Article ; Online: Shared genomic segment analysis with equivalence testing.
2020 Volume 44, Issue 7, Page(s) 741–747
Abstract: An important aspect of disease gene mapping is replication, that is, a putative finding in one group of individuals is confirmed in another set of individuals. As it can happen by chance that individuals share an estimated disease position, we developed ... ...
Abstract | An important aspect of disease gene mapping is replication, that is, a putative finding in one group of individuals is confirmed in another set of individuals. As it can happen by chance that individuals share an estimated disease position, we developed a statistical approach to determine the p-value for multiple individuals or families to share a possibly small number of candidate susceptibility variants. Here, we focus on candidate variants for dominant traits that have been obtained by our previously developed heterozygosity analysis, and we are testing the sharing of candidate variants obtained for different individuals. Our approach allows for multiple pathogenic variants in a gene to contribute to disease, and for estimated disease variant positions to be imprecise. Statistically, the method developed here falls into the category of equivalence testing, where the classical null and alternative hypotheses of homogeneity and heterogeneity are reversed. The null hypothesis situation is created by permuting genomic locations of variants for one individual after another. We applied our methodology to the ALSPAC data set of 1,927 whole-genome sequenced individuals, where some individuals carry a pathogenic variant for the BRCA1 gene, but no two individuals carry the same variant. Our shared genomic segment analysis found significant evidence for BRCA1 pathogenic variants within ±5 kb of a given DNA variant. |
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MeSH term(s) | BRCA1 Protein/genetics ; Chromosome Mapping/methods ; Genes, BRCA1 ; Genetic Predisposition to Disease/genetics ; Genetics, Population/methods ; Genomics/methods ; Heterozygote ; Humans ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Whole Genome Sequencing/methods |
Chemical Substances | BRCA1 Protein ; BRCA1 protein, human |
Language | English |
Publishing date | 2020-07-16 |
Publishing country | United States |
Document type | Journal Article ; Research Support, Non-U.S. Gov't |
ZDB-ID | 605785-8 |
ISSN | 1098-2272 ; 0741-0395 |
ISSN (online) | 1098-2272 |
ISSN | 0741-0395 |
DOI | 10.1002/gepi.22335 |
Database | MEDical Literature Analysis and Retrieval System OnLINE |
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