin: validation
and extension using human genome diversity panels:
Results
In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East…
razib | July 7, 2009Blogger Thomas Mailund is an author on a new paper, Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach:
With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the number of generations between speciation events. We use a hidden Markov model parametrized according to coalescent theory in order to infer the genealogy along a four-species genome alignment of closely related species…
dgmacarthur | April 30, 2009This is a profoundly impressive paper - a study of the patterns of genetic variation in 2,400 individuals from 113 African populations, by far the most comprehensive analysis of African genetic diversity ever performed.
I had heard that Sarah Tishkoff's group had assembled a large
collection of African DNA samples, a daunting achievement in itself
given the logistical, ethical and social challenges involved (New Scientist
notes that "the researchers often had to use their vehicle batteries to
power the
centrifuges used to separate out white blood cells from their samples")
- but the breadth…
dgmacarthur | March 13, 2009Nalls, M., Simon-Sanchez, J., Gibbs, J., Paisan-Ruiz, C., Bras, J., Tanaka, T., Matarin, M., Scholz, S., Weitz, C., Harris, T., Ferrucci, L., Hardy, J., & Singleton, A. (2009). Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics PLoS Genetics, 5 (3) DOI: 10.1371/journal.pgen.1000415
A new study indicates that increases in mobility, urbanisation, and cross-population mating over the last century have substantially reduced inbreeding, and left a distinctive trace in the genome of modern Americans.
The study, published in the latest…