The effect of reference panels and software tools on genotype imputation.

Kwangsik Nho, Li Shen, Sungeun Kim, Shanker Swaminathan, Shannon L. Risacher, Andrew Saykin, Disease Neuroimaging Initiative (ADNI) Alzheimer's Disease Neuroimaging Initiative (ADNI)

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Genotype imputation is increasingly employed in genome-wide association studies, particularly for integrative and cross-platform analysis. Several imputation algorithms use reference panels with a larger set of genotyped markers to infer genotypes at ungenotyped marker locations. Our objective was to assess which method and reference panel was more accurate when carrying out imputation. We investigated the influence of choice of two most popular imputation methods, IMPUTE and MACH, on two reference panels from the HapMap and the 1000 Genomes Project. Our results indicated that for the HapMap, MACH consistently yielded more accurate imputation results than IMPUTE, while for the 1000 Genomes Project, IMPUTE performed slightly better. The best imputation results were achieved by IMPUTE with the combined reference panel (HapMap + 1000 Genomes Project). IMPUTE with the combined reference panel is a promising strategy for genotype imputation, which should facilitate fine-mapping for discovery as well as known disease-associated candidate regions.

Original languageEnglish
Pages (from-to)1013-1018
Number of pages6
JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
Volume2011
StatePublished - 2011

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HapMap Project
Software
Genotype
Genome
Genome-Wide Association Study

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Nho, K., Shen, L., Kim, S., Swaminathan, S., Risacher, S. L., Saykin, A., & Alzheimer's Disease Neuroimaging Initiative (ADNI), D. N. I. ADNI. (2011). The effect of reference panels and software tools on genotype imputation. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 2011, 1013-1018.

The effect of reference panels and software tools on genotype imputation. / Nho, Kwangsik; Shen, Li; Kim, Sungeun; Swaminathan, Shanker; Risacher, Shannon L.; Saykin, Andrew; Alzheimer's Disease Neuroimaging Initiative (ADNI), Disease Neuroimaging Initiative (ADNI).

In: AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, Vol. 2011, 2011, p. 1013-1018.

Research output: Contribution to journalArticle

Nho, K, Shen, L, Kim, S, Swaminathan, S, Risacher, SL, Saykin, A & Alzheimer's Disease Neuroimaging Initiative (ADNI), DNIADNI 2011, 'The effect of reference panels and software tools on genotype imputation.', AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, vol. 2011, pp. 1013-1018.
Nho, Kwangsik ; Shen, Li ; Kim, Sungeun ; Swaminathan, Shanker ; Risacher, Shannon L. ; Saykin, Andrew ; Alzheimer's Disease Neuroimaging Initiative (ADNI), Disease Neuroimaging Initiative (ADNI). / The effect of reference panels and software tools on genotype imputation. In: AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2011 ; Vol. 2011. pp. 1013-1018.
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