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

Dingge Ying; Pak Chung Sham; David Keith Smith; Lu Zhang; Yu Lung Lau; Wanling Yang

doi:10.1186/s13059-015-0662-9

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

Dingge Ying
, Pak Chung Sham
, David Keith Smith
, Lu Zhang
, Yu Lung Lau
, Wanling Yang^*

^*Corresponding author for this work

Department of Computer Science

Research output: Contribution to journal › Journal article › peer-review

6 Citations (Scopus)

Abstract

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.

Original language	English
Article number	92
Number of pages	14
Journal	Genome Biology
Volume	16
Issue number	1
Early online date	9 May 2015
DOIs	https://doi.org/10.1186/s13059-015-0662-9
Publication status	Published - Dec 2015

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SDG 3 Good Health and Well-being

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Cite this

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title = "HaploShare: identification of extended haplotypes shared by cases and evaluation against controls",

abstract = "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.",

author = "Dingge Ying and Sham, \{Pak Chung\} and Smith, \{David Keith\} and Lu Zhang and Lau, \{Yu Lung\} and Wanling Yang",

note = "This project was partially supported by S K Yee Medical Foundation general award (to YLL and WY). DY and LZ are partially supported by SRT Genomic program of The University of Hong Kong and Edward the Sai Kim Hotung Paediatric Education and Research Fund. We also thank support from RGC of Hong Kong SAR (GRF HKU783813M, 17125114, HKU 784611 M, and HKU 770411 M). Publisher Copyright: {\textcopyright} 2015 Ying et al.; licensee BioMed Central.",

year = "2015",

month = dec,

doi = "10.1186/s13059-015-0662-9",

language = "English",

volume = "16",

journal = "Genome Biology",

issn = "1474-7596",

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T2 - identification of extended haplotypes shared by cases and evaluation against controls

AU - Ying, Dingge

AU - Sham, Pak Chung

AU - Smith, David Keith

AU - Zhang, Lu

AU - Lau, Yu Lung

AU - Yang, Wanling

N1 - This project was partially supported by S K Yee Medical Foundation general award (to YLL and WY). DY and LZ are partially supported by SRT Genomic program of The University of Hong Kong and Edward the Sai Kim Hotung Paediatric Education and Research Fund. We also thank support from RGC of Hong Kong SAR (GRF HKU783813M, 17125114, HKU 784611 M, and HKU 770411 M). Publisher Copyright: © 2015 Ying et al.; licensee BioMed Central.

PY - 2015/12

Y1 - 2015/12

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84939129135

UR - https://link.springer.com/article/10.1186/s13059-015-0662-9

U2 - 10.1186/s13059-015-0662-9

DO - 10.1186/s13059-015-0662-9

M3 - Journal article

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AN - SCOPUS:84939129135

SN - 1474-7596

VL - 16

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 92

ER -

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

Abstract

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