The further development of DNA pooling for gene discovery and public health genomics

Abstract

A model based on quantitative haemoglobin (Hb) genetics was explored to seek alleles that may have been "trans-selected" by beta thalassaemia. Hb is a duplex of two heterodimers (or 2αβ). Quantitative data on Rb variants such as Rb S, in the context of different genotypes, suggested a model that could be suitable to account for the broad range of severity in various complex diseases that are caused by multiple al1eles with quantitative effects. Interplay between two to three alleles at two to three loci (α,β,γ) could be associated with levels of a heterodimeric molecule such as Hb S, from as little as 5% to as much as 100% of total Hb. A search for other heterodimers was conducted based on the assumption that like Hb, duplexes of heterodimers, having subunits coded on non-syntenic chromosomes could display expression profiles over a broad range of values due to interplay of subunits at the level of protein assembly. Five heterodimers involved in inflammation, having one of their sub units coded by either chromosome 11 or 16 were selected from databases. Fifteen single nucleotide polymorphisms (SNPs) were quantified in the random (neonate) Maltese population and in adult β thalassaemia heterozygotes. Two of the single nucleotide variants (Integrin alpha-M (ITGAM) c.3436C>T and ITGAM c.2573C>T), which were in linkage disequilibrium (LD) with each other, resulted in odds ratios of 1.3 in the comparison between beta thalassaemia heterozygotes and controls. The two SNPs are located on chromosome 16 in the gene coding for the ITGAM subunit of the ITGAM/beta-2 heterodimer. The beta 2 (β2) gene is located on chromosome 21. Furthermore, whole exome sequencing on the Maltese random neonate DNA pool (n=50) gave a strong linear correlation (R² = 0.9066) between known Maltese allele frequencies and allele frequencies obtained from whole exome sequencing. Sequencing of DNA pools is a well-suited technique for quantification of allele frequencies and discovery of other alleles that may have been subjected to trans-selection. ITGAM/β2 is coded for by non-syntenic genes. Therefore selection pressure on one of the sub units may have been transmitted to the other as in the case of the alpha and beta globin subunits of Hb.