genetic variation
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 JapanPopulation substructure of Mexican MestizosEuropean population substructureGenetic Map of East AsiaThe genetics of Fenno-ScandinaviaFinns as European outliersUyghurs are hybridsGenetic structure of Eastern European populationsGenetic map of Europe; genes vary as a function of distance More genetic maps of EuropeHuman population structure…
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 | June 5, 2009In Natural selection of a human gene: FUT2 I referred to a paper, Signals of recent positive selection in a worldwide sample of human populations (see my earlier review). Now the same group has a follow up paper which takes a slightly different tack, The Role of Geography in Human Adaptation:
Since the beginning of the study of evolution, people have been fascinated by recent human evolution and adaptation. Despite great progress in our understanding of human history, we still know relatively little about the selection pressures and historical factors that have been important over the past…
razib | June 3, 2009A few months ago I reviewed a paper which examined the various complexities of interpreting signals of natural selection from recently developed genomic tests in response to the avalanche of human sequence data. In the paper, Signals of recent positive selection in a worldwide sample of human populations, the authors state:
We find that putatively selected haplotypes tend to be shared among geographically close populations. In principle, this could be due to issues of statistical power: broad geographical groupings share a demographic history and thus have similar power profiles. However,…
razib | June 2, 2009Two interesting papers, one which relates KITLG and cancer, and another which connects ABCC11 and cancer. These are familiar genes. KITLG has been implicated in depigmentation, both of skin and hair. ABCC11 in earwax form and body odor. If you knock around a gene there is a high probability that you'll perturb multiple traits. Somethings the relationship between variation on a gene and pathology is more straightforward. Some of the genes responsible for normal human variation in pigmentation were originally of interest due to their implication in albinism, which is a disease with some non-…
razib | May 22, 2009It is well known that different ethnic groups vary when it comes to diseases such as Type II Diabetes. Or, more specifically they vary in terms of risk, all things equal (if you use an online Type II Diabetes calculator you'll see immediately as they sometimes have a parameter for ethnicity). American blacks for example are heavier than American whites. This seems to be true even when you control for socioeconomic status (though as Oprah once said, "You don't need to do a 'study' to figure that out"). There has been research on genetic loci correlating to obesity in European populations…
razib | May 19, 2009400-500 years ago in the midst of the Great Dying somewhere the indigenous inhabitants of the New World suffered mortality rates on the order of 90-95%. This was almost certainly due to the facts of evolutionary history; the indigenous peoples had little defense against Eurasian pathogens. A result has been the reality that most of the New World is inhabited by European, African or mixed populations. But there are exceptions. In Mesoamerica there is still an indigenous dominated region from southern Mexico into the highlands of Guatemala. More substantially the highlands of the Andes, and…
razib | May 15, 2009Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans:
Studying genomic patterns of human population structure provides important insights into human evolutionary history and the relationship among populations, and it has significant practical implications for disease-gene mapping. Here we describe a principal component (PC)-based approach to studying intracontinental population structure in humans, identify the underlying markers mediating the observed patterns of fine-scale population structure, and infer the predominating evolutionary forces…
razib | May 14, 2009One of the peculiarities of American discussion about race is that skin color is assumed to be synonymous with racial distinctions. That is, skin color is not just a trait, but it is the trait which defines between population differences. There's a reason for this, the skin is the largest organ and it is very salient. Populations with little phylogenetic relationship to each other, from India to the Pacific to Southeast Asia have been referred to as "black" by lighter-skinned populations. No population is referred to by their neighbors as those "straight hairs," to my knowledge. But another…
razib | May 12, 2009Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico:
Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population.…
razib | May 10, 2009A few months ago I relayed preliminary data which suggested that Estonians are not like Finns. Now a new paper, Genetic Structure of Europeans: A View from the North-East:
Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis…
razib | May 5, 2009In the comments below on the post on human population structure there was some request for a bigger global perspective. Below the fold I've placed a table with FST values which compare each population to the other. This an older population genetic statistic derived from the work of Sewall Wright, but you are almost certainly familiar with the talking point that "85% of variation is within races, and only 15% between." That is an FST insight. The higher the FST the greater the proportion of genetic variation which can be attributed to between population differences, so it serves as a rough…
razib | May 3, 2009I still remember when L. L. Cavalli-Sforza's The History and Geography of Human Genes was a candle in the dark, illuminating human history with slivers of genetic data laboriously gathered and analyzed over decades. We've come a long way. Dienekes points me to a new paper, Fine-scaled human genetic structure revealed by SNP microarrays:
We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have…
razib | April 30, 2009I've been fine tuning Ubuntu all day with goodies and getting drivers to work right, so I missed this paper on African genetics:
Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, 4 African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared…
razib | April 29, 2009Haplotypic Background of a Private Allele at High Frequency in the Americas:
Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these…
razib | April 28, 2009Dan MacArthur has a post, Genetics of complex traits in Europeans and East Asians: similarities and differences:
With those goals in mind, you can expect to see many more GWAS of non-European populations over the next couple of years, and some explicit comparisons of the differing genetic architecture of complex traits between populations. Exciting times for those of us interested in the genetic and evolutionary basis of between-population differences...
This reminds me of A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction:…
razib | April 27, 2009On the order of ~1 million years ago humans seem to have evolved dark skin. While light skin evolved several times, it looks like dark skin exhibits an "consensus sequence," so that all dark skinned peoples seem to have the same genetic architecture.
This chart (from Signatures of Positive Selection in Genes Associated with Human Skin Pigmentation as Revealed from Analyses of Single Nucleotide Polymorphisms) shows that when it comes to skin color related genes the populations of Bougainville Island (off the eastern coast of Papua New Guinea) and Sub-Saharan Africa are far closer than you…
razib | April 26, 2009Thankfully. Familial Resemblance of Borderline Personality Disorder Features: Genetic or Cultural Transmission?:
Borderline personality disorder is a severe personality disorder for which genetic research has been limited to family studies and classical twin studies. These studies indicate that genetic effects explain 35 to 45% of the variance in borderline personality disorder and borderline personality features. However, effects of non-additive (dominance) genetic factors, non-random mating and cultural transmission have generally not been explored. In the present study an extended twin-…
razib | April 23, 2009There are some papers out on the genome of the domestic cow out right now. ScienceNews has an overview:
Two competing research teams have cataloged the "essence of bovinity" found in the DNA of cattle, but not without disagreement on some essential points.
Reporting online April 23 in Science and April 24 in Genome Biology, the two groups compiled drafts of the bovine genome, identifying genes important for fighting disease, digesting food and producing milk.
I don't see the Genome Biology paper on the site yet, but there are two in Science. First, The Genome Sequence of Taurine Cattle: A…
razib | April 20, 2009In response to the NEJM issue on personal genomics and the CDCV hypothesis, p-ter offers a proposal:
Let's follow Goldstein's back-of-the-envelope calculations: assume there are ~100K polymorphisms (assuming Goldstein isn't making the mistake I attribute to him, this includes polymorphisms both common and rare) that contribute to human height, that we've found the ones that account for the largest fractions of the variance, and that these fractions of variance follow an exponential distribution.
Now, assume you have assembled a cohort of 5000 individuals and done a genome-wide association…