ID

45181

Description

Principal Investigator: David Herrington, MD, MHS, Wake Forest University Baptist Medical Center, Winston Salem, NC, USA MeSH: Atherosclerosis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000349 The SEA study is a genome-wide association study to identify genetic variants associated with premature atherosclerosis in subjects included in the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) repository - a unique NHLBI resource including data, DNA and arterial specimens from over 3000 multi-ethnic subjects 15-34 years of age who died of non-atherosclerotic causes (mostly trauma). All PDAY subjects had post-mortem quantitative assessment of raised atherosclerotic lesions in their aorta and coronary arteries - making this the largest and most carefully phenotyped cohort for premature atherosclerosis in the world. The goal of the current project was to use the quantitative measure of raised atherosclerotic lesions in the PDAY cohort as the target phenotype for a genome-wide association study and to use quantitative measures of subclinical atherosclerosis (coronary calcium and carotid IMT) in the Multi-Ethnic Study of Atherosclerosis (MESA) to confirm or refute candidate loci identified from the PDAY analysis. Identifying genetic factors that predispose individuals to premature atherosclerosis could lead to more effective screening and early treatment of high risk individuals and suggest novel molecular targets for treatment and prevention interventions.

Link

dbGaP study = phs000349

Keywords

Versions (2)
  1. 8/20/22 8/20/22 - Simon Heim
  2. 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder

David Herrington, MD, MHS, Wake Forest University Baptist Medical Center, Winston Salem, NC, USA

Uploaded on

October 12, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000349 SNPs and Extent of Atherosclerosis (SEA) Study

English

Eligibility Criteria

4 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

*PDAY Population and Atherosclerosis Phenotype*: From 1987 to 1994 PDAY centers collected standardized autopsy specimens and selected risk factor data from black and white males and females, age 15-34 yrs, who died within 72 hours after injury. Using an unlinked anonymous coding system, the specimens and data were submitted to central pathology laboratories for detailed histopathologic analyses. The right coronary artery and left half of the aorta were stained with Sudan IV and the percent of intimal surface involved with raised atherosclerotic lesions in the distal and thoracic aorta and right coronary artery was independently estimated by three pathologists. This produced a pathologically specific and quantitatively precise description of atherosclerosis extent that was strongly correlated with blood lipids and other conventional risk factors in the PDAY cohort*. For the current project the percent surface involvement in the distal and thoracic aorta and right coronary artery was summed and then adjusted for age^2, race and gender to produce a total raised lesion score which was the primary phenotype for our genetic association analyses.
Description

*PDAY Population and Atherosclerosis Phenotype*: From 1987 to 1994 PDAY centers collected standardized autopsy specimens and selected risk factor data from black and white males and females, age 15-34 yrs, who died within 72 hours after injury. Using an unlinked anonymous coding system, the specimens and data were submitted to central pathology laboratories for detailed histopathologic analyses. The right coronary artery and left half of the aorta were stained with Sudan IV and the percent of intimal surface involved with raised atherosclerotic lesions in the distal and thoracic aorta and right coronary artery was independently estimated by three pathologists. This produced a pathologically specific and quantitatively precise description of atherosclerosis extent that was strongly correlated with blood lipids and other conventional risk factors in the PDAY cohort*. For the current project the percent surface involvement in the distal and thoracic aorta and right coronary artery was summed and then adjusted for age^2, race and gender to produce a total raised lesion score which was the primary phenotype for our genetic association analyses.

Data type

boolean

Alias
UMLS CUI [1,1]
C0200345
UMLS CUI [1,2]
C0332142
UMLS CUI [1,3]
C0442818
UMLS CUI [1,4]
C0221198
UMLS CUI [1,5]
C0205042
UMLS CUI [1,6]
C0003483
Cases were defined as the PDAY subjects at >90th% for total raised lesion score.
Description

Cases were defined as the PDAY subjects at >90th% for total raised lesion score.

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C0442818
UMLS CUI [1,3]
C0221198
UMLS CUI [1,4]
C0449820
Controls were selected from among PDAY subjects with a total raised lesion score = 0 after matching to cases (2:1) on age, race and gender.
Description

Controls were selected from among PDAY subjects with a total raised lesion score = 0 after matching to cases (2:1) on age, race and gender.

Data type

boolean

Alias
UMLS CUI [1,1]
C0009932
UMLS CUI [1,2]
C0442818
UMLS CUI [1,3]
C0221198
UMLS CUI [1,4]
C0449820
In Phase I of the SEA Study quantitative genotyping was used to estimate allele frequency for >2.4 million SNPs in each of eight pools of DNA (3 case and 5 control pools). Pools were balanced for age, gender and genetic ancestry based on analysis of 311 ancestry informative markers typed on every sample before pool formation. Phase II and III of the SEA study involved individual level genotyping of promising SNPs in the PDAY subjects and subsequent replication in the MESA cohort. Phase II and III data are not included in the dbGap data set.
Description

In Phase I of the SEA Study quantitative genotyping was used to estimate allele frequency for >2.4 million SNPs in each of eight pools of DNA (3 case and 5 control pools). Pools were balanced for age, gender and genetic ancestry based on analysis of 311 ancestry informative markers typed on every sample before pool formation. Phase II and III of the SEA study involved individual level genotyping of promising SNPs in the PDAY subjects and subsequent replication in the MESA cohort. Phase II and III data are not included in the dbGap data set.

Data type

boolean

Alias
UMLS CUI [1,1]
C0392762
UMLS CUI [1,2]
C1509144
UMLS CUI [1,3]
C1285573
UMLS CUI [2,1]
C1285573
UMLS CUI [2,2]
C0237401
*A more detailed description of the measurement of raised lesions in the PDAY cohort can be found in: Strong JP, Malcom GT, McMahan CA et al. Prevalence and extent of atherosclerosis in adolescents and young adults. Implications for prevention from the Pathobiological Determinants of Atherosclerosis in Youth study. JAMA 1999;281:727-35; PMID: 10052443.
Description

*A more detailed description of the measurement of raised lesions in the PDAY cohort can be found in: Strong JP, Malcom GT, McMahan CA et al. Prevalence and extent of atherosclerosis in adolescents and young adults. Implications for prevention from the Pathobiological Determinants of Atherosclerosis in Youth study. JAMA 1999;281:727-35; PMID: 10052443.

Data type

boolean

Alias
UMLS CUI [1,1]
C1546922
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Similar models

Eligibility Criteria

4 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
*PDAY Population and Atherosclerosis Phenotype*: From 1987 to 1994 PDAY centers collected standardized autopsy specimens and selected risk factor data from black and white males and females, age 15-34 yrs, who died within 72 hours after injury. Using an unlinked anonymous coding system, the specimens and data were submitted to central pathology laboratories for detailed histopathologic analyses. The right coronary artery and left half of the aorta were stained with Sudan IV and the percent of intimal surface involved with raised atherosclerotic lesions in the distal and thoracic aorta and right coronary artery was independently estimated by three pathologists. This produced a pathologically specific and quantitatively precise description of atherosclerosis extent that was strongly correlated with blood lipids and other conventional risk factors in the PDAY cohort*. For the current project the percent surface involvement in the distal and thoracic aorta and right coronary artery was summed and then adjusted for age^2, race and gender to produce a total raised lesion score which was the primary phenotype for our genetic association analyses.
Item
*PDAY Population and Atherosclerosis Phenotype*: From 1987 to 1994 PDAY centers collected standardized autopsy specimens and selected risk factor data from black and white males and females, age 15-34 yrs, who died within 72 hours after injury. Using an unlinked anonymous coding system, the specimens and data were submitted to central pathology laboratories for detailed histopathologic analyses. The right coronary artery and left half of the aorta were stained with Sudan IV and the percent of intimal surface involved with raised atherosclerotic lesions in the distal and thoracic aorta and right coronary artery was independently estimated by three pathologists. This produced a pathologically specific and quantitatively precise description of atherosclerosis extent that was strongly correlated with blood lipids and other conventional risk factors in the PDAY cohort*. For the current project the percent surface involvement in the distal and thoracic aorta and right coronary artery was summed and then adjusted for age^2, race and gender to produce a total raised lesion score which was the primary phenotype for our genetic association analyses.
boolean
C0200345 (UMLS CUI [1,1])
C0332142 (UMLS CUI [1,2])
C0442818 (UMLS CUI [1,3])
C0221198 (UMLS CUI [1,4])
C0205042 (UMLS CUI [1,5])
C0003483 (UMLS CUI [1,6])
Cases were defined as the PDAY subjects at >90th% for total raised lesion score.
Item
Cases were defined as the PDAY subjects at >90th% for total raised lesion score.
boolean
C1706256 (UMLS CUI [1,1])
C0442818 (UMLS CUI [1,2])
C0221198 (UMLS CUI [1,3])
C0449820 (UMLS CUI [1,4])
Controls were selected from among PDAY subjects with a total raised lesion score = 0 after matching to cases (2:1) on age, race and gender.
Item
Controls were selected from among PDAY subjects with a total raised lesion score = 0 after matching to cases (2:1) on age, race and gender.
boolean
C0009932 (UMLS CUI [1,1])
C0442818 (UMLS CUI [1,2])
C0221198 (UMLS CUI [1,3])
C0449820 (UMLS CUI [1,4])
In Phase I of the SEA Study quantitative genotyping was used to estimate allele frequency for >2.4 million SNPs in each of eight pools of DNA (3 case and 5 control pools). Pools were balanced for age, gender and genetic ancestry based on analysis of 311 ancestry informative markers typed on every sample before pool formation. Phase II and III of the SEA study involved individual level genotyping of promising SNPs in the PDAY subjects and subsequent replication in the MESA cohort. Phase II and III data are not included in the dbGap data set.
Item
In Phase I of the SEA Study quantitative genotyping was used to estimate allele frequency for >2.4 million SNPs in each of eight pools of DNA (3 case and 5 control pools). Pools were balanced for age, gender and genetic ancestry based on analysis of 311 ancestry informative markers typed on every sample before pool formation. Phase II and III of the SEA study involved individual level genotyping of promising SNPs in the PDAY subjects and subsequent replication in the MESA cohort. Phase II and III data are not included in the dbGap data set.
boolean
C0392762 (UMLS CUI [1,1])
C1509144 (UMLS CUI [1,2])
C1285573 (UMLS CUI [1,3])
C1285573 (UMLS CUI [2,1])
C0237401 (UMLS CUI [2,2])
*A more detailed description of the measurement of raised lesions in the PDAY cohort can be found in: Strong JP, Malcom GT, McMahan CA et al. Prevalence and extent of atherosclerosis in adolescents and young adults. Implications for prevention from the Pathobiological Determinants of Atherosclerosis in Youth study. JAMA 1999;281:727-35; PMID: 10052443.
Item
*A more detailed description of the measurement of raised lesions in the PDAY cohort can be found in: Strong JP, Malcom GT, McMahan CA et al. Prevalence and extent of atherosclerosis in adolescents and young adults. Implications for prevention from the Pathobiological Determinants of Atherosclerosis in Youth study. JAMA 1999;281:727-35; PMID: 10052443.
boolean
C1546922 (UMLS CUI [1,1])
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