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

Tore, Silvia and Casula, Stefania and Casu, Giuseppina and Concas, Maria Pina and Pistidda, Paola and Persico, Ivana and Sassu, Alessandro and Maestrale, Giovanni Battista and Mele, Caterina and Caruso, Maria Rosa and Bonerba, Bibiana and Usai, Paolo and Deiana, Ivo and Thornton, Thimoty and Pirastu, Mario and Forabosco, Paola (2011) Application of a new method for GWAS in a related case/control sample with known pedigree structure: identification of new loci for nephrolithiasis. Plos Genetics, Vol. 7 (1), e1001281. ISSN 1553-7390. Article.

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DOI: 10.1371/journal.pgen.1001281

Abstract

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.

Item Type:Article
ID Code:6244
Status:Published
Refereed:Yes
Uncontrolled Keywords:Uric acid nephrolithiasis (UAN), urolithiasis, kidney stones, ROADTRIPS, isolated population of Talana, Sardinia
Subjects:Area 06 - Scienze mediche > MED/03 Genetica medica
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > CNR-Consiglio Nazionale delle Ricerche > Istituto di genetica delle popolazioni, Alghero
Publisher:Public Library of Science
ISSN:1553-7390
Copyright Holders:© 2011 Tore et al.
Deposited On:11 Jul 2011 16:42

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