ALFRED: An allele frequency database for anthropology

Osier, Michael V.; Cheung, Kei‐Hoi; Kidd, Judith R.; Pakstis, Andrew J.; Miller, Perry L.; Kídd, Kenneth K.

doi:10.1002/ajpa.10094

Cited by 54 publications

(31 citation statements)

References 26 publications

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“…Allele frequencies and numbers of individuals typed for all of the sites in all of the populations can be found in ALFRED 36 under the site UIDs ( Table 1). All of the markers are in Hardy -Weinberg equilibrium; 88% of the 1008 heterozygosities (63 markers in 16 populations) are greater than 9.5%.…”

Section: Resultsmentioning

confidence: 99%

“…Descriptions of the markers, their allele frequencies, and the typing method used are present in ALFRED (http:// alfred.med.yale.edu). 36 Markers were typed variously by RFLP, fluorescence polarization, 37 and dynamic allelespecific hybridization (DASH), 38 and TaqMan. 39 Several markers at RET-D10S94 and DRD2-NCAM1 were identified by resequencing using an ethnically diverse panel of 10 individuals (three Africans (Biaka, Lisongo, Yoruba), three Europeans (Adygei, Russian, Dane), two Chinese, and two Native Americans (Pima, Cheyenne)); a potential polymorphism was pursued if a variant occurred at least twice in the 20 chromosomes.…”

Section: Markers Typedmentioning

confidence: 99%

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Linkage disequilibrium patterns vary substantially among populations

et al. 2005

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A major initiative to create a global human haplotype map has recently been launched as a tool to improve the efficiency of disease gene mapping. The 'HapMap' project will study common variants in depth in four (and to a lesser degree in up to 12) populations to catalogue haplotypes that are expected to be common to all populations. A hope of the 'HapMap' project is that much of the genome occurs in regions of limited diversity such that only a few of the SNPs in each region will capture the diversity and be relevant around the world. In order to explore the implications of studying only a limited number of populations, we have analyzed linkage disequilibrium (LD) patterns of three 175 -320 kb genomic regions in 16 diverse populations with an emphasis on African and European populations. Analyses of these three genomic regions provide empiric demonstration of marked differences in frequencies of the same few haplotypes, resulting in differences in the amount of LD and very different sets of haplotype frequencies. These results highlight the distinction between the statistical concept of LD and the biological reality of haplotypes and their frequencies. The significant quantitative and qualitative variation in LD among populations, even for populations within a geographic region, emphasizes the importance of studying diverse populations in the HapMap project to assure broad applicability of the results.

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Section: Resultsmentioning

confidence: 99%

Section: Markers Typedmentioning

confidence: 99%

Linkage disequilibrium patterns vary substantially among populations

et al. 2005

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“…The NAN Melanesian (NonAustronesian Melanesian) population is very poorly specified in refs. 36 and 37, but it most probably represents (66,67) (70), and for 50 alleles no such information could be retrieved. Moreover, 124 pairs were duplicated between the two databases, and 9 were deleted because they introduced systematic missing data in sub-Saharan Africa.…”

Section: Methodsmentioning

confidence: 99%

Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin

Dediu

Ladd

2007

Proc. Natl. Acad. Sci. U.S.A.

246

242

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The correlations between interpopulation genetic and linguistic diversities are mostly noncausal (spurious), being due to historical processes and geographical factors that shape them in similar ways. Studies of such correlations usually consider allele frequencies and linguistic groupings (dialects, languages, linguistic families or phyla), sometimes controlling for geographic, topographic, or ecological factors. Here, we consider the relation between allele frequencies and linguistic typological features. Specifically, we focus on the derived haplogroups of the brain growth and development-related genes ASPM and Microcephalin, which show signs of natural selection and a marked geographic structure, and on linguistic tone, the use of voice pitch to convey lexical or grammatical distinctions. We hypothesize that there is a relationship between the population frequency of these two alleles and the presence of linguistic tone and test this hypothesis relative to a large database (983 alleles and 26 linguistic features in 49 populations), showing that it is not due to the usual explanatory factors represented by geography and history. The relationship between genetic and linguistic diversity in this case may be causal: certain alleles can bias language acquisition or processing and thereby influence the trajectory of language change through iterated cultural transmission.learning biases ͉ tone language ͉ linguistic typology ͉ cultural transmission

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“…The allele and haplotype frequencies are being entered in ALFRED (http://alfred. med.yale.edu/) (17). F st -based pairwise genetic distances were calculated (18), and a best least-squares tree was derived (19,20).…”

Section: Research Design and Methods -The Pima Indians Ofmentioning

confidence: 99%

Effects of Traditional and Western Environments on Prevalence of Type 2 Diabetes in Pima Indians in Mexico and the U.S.

et al. 2006

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OBJECTIVE -Type 2 diabetes and obesity have genetic and environmental determinants. We studied the effects of different environments on these diseases in Pima Indians in Mexico and the U.S. RESEARCH DESIGN AND METHODS -AdultPima-Indian and non-Pima populations in the Sierra Madre mountains of Mexico were examined using oral glucose tolerance tests and assessments for obesity, physical activity, and other risk factors. Results were compared with those from Pima Indians in Arizona. Both Pima populations were typed for DNA polymorphisms to establish their genetic similarity.RESULTS -The age-and sex-adjusted prevalence of type 2 diabetes in the Mexican Pima Indians (6.9%) was less than one-fifth that in the U.S. Pima Indians (38%) and similar to that of non-Pima Mexicans (2.6%). The prevalence of obesity was similar in the Mexican Pima Indians (7% in men and 20% in women) and non-Pima Mexicans (9% in men and 27% in women) but was much lower than in the U.S. Pima Indians. Levels of physical activity were much higher in both Mexican groups than in the U.S. Pima Indians. The two Pima groups share considerable genetic similarity relative to other Native Americans.CONCLUSIONS -The much lower prevalence of type 2 diabetes and obesity in the Pima Indians in Mexico than in the U.S. indicates that even in populations genetically prone to these conditions, their development is determined mostly by environmental circumstances, thereby suggesting that type 2 diabetes is largely preventable. This study provides compelling evidence that changes in lifestyle associated with Westernization play a major role in the global epidemic of type 2 diabetes. Diabetes Care 29:1866 -1871, 2006T he global prevalence of diabetes in the 20-to 79-year age range in 2003 was estimated to be 5.1%, but the prevalence varied dramatically by region and race (1). Rural areas of developing countries have a low prevalence of type 2 diabetes, but in many countries, prevalence is increasing rapidly due to increasing urbanization and aging of the population (2). Certain populations experience a disproportionately elevated prevalence of diabetes. For example, type 2 diabetes reaches epidemic proportions in Nauru (3), in the Aborigines of Australia (4), and many in American-Indian groups in the U.S. (5-7), and the prevalence is much higher in these ethnic groups than in others in the same countries. These observations, together with strong evidence of the importance of genetic susceptibility in type 2 diabetes (8), indicate that type 2 diabetes results from an interaction between genetic predisposition and lifestyles associated with unfavorable environments.To elucidate the nature and contribution of environmental influences on type 2 diabetes, we studied two groups of Pima Indians in Mexico and in the U.S. The high prevalence of type 2 diabetes in the Pima Indians in the U.S. is well established (5,6), but the prevalence among their counterparts living in Mexico was previously unknown. The Pima Indians in the U.S. reside mainly in the desert regions of Arizon...

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ALFRED: An allele frequency database for anthropology

Cited by 54 publications

References 26 publications

Linkage disequilibrium patterns vary substantially among populations

Linkage disequilibrium patterns vary substantially among populations

Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin

Effects of Traditional and Western Environments on Prevalence of Type 2 Diabetes in Pima Indians in Mexico and the U.S.

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