Open AccessRules for resolving Mendelian inconsistencies in nuclear pedigrees typed for two-allele markers
Author(s) -
Sajjad Ahmad Khan,
Sadaf Manzoor,
Alamgir,
Amjad Ali,
Dost Muhammad Khan,
Umair Khalil
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0172807
Subject(s) - pedigree chart , genotyping , mendelian inheritance , genetics , allele , genotype , data set , single nucleotide polymorphism , set (abstract data type) , computer science , computational biology , biology , gene , artificial intelligence , programming language
Gene-mapping studies, regularly, rely on examination for Mendelian transmission of marker alleles in a pedigree as a way of screening for genotyping errors and mutations. For analysis of family data sets, it is, usually, necessary to resolve or remove the genotyping errors prior to consideration. At the Center of Inherited Disease Research (CIDR), to deal with their large-scale data flow, they formalized their data cleaning approach in a set of rules based on PedCheck output. We scrutinize via carefully designed simulations that how well CIDR’s data cleaning rules work in practice. We found that genotype errors in siblings are detected more often than in parents for less polymorphic SNPs and vice versa for more polymorphic SNPs. Through computer simulations, we conclude that some of the CIDR’s rules work poorly in some circumstances, and we suggest a set of modified data cleaning rules that may work better than CIDR’s rules.