GCD Datasets Requiring Release
The Requires Release table lists the specifications of known global coherent datasets with identified or anticipated legal release problems that must be addressed prior to public posting. Note that for Datasets with more than one tissue the "approximate numbers of individuals" refers to the tissue with the greatest number of individuals and all tissues may not have this degree of coverage.
To add to or update this list please contact repdata@sagebase.org.
| Dataset Name | Tumor/Tissue Type | Species | Disease | Approx No. Individuals |
Investigator | Institution | Reference PMID/ Description |
| Human_Cancer_Breast_ Stanford |
Breast | Human | Cancer | 89 | Jonathan Pollack | Stanford | 16897746 |
| Human_Cancer_Breast_KI | Breast | Human | Cancer | 650 | Jonas Bergh | Karolinska | Description |
| Human_Metabolic_Adipose_ Blood_deCODE |
Adipose_Blood | Human | Metabolic | 1,002 | Kari Stefansson | deCODE | 18344981 |
| Human_Metabolic_Adipose: Omental/subQ_Liver_Stomach_ Harvard |
Adipose:Omental/subQ_ Liver_Stomach |
Human | Metabolic | 975 | Lee Kaplan | Harvard | Description |
| Human_Respiratory_Lung_ UBC/Laval/Groningen |
Lung | Human | Respiratory | 1,180 | Parre/Bosse/Timmens | UBC/Laval/ Groningen |
|
| Human_Metabolic_Adipose_ Muscle_NIDDK |
Adipose_Muscle | Human | Metabolic | 225 | Cliff Bogardus | NIDDK | Description |
| Human_Multiple_Blood_NHLBI | Blood | Human | Multiple | 5,000 | Dan Levy | NHLBI | Description |
| Human_CVD_Macrophage_Liver_ Carotid_IMA_Adipose_Muscle_ Plaque_Blood_Karolinska |
Macrophage_Liver_Carotid_ IMA_Adipose_Muscle_ Plaque_Blood |
Human | CVD | 100 | Johan Bjorkegren | Karolinska | 19997623 |
| Human_Inflammatory Disease_ Blood_UCL |
Blood | Human | Inflammatory Disease | 1,469 | David van Heel | UCL | 20190752 |
| Human_Asthma_Blood_Imperial | Blood | Human | Asthma | 400 | William Cookson | Imperial | 17873877 |
| Human_CVD_PBMC_UTSW | PBMC | Human | CVD | 1,240 | John Blangero | UTSW | 17873875 |
| Mouse_Metabolic_Islet_Liver_ Adipose_Hypothalamus_Kidney_ Muscle_Wisconsin |
Islet_Liver_Adipose_ Hypothalamus_Kidney_ Muscle |
Mouse | Metabolic | 500 | Alan Attie | Wisconsin | Description |
| Mouse_Sleep_Hypothalamus_ Thalamus_Frontal Cortex_Liver_ Northwestern |
Hypothalamus_Thalamus_ Frontal Cortex_Liver |
Mouse | Sleep | 250 | Fred Turek | Northwestern | 19360106 |
| Mouse_Sleep_Hypothalamus_ Thalamus_Frontal Cortex_ Hippocampus_Northwestern |
Hypothalamus_Thalamus_ Frontal Cortex_Hippocampus |
Mouse | Sleep | 220 | Fred Turek | Northwestern | Description |
| Mouse_Metabolic_Adipose_Liver_ Duodenum_Islets_UCLA |
Adipose_Liver_Duodenum_ Islets |
Mouse | Metabolic | 500 | Jake Lusis | UCLA | Description |
| Mouse_Respiratory_Lung_Harvard | Lung | Mouse | Respiratory | 200 | David Beier | Harvard | Description |
| Mouse_Metabolic_Liver_Adipose_ Hypothalamus_Arizona |
Liver_Adipose_ Hypothalamus |
Mouse | Metabolic | 308 | Daniel Pomp | Arizona | 19463160 |
| Mouse_Metabolic_Adipose_Liver_ Hypothalamus_Muscle_Merck |
Adipose_Liver_ Hypothalamus_Muscle |
Mouse | Metabolic | 1,650 | Eric Schadt | Merck | Description |
| Mouse_CVD_Adipose_Kidney cortex_ Kidney medulla_Liver_Merck |
Adipose_Kidney cortex_Kidney medulla_Liver | Mouse | CVD | 350 | Eric Schadt | Merck | Description |
| Mouse_Multiple_Multiple Tissues_ Tennessee |
Multiple Tissues | Mouse | Multiple | 60 | Rob Williams | Tennessee | genenetwork.org |
| Mouse_CVD_Liver_UCLA | Liver | Mouse | CVD | 100 | Jake Lusis | UCLA | 20054062 |
| Mouse_Multiple_Hippocampus_ Lung_Liver_Oxford |
Hippocampus_Lung_Liver | Mouse | Multiple | 1,900 | Jonathan Flint | Oxford | 19376938 |
| Mouse_Sarcopenia_Muscle_PSU | Muscle | Mouse | Sarcopenia | 811 | Arimantas Lionikas | PSU | Description |
| Mouse_Cancer_Skin_UCSF | Skin | Mouse | Cancer | 71 | Allan Balmain | UCSF | 19136944 |
| Human_Cancer_Lung_Mayo | Lung | Human | Cancer | 70 | Ping Yang | Mayo | 20304703 |
| Mouse_Cancer_Breast_UNC | Breast | Mouse | Cancer | 615 | Ryan Gordon | UNC | 20354763 |
| Human_Alzheimers_Cortex_Miami | Cortex | Human | Alzheimers | 364 | Amanda Myers | Miami | 19361613 |
| Mouse_Metabolic_Adipose_Liver_ Brain_Muscle_UCLA |
Adipose, Liver, Brain, Muscle | Mouse | Metabolic | 442 | Jake Lusis | UCLA | Description |
| Mouse_Metabolic_Adipose_Liver_ Brai_ Muscle_UCLA |
Adipose, Liver, Brain, Muscle | Mouse | Metabolic | 309 | Jake Lusis | UCLA | 18462017 |
Descriptions
Human_Cancer_Breast_KI
During the period of 1997 to 2005, fresh breast neoplasms were collected from women treated for primary breast cancer by surgery at the Karolinska Institute Center, Sweden. Fresh tissue samples were immediately frozen in liquid nitrogen and stored at -80°C. Clinical outcomes in the cohort include: Response to therapy (CT scans, MRI, clinical criteria), metastatic v non-metastatic, Time to progression.
Human_Metabolic_Adipose:Omental/subQ_Liver_Stomach_Harvard
High throughput genotyping and expression profiling in three relevant tissues (liver, omental adipose, subcutaneous adipose) from ~1000 patients undergoing roux en y gastric bypass surgery to identify expression SNPs (eSNPs) and the genetics of weight loss and diabetes correction due to bypass surgery; microRNA profiling of liver samples and adipose tissues to understand the role of microRNA in metabolic disorders.
Human_Respiratory_Lung_UBC/Laval/Groningen
A cohort assembled from 3 centres to define the genetics of gene expression in the lung. Samples are collected from a range of pathological conditions with the majority being either COPD or adjacent normal tissue from Lung cancer patients. Gene expression carried out on a custom Affymetrix chip, genotyping on the Illumina 1M panel. Clinical outcomes available include measures of lung function.
Human_Metabolic_Adipose_Muscle_NIDDK
The Pima Indians have an extraordinarily high prevalence of type II diabetes and have been the subject of longitudinal genetic studies by NIDDK. This dataset comprises 225 skeletal muscle and adipose samples profiled on a exon array with accompanying genotypes (~1 million SNPs). Longitudinal clinical outcomes include a variety of tests to measure body composition, oral and intravenous glucose tolerance, measures of insulin sensitivity using the hyperinsulinemic, euglycemic clamp, measures of insulin secretory function, as well as measures of 24-hour energy expenditure and substrate oxidation rates in a human calorimeter.
Human_Multiple_Blood_NHLBI
The Framingham Heart Study comprises a longitudinal three-generation population study (n~15,000). Genotyping at 500K SNPs is available for ~9,500 individuals and gene expression for blood on 5,000-7,000. Phenotypes in the cohort include serum lipid/cholesterol, CRP, glucose levels, adiposity measures, hypertension, T2D, chronic kidney disease, imaging measures and heart disease outcomes (MI, failure)
Mouse_Metabolic_Islet_Liver_Adipose_Hypothalamus_Kidney_Muscle_Wisconsin
The C57BL/6J (B6) mice, when made genetically obese (B6-ob/ob), develop only transient mild hyperglycemia. In striking contrast, when BTBR T+ tf/J (BTBR) mice are made genetically obese (BTBR-ob/ob), the mice develop severe diabetes. At 6 weeks of age, B6-ob/ob mice have an average fasting plasma insulin level of ~10 ng/ml vs.17 ng/ml in BTBR-ob/ob mice (normal insulin in a lean mouse: <2.0 ng/ml.). B6-ob/ob mice showed slightly increased fasting glucose at 8 weeks of age, but returned to a plateau by 10 weeks. The B6-ob/ob mice maintain the normal glucose level by progressively increasing insulin to 30 ng/ml, from 6 to 14 weeks of age. On the other hand, the BTBR-ob/ob mice fail to secrete sufficient insulin. Consequently, their fasting glucose rises to >400 mg/dl by 10 weeks of age. Preliminary data show insufficient β-cell mass in BTBR-ob/ob mice, which leads to the hypothesis that the BTBR-ob/ob mice are diabetic because they fail to maintain sufficient β-cell mass to compensate for insulin resistance. The β-cells in the islets of Langerhans make up the most important tissue in the development of type-2 diabetes and therefore make a logical choice for new diabetes targets. This BTBR X C57BL6 ob/ob F2 cross study, was designed to simultaneously study tissues involved in insulin resistance (liver, muscle, adipose) and insulin secretion (islets) and derive the gene networks that underlie there phenotypes.
Mouse_Sleep_Hypothalamus_Thalamus_Frontal Cortex_Hippocampus_Northwestern
An F2 cross between C57BL/6J and 129SvJ mice. EEG and EMG characterized sleep states were assigned for a total of 50 hrs that included 24 baseline, 6 sleep deprivation, and 20 recovery. The objective of the study was to relate genes that control sleep patterns to psychiatric and sleep deprevation traits.
Mouse_Metabolic_Adipose_Liver_Duodenum_Islets_UCLA
The classic model of diabetes in mouse is the C57BLKS db/db strain. While C57BL/6 db/db animals show hyperinsulinemia with age, they do not progress to frank diabetes, although they are somewhat hyperglycemic. By contrast, C57BLKS db/db animals are insulin resistant at a very young age and progress to beta cell failure and hyperglycemia over a few months. At 12 weeks, these mice show the beginnings of diabetic complications including nephropathy, neuropathy and cardiomyopathy. The C57BLKS mouse is genetically identical to C57BL/6 over 70% of its genome. Most of the remainder comes from DBA (with some small residual from an unknown strain). Thus, the diabetic susceptibility of C57BLKS most likely originates from the DBA regions of its genome. Further, there are several indications that DBA is more susceptible to diabetes than C57BLKS. For instance compared with C57BLKS and DBA, C57BL/6 islets show strongest glucose-stimulated insulin release and beta-cell proliferation. Similarly, C57BL/6 has the least glucose induced beta-cell apoptosis. Between C57BLKS and DBA, the DBA strain is consistently the most diabetes susceptible by these measures. It is surmised that the DBA strain carries additional diabetes susceptibility loci beyond those carried in the 20% of DBA present in C57BLKS. It is anticipated that the BXD db/db cross will give mapping information for the susceptibility loci in C57BLKS plus the additional loci in DBA.
Mouse_Respiratory_Lung_Harvard
This backcross is designed to uncover the genetic drivers of naïve airway hyperresponsiveness (AHR) in the mouse. The cohort comprises a set of ~200 backcross mice from C57BL/6 and A/J inbred lines and have been phenotyped for methacholine-induced AHR. Genotypes and gene expression for Lung are available.
Mouse_Metabolic_Adipose_Liver_Hypothalamus_Muscle_Merck
This backcross cohort consists of 4 separate populations of C57BL6/JxDBA/2 (n=2), C57BL6/Jx129SvImJ F2 and C57BL6/JxA/J F2s numbering 300-500 animals each. 3 of the populations, comprising the 3 different cross backgrounds, underwent a 20 week protocol prior to sacrifice including 12 weeks on high fat diet (HFD) while the 2nd C57BL6/JxDBA/2 cohort underwent the identical protocol for the first 20 weeks of life but was then aged out to week 62 before sacrifice, with repetition of the 12 weeks of HFD for the last period of life. Phenotypes collected in these mice include weight, body composition and measures of glucose metabolism. Gene expression profiles have been generated from all animals for adipose, liver hypothalamus and muscle.
Mouse_CVD_Adipose_Kidney cortex_Kidney medulla_Liver_Merck
F2 cross designed to identify the genes and networks that regulate blood pressure. In addition to blood pressure traits, echocardiographic traits were measured in this cross in addition to body composition, lipids, and bone traits.
Mouse_Sarcopenia_Muscle_PSU
The Center for Developmental and Health Genetics at Penn State University (PSU) has been working for a number of years on mapping the genetic determinants of age-related phenotypes in a B6D2F2 intercross. This project aims to apply an integrated genetic analysis to the B6D2F2 cohort to look at the effects of aging on the genetics underlying a number of phenotypic traits, particularly gastrocnemius muscle mass data collected in d200, d500 and d800 cohorts. Integration of the muscle gene expression data generated will enable the genes and networks that regulate muscle mass to be identified and the effect of age to be assessed.
Mouse_Metabolic_Adipose, Liver, Brain, Muscle_UCLA
An F2 cross between C57BL/6J (B6) and Castaneus (CAST) mice. All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow containing 4% fat until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) containing 42% fat and 0.15% cholesterol for the subsequent 8 wk. Designed to identify the genes and networks that regulate metabolic traits including body composition, lipids, glucose, and bone traits.