The Finland-United States Investigation of NIDDM Genetics (FUSION) Tissue Biopsy Study

The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits (QTs). Skeletal muscle and adipose are major insulin target tissues and play key roles in insulin resistance. We hypothesize that a subset of T2D and related QT variants alter gene expression in skeletal muscle and adipose tissue. For this FUSION Tissue Biopsy Study, we have obtained and are analyzing RNA-Seq, microRNA (miRNA)-Seq, and DNA methylation (methyl)-Seq data on biopsy samples from 331 individuals from across the range of glucose tolerance: 124 normal glucose tolerance (NGT), 77 impaired glucose tolerance (IGT), 44 impaired fasting glucose (IFG), and 86 newly-diagnosed T2Ds. Participants completed two study visits, two weeks apart. First visits comprised most of the clinical phenotyping, including four-point OGTT (fasting, and 30, 60, and 120 minute post-load); BMI, WHR; lipids; blood pressure; and many other variables. Participants also completed FUSION health history, medication, and lifestyle questionnaires. At second visit, we obtained ~250mg vastus lateralis skeletal muscle, ~750mg abdominal subcutaneous adipose, and a ~5x15mm section of abdominal skin. Visits were completed in March 2013. RNA isolation is ongoing in the Collins laboratory at the NIH, RNA and miRNA sequencing at the NIH Intramural Sequencing Center (NISC), and genotyping at the Center for Inherited Disease Research (CIDR). Individual-level data is available here for the 306 individuals who consented to data deposit.

To focus on evaluation of gene expression and its regulation in skeletal muscle, we analyzed mRNA extracted from vastus lateralis skeletal muscle obtained from 271 of the 331 individual subjects from Finland, along with genome-wide genotypes. Individual-level data is available here for the 250 subjects who reconsented to the use of their data. Release phs001048.v2.p1 adds muscle data for an additional 42 subjects and data from adipose tissue for 276 subjects. Total RNA was isolated using Trizol extraction in the Collins laboratory at the NIH. The mRNA was poly-A selected, 24-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol and RNA sequencing was performed on HiSeq2000 sequencers using 101bp paired-end reads at NISC. miRNA libraries were prepared from total RNA from 296 muscle and 270 adipose samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. Data for 272 muscle and 251 adipose samples are available here for individuals with consent for data deposit. DNA was extracted from blood in the Collins laboratory, and genotyping on the Illumina Omni2.5M array was performed at CIDR. Genotypes were imputed using the HRC 2016 reference panel. In order to assess regions of open chromatin in skeletal muscle, we obtained muscle tissue from a commercial provider to perform ATAC-seq; these samples were sequenced at the University of Michigan DNA Sequencing Core.

Greater than 90% of the approximately 80 loci associated with T2D and the 100s of loci associated with T2D-related traits (glucose and insulin, anthropometrics, lipids) through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Regulatory element activity is often tissue-specific, which further complicates discovery of the causal/functional variation. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains whole genome sequence and whole genome bisulfite sequence, and/or Illumina MethylationEPIC Array data, of two tissues relevant to T2D: skeletal muscle and adipose tissue from individuals with glucose tolerance categories ranging from normal to T2D, providing a comprehensive survey of both individual genetic variation as well as DNA methylation across different tissues from multiple individuals.

• Study Design:
  • Prospective Longitudinal Cohort
• Study Type:
  • Cohort
  • Prospective
• dbGaP estimated ancestry using GRAF-pop
• Total number of consented subjects: 307
• Subject Sample Telemetry Report (SSTR)

• BioProject
• PubMed
• Sequence Read Archive
• BioSample
• MeSH
• Gene
• PMC

We attempted to contact still-living FUSION spouses and offspring who participated in FUSION study visits between 1994 and 1998, individuals who had participated in the population-based Savitaipale Prospective Diabetes Study, the FINRISK 2007 survey, the Dose Responses to Exercise Training (DR's EXTRA) study and the Metabolic Syndrome in Men (METSIM) study. Additional subjects were recruited by newspaper advertisements.

We excluded individuals: (1) with drug treatment for diabetes, (2) with diseases that might be expected to confound the analyses (for example, cancer, skeletal muscle diseases, acute or chronic inflammatory diseases), (3) with diseases that increase hemorrhage risk during biopsy (for example, von Willebrand's disease, hemophilia, severe liver diseases), (4) taking medications that need to be taken daily and increase hemorrhage risk in the biopsies including warfarin (patients on acetosalicylic acid were instructed to stop for 7 days prior to biopsy), (5) taking medications that could confound the analyses (for example, oral corticosteroids, other anti-inflammatory drugs such as 5-ASA, infliximab or methotrexate), and (6) of age <18 years.

• Primary Phenotype: Diabetes Mellitus, Type 2

• ANK1

• Principal Investigators
  • Michael Boehnke. University of Michigan, Ann Arbor, MI, USA.
  • Francis S. Collins. National Institutes of Health, Bethesda, MD, USA.
  • Richard Bergman. Cedars-Sinai Medical Center, West Hollywood, CA, USA.
  • Jaakko Tuomilehto. National Institute for Health and Welfare, Helsinki, Finland.
  • Heikki Koistinen. National Institute for Health and Welfare, Helsinki, Finland.
  • Karen Mohlke. University of North Carolina, Chapel Hill, NC, USA.
  • Markku Laakso. University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland.
  • Laura Scott. University of Michigan, Ann Arbor, MI, USA.
• Principal Investigator for WGS/WGBS
  • Richard K. Wilson. McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
• Co-Investigators
  • Stephen Parker. University of Michigan, Ann Arbor, MI, USA.
  • Ryan Welch. University of Michigan, Ann Arbor, MI, USA.
  • Heather Stringham. University of Michigan, Ann Arbor, MI, USA.
  • Lori Bonnycastle. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Mike Erdos. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Narisu Narisu. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
• Sequencing Centers
  • NIH Intramural Sequencing Center. National Institutes of Health, Bethesda, MD, USA.
  • University of Michigan DNA Sequencing Core. University of Michigan, Ann Arbor, MI, USA.
  • McDonnell Genome Institute. Washington University School of Medicine, St. Louis, MO, USA.
• Genotyping Center
  • Center for Inherited Disease Research (CIDR). Johns Hopkins University, Baltimore, MD, USA.
• Funding Sources
  • U01DK062370. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
  • R00DK099240. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
  • R01DK072193. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
  • 1-ZIA-HG000024. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Z1B-HG000196. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • 1-14-INI-07. American Diabetes Association, Alexandria, VA, USA.
  • Grant - 271961. Academy of Finland, Helsinki, Finland.
  • Grant - 272741. Academy of Finland, Helsinki, Finland.
  • Grant - 258753. Academy of Finland, Helsinki, Finland.
• Funding Source for CIDR Genotyping
  • HHSN268201200008I NIH contract "High throughput genotyping for studying the genetic contributions to human disease". National Institutes of Health, Bethesda, MD, USA.
• Funding Source for WGS/WGBS
  • U54 HG003079. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.