Ethnicity and Human Genetic Linkage Maps

Department of Genetics, Stanford University, Stanford, CA, USA.
The American Journal of Human Genetics (Impact Factor: 10.93). 03/2005; 76(2):276-90. DOI: 10.1086/427926
Source: PubMed


Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined--for the first time, to our knowledge--racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, and Blood Institute-funded Family Blood Pressure Program, the largest sample used for map construction to date. Although the maps for the different groups are generally similar, we did find regional and genomewide differences across ethnic groups, including a longer genomewide map for African Americans than for other populations. Some of this variation was explained by genotyping artifacts--namely, null alleles (i.e., alleles with null phenotypes) at a number of loci--and by ethnic differences in null-allele frequencies. In particular, null alleles appear to be the likely explanation for the excess map length in African Americans. We also found that nonrandom missing data biases map results. However, we found regions on chromosome 8p and telomeric segments with significant ethnic differences and a suggestive interval on chromosome 12q that were not due to genotype artifacts. The difference on chromosome 8p is likely due to a polymorphic inversion in the region. The results of our investigation have implications for inferences of possible genetic influences on human recombination as well as for future linkage studies, especially those involving populations of nonwhite ethnicity.

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Available from: Richard Cooper, Oct 08, 2014
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    • "We observed different map sizes in the consensus female maps; the map constructed with combined haploid and diploid families had a size of 6596.7 cM, which is significantly larger than the coho map created with haploids alone (3602.6 cM). There are several reasons that might explain the differences such as nonrandom missing values (Jorgenson et al. 2005), genotyping errors (Hackett and Broadfoot 2003), and numbers of markers mapped. "
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    • "There are three reasons that might explain the differences. Nonrandom missing values (Jorgenson et al. 2005) and genotyping errors (Hackett and Broadfoot 2003) can inflate map distances. We found that missing values were not randomly distributed across individuals (x 2 test for uniform distribution across individuals: P-value ~0 for each family). "
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    • "In Asians, the physical distance between the same markers would generally be concordant with the reference map (with correspondingly ''normal'' genetic distances). Comparison of the intermarker genetic distances between Africans and Asians consequently gives an impression of increased local recombination in Africans (Jorgenson et al. 2005), whereas the converse would be expected for markers distantly separated on the genome reference map. Like the 17q21.31 "
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