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Beyond Homozygosity Mapping: Family-Control analysis based on Hamming distance for prioritizing variants in exome sequencing
Imai, Atsuko1,2; Nakaya, Akihiro2; Fahiminiya, Somayyeh3,4; Tetreault, Martine3,4; Majewski, Jacek3,4; Sakata, Yasushi1; Takashima, Seiji1,5; Lathrop, Mark3,4; Ott, Jurg6,7
2015-07-06
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
SubtypeArticle
Volume5Issue:0Pages:12028
AbstractA major challenge in current exome sequencing in autosomal recessive (AR) families is the lack of an effective method to prioritize single-nucleotide variants (SNVs). AR families are generally too small for linkage analysis, and length of homozygous regions is unreliable for identification of causative variants. Various common filtering steps usually result in a list of candidate variants that cannot be narrowed down further or ranked. To prioritize shortlisted SNVs we consider each homozygous candidate variant together with a set of SNVs flanking it. We compare the resulting array of genotypes between an affected family member and a number of control individuals and argue that, in a family, differences between family member and controls should be larger for a pathogenic variant and SNVs flanking it than for a random variant. We assess differences between arrays in two individuals by the Hamming distance and develop a suitable test statistic, which is expected to be large for a causative variant and flanking SNVs. We prioritize candidate variants based on this statistic and applied our approach to six patients with known pathogenic variants and found these to be in the top 2 to 10 percentiles of ranks.
Indexed BySCI
Language英语
WOS IDWOS:000357379100001
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.psych.ac.cn/handle/311026/13342
Collection健康与遗传心理学研究室
Affiliation1.Osaka Univ, Dept Cardiovasc Med, Grad Sch Med, Osaka, Japan
2.Osaka Univ, Dept Genome Informat, Grad Sch Med, Osaka, Japan
3.McGill Univ, Montreal, PQ H3A 1B1, Canada
4.Genome Quebec Innovat Ctr, Montreal, PQ H3A 1B1, Canada
5.Osaka Univ, Dept Med Biochem, Grad Sch Med, Osaka, Japan
6.Chinese Acad Sci, Inst Psychol, Beijing 100101, Peoples R China
7.Rockefeller Univ, New York, NY 10065 USA
Recommended Citation
GB/T 7714
Imai, Atsuko,Nakaya, Akihiro,Fahiminiya, Somayyeh,et al. Beyond Homozygosity Mapping: Family-Control analysis based on Hamming distance for prioritizing variants in exome sequencing[J]. SCIENTIFIC REPORTS,2015,5(0):12028.
APA Imai, Atsuko.,Nakaya, Akihiro.,Fahiminiya, Somayyeh.,Tetreault, Martine.,Majewski, Jacek.,...&Ott, Jurg.(2015).Beyond Homozygosity Mapping: Family-Control analysis based on Hamming distance for prioritizing variants in exome sequencing.SCIENTIFIC REPORTS,5(0),12028.
MLA Imai, Atsuko,et al."Beyond Homozygosity Mapping: Family-Control analysis based on Hamming distance for prioritizing variants in exome sequencing".SCIENTIFIC REPORTS 5.0(2015):12028.
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