NDLI: Multiple Rare Variants as a Cause of a Common Phenotype: Several Different Lactase Persistence Associated Alleles in a Single Ethnic Group

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Multiple Rare Variants as a Cause of a Common Phenotype: Several Different Lactase Persistence Associated Alleles in a Single Ethnic Group

Content Provider	Springer Nature Link
Author	Ingram, Catherine J. E. Raga, Tamiru Oljira Tarekegn, Ayele Browning, Sarah L. Elamin, Mohamed F. Bekele, Endashaw Thomas, Mark G. Weale, Michael E. Bradman, Neil Swallow, Dallas M.
Copyright Year	2009
Abstract	Persistence of intestinal lactase into adulthood allows humans to use milk from other mammals as a source of food and water. This genetic trait has arisen by convergent evolution and the derived alleles of at least three different single nucleotide polymorphisms (–13910C>T, –13915T>G, –14010G>C) are associated with lactase persistence in different populations. Each allele occurs on an extended haplotype, consistent with positive directional selection. The SNPs are located in an ‘enhancer’ sequence in an intron of a neighboring gene (MCM6) and modulate lactase transcription in vitro. However, a number of lactase persistent individuals carry none of these alleles, but other low-frequency single nucleotide polymorphisms have been observed in the same region. Here we examine a cohort of 107 milk-drinking Somali camel-herders from Ethiopia. Eight polymorphic sites are identified in the enhancer. –13915G and –13907G (a previously reported candidate) are each significantly associated with lactase persistence. A new allele, –14009*G, has borderline association with lactase persistence, but loses significance after correction for multiple testing. Sequence diversity of the enhancer is significantly higher in the lactase persistent members of this and a second cohort compared with non-persistent members of the two groups (P = 7.7 × 10−9 and 1.0 × 10−3). By comparing other loci, we show that this difference is not due to population sub-structure, demonstrating that increased diversity can accompany selection. This contrasts with the well-documented observation that positive selection decreases diversity by driving up the frequency of a single advantageous allele, and has implications for association studies.
Starting Page	579
Ending Page	588
Page Count	10
File Format	PDF
ISSN	00222844
Journal	Journal of Molecular Evolution
Volume Number	69
Issue Number	6
e-ISSN	14321432
Language	English
Publisher	Springer-Verlag
Publisher Date	2009-11-24
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Lactase persistence Population genetics Evolutionary genetics Gene-culture co-evolution Selection Africa Milk Humans Animal Genetics and Genomics Plant Genetics & Genomics Plant Sciences Microbiology Evolutionary Biology Cell Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Ecology, Evolution, Behavior and Systematics

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Multiple Rare Variants as a Cause of a Common Phenotype: Several Different Lactase Persistence Associated Alleles in a Single Ethnic Group

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Multiple Rare Variants as a Cause of a Common Phenotype: Several Different Lactase Persistence Associated Alleles in a Single Ethnic Group