Cristen Willer, Ph.D
Department of Computational Medicine and Bioinformatics,
University of Michigan, Ann Arbor, MI, USA.
Pradeep Natarajan, M.D, MMSc.
Massachusetts General Hospital, Broad Institute of Harvard and MIT
Boston, MA, USA
ADVANCE (Atherosclerotic Disease, VAscular FuNction, & GenetiC Epidemiology study)
ADVANCE is an epidemiological case-control study of genetic and non-genetic determinants of coronary artery disease (CAD) that started in 2000 as a collaborative effort between researchers at Stanford University and Kaiser Permanente of Northern California (KPNC)2. Between October 2001 and December 2003, a total of 3,179 subjects from KPNC were enrolled into three case groups and two control groups. A multi-ethnic subset of ~520 cases underwent GWAS in 2007 along with a set of controlsfrequency-matched to cases by age and sex. All remaining older onset cases (n = 974) and older controls (n =705) of white/European ancestry underwent Metabochipgenotyping in 2010. Included in this analysis are all controls not on lipid altering therapy at the time of determination of serum lipid levels.
2. Assimes, T.L. et al. Susceptibility locus for clinical and subclinical coronary artery disease at chromosome 9p21 in the multi-ethnic ADVANCEstudy. Hum Mol Genet17, 2320-8 (2008).
AMC-PAS (The Academic Medical Center of Amsterdam Premature Atherosclerosis Cohort)
AMC-PAS is aprospective study cohort recruited from the Academic Medical Centre Amsterdam that consists of patients with Premature AtheroSclerosis (PAS), defined as symptomatic CAD before the age of 51 years, or MI, coronary revascularization, or evidence of at least 70% stenosis in a major epicardial artery3. The total sample size at time of genotyping was 1,089; only cases with sufficient good quality DNA were included.
3. Samani, N.J. et al. Large scale association analysis of novel genetic loci for coronary artery disease. Arterioscler Thromb Vasc Biol29, 774-80 (2009).
The Old Order Amish individuals included in this study were participants of several ongoing studies of cardiovascular health carried out at the University of Maryland among relatively healthy volunteers from the Old Order Amish community of Lancaster County, PA and their family members4,5. The 1,200 subjects on whom the Metabochip was genotyped were recruited between 2002 and 2006 and examined at the Amish Research Clinic in Strasburg, PA.
4. Mitchell, B.D. et al. The genetic response to short-term interventions affecting cardiovascular function: rationale and design of the Heredity and Phenotype Intervention (HAPI) Heart Study. Am Heart J155, 823-8 (2008).
5. Post, W. et al. Determinants of coronary artery and aortic calcification in the Old Order Amish. Circulation115, 717-24 (2007).
BC58 (1958 British Birth Cohort)
The 1958 British Birth Cohort was initiated as a study of perinatal mortality focusing on just over 17,000 births in England, Wales, and Scotland, during one week in 1958, with the aim of identifying social and obstetric factors linked to stillbirth and neonatal death6-8. The individuals were followed into adult life, with a biomedical survey of the cohort conducted when they were aged 44-45 years. The survey included anthropometric measurements, blood sampling for lipids, and blood pressure measurements. The sample comprises 5,639 individuals of white European ethnicity, of which 2,136 were analyzed (http://www.b58cgene.sgul.ac.uk/collection.php).
6. Power, C. & Elliott, J. Cohort profile: 1958 British birth cohort (National Child Development Study). Int J Epidemiol35, 34-41 (2006).
7. Strachan, D.P. et al. Lifecourse influences on health among British adults: effects of region of residence in childhood and adulthood. Int J Epidemiol36, 522-31 (2007).
8. Atherton, K., Fuller, E., Shepherd, P., Strachan, D.P. & Power, C. Loss and representativeness in a biomedical survey at age 45 years: 1958 British birth cohort. J Epidemiol Community Health62, 216-23 (2008).
The purpose of the study is to gather information about prevalence of diabetes and cardiovascular diseases and of the risk factors associated with these within the Finnish population9. The survey assists in the evaluation of the effects of the national type 2 diabetes prevention plan. The study sample consists of 4,500 people randomly selected from the Finnish population register between the ages of 45 and 74 years and living in one of the three hospital districts chosen for the study: South Ostrobothnia, Central Finland, and Pirkanmaa.
9. Kotronen, A. et al. Non-alcoholic and alcoholic fatty liver disease - two diseases of affluence associated with the metabolic syndrome and type 2 diabetes: the FIN-D2D survey. BMC Public Health10, 237 (2010).
The deCODE lipid study includes lipid measurements from Icelanders recruited through various genetic studies at deCODE, primarily cardiovascular studies10. The measurements were done between the years 1987 and 2010. For the current analysis we excluded individuals using lipid lowering drugs. Genotypes and lipidmeasurements were available for 15,612 Icelanders. The study was approved by the Icelandic Data Protection Commission and the National Bioethics Committee. All study participants signed informed consent and donated blood samples. Personal identities were encrypted by a third party system provided by the Icelandic Data Protection Commission.
10. Helgadottir, A. et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science316, 1491-3 (2007).
DIAGEN (The DIAbetes GENetic Study)
DIAGEN is a large, prospective study of diabetes genetics that began in 1997 and seeks to understand the genetic causes of diabetes development; 6,282 individuals have been studied to date11. DIAGEN recruits and phenotypes individuals at high risk of T2D; 3,611 individuals from German families with a history of T2D, obesity, or dyslipoproteinemia have been studied to date from Dresden and surrounding areas.
11. Schwarz, P.E. et al. Hypoadiponectinemia is associated with progression toward type 2 diabetes and genetic variation in the ADIPOQ gene promoter. Diabetes Care29, 1645-50 (2006).
DILGOM (The Dietary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome study)
DILGOM consists of 5,025 individuals who took part in the larger FINRISK 2007 collection12. The DILGOM sample was collected to study in greater detail the components affecting obesity and metabolic syndrome.
12. Vartiainen, E. et al. Thirty-five-year trends in cardiovascular risk factors in Finland. Int J Epidemiol39, 504-18 (2010).
DPS (The Finnish Diabetes Prevention Study)
DPS is a prospective randomized controlled trial aimed at preventing the progression from IGT to diabetes13. The original DPS was initiated in 1993. A total of 522 middle-aged, overweight subjects with IGT at baseline were randomized into either a lifestyle intervention or a standard-care control group. They were followed for occurrence of diabetes until the year 2000, when the first interim analysis of the data was carried out as originally planned. At this point, the randomized trial was prematurely terminated due to markedly lower diabetes incidence rate in the lifestyle intervention group as compared to the control group. Since the termination of the randomized phase of the DPS, the original cohorts are no longer offered different treatments. However, all participants are monitored with yearly visits for long-term development of type 2 diabetes and complications.
13. Tuomilehto, J. et al. Prevention of type 2 diabetes mellitus by changes in lifestyle among subjects with impaired glucose tolerance. N Engl J Med344, 1343-50 (2001).
DR'S EXTRA (The Dose Responses to Exercise Training Study)
DR's EXTRA is a 4-year randomized controlled trial on the health effects of aerobic and resistance exercise training and a diet with lowsaturated fat, highunsaturatedfat, and highfiber in a population sample of middle-aged and older men and women14. The target population was a representative sample of 3,000 individuals (1,500 men, 1,500 women) who lived in the city of Kuopio in Finland and who were 55-74 years of age in 2002, when they were randomly selected from the national population register. Of these individuals, 2,062 were willing to participate and 1,479 (72%) participated in the baseline examinations in 2005-2006. 1,410 individuals were randomly allocated into one of the six study groups, each of which included about 235 persons.
14. Kouki, R. et al. Diet, fitness and metabolic syndrome - The DR's EXTRA Study. Nutr Metab Cardiovasc Dis (2010).
EAS (Edinburgh Artery Study)
EASis a prospective study of 1,592 men and women whose age at baseline ranged from 55 to 74 years15. The population was selected at random, in 5-year age bands, from 10 general practices spread socioeconomically across the city of Edinburgh, Scotland. A large number of biomarkers and phenotypes, focusing predominantly on putative vascular risk factors, have been measured. To identify all deaths, participant records were flagged at the UK NHS Central Registry. To obtain details of possible non-fatal events, information was sought from general practitioners, hospitals, the Information Services Division of NHS Scotland and by annual questionnaire to the subjects themselves. All cardiovascular events and deaths were further investigated using hospital or general practitioner records. The study was approved by the Lothian Health Board Ethics Committee and informed consent was obtained from each participant.
15. Fowkes, F.G. et al. Edinburgh Artery Study: prevalence of asymptomatic and symptomatic peripheral arterial disease in the general population. Int J Epidemiol20, 384-92 (1991).
EGCUT (Estonian Genome Center of University of Tartu)
The Estonian cohort is from the population-based biobank of the Estonian Genome Project of University of Tartu (EGCUT)16. The project is conducted according to the Estonian Gene Research Act, and all participants have signed the broad informed consent. The current cohort size is > 51,515, 18 years of age and older, which reflects closely the age distribution in the adult Estonian population. Subjects are recruited by the general practitioners (GP) and physicians in the hospitals were randomly selected from individuals visiting GP offices or hospitals. Each participant filled out a computer-assisted personal interview during 1-2 hours at a doctor's office, including personal data (place of birth, place(s) of living, nationality. etc.), genealogical data (three generation family history), educational and occupational history, and lifestyle data (physical activity, dietary habits, smoking, alcohol consumption, women's health, quality of life). For the current study, 2,770 individuals were genotyped with Metabochip; 1,072 of these had lipids data available.
16. Nelis, M. et al. Genetic structure of Europeans: a view from the North-East. PLoS One4, e5472 (2009).
The Ely study commenced in 1990 as a prospective population-based cohort study of the etiology and pathogenesis of type 2 diabetes and related metabolic disorders. Study aims are: 1) understanding the pathogenesis of type 2 diabetes in a Caucasian population through longitudinal examination of people free of diabetes at baseline; 2) determining early markers of future risk of progression of glucose intolerance and providing the means to identify populations at high risk of diabetes; and 3) quantifying and specifying the role of key exposures in adult life, particularly diet and physical activity17.
17. Williams, D.R. et al. Undiagnosed glucose intolerance in the community: the Isle of Ely Diabetes Project. Diabet Med12, 30-5 (1995).
EPIC-CAD and EPIC-T2D (The European Prospective Investigation into Cancer and Nutrition)
EPIC was designed to investigate the relationships between diet, nutritional status, lifestyle and environmental factors and the incidence of cancer and other chronic diseases. EPIC is a large study of diet and health having recruited 520,000 individuals18,19.
18. Day, N. et al. EPIC-Norfolk: study design and characteristics of the cohort. European Prospective Investigation of Cancer. Br J Cancer80 Suppl 1, 95-103 (1999).
19. Harding, A.H. et al. Dietary fat and the risk of clinical type 2 diabetes: the European prospective investigation of Cancer-Norfolk study. Am J Epidemiol159, 73-82 (2004).
Fenland is a population-based study of lifestyle and health. The study will investigate the influence of diet, lifestyle, and genetic factors on the development of diabetes and obesity. The participants are from the general population in the East Cambridgeshire and Fenland area and were born between 1950 and 1975.
FINCAVAS (The Finnish Cardiovascular Study)
The purpose of the FINCAVAS is to construct a risk profile - using genetic, haemodynamic, and electrocardiographic (ECG) markers - of individuals at high risk of cardiovascular diseases, events, and deaths20. All patients scheduled for an exercise stress test at Tampere University Hospital and willing to participate were recruited between October 2001 and December 2007. The final number of participants is 4,567. In addition to repeated measurement of heart rate and blood pressure, digital high-resolution ECG at 500 Hz is recorded continuously during the entire exercise test, including the resting and recovery phases. About 20% of the patients are examined with coronary angiography. Genetic variations known or suspected to alter cardiovascular function or pathophysiology are analyzed to elucidate the effects and interactions of these candidate genes, exercise, and commonly used cardiovascular medications. Genotyping has been done with the Metabochip for 2,795 participants. After exclusions, both genotype and lipid data were available for 1,201 participants.
20. Nieminen, T. et al. The Finnish Cardiovascular Study (FINCAVAS): characterising patients with high risk of cardiovascular morbidity and mortality. BMC Cardiovasc Disord6, 9 (2006).
FRISCII (Fragmin and Fast Revascularization during Instability in Coronary Artery Disease)
CAD patients were randomly assigned an early invasive or non-invasive treatment strategy with placebo-controlled long-term low-molecular-mass heparin (dalteparin) for 3 months as part of a clinical trial21. Total sample size of cases is 3,489. Healthy controls (N=500) were selected to match in age and sex to the cases. In total, 2,963 individuals have been analyzed (N cases = 2,552 N controls = 411).
21. Wallentin, L. et al. Outcome at 1 year after an invasive compared with a non-invasive strategy in unstable coronary-artery disease: the FRISC II invasive randomised trial. FRISC II Investigators. Fast Revascularisation during Instability in Coronary artery disease. Lancet356, 9-16 (2000).
FUSION2 includes subjects chosen from the following studies: Dehko 2D (D2D) 2004: a population-based study to screen individuals regarding T2D risk and to prevent T2D development; Finrisk 1987: an early round of the 5-yearly Finrisk national population-based health surveys; Finrisk 2002: a population-based survey of non-communicable diseases in ≥ 13,000 individuals aged 25-74 years living in 80 communities of Finland; Action LADA: a study of latent autoimmune diabetes in adults (LADA)22. Action LADA investigators screened individuals aged 30-69 years with recently-diagnosed diabetes and identified 373 T2D cases who agreed to participate in FUSION; Health 2000: a population-based study of people aged .30 years from throughout Finland; Savitaipale Diabetes Study: a study of diabetes in the town of Savitaipale in eastern Finland.
22. Scott, L.J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science316, 1341-5 (2007).
GLACIER (Gene x Lifestyle interactions And Complex traits Involved in Elevated disease Risk)
GLACIER is an ongoing population-based prospective cohort study comprising 19,547 adults from the northern Swedish county of Västerbotten, nested within the Northern Sweden Health and Disease Study23. All GLACIER participants underwent detailed health and lifestyle examinations as part of the Västerbotten Intervention Programme (VIP), an ongoing population-wide project focused on type 2 diabetes, cardiovascular disease, and common cancers. Since 1985, all residents of the county aged 40, 50, and 60 years have been invited to visit their primary health care centers for clinical examinations according to a standardized protocol. Baseline examinations of GLACIER participants were undertaken from 1985 through 2004. In the present study, 5,764 individuals were included in the analysis.
23. Renstrom, F. et al. Genetic predisposition to long-term nondiabetic deteriorations in glucose homeostasis: Ten-year follow-up of the GLACIER study. Diabetes60, 345-54 (2011).
Go-DARTs (Genetics of Diabetes and Audit Research Tayside)
A high quality resource, initially funded by the Wellcome Trust and supported by Diabetes UK, has been created with successful recruitment of consented patients with type 2 diabetes and matching controls (non diabetics) throughout Tayside24.
24. Kimber, C.H. et al. TCF7L2 in the Go-DARTS study: evidence for a gene dose effect on both diabetes susceptibility and control of glucose levels. Diabetologia50, 1186-91 (2007).
HUNT (Nord-Trøndelag Health Study 2)
The HUNT study is a large population-based health study in Nord-Trøndelag county, central Norway (population 127,000). HUNT 2 was carried out in 1995-1997; data were collected through questionnaires, clinical exam, and blood and urine samples. 74,000 individuals (71%) participated.
IMPROVE is a cohort of European subjects with .3 classical CVD risk factors, recruited from seven centers in five countries25. Of 3,418 subjects with genotyping and detailed ultrasonic phenotyping of carotid inter-media thickness, 1,769 subjects were included in this study.
25. Baldassarre, D. et al. Cross-sectional analysis of baseline data to identify the major determinants of carotid intima-media thickness in a European population: the IMPROVE study. Eur Heart J31, 614-22 (2010).
KORA F3 (Cooperative Research in the Region of Augsburg)
KORA is a series of independent population-based epidemiological surveys and follow-up studies of participants living in the region of Augsburg, Southern Germany26. All participants are residents of Germany. In KORA S3, 4,856 subjects have been examined. 3,184 subjects participated in a 10-year follow-up examination of S3 in 2004/05. The present study includes data of 2,816 individuals of the follow-up study KORA F3. All participants gave signed informed consent. The local ethics committee has approved the studies.
26. Wichmann, H.E., Gieger, C. & Illig, T. KORA-gen--resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen67 Suppl 1, S26-30 (2005).
KORA F4 (Cooperative Research in the Region of Augsburg)
KORAis a series of independent population-based epidemiological surveys and follow-up studies of participants living in the region of Augsburg, Southern Germany26. All participants are residents of Germany. In the KORA S4 study, 4,261 subjects have been examined. 3,080 subjects participated in a 10-year follow-up examination of S4 in 2006-2008. The present study includes data of 2,678 individuals of the follow-up study KORA F4. All participants gave signed informed consent. The local ethics committee has approved the studies.
LURIC (Ludwigshafen Risk and Cardiovascular Health Study)
LURIC includes 3,316 consecutive white patients of Caucasian origin (17 to 92 years of age) hospitalized for coronary angiography between June 1997 and May 200127. Clinical indications for angiography were chest pain or non-invasive tests consistent with myocardial ischemia. To limit clinical heterogeneity, individuals suffering from acute illness other than acute coronary syndromes, chronic non-cardiac diseases and a history of malignancy within the five past years were excluded. For this study, 1,506 samples were included in the analysis.
27. Winkelmann, B.R. et al. Rationale and design of the LURIC study--a resource for functional genomics, pharmacogenomics and long-term prognosis of cardiovascular disease. Pharmacogenomics2, S1-73 (2001).
MDC (Malmo Diet and Cancer Study)
Prospective observational population-based study with a baseline examination 1991-1996 (n = 28,098) and follow ups of mortality and morbidity by means of registries28. The main focus is on cancer and cardiovascular disease.
28. Berglund, G., Elmstahl, S., Janzon, L. & Larsson, S.A. The Malmo Diet and Cancer Study. Design and feasibility. J Intern Med233, 45-51 (1993).
METSIM (METabolic Syndrome In Men)
The METSIM study aims to investigate the metabolic syndrome, type 2 diabetes, cardiovascular disease, and cardiovascular risk factors29. It is an ongoing study of men aged 50 to 70 years, randomly selected from the population registry of the town of Kuopio, in Eastern Finland.
29. Stancakova, A. et al. Changes in insulin sensitivity and insulin release in relation to glycemia and glucose tolerance in 6,414 Finnish men. Diabetes58, 1212-21 (2009).
NFBC1986 (Northern Finland Birth Cohort 1986)
NFBC1986 is a longitudinal one-year birth cohort study from an unselected population. The cohort included all the mothers (N = 9,362) with children whose expected date of birth fell between July 1, 1985 and June 30, 1986 in the two northernmost provinces of Finland (Oulu and Lapland). Altogether 9,479 children were born into the cohort, 9,432 of them live-born. In the 15/16-year follow-up study, blood samples were taken from 6,400 individuals of whom 4,900 were genotyped.
NSHD (MRC National Survey of Health and Development)
The Medical Research Council National Survey of Health and Development (NSHD), MRC 1946 Study30. This is an ongoing prospective birth cohort study consisting of all births in England, Scotland, and Wales in one week in March 1946. The sample includes single, legitimate births whose fathers were in non-manual or agricultural occupations and a randomly selected one in four of all others, whose fathers were in manual labor. The original cohort, now 62 years of age, comprised 2,547 women and 2,815 men who have been followed up > 20 times since birth. The data collected to date include cognitive function, physical, lifestyle and anthropomorphic measures as well as blood analytes, and other measures. Through MRC Unit funding, the cohort is currently undergoing a particularly intensive phase of clinical assessment and biological sampling, with blood and urine sampling and analysis, cardiac and vascular imaging (http:www.nshd.mrc.ac.uk).
30. Wadsworth, M., Kuh, D., Richards, M. & Hardy, R. Cohort Profile: The 1946 National Birth Cohort (MRC National Survey of Health and Development). Int J Epidemiol35, 49-54 (2006).
PIVUS (Prospective Investigation of the Vasculature in Uppsala Seniors)
Participants were randomly sampled from all men and women aged 70 years living in Uppsala County in 2001 (www.medsci.uu.se/PIVUS)31. Of the 2,025 individuals invited, 1,016 participated. Participants underwent a medical examination including a detailed questionnaire on lifestyle and socioeconomic factors, fasting blood sampling, blood pressure measurement and anthropometric measurements, as previously described.18 Blood and plasma samples were frozen until analysis, and blood tests performed included a wide variety of traditional and more recent CVD risk factors, along with DNA extraction. In addition, individuals have undergone extensive phenotyping including whole body MRI, echocardiography, endothelial function measurements, carotid ultrasound, DXA, and spirometry.
31. Ingelsson, E., Hulthe, J. & Lind, L. Inflammatory markers in relation to insulin resistance and the metabolic syndrome. Eur J Clin Invest38, 502-9 (2008).
SardiNIA (SardinNIA Study on Aging)
The SardiNIA study is a cohort of 6,148 participants, aged 14-102 years, from four clustered towns in Sardinia; it includes 34,469 relative pairs32. Phenotype data are available on hundreds of traits. GWAS data has been collected on ~4,700 individuals and the entire sample has been genotyped with the Metabochip.
32. Pilia, G. et al. Heritability of cardiovascular and personality traits in 6,148 Sardinians. PLoS Genet2, e132 (2006).
A case-control study recruited from the Stockholm region of Sweden. Controls subjects were matched (for age and geographical location) to subjects with MI. Of a total of 3,400 subjects, 2,973 were included in this study.
STR (Swedish Twin Register)
Four sub-studies within the Swedish Twin Register were utilized in current study, including Sex differences in health and aging (GENDER), Individual differences among the oldest-old (OCTO-Twin), and Swedish Adoption/Twin Study of Aging (SATSA)33. Similar examinations with both questionnaires and blood sampling were done in each study.
Information has been updated annually on mortality and morbidity using national registries, such as the Cause of Death Registry, the National Patient Registry, and the Prescribed Drug Registry. Different biomarkers have been measured, such as markers of inflammation, lipoproteins, fatty acid composition, glucose and insulin metabolism. We required overnight fasting before blood draw except for OCTO-Twin study.
33. Reynolds, C.A. et al. A survey of ABCA1 sequence variation confirms association with dementia. Hum Mutat30, 1348-54 (2009).
THISEAS (The Hellenic study of Interactions between SNPs and Eating in Atherosclerosis Susceptibility)
THISEAS is a case-control study designed to investigate the association between genetic and lifestyle environmental factors and the risk of coronary artery disease in adults34,35. Study participants were recruited from 8 hospitals and from Open Care Centers for the elderly in the region of Athens. Cases were subjects presenting with either ACS or stable CAD defined as > 50% stenosis in at least one of the three main coronary vessels assessed by coronary angiography. ACS was defined as acute MI or unstable angina corresponding to class III of the Braunwald classification. ACS patients have also undergone coronary angiography examination that verified the presence of significant stenosis. Controls were subjects with negative coronary angiography findings, or negative stress test, or subjects without symptoms of disease that were admitted at the same hospitals as cases and were free of any cardiovascular disease, cancer, or inflammatory diseases. Exclusion criteria for both study groups were renal or hepatic disease. The bioethics committee of Harokopio University approved the study and all participants gave their informed consent. Hematological, biochemical, and anthropometric measurements were conducted for all participants. Dietary assessment through a semi-quantitative food frequency questionnaire and physical activity data were collected through face-to-face interview by well trained scientists.
34. Theodoraki, E.V. et al. Fibrinogen beta variants confer protection against coronary artery disease in a Greek case-control study. BMC Med Genet11, 28 (2010).
35. Theodoraki, E.V. et al. ROS1 Asp2213Asn polymorphism is not associated with coronary artery disease in a Greek case-control study. Clin Chem Lab Med47, 1471-3 (2009).
TROMSO (Tromsø 4)
The Tromsø is a prospective population-based study in the city of Tromsø in Northern Norway (population 64,000)36. There have been five study waves to date. The participation rate was > 75% each time; 38,164 adults have participated at least once. For Tromsø 4(1994), all inhabitants aged .25 years were invited and 27,159 (77%) participated.
36. Jacobsen, B.K., Eggen, A.E., Mathiesen, E.B., Wilsgaard, T. & Njolstad, I. Cohort profile: The Tromso Study. Int J Epidemiol (2011).
ULSAM (Uppsala Longitudinal Study of Adult Men)
ULSAM was initiated as a health investigation focused on identifying metabolic risk factors for cardiovascular disease, to which all 50-year-old men living in Uppsala County, Sweden, in 1970-74 were invited37. Of these, 82% (2,322 men) participated in the investigation. The men have been investigated at the ages of 50, 60, 71, 77, 82, and 88 years. The examination performed at age 71 (in 1991-1995), when the DNA was collected, included medical examination, questionnaire, cognitive function testing, 7-day dietary assessment, anthropometric measurements, blood sampling (after an overnight fast), blood pressure measurement, 24-hour ambulatory blood pressure measurement, electrocardiography, echocardiography, OGTT, muscle biopsy, and euglycemic insulin clamp. Outcome data have been updated annually on mortality and morbidity using national registries, such as the Cause of Death Registry, the National Patient Registry, and the Prescribed Drug Registry. Many biomarkers have been measured, such as markers of inflammation/oxidation, lipoproteins, fatty acid composition, and glucose and insulin metabolism. Insulin sensitivity was determined using the euglycemic insulin clamp technique, with a slight modification; insulin was infused at a constant rate of 56 instead of 40 mU/(min*m2) to achieve nearly complete suppression of hepatic glucose output.
37. Ingelsson, E., Sundstrom, J., Arnlov, J., Zethelius, B. & Lind, L. Insulin resistance and risk of congestive heart failure. JAMA294, 334-41 (2005).
The Whitehall II Study recruited 10,308 participants (70% men) between 1985 and 1989 and involved 20 London-based civil service departments38. In this longitudinal study, clinical data were collected in phase 1 (1985-1988), phase 3 (1991-1993), phase 5 (1997-1999), and phase 7 (2003-2004). DNA was stored from phase 7 from > 6,000 participants. The study individuals are all well phenotyped for cardiovascular and other ageing related health outcomes.
38. Marmot, M. & Brunner, E. Cohort Profile: the Whitehall II study. Int J Epidemiol34, 251-6 (2005).
CLHNS (Cebu Longitudinal Health and Nutrition Survey)
CLHNSis an on-going community-based study that began in 198339. The baseline survey randomly recruited 3,327 mother-child pairs from 17 urban and 16 rural areas from the Metropolitan Cebu area, the Philippines. Overnight fasting blood samples for biomarkers and DNA were obtained at the 2005 survey. In this study, 1,771 offspring samples were included in analysis.
39. Adair, L.S. et al. Cohort profile: the Cebu longitudinal health and nutrition survey. Int J Epidemiol40, 619-25 (2011).
TAICHI (TAIwanmetaboCHIp consortium)cohorts
The TaiChi consortium was formed through a collaborative effort between investigators based in the U.S. and Taiwan. The consortium's primary aim is to identify genetic determinants of atherosclerosis and diabetes related traits in East Asians and to fine-map validated loci identified in other race/ethnic groups.The main academic sites in Taiwan include Taipei and Taichung Veteran's General Hospitals (VGH), National Health Research Institute (NHRI), Tri-Service General Hospital (TSGH), and National Taiwan University Hospital (NTUH). The main U.S academic sites participating in the TaiChi consortium include Stanford University School of Medicine in Stanford, California; Hudson-Alpha Biotechnology Institute in Huntsville, Alabama; and Cedars-Sinai Medical Center (CSMC) in Los Angeles, California. There are 7 principal Taiwan based cohorts that make up the current TaiChi bio-resource with a total of 11,859 subjects in the current study. Each cohort is described in more detail in the supplementary text.
- a. Taiwan DRAGON (Taiwan Diabetes and RelAted Genetic COmplicatioN) study is a cohort study with T2DM at the Veteran's General Hospital in Taichung, Taiwan (Taichung VGH). Participants include individuals with either newly diagnoses or established diabetes who visit the diabetes outpatient clinic on a regular basis. Subjects with hyperglycemia who do not meet criteria for Type 2 DM defined by IDF are not included. Individuals participate in a health examination program at Taichung VGH are also interviewed. Specialized tests include an oral glucose tolerance tests (OGTT) in subjects without an established diagnosis of diabetes.
- b. HALST (Healthy Aging Longitudinal Study in Taiwan) is a population based multi-site cohort study of ambulatory adults aged > 55 years living in 7 major geographic regions of Taiwan, established by the NHRI. The aim of the study is to investigate themultidimensional determinants, including lifestyle, genetic, metabolic, and inflammatory factors, of an older Asian population.These 7 locations include both urban and rural areas: two are in the north (Taipei's Shilin District and Taoyuan County's Yangmei Township), two in central Taiwan (Miaoli City in Miaoli County and Changhua City in Changhua County), two in the south (Puzi, Chiayi County, and Kaohsiung's Lingya District), and one in the east (Hualien City/County). The only exclusion criteria are presence of highly contagious diseases, advanced illnesses with limited life span or bedridden status, dementia, other advanced neurological deficit, severe hearing loss, and institutionalization in a chronic care facility for any reason. Over 5000 subjects are being recruited over a five-year period (2008-2012) from seven recruitment sites across the country. Following completion of recruitment of the initial HALST cohort, follow-up in person visits will be scheduled during a second 5-year study cycle scheduled to begin in 2013 (~1000 subjects / year). Within each wave, participants are to be followed up by telephone contact every year for vital status and for updates on health-related conditions. Medical records are requested to confirm the development of any new health conditions. Vital status, health claims, health care utilization data are being collected for the cohort on a regular basis by linking to the National Death Registry DatabaseandtheNational Health Insurance Database.
- c. SAPPHIRe (Stanford-Asian Pacific Program in Hypertension and Insulin Resistance) is a family based study established in 1995 with an initial goal of identifying major genetic loci underlying hypertension and insulin resistance through linkage in East Asian populations. SAPPHIRe was also one of four networks participating the NHLBI's Family Blood Pressure Program (FBPP). At the outset, SAPPHIRe involved recruitment sites in the San Francisco Bay Area, Hawaii, and Taiwan. However, a majority of the ~1,700 sibpairs in SAPPHIRe were recruited from 3 centers in Taiwan (NTUH, Taipei VGH and Taichung VGH) with NHRI being the DCC. Sibpairs were either highly concordant or discordant for blood pressure and a subset underwent an insulin suppression test. Many metabolicvariables associated with blood pressure and insulin resistance were examined in the first 5-year investigative cycle funded by the NIH (1995-2000). Further extensive phenotyping through return visits and regular follow ups occurred between 2001 and 2008 in the Taiwanese SAPPHIRe participants which included echocardiographic and multi-detector row CT imaging procedures. During this time, SAPPHIRe was referred to as the HIRGs study in Taiwan.
- d. TACT (TAiwan Coronary and Transcatheter intervention) cohort study enrolled patients with angina pectoris and objective documentation of myocardial ischemia who underwent diagnostic coronary angiography and/or revascularization any time after October 2000 at the National Taiwan University Hospital (NTUH). This cohort is very similar to TCAGEN but was collected independently. Participants provided clinically relevant information including use of cardiovascular related medication through a standardized questionnaire. Clinically relevant information is also available through a comprehensive electronic medical records database that includes information on drug use and surgical interventions. Fasting blood samples were collected before cardiac catheterization.
- e. TCAD (Taichung CAD study) includes patients with a variety of cardiovascular diseases receiving care at the Taichung Veterans General Hospital. Specifically, individuals who were hospitalized for diagnostic and interventional coronary angiography examinations and treatment are included in TAI CHI. Also included in TAI CHI are subjects with a history of myocardial infarction or revascularizationof any type (percutaneous coronary intervention or coronary artery bypass).
- f. TCAGEN (Taiwan Coronary Artery Disease GENetic) study is an ongoing cohort study that has been enrolling patients undergoing coronary angiography or percutaneous intervention at the National Taiwan University Hospital (NTUH) in the setting of either stable angina pectoris or prior myocardial infarction. Participants are not only from the north of Taiwan where the main NTU medical school/hospital is located, but also from Yulin branch of NTUH, located in south/central Taiwan. The hospital uses an elaborate electronic medical record system that provides access to clinic visit notes, diagnostic codes of clinic encounters, prescriptions, and laboratory data in a searchable form. Fasting blood samples were collected before cardiac catheterization while 10 ml of peripheral blood was collected in the catheter lab specifically for buffy coat isolation and DNA extraction.
- g. TUDR (Taiwan USA Diabetes Retinopathy) is a cohort that enrolled subjects with T2DM receiving care at Taiching Veteran's General Hospital, a small number of subjects were included from Tri-Service General Hospital(TSGH). All TUDR subjects underwent a complete fundoscopic examination to carefully document the presence and extent of retinopathy. To date, a total of 2222 unrelated type 2 DM subjects with and without retinopathy were ascertained and have undergone metabochip genotyping.
AIDHS/SDS (Asian Indian Diabetic Heart Study/Sikh Diabetes Study)
A total of 3,958 participants from AIDHS are from two different cohorts comprising 2,902 individuals from the Sikh Diabetes Study (SDS) and 1,056 migrant Asian Indians living in the US40,41. Of these, 1,516 subjects (800 males/ 716 females) available with genome-wide genotyping data (llumina's 660W-Quad BeadChip) were used in the present study. These individuals were recruited through public advertisements from Northern states of India including Punjab, Haryana, and Delhi. Both men and women aged 17-90 years participated. Individuals with non-Punjabi ancestry and non-Asian Indian ancestry were not enrolled. Normoglycemic control subjects were random individuals recruited from the same Asian Indian community as the patients, and matched for ethnicity and geographic location. Diagnoses of type 2 diabetes were confirmed by reviewing medical records for symptoms, use of medication, and measuring fasting glucose levels following the guidelines of the American Diabetes Association (2004)42. A medical record indicating either (1) a fasting plasma glucose level .7.0 mmol/L or .126 mg/dL after a minimum 12h fast or (2) a 2h post-glucose level (2h oral glucose tolerance test) .11.1mmol/L or .200 mg/dL on more than one occasion, combined with symptoms of diabetes confirmed the diagnosis. Impaired fasting glucose (IFG) is defined as a fasting blood glucose level .100 mg/dL (5.6 mmol/L) but .126 mg/dL (7.0 mmol/L). Impaired glucose tolerance (IGT) is defined as a 2h OGTT > 140mg dL (7.8mmol/L) but < 200mg /dL(11.1mmol/L).Subjects with IFG or IGT were excluded from this study. The 2h OGTTs were performed following the criteria of the World Health Organizations (WHO) (75 g oral load of glucose). The selection of normoglycemic controls was based on a fasting glycemia < 100.8 mg/dL or a 2h glucose < 141.0 mg/dL. Serum lipids (total cholesterol, LDL cholesterol, HDL cholesterol, VLDL cholesterol, and triglycerides) were quantified using standard enzymatic methods (Roche, Basel, Switzerland).All quantitative parameters were determined by following manufacturer's instructions using a Hitachi 902 auto-analyzer (Roche, Basel, Switzerland). All blood samples were obtained at the baseline visits. All participants signed a written informed consent for the investigations. The study was reviewed and approved by the University of Oklahoma Health Sciences Center's Institutional Review Board, as well as the Human Subject Protection Committees at the participating hospitals and institutes in India.
40. Sanghera, D.K. et al. Impact of nine common type 2 diabetes risk polymorphisms in Asian Indian Sikhs: PPARG2 (Pro12Ala), IGF2BP2, TCF7L2 and FTO variants confer a significant risk. BMC Med Genet9, 59 (2008).
41. Been, L.F. et al. Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: a study of 3,310 subjects from India and the US. BMC Med Genet12, 18 (2011).
42. Hammond, C.J., Andrew, T., Tat Mak, Y. & Spector, T.D. A Susceptibility Locus for Myopia in the Normal Population Is Linked to the PAX6 Gene Region on Chromosome 11: A Genomewide Scan of Dizygotic Twins. Am J Hum Genet75, 294-304 (2004).
PROMIS (The Pakistan Risk Of Myocardial Infarction Study)
PROMIS is an ongoing case-control study of acute myocardial infarction (MI) in urban Pakistan, which by mid-2009 included 5,500 MI cases and 5,500 controls43. Cases have typical ECG characteristics, a positive troponin test, and MI symptoms within the previous 24 hours. Controls are individuals frequency-matched to cases by sex and age (in 5 year bands) and identified in the same hospitals as the index cases. Controls have been recruited in the following order of priority: (i) visitors of patients attending the out-patient department; (ii) patients attending the out-patient department for routine non-cardiac complaints, or (iii) non-blood related visitors of index MI cases. A locally-piloted and validated epidemiological questionnaire has been administered to participants by medically qualified research officers that seeks > 200 items of information in relation to: ethnicity (eg, personal and paternal ethnicity, spoken language, place of birth and any known consanguinity); demographic characteristics; lifestyle factors (eg, tobacco and alcohol consumption, dietary intake, and physical activity); personal and family history of cardiovascular disease; and medication usage. PROMIS has received approval by the relevant research ethics committee of each of the institutions involved in participant recruitment. Informed consent has been obtained from each participant recruited into the study, including consent to use the samples in genetic, biochemical, and other analyses.
43. Saleheen, D. et al. The Pakistan Risk of Myocardial Infarction Study: a resource for the study of genetic, lifestyle and other determinants of myocardial infarction in South Asia. Eur J Epidemiol24, 329-38 (2009).
FBPP (Family Blood Pressure Project GenNet and HyperGEN studies)
The FBPP GenNet study recruited European-American (N=1,497) and African American (N=1,101) participants at two field centers between 1995 and 2003, based on a hypertensive proband44. Non-Hispanic white subjects were recruited from Tecumseh, Michigan, and African American subjects were recruited from Maywood, Illinois. Probands were defined as individuals aged 18-50 years with blood pressures in the upper 20th to 25th percentile of the age/gender specific blood pressure distribution. Once the proband was identified, an attempt was made to enroll all siblings and parents of the proband, irrespective of their blood pressure or hypertension treatment status. Blood pressure measurements were carried out according to standard procedures in a sitting position after a resting period. Subjects were not allowed to smoke or drink coffee before the visit. The average of two manual BP measurements was used as the phenotype. DNA was available for 1,381 European American and 848 African-American participants (www.biostat.wustl.edu/fbpp/FBPP.shtml). The Hypertension Genetic Epidemiology Network recruited two types of participants (hypertensive sibships and random samples of subjects) in European American and African American samples. Recruitment of the study participants, including the hypertensive probands, was carried out at five field centers based largely on ongoing population based studies. For European Americans, HyperGEN recruited and characterized a total of 1,142 hypertensive subjects from 480 sibships, yielding a total of 992 self-reported sib-pairs, and a random sample of 472 biologically unrelated participants. For African Americans,HyperGEN recruited and characterized a total of 1,261 hypertensive subjects from 596 sibships yielding a total of 826 self-reported sib-pairs, and a random sample of 446 biologically unrelated African Americans (www.biostat.wustl.edu/fbpp/FBPP.shtml). Blood pressure measurements were carried out according to standard procedures in a sitting position after a resting period.
44. Multi-center genetic study of hypertension: The Family Blood Pressure Program (FBPP). Hypertension39, 3-9 (2002).
GXE (Kingston GXE; subset of International Collaborative Study of Hypertension in Blacks (ICSHIB))
The Kingston GXE cohort was obtained from a survey conducted inKingston, Jamaica as part of a larger project to examine gene by environment interactions in the determination of blood pressure among adults 25-74 years45. The principal criterion for eligibility was a body mass index in either the top or bottom third of BMI for the Jamaican population. Participants were identified principally from the records of the Heart Foundation of Jamaica, a non-governmental organization based in Kingston, which provides low-cost screening services (height and weight, blood pressure, glucose, cholesterol) to the general public. Other participants were identified from among participants in family studies of blood pressure at the Tropical Metabolism Research Unit (TMRU) and from among staff members at the University of the West Indies, Mona.
45. Lettre, G. et al. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. PLoS Genet7, e1001300 (2011).
MRC/UVRI GPC (General Population Cohort (GPC) Study, Kyamulibwa, Uganda)
MRC/UVRI GPC is a population-based cohort study of > 18,000 people living within the Kyamulibwa sub-county of Kalungu District in rural south-west Uganda. The cohort was established in 1989 by the Medical Research Council (MRC) Programme on AIDS in Uganda to describe trends in the prevalence and incidence of HIV infection and their determinants in the general population. Today the study also aims to estimate the prevalence and distribution of cardiometabolic risks factors and diseases in the population. This cohort has GWAS data but only the SNPs overlapping with metabochip were included.
SEY (Seychelles Tandem Study)
SEY recruited 494 participants, aged over 18 years, from 76 families of East African descent from the Republic of Seychelles (Indian Ocean), collected for the primary purpose of a candidate gene study of arterial hypertension46. Families were selected from a national register that includes all patients with hypertension. Families were selected if there were two or more full siblings with hypertension (defined as being on current antihypertensive treatment or having an average (6 measures) office systolic/diastolic blood pressure greater than or equal to 140/90 mm Hg). Participants were recruited from July 1999 until January 2002. Blood was collected in the morning between 7 am and noon after overnight fasting.
46. Bochud, M. et al. Heritability of renal function in hypertensive families of African descent in the Seychelles (Indian Ocean). Kidney Int67, 61-9 (2005).
SPT (Spanishtown; subset of International Collaborative Study of Hypertension in Blacks (ICSHIB))
Participants were recruited from Spanish Town, a stable, residential urban area neighboring the capital city of Kingston, Jamaica as part of the International Collaborative Study of Hypertension in Blacks (ICSHIB)47. A stratified random sampling scheme was used to recruit adult males and females aged 25-74 years from the general population. Spanish Town was chosen because its demographic make-up was broadly representative of Jamaica as a whole.
47. Cooper, R. et al. The prevalence of hypertension in seven populations of west African origin. Am J Public Health87, 160-8 (1997).
PARC (Pharmacogenomics and Risk of Cardiovascular Disease)
Samples for analysis were from the Cholesterol and Atherosclerosis Pharmacogenetics (CAP) Study49. CAP was a clinical trial designed to identify genetic influences responsible for inter-individual variation in response to simvastatin. CAP participants were 944 Caucasiansand African Americans, aged 30 and above, who received open label 40 mg simvastatin daily for 6 weeks. They were recruited on the basis of having serum total cholesterol levels of 4.14-10.36 mmol/L (160-400 mg/dL). Complete phenotypes of lipids before and after statin treatment and Metabochip data are available on 530 Caucasian CAP participants.
49. Simon, J.A. et al. Phenotypic predictors of response to simvastatin therapy among African-Americans and Caucasians: the Cholesterol and Pharmacogenetics (CAP) Study. Am J Cardiol97, 843-50 (2006).
MORGAM (MOnica Risk, Genetics, Archiving and Monograph)
MORGAM is a multinational collaborative study exploring the relationships between the development of cardiovascular diseases, their classic and genetic risk factors and biomarkers50.
50. Evans, A. et al. MORGAM (an international pooling of cardiovascular cohorts). Int J Epidemiol34, 21-7 (2005).
When using downloaded data, please cite the corresponding paper:
A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.
Ramdas et al.Am J Hum Genet. 109(8):1366-1387 (2022).
Rare coding variants in 35 genes associate with circulating lipid levels-A multi-ancestry analysis of 170,000 exomes.
Hindy et al.Am J Hum Genet. 109(1):81-96 (2022).
The power of genetic diversity in genome-wide association studies of lipids.
Graham et al.Nature volume 600, pages 675–679 (2021).
Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.
Lu et al.Nat Genet. 49(12):1722-1730. (2017).
Exome-wide association study of plasma lipids in >300,000 individuals.
Liu et al.Nat Genet. 49(12):1758-1766 (2017).
Discovery and refinement of loci associated with lipid levels.
Global Lipids Genetics Consortium et al.Nat Genet. 45, 1274-83 (2013).
Biological, clinical and population relevance of 95 loci for blood lipids.
Teslovich TM et al.Nature 466, 707-13 (2010).
Common variants at 30 loci contribute to polygenic dyslipidemia.
Kathiresan S et al.Nat Genet. 41, 56-65 (2009).
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
Willer CJ et al.Nat Genet. 40, 161-9 (2008).
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
Kathiresan S et al.Nat Genet. 40, 1 89-97 (2008).
Implicating genes, pleiotropy and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
Stavroula Kanoni and Gina Peloso, et al.
Whole genome sequencing of over 65,000 individuals.
TOPMed; Pradeep Natarajan et al.