Genomic organization and sequence variation of the human integrin subunit α8 gene (ITGA8)

Catherine Ekwa-Ekoka, George A. Diaz, Chris Carlson, Tomonobu Hasegawa, Ram Samudrala, Kim Chew Lim, Julie M. Yabu, Brynn Levy, Lynn M. Schnapp

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8 Citations (Scopus)

Abstract

The integrin α8 is highly expressed during kidney and lung development. α8-deficient mice display abnormal renal development suggesting that α8 plays a critical role in organogenesis. Therefore, it would be of considerable interest to understand the genomic structure, localization and sequence variation of the α8 gene. Using FISH and genomic database analysis, we show that α8 gene maps to chromosome 10p13 and consists of >200 kbp organized into 30 exons. Examination of 47 individuals from two different ethnic groups (European and African descent) identified 286 varying sites. The diversity of α8 is comparable to that of other regions within the human genome. Eight of the varying sites were located in the coding regions: six resulted in nonsynonymous substitutions of which two lead to non-conservative changes in protein. None of the sites showed significant deviation from Hardy-Weinberg equilibrium. We mapped the coding region single nucleotide polymorphisms (SNPs) onto a model of the predicted α8 structure and found all the SNPs were located in the "calf" of the extracellular domain. In the European population, the linkage disequilibrium statistic D′ showed three blocks of relatively non-recombinant regions in the α8 gene while the African population showed more evidence of recombination. The observed patterns of the linkage disequilibrium statistic R 2 suggest that a large number of sites will need to be genotyped to ensure coverage of the entire gene for genetic association studies. Identification of the sequence variation will allow genetic association studies of α8 in kidney and lung disease.

Original languageEnglish
Pages (from-to)487-496
Number of pages10
JournalMatrix Biology
Volume23
Issue number7
DOIs
Publication statusPublished - 2004 Nov 1

Keywords

  • Integrin alpha chain
  • Polymorphism
  • single nucleotide

ASJC Scopus subject areas

  • Molecular Biology

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    Ekwa-Ekoka, C., Diaz, G. A., Carlson, C., Hasegawa, T., Samudrala, R., Lim, K. C., Yabu, J. M., Levy, B., & Schnapp, L. M. (2004). Genomic organization and sequence variation of the human integrin subunit α8 gene (ITGA8). Matrix Biology, 23(7), 487-496. https://doi.org/10.1016/j.matbio.2004.08.005