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A test for linkage and association in general pedigrees: the pedigree disequilibrium test.

Abstract：

:Family-based tests of linkage disequilibrium typically are based on nuclear-family data including affected individuals and their parents or their unaffected siblings. A limitation of such tests is that they generally are not valid tests of association when data from related nuclear families from larger pedigrees are used. Standard methods require selection of a single nuclear family from any extended pedigrees when testing for linkage disequilibrium. Often data are available for larger pedigrees, and it would be desirable to have a valid test of linkage disequilibrium that can use all potentially informative data. In this study, we present the pedigree disequilibrium test (PDT) for analysis of linkage disequilibrium in general pedigrees. The PDT can use data from related nuclear families from extended pedigrees and is valid even when there is population substructure. Using computer simulations, we demonstrated validity of the test when the asymptotic distribution is used to assess the significance, and examined statistical power. Power simulations demonstrate that, when extended pedigree data are available, substantial gains in power can be attained by use of the PDT rather than existing methods that use only a subset of the data. Furthermore, the PDT remains more powerful even when there is misclassification of unaffected individuals. Our simulations suggest that there may be advantages to using the PDT even if the data consist of independent families without extended family information. Thus, the PDT provides a general test of linkage disequilibrium that can be widely applied to different data structures.

journal_name

Am J Hum Genet

journal_title

American journal of human genetics

authors

Martin ER,Monks SA,Warren LL,Kaplan NL

doi

10.1086/302957

subject

Has Abstract

pub_date

2000-07-01 00:00:00

pages

146-54

issue

1

eissn

0002-9297

issn

1537-6605

pii

S0002-9297(07)62440-9

journal_volume

67

pub_type

杂志文章

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