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Michigan Imputation Server specifications

Information


Unique identifier OMICS_17672
Name Michigan Imputation Server
Interface Web user interface
Restrictions to use None
Input format VCF files compressed by bgzip.
Computer skills Basic
Version 1.22.0
Stability Stable
Maintained Yes

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Publication for Michigan Imputation Server

Michigan Imputation Server citations

 (44)
call_split

Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

2018
Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
call_split See protocol

[…] datasets have been excluded. Ancestry outliers were identified in TCGA using principal components analysis in plink 1.9. Resulting files were imputed using Eagle 2 and Minimac3 as implemented on the Michigan imputation server (https://imputationserver.sph.umich.edu) using the Haplotype Reference Consortium Version r1.1 2016 as a reference panel–. Somatic characterization of TCGA cases was obtaine […]

library_books

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

2018
Nat Commun
PMCID: 5940825
PMID: 29739930
DOI: 10.1038/s41467-018-03621-1

[…] /~wrayner/tools/) was used to perform some final filtering and split data by chromosome. Phasing (via eagle v2.3) and imputation against the HRC r1.1 2016 panel (via minimac3) were carried out by the Michigan Imputation Server. […]

library_books

Genome wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

2018
Nat Commun
PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] aplotypes) as reference panels. Specifically, SNP genotypes were imputed in two steps. First, genotypes on each chromosome were phased using ShapeIT (v2.r837). Then, phased data were submitted to the Michigan Imputation Server, and imputed using Minimac3. The protocol of the study was approved by the Institutional Review Board of Brigham and Women’s Hospital and the Harvard School of Public Health […]

library_books

Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis

2018
Wellcome Open Res
PMCID: 5904730
PMID: 29744390
DOI: 10.21956/wellcomeopenres.15031.r30762

[…] iation studies in neurodevelopmental disorders ( ; ). These two SNPs were not directly genotyped on the Illumina arrays and were therefore imputed for all individuals. Imputation was performed on the Michigan Imputation Server, an online server which generates phased and imputed genotypes using high-density reference panels. Variant Call Files (VCF) were uploaded for 15,936 SNPs genotyped on chrom […]

library_books

One for all and all for One: Improving replication of genetic studies through network diffusion

2018
PLoS Genet
PMCID: 5933817
PMID: 29684019
DOI: 10.1371/journal.pgen.1007306

[…] analyses. Genotypes for a much larger set of SNPs were imputed using the Haplotype Reference Consortium panel release 1.1 [, ], which includes 64,976 haplotypes derived from 39,235,157 SNPs, and the Michigan Imputation Server (https://imputationserver.sph.umich.edu/) running MiniMac3 [, ]. […]

library_books

A genome wide association study of red blood cell fatty acids and ratios incorporating dietary covariates: Framingham Heart Study Offspring Cohort

2018
PLoS One
PMCID: 5898718
PMID: 29652918
DOI: 10.1371/journal.pone.0194882

[…] Genotypes were originally measured using both an Affymetrix 500K and a 50K Human Gene Focused Panel as previously described []. We imputed these markers on the University of Michigan imputation server using the 1000 genomes Phase 1 imputation, yielding 9.3 million variants meeting standard quality control criteria and with MAF>1% []. The Michigan Imputation Server phased […]

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Michigan Imputation Server institution(s)
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA; Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, US National Institutes of Health, Bethesda, MD, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Psychology, University of Minnesota, Minneapolis, MN, USA; Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Neurobiology–Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, MD, USA; Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), affiliated with the University of Lübeck, Bolzano, Italy
Michigan Imputation Server funding source(s)
Supported by the National Institutes of Health grants HG007022 and HL117626, HG000376, and R01DA037904, Austrian Science Fund grant J-3401, the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 602133 and also in part by the Intramural Research Program of the National Institute on Aging, National Institutes of Health.

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