BOLT-LMM statistics

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BOLT-LMM specifications


Unique identifier OMICS_13504
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data High-confidence set of SNPs, imputed SNPs, phenotypes, covariates, missing data treatment, genotype QC, user-specified filters
Output data Association statistics in a tab-delimited file
Operating system Unix/Linux
Computer skills Advanced
Version 2.3.2
Stability Stable
Maintained Yes



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  • person_outline Po-Ru Loh <>

Publication for BOLT-LMM

BOLT-LMM in publications

PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] in addition to birth year as a covariate., variance explained by genetic variants in the current study were estimated using the restricted estimate maximum likelihood (reml) method implemented in bolt-lmm. we tested different snp sets: (i) directly genotyped variants within 250 kb up- or down-stream of the previously reported european lead variants,, and (ii) all directly genotyped variants […]

PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] model snps and ~ 7.8 million imputed variants with maf ≥ 1%, imputation quality (info) > 0.3 using the full data set., next, we performed a gwas for each trait using a linear mixed model method (bolt-lmm) under the additive genetic model including ~ 7.8 million imputed snps with maf ≥ 1% and info > 0.3. we used the heritability estimation obtained from bolt-reml., for δhrex and δhrex […]

PMCID: 5912948
PMID: 29641994
DOI: 10.1016/j.celrep.2018.03.070

[…] by assuming that the meta-test statistics were normally distributed., all genotype-phenotype association data were generated starting from 451,099 individuals defined as european ancestry and using bolt-lmm version 1.2, which uses an ld score regression approach to account for structure caused by relatedness (close and distant). all association testing was based on an additive, per allele model […]

PMCID: 5832790
PMID: 29497042
DOI: 10.1038/s41467-018-03395-6

[…] or hr-altering medication were assessed using a chow test., in total, 58,818 participants were included in the gwas. the genome-wide association study and heritability analyses were performed using bolt-lmm and bolt-reml, respectively. a conjugate gradient-based iterative framework for fast mixed-model computations was employed to accurately account for population structure and relatedness; […]

PMCID: 5886200
PMID: 29309628
DOI: 10.1093/hmg/ddx429

[…] to a reference panel of a combined 1000 genomes project consortium and uk10k project consortium. we tested for association with birth weight of first child using a linear mixed model implemented in bolt-lmm () to account for cryptic population structure and relatedness. genotyping array was included as a binary covariate in the regression model. total chip heritability (i.e. the variance […]

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BOLT-LMM institution(s)
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Endocrinology, Children’s Hospital Boston, Boston, MA, USA; Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
BOLT-LMM funding source(s)
Supported by NIH grant R01 HG006399 and NIH fellowship F32 HG007805; by the Fannie and John Hertz Foundation; by HL043851 and HL080467 from the National Heart, Lung, and Blood Institute and CA047988 from the National Cancer Institute, the Donald W. Reynolds Foundation and the Fondation Leducq, with collaborative scientific support and funding for genotyping provided by Amgen.

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