Pooled genotyping of microsatellite markers in parent-offspring trios

Kirov, George ORCID: https://orcid.org/0000-0002-3427-3950, Williams, Nigel Melville ORCID: https://orcid.org/0000-0003-1177-6931, Sham, P., Craddock, Nicholas John ORCID: https://orcid.org/0000-0003-2171-0610 and Owen, Michael John ORCID: https://orcid.org/0000-0003-4798-0862 2000. Pooled genotyping of microsatellite markers in parent-offspring trios. Genome Research 10 (1) , pp. 105-115.

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Abstract

We studied the extent to which genotyping of simple sequence repeat polymorphisms (SSRs) in pooled DNA samples can be used to predict differences in allele frequencies between parents and their affected offspring. We also developed a simple method of correction for the effects of stutter and differential amplification on the analysis of SSRs in pooled DNA samples based on widely available software. We genotyped individually eight polymorphic microsatellite markers in 110 parent-offspring trios affected with bipolar affective disorder (BP). Analysis of pooled DNA samples predicted very accurately the differences in individual allele frequency distributions between children and their parents. The mean error was <1% (range 0%-3.2%) when marker-specific corrections for stutter and differential amplification were performed. We show that if an individual allele is significantly preferentially transmitted from parents to affected offspring, the difference in the frequency of that allele would be sufficiently large to be detected with pooling in most situations. We propose recommendations for disequilibrium mapping with pooling in which both case-control samples and trios are used in an initial screen and markers are genotyped individually only if they satisfy very relaxed criteria for statistical significance. The use of case-control samples should reduce the false-negative rate as the differences in allele frequencies between cases and controls are twice as high in the presence of the same genetic effect. The use of trios will confirm or reject any suggested differences, thus reducing the false-positive rate that can be created by hidden population stratification.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG) Neuroscience and Mental Health Research Institute (NMHRI)
Subjects:	R Medicine > R Medicine (General) R Medicine > RZ Other systems of medicine
Publisher:	Cold Spring Harbor Laboratory Press
ISSN:	1088-9051
Last Modified:	27 Oct 2022 08:39
URI:	https://orca.cardiff.ac.uk/id/eprint/63046

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