HaploShare: identification of extended haplotypes shared by cases and evaluation against controls

• Published in: Genome Biology Vol. 16; no. 1; p. 92
• Main Authors: Ying, Dingge, Sham, Pak Chung, Smith, David Keith, Zhang, Lu, Lau, Yu Lung, Yang, Wanling
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.05.2015; Springer Nature B.V
• Subjects: Algorithms; Animal Genetics and Genomics; Asian Continental Ancestry Group - genetics; Bioinformatics; Biomedical and Life Sciences; Case-Control Studies; Computational Biology; computer software; Disease; Evolutionary Biology; False Positive Reactions; Genetic Association Studies - methods; genome; Genomes; Haplotypes; Hirschsprung Disease - diagnosis; Hirschsprung Disease - genetics; Human Genetics; Humans; Life Sciences; Method; Microbial Genetics and Genomics; Mutation; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; Power; Sensitivity and Specificity; Statistical analysis; Shared Haplotype; Linkage Disequilibrium Block; False Positive Rate; Founder Mutation; Linkage Disequilibrium
• ISSN: 1465-6906; 1474-7596; 1474-760X; 1465-6914; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/s13059-015-0662-9

Recent founder mutations may play important roles in complex diseases and Mendelian disorders. Detecting shared haplotypes that are identical by descent (IBD) could facilitate discovery of these mutations. Several programs address this, but are usually limited to detecting pair-wise shared haplotypes and not providing a comparison of cases and controls. We present a novel algorithm and software package, HaploShare, which detects extended haplotypes that are shared by multiple individuals, and allows comparisons between cases and controls. Testing on simulated and real cases demonstrated significant improvements in detection power and reduction of false positive rate by HaploShare relative to other programs.