Population mutation scanning of human GHR by meltMADGE and identification of a paucimorphic variant

Alharbi, Khalid K., Hou, Guangwei, Chen, Xiao-he, Gaunt, Tom R., Syddall, Holly E., Sayer, Avan Aihie, Dennison, Elaine M., Phillips, David I. W., Cooper, Cyrus and Day, Ian N. W. (2011) Population mutation scanning of human GHR by meltMADGE and identification of a paucimorphic variant. Genetic Testing and Molecular Biomarkers, 15, 855-860. (PMID:21689014)

Abstract

Current studies of human genetic diversity are focused in two areas: first, detection of rare mutations in highly selected clinical cases; and second, in common single-nucleotide polymorphism (SNP) and haplotype effects in the general population. Less frequent SNPs and "paucimorphisms" remain underexplored, although lower frequency coding SNPs are more likely to have functional impact. We have developed a cost-efficient mutation scanning technology, meltMADGE, for population mutation scanning. Previous research in GHR has explored its role in extreme (-3 SD) growth retardation and, subsequently, "moderate" (-2 SD) growth retardation cases. Here, we describe meltMADGE assays for the entire coding region of GHR. As a first step we have established long polymerase chain reaction subbanks for GHR from 2423 unselected subjects and have applied meltMADGE scanning assays of exons 4 and 5 to these subbanks. A novel paucimorphism present at 439+30A>C (allele frequency: 0.0021) in intron 5 (location chr5:42,695,221 in GRCh37/hg19) was identified in 10 individuals, confirmed by sequencing and analysis made for major phenotypic effects. This approach is relevant to the deep sampling of populations for less frequent sequence diversity, some of which is expected to exert significant phenotypic effects.

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Contributors

Author: Holly E. Syddall

Author: Elaine M. Dennison

Author: Cyrus Cooper

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