Application of a new method for GWAS in a related case/control sample with known pedigree structure: identification of new loci for nephrolithiasis.

In contrast to large GWA studies based on thousands of individuals and large meta-analyses combining GWAS results, we analyzed a small case/control sample for uric acid nephrolithiasis. Our cohort of closely related individuals is derived from a small, genetically isolated village in Sardinia, with well-characterized genealogical data linking the extant population up to the 16(th) century. It is expected that the number of risk alleles involved in complex disorders is smaller in isolated founder populations than in more diverse populations, and the power to detect association with complex traits may be increased when related, homogeneous affected individuals are selected, as they are more likely to be enriched with and share specific risk variants than are unrelated, affected individuals from the general population. When related individuals are included in an association study, correlations among relatives must be accurately taken into account to ensure validity of the results. A recently proposed association method uses an empirical genotypic covariance matrix estimated from genome-screen data to allow for additional population structure and cryptic relatedness that may not be captured by the genealogical data. We apply the method to our data, and we also investigate the properties of the method, as well as other association methods, in our highly inbred population, as previous applications were to outbred samples. The more promising regions identified in our initial study in the genetic isolate were then further investigated in an independent sample collected from the Italian population. Among the loci that showed association in this study, we observed evidence of a possible involvement of the region encompassing the gene LRRC16A, already associated to serum uric acid levels in a large meta-analysis of 14 GWAS, suggesting that this locus might lead a pathway for uric acid metabolism that may be involved in gout as well as in nephrolithiasis.

The homozygous state of Hb J Sardegna.

Hb J Sardegna is a well known innocent Hb variant which is widespread in Sardinia. As yet, homozygosity for Hb J Sardegna has not been documented. This report deals with the homozygous state for Hb J which we demonstrate by molecular analysis in two Sardinian siblings in which beta-thalassemia coexists. The Hb J specific mutation was determined both by enzyme digestion and by sequencing specific segments of PCR amplified alpha-globin genes. A pregnant girl showed mild non-sideropenic microcytic anemia, normal Hb A(2) levels (2.4%) on DE-52 microchromatography, 50% of Hb variant on HPLC and 2.1 alpha/beta globin chain biosynthetic ratio. She proved to be a carrier of the beta degrees 6(-A) thalassemia determinant. The alpha-globin gene mapping did not reveal alpha-thalassemia. Btg I restriction analysis of both alpha(2)-globin genes showed a recognition site defect for this enzyme in both chromosomes, which resulted to be the C-->A point mutation in homozygosity at the first nt of alpha(2)-globin gene 50th codon by sequencing. This defect, typical of Hb J Sardegna, was also present in her brother. From a practical point of view, this study demonstrates that the association of beta-thalassemia with Hb J, may show falsely reduced Hb A(2) levels on routine Hb A(2) quantitation techniques, such as DE-52 microchromatography. This possibility implies that identification methods such as simple Hb electrophoresis, which permit visualization of Hb A(J)(2) should be used in thalassemia screening involving populations in which Hb J and beta-thalassemia coexist.