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| Item Type: | Article |
|---|---|
| Title: | Statistical considerations for genome-wide scans: design and application of a novel software package POLYMORPHISM |
| Creators Name: | Niu, T., 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 |
| ISSN: | 0001-5652 |
| Publisher: | Karger |
| Volume: | 52 |
| Number: | 2 |
| Page Range: | 102-109 |
| Date: | July 2001 |
| Official Publication: | https://doi.org/10.1159/000053361 |
| PubMed: | View item in PubMed |
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