About

Michael Boehnke is the Richard G. Cornell Distinguished University Professor of Biostatistics at the University of Michigan. He is the Director of the University of Michigan Center for Statistical Genetics and the Genome Science Training Program. His research addresses problems of study design and statistical analysis of human genetic data, with a particular emphasis on statistical methods for human gene mapping. His current focus is on disease and trait association studies based on genome sequence and genotype-array data. Dr. Boehnke has contributed significantly to understanding the genetic basis of complex diseases, especially type 2 diabetes and related traits. He is a principal investigator of the Finland-United States Investigation of NIDDM (FUSION) study and a founder and steering committee member of several large-scale genome-wide association consortia, including DIAGRAM, DIAMANTE, MAGIC, GIANT, and Global Lipids. With over 400 refereed publications, he has chaired numerous doctoral committees and supervised many post-doctoral fellows, many of whom have gone on to faculty positions at major research universities. His educational background includes a BA in Mathematics from the University of Oregon and a PhD in Biomathematics from UCLA.

Research topics

• Genetics
• Biology
• Computer Science
• Computational biology
• Medicine
• Evolutionary biology
• Endocrinology
• Internal medicine
• Demography
• Sociology
• Bioinformatics
• Psychology
• Data science
• Physical medicine and rehabilitation
• Psychiatry
• Neuroscience
• Astronomy
• Clinical psychology
• Environmental health
• Mathematics
• Physics

Selected publications

• Genomic analyses implicate hormonal and metabolic dysregulation in polycystic ovary syndrome

  Nature Genetics · 2026-04-23

  articleOpen access

  Polycystic ovary syndrome (PCOS) and its underlying features remain poorly understood. In this genetic study (n = 544,513), we expand the number of genetic loci from 16 to 29, and additionally identify 31 associated plasma proteins. Many risk-increasing loci were associated with later age at menopause, underscoring the reproductive longevity related to an increased oocyte number and/or availability across the lifespan. Hormonal regulation in the etiology of this condition, through metabolic and reproductive features, was emphasized. The proteomic analysis highlighted metabolic biology known to be related to PCOS. A polygenic risk score (PRS) was associated with adverse cardiometabolic outcomes, with differing relevance of testosterone and body mass index in women and men. Finally, while oligo-anovulation and anovulatory infertility are features of PCOS, we observed no impact of PCOS susceptibility on childlessness. We suggest that PCOS susceptibility confers balanced pleiotropic influences on fertility in women, and life-long adverse metabolic consequences in both sexes.

  PublisherOA PDFDOI

• Polygenic risk score for type 2 diabetes shows context-dependent effects across populations

  UNC Libraries · 2025-11-07

  articleOpen access
  PublisherDOI

• Fine-mapping genomic loci refines bipolar disorder risk genes

  Nature Neuroscience · 2025-06-25 · 20 citations

  articleOpen access

  Bipolar disorder is a heritable mental illness with complex etiology. While the largest published genome-wide association study identified 64 bipolar disorder risk loci, the causal SNPs and genes within these loci remain unknown. We applied a suite of statistical and functional fine-mapping methods to these loci and prioritized 17 likely causal SNPs for bipolar disorder. We mapped these SNPs to genes and investigated their likely functional consequences by integrating variant annotations, brain cell-type epigenomic annotations, brain quantitative trait loci and results from rare variant exome sequencing in bipolar disorder. Convergent lines of evidence supported the roles of genes involved in neurotransmission and neurodevelopment, including SCN2A, TRANK1, DCLK3, INSYN2B, SYNE1, THSD7A, CACNA1B, TUBBP5, FKBP2, RASGRP1, FURIN, FES, MED24 and THRA among others in bipolar disorder. These represent promising candidates for functional experiments to understand biological mechanisms and therapeutic potential. Additionally, we demonstrated that fine-mapping effect sizes can improve performance of bipolar disorder polygenic risk scores across diverse populations and present a high-throughput fine-mapping pipeline.

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• Extensive differential gene expression and regulation by sex in human skeletal muscle

  UNC Libraries · 2025-11-07

  articleOpen access1st authorCorresponding
  PublisherDOI

• Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

  UNC Libraries · 2025-11-07

  articleOpen access
  PublisherDOI

• Genetic Determinants of Circulating Glycine Levels and Risk of Coronary Artery Disease

  2025-11-07

  articleOpen access

  Background Recent studies have revealed sexually dimorphic associations between the carbamoyl-phosphate synthase 1 locus, intermediates of the metabolic pathway leading from choline to urea, and risk of coronary artery disease ( CAD ) in women. Based on evidence from the literature, the atheroprotective association with carbamoyl-phosphate synthase 1 could be mediated by the strong genetic effect of this locus on increased circulating glycine levels. Methods and Results We sought to identify additional genetic determinants of circulating glycine levels by carrying out a meta-analysis of genome-wide association study data in up to 30 118 subjects of European ancestry. Mendelian randomization and other analytical approaches were used to determine whether glycine-associated variants were associated with CAD and traditional risk factors. Twelve loci were significantly associated with circulating glycine levels, 7 of which were not previously known to be involved in glycine metabolism ( ACADM , PHGDH , COX 18- ADAMTS 3, PSPH , TRIB 1, PTPRD , and ABO ). Glycine-raising alleles at several loci individually exhibited directionally consistent associations with decreased risk of CAD . However, these effects could not be attributed directly to glycine because of associations with other CAD -related traits. By comparison, genetic models that only included the 2 variants directly involved in glycine degradation and for which there were no other pleiotropic associations were not associated with risk of CAD or blood pressure, lipid levels, and obesity-related traits. Conclusions These results provide additional insight into the genetic architecture of glycine metabolism, but do not yield conclusive evidence for a causal relationship between circulating levels of this amino acid and risk of CAD in humans.

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• Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits

  UNC Libraries · 2025-11-08

  articleOpen access

  Understanding differences in adipose gene expression between individuals with different levels of clinical traits may reveal the genes and mechanisms leading to cardiometabolic diseases. However, adipose is a heterogeneous tissue. To account for cell-type heterogeneity, we estimated cell-type proportions in 859 subcutaneous adipose tissue samples with bulk RNA sequencing (RNA-seq) using a reference single-nuclear RNA-seq data set. Cell-type proportions were associated with cardiometabolic traits; for example, higher macrophage and adipocyte proportions were associated with higher and lower BMI, respectively. We evaluated cell-type proportions and BMI as covariates in tests of association between >25,000 gene expression levels and 22 cardiometabolic traits. For >95% of genes, the optimal, or best-fit, models included BMI as a covariate, and for 79% of associations, the optimal models also included cell type. After adjusting for the optimal covariates, we identified 2,664 significant associations (P ≤ 2e-6) for 1,252 genes and 14 traits. Among genes proposed to affect cardiometabolic traits based on colocalized genome-wide association study and adipose expression quantitative trait locus signals, 25 showed a corresponding association between trait and gene expression levels. Overall, these results suggest the importance of modeling cell-type proportion when identifying gene expression associations with cardiometabolic traits. 

  PublisherDOI

• Rare-variant association studies: When are aggregation tests more powerful than single-variant tests?

  The American Journal of Human Genetics · 2025-07-29 · 2 citations

  articleOpen accessSenior author
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• Loci for insulin processing and secretion provide insight into type 2 diabetes risk

  UNC Libraries · 2025-11-08

  articleOpen access
  PublisherDOI

• Human germline biallelic loss-of-function <i>OSMR</i> variants cause severe allergic disease

  medRxiv · 2025-08-08 · 1 citations

  preprintOpen access

  ABSTRACT OSMRβ (Oncostatin M receptor beta), a member of the IL-6 superfamily of cell surface receptors, binds OSM and IL-31 and plays a critical role in human immunity. We identified probands from four kindreds with biallelic damaging variants in OSMR , which encodes OSMRβ. Patients had a unifying phenotype for severe widespread, early-onset atopic dermatitis, peripheral eosinophilia, and elevated serum IgE. Patient OSMRβ variants were not appropriately expressed on the cell surface compared to OSMRβ WT . Patient OSMR variants showed significantly reduced OSM-mediated activation of STAT1, STAT3, and STAT5 and distinct transcriptional changes in primary dermal fibroblasts, including loss of interferon and inflammatory signatures. These defects were rescued upon lentiviral transduction of WT- OSMR . Together, these data establish that human germline biallelic loss-of-function OSMR variants cause severe allergic disease. We anticipate that this discovery will facilitate the recognition of additional affected individuals and the full definition of this novel primary atopic disorder.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01MH094145

  NIH · $2.0M · 2016

• Design and Analysis of Human Gene Mapping Studies

  NIH · $2.5M · 2018–2024

• University of Michigan Training Program in Genomic Science

  NIH · $16.8M · 1995–2030

• Identifying Genes for Type 2 Diabetes: FUSION

  NIH · $11.6M · 2002–2022

• NIH Grant U01DK085584

  NIH · $4.1M · 2015

Frequent coauthors

• Karen L. Mohlke

  1767 shared

• Jaspal S. Kooner

  Imperial College London

  1757 shared

• John C. Chambers

  University of Cambridge

  1734 shared

• Ruth J. F. Loos

  Novo Nordisk (United States)

  1713 shared

• Nicholas J. Wareham

  MRC Epidemiology Unit

  1688 shared

• Gonçalo R. Abecasis

  University of Michigan–Ann Arbor

  1677 shared

• Anne Jackson

  1627 shared

• Cornelia M. van Duijn

  1579 shared

Awards & honors

• Member of the National Academy of Medicine
• Fellow of the American Statistical Association
• Fellow of the American Association for the Advancement of Sc…