title: Rules for resolving Mendelian inconsistencies in nuclear pedigrees typed for two-allele markers.
abstract: 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.
authors.affiliation: Department of Statistics, Abdul Wali Khan University Mardan, Khyber Pukhtunkhwa, Pakistan.|Department of Statistics, Islamia College, Peshawar, Khyber Pukhtunkhwa, Pakistan.
authors.forename: Sajjad Ahmad
authors.initials: SA
authors.lastname: Khan
authors.affiliation: Department of Statistics, Islamia College, Peshawar, Khyber Pukhtunkhwa, Pakistan.
authors.forename: Sadaf
authors.initials: S
authors.lastname: Manzoor
authors.affiliation: Department of Statistics, University of Peshawar, Khyber Pukhtunkhwa, Pakistan.
authors.lastname: Alamgir
authors.affiliation: Department of Statistics, Islamia College, Peshawar, Khyber Pukhtunkhwa, Pakistan.
authors.forename: Amjad
authors.initials: A
authors.lastname: Ali
authors.affiliation: Department of Statistics, Abdul Wali Khan University Mardan, Khyber Pukhtunkhwa, Pakistan.
authors.forename: Dost Muhammad
authors.initials: DM
authors.lastname: Khan
authors.affiliation: Department of Statistics, Abdul Wali Khan University Mardan, Khyber Pukhtunkhwa, Pakistan.
authors.forename: Umair
authors.initials: U
authors.lastname: Khalil
mesh_terms: D000328:Adult; D000483:Alleles; D002648:Child; D005260:Female; D005787:Gene Frequency; D005819:Genetic Markers / Q000235:genetics*; D006801:Humans; D008297:Male; D010375:Pedigree; D012107:Research Design; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D005819:Genetic Markers