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MIXSCORE specifications


Unique identifier OMICS_17450
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes




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  • person_outline Michael Seldin <>

Publication for MIXSCORE

MIXSCORE citations


Genome wide admixture and association study of subclinical atherosclerosis in the Women’s Interagency HIV Study (WIHS)

PMCID: 5714351
PMID: 29206233
DOI: 10.1371/journal.pone.0188725

[…] the supplementary methods section () and the results are presented in . the comparison shows that the power is highest for the qsum test that adjusts for both local and global ancestries using the mixscore program. pasaniuc et al. reported that the qatt test performed better for quantitative traits but also noted that the qsum test might perform better given a set of conditions where high […]


Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping

PMCID: 5435963
PMID: 28332560
DOI: 10.1038/gene.2017.6

[…] am analysis. a case-only admixture score and a mixed χ2(1df) score (mix) to jointly evaluate both single-nucleotide polymorphism (snp) and admixture association (p<5.00e-08) were computed using mixscore. in addition, a permutation scheme was implemented to derive multiplicity adjusted p-values (genome-wide 0.05 significance threshold: p<9.46e-05). after empirical multiplicity adjustment, […]


Genetic architecture of age related cognitive decline in African Americans

PMCID: 5206965
PMID: 28078323
DOI: 10.1212/NXG.0000000000000125

[…] was performed using metal software., to detect chromosomal segments of distinct ancestry in aas, we used the hapmix algorithm. the quantitative and case-control admixture scan was performed using mixscore (version 1.3) software. a description of the admixture analysis is provided in the e-methods., we performed a pathway enrichment analysis using magenta software and adopting ingenuity […]


The Role of Local Ancestry Adjustment in Association Studies Using Admixed Populations

PMCID: 5079159
PMID: 25043967
DOI: 10.1002/gepi.21835

[…] the signals from admixture mapping and single snp associations provide independent information and could complement each other, and suggested a joint test under a family design []. two joint tests (mixscore) were developed in the context of case/control gwas study, and a gain of power was reported []. a bayesian method (bmix) has also been proposed []., when the causal variants are not directly […]


Admixture Fine Mapping in African Americans Implicates XAF1 as a Possible Sarcoidosis Risk Gene

PMCID: 3963923
PMID: 24663488
DOI: 10.1371/journal.pone.0092646

[…] faff: frequency of modeled allele in sarcoidosis-affected individuals; funf: frequency of modeled allele in unaffected individuals; or: odds ratio; 95%ci: 95% confidence interval; p: p-value; mix: mixscore test., minor allele in african americans is bolded; modeled by generalized estimating equations adjusting for percent global west african ancestry and sex., “imputed” indicates a snp […]

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MIXSCORE institution(s)
Rowe Program in Human Genetics, Department of Biochemistry and Molecular Medicine and Department of Medicine, University of California Davis, Davis, CA, USA; Department of Epidemiology and the Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; the Broad Institute of MIT and Harvard, Cambridge, MA, USA
MIXSCORE funding source(s)
This work was funded by US National Institutes of Health grants RC1 GM091332, R01 AR050267 and R01 DK071185.

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