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Statistical considerations for genome-wide scans: design and application of a novel software package POLYMORPHISM

Item Type:Article
Title:Statistical considerations for genome-wide scans: design and application of a novel software package POLYMORPHISM
Creators Name:Niu, T. and Struk, B. and Lindpaintner, K.
Abstract:OBJECTIVE: Given the cost and complexity of genome-wide scans, optimization of study design is of critical importance. Available algorithms only partially satisfy this need. We designed a software package called 'POLYMORPHISM' to meet these needs. METHODS: The program is designed to calculate linkage parameters for both 'single-point' and 'two-point' settings that are applicable also to incompletely informative microsatellite markers. In single-point analysis, the heterozygosity, polymorphism information content (PIC) and linkage information content (LIC) statistics based on marker allele frequencies are provided. In two-point analysis, joint PIC values for two markers, the conditional probability of detecting linkage phase, the frequency of double heterozygotes and the expected number of informative meioses are calculated. RESULTS: Results were obtained using S.A.G.E./DESPAIR (Design of Linkage Studies Based on Pairs of Relatives) in addition to applying this program to a Centre d'Etude du Polymorphisme pedigree-derived genotyping data set, which estimated critical parameters used in a two-stage genome scan. A single nucleotide polymorphism (SNP)-based one-stage genomic screen strategy is also considered. CONCLUSIONS: LIC values are crucial for getting accurate estimates on those parameters that are important for a two-stage genome screening study. Optimization of the cost-effectiveness of an SNP-based genomic screen strategy is possible by modeling a balance between marker information content and marker density.
Keywords:Marker Polymorphism, Nonparametric, Linkage Analysis, Sib Pairs
Source:Human Heredity
Publisher:Karger (Switzerland)
Page Range:102-109
Date:July 2001
Official Publication:https://doi.org/10.1159/000053361
PubMed:View item in PubMed

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