Genetic Data Available for Distribution Files through dbGaP
The three types of files available that can be used for performing genetic studies are described below and are available through dbGaP.
- Family structure files
- Genotype files
- Phenotype files
Family Structure File
FHS participants are readily divided into three groups, the Original Cohort (Gen1), the Offspring Cohort (Gen2), and the Third Generation (Gen3) Cohort. The Original Cohort consists of 5209 participants. The Offspring Cohort consists of 5124 participants and includes biological descendants of the Original Cohort as well as spouses and adopted offspring. The Third Generation Cohort consists of 4095 participants and is the biological descendants of the Offspring Cohort and adopted offspring. The Family Structure File contains information for biologically related Framingham participants. A total of 1538 families are present; the mean pedigree size is 10 and ranges from 3 to 639. Of note is that there are siblings (brothers and sisters) among the participants of the Original Cohort as well as parent-offspring pairs. Thus, the extended family relationships in the Framingham Study can include parents and offspring from the same Cohort, and sibships in which the members are from different Cohorts. Also of note is that not all members of the three cohorts have biological relatives and thus are absent from the Family File. Conversely, not all individuals present in the Family File are Framingham Study participants. Place holding individuals were imputed when necessary to reflect biological relationships among participants. For example, parents of the Original Cohort, who are not Framingham Study participants, were created for the Family Structure File, to identify sibships in the Original Cohort. The Framingham Study has no biological samples or direct phenotypic data for these place holders. The biological relationships are coded in a manner that is commonly used in genetic epidemiological studies. Siblings are identified by having common parents. Spouse pairs are identified by having descendants. Note: Full siblings will have the same father and mother ID, while half-siblings will only share one of these IDs, either a common father or a common mother, but not both.
- Family ID number (pedno): A unique number assigned to all members of an extended pedigree.
- Random ID number (shareid): A unique number assigned to each participant.
- Father ID (fshare): The ID for the father of the subject. All brothers and sisters that share a common father will share the same father ID number.
- Mother ID (mshare): The ID for the mother of the subject. All brothers and sisters that share a common mother will share the same mother ID number.
- Sex (sex): the sex of the individual, coded male=1, female=2.
- Identical twin ID (itwin): This field designates biologically identical individuals within families. The pairs within families have the same number, so that the first identical pair of twins is designated as 1; the second pair designated as 2. No pedigrees contain more than two identical twin pairs.
Genetic data sets described below are available at the dbGaP website.
Note that participants may refuse to participate in genetic studies (while continuing to participate in other aspects of the Study). The data in the genotype files are from those individuals who have given explicit permission for genetic studies. As Framingham is an ongoing study, the participants can revoke their permission at any time. The genotype files are updated periodically to reflect changes in permission.
- Marshfield Scan data
Ten cM genome scan data in FHS family members, 453 from the original and 1380 from the offspring cohort. Genotyping of approximately 400 markers per individual was performed by the Mammalian Genotyping Service in Marshfield, Wisconsin, in six batches (composed of different sub-samples of individuals) between 1996 and 2005. View website.Due to changes in markers present in Marshfield Screening sets from 8 to 13 during that period, as well as the addition of markers genotyped in the FHS Genetics Laboratory, a total of 604 markers are present in the file. An accompanying map file is included.
- 100k data
Affymetrix GeneChip Human Mapping 100K set SNP genotype results for 1345 FHS family members, 258 in the original and 1087 in the offspring cohort. Genotyping was performed through an ancillary study to Drs. Michael Christman and Alan Herbert in the Department of Genetics and Genomics at Boston University School of Medicine. Genotypes were determined using the Dynamic Modeling (DM) algorithm. A file with selected information about each SNP is also included.
- CardioGenomics PGA data
Genotyping results for 709 SNPs from 1754 FHS offspring cohort members. This genotyping was performed through an ancillary study at the Genomics of Cardiovascular Development, Adaptation, and Remodeling, an NHLBI Program for Genomic Applications, Harvard Medical School. (NHLBI Grant Number 1U01HL66582, 10/01/00-07/31/05, PGA PI Dr. S. Izumo and Project 5 PI Dr. EJ Benjamin, Functional Genomics of the Cardiovascular System: Component 5, Framingham Heart Study. View website.These SNPs come from candidate genes believed to be associated with echocardiographic measures of left ventricular size and function. A file with selected information about each SNP is also included.
- Framingham Obesity Genetic data
Genotyping results for 1485 SNPs in 1343 FHS family members; 257 from the original and 1086 from the offspring cohort. This genotyping was performed at Illumina Inc. by the Framingham Obesity Genetics (FOG) project supported by NIDDK grant number R01 DK66241, Dr. Larry Atwood, Department of Neurology at Boston University School of Medicine). The SNPs compose fine mapping data from regions on chromosomes 6, 10 and 11. The accompanying SNP information file provided from Illumina is also included.
- ApoE and ApoA4 Genetic data
Genotyping results of APoE and ApoA4 polymorphisms in 5198 FHS members; 1258 from the original and 3940 from the offspring cohort. Please see relevant FHS publications for genotype information.
- SHARe data
Affymetrix GeneChip Human Mapping 500K Array and the 50K Human Gene Focused Panel results for 9274 unique FHS participants, including 1529 original cohorts, 3753 offspring, 99 offspring spouses, and 3893 third generation participants. Genotypes were determined using the BRLMM algorithm. A file with selected information about the 549,915 SNPs is also included.
The phenotype data sets described below are available through the dbGaP website.
The phenotype files provide for each study participant phenotypes measured over the course of the study. The Original Cohort began Exam 1 in 1948 (9/1948 - 4/1953) and has continued with biennial examinations to the present. The Offspring Cohort began Exam 1 in 1971 (8/1971 - 9/1975) and has on average been examined every 3 to 4 years since enrollment. However, there was an eight year window between exam 1 and exam 2. At this time, the first examination has been performed in the third generation (4/2002 - 7/2005). In addition to these core study examinations, a number of ancillary studies involving Framingham participants were also performed over the years and their phenotypic results are also posted.
A total of 27 original cohort examination files are present, as well as files of ancillary study phenotype data. A total of 7 Offspring cohort examination files are present, as well as files of ancillary study phenotype data. The data from the sole GEN3 examination that was performed 4/2002 - 7/2005 is present, as well as files of ancillary study phenotype data. Finally, files with data from the various cohorts combined are also included. Extensive documentation for each data set and variable definitions are available at the dbGAP website.
Genetic Ancillary studies requesting DNA, other biological specimens, or genetic data not yet available on the dbGaP website require a Research Application for review by the DNA Committee. Submission deadlines are January 15, April 15, July 15 and October 15. The review meetings take place approximately 3 weeks after the submission deadline. In addition to the electronic submission of an application please attach a Biographical Sketch and any additional documentation that would be helpful in the evaluation of the proposal, such as a pending grant application, grant award statement, accepted or published manuscripts or abstracts, recent supporting literature.