0 Ratings
ID

45457

Description

Principal Investigator: Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA MeSH: Neoplasms,Breast Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Lung Neoplasms,Lymphoma, Non-Hodgkin,Ovarian Neoplasms,Melanoma,Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000559 As part of Population Architecture using Genomics and Epidemiology PAGE study (Phase I), the Epidemiologic Architecture using Genomics and Epidemiology (EAGLE I) project accessed both epidemiologic- and clinic-based collections. The epidemiologic-based collection of EAGLE I included the National Health and Nutritional Examination Surveys (NHANES), ascertained between 1991-1994 (NHANES III), 1999-2002, and 2007-2008. NHANES is a population-based cross-sectional survey now conducted every year in the United States to assess the health status of Americans at the time of ascertainment and to assess trends over the years of survey. Genetic NHANES consists of 19,613 DNA samples linked to thousands of variables including demographics, health and lifestyle variables, physical examination variables, laboratory variables, and exposures. NHANES is diverse with almost one-half of the samples (46.4%) coming from self-reported Mexican Americans and non-Hispanic blacks. In contrast to NHANES, BioVU is a clinic-based collection of 150,000 DNA samples from Vanderbilt University Medical Center linked to de-identified electronic medical records (EMRs). Approximately 12% of BioVU's overall DNA sample collection is from African American, Hispanic, and Asian patients. The overall goals of PAGE I and EAGLE I were broad and several-fold:- Replicate genome-wide association study (GWAS)- identified variants in European Americans; - Identify population-specific and trans-population genotype-phenotype associations; - Identify genetic and environmental modifiers of these associations. NHANES is an excellent resource for the study of quantitative traits associated with common human diseases. However, given that the age range of NHANES spans childhood to late adulthood and not all diseases are surveyed, NHANES is less useful for the study of adult-onset diseases such as major cancers. Therefore, under American Recovery and Reinvestment Act (ARRA) funding, EAGLE as part of PAGE I defined eight major cancers sites for genetic analysis in BioVU, Vanderbilt's biorepository linked to de-identified EMRs. The eight major cancers defined for this study included melanoma, breast, ovarian, prostate, colorectal, lung, endometrial, and Non-Hodgkin's lymphoma (NHL). Cancer cases were defined using a combination of ICD-9 codes and tumor registry entries. Controls include BioVU participants without cancer and encompassing the age and gender distributions of cancer cases. Targeted genotyping of GWAS-identified variants for these diseases (124 SNPs) and ancestry informative markers (128 AIMs) was performed by the Center for Human Genetics Research Vanderbilt DNA Resources Core. After quality control, a total of 116 cancer-associated SNPs and 122 AIMs were available for downstream analyses.

Link

dbGap-study=phs000559

Keywords

Versions (2)
  1. 10/27/22 10/27/22 - Simon Heim
  2. 12/12/22 12/12/22 - Kristina Keller
Copyright Holder

Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA

Uploaded on

December 12, 2022

DOI

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License

Creative Commons BY 4.0
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    dbGaP phs000559 PAGE: Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project

    English

    Eligibility Criteria

    5 forms  
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. Subject ID and consent group of participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      3. Subject ID, sample ID and sample use variable obtained from participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      4. Subject ID, age, sex, race, ethnicity, smoking status, smoking ICD9 code, CEU population, follow-up time of cancer participant visit, cancer status, cancer diagnosis, cancer site, CEU population, total population, smoking status, year of diagnosis, cancer type, cancer stage, breast cancer, colorectal cancer, lung cancer, melanoma, non-Hodgkin's lymphoma, ovarian cancer, prostate cancer, endometrial cancer, multiply cancer and follow-up time of cancer participant's visit of subjects with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      5. Sample ID, body site where sample was collected [blood], analyte type, tumor status, and histological type of sample obtained from participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
    Inclusion and exclusion criteria
    Description

    Inclusion and exclusion criteria

    Cancer cases and controls were identified using a combination of in-patient and out-patient data as well as tumor registry entries. These data include primary site designations and histology information collected for clinical reporting purposes for the North America Association of Central Cancer Registries. A combination of the tumor registry data, along with ICD-9 billing codes, procedure codes, vital signs, and free text clinical notes, were used to identify cases for eight cancers among all patients aged 18 or greater in the SD with DNA samples using the following algorithms:
    Description

    Cancer cases and controls were identified using a combination of in-patient and out-patient data as well as tumor registry entries. These data include primary site designations and histology information collected for clinical reporting purposes for the North America Association of Central Cancer Registries. A combination of the tumor registry data, along with ICD-9 billing codes, procedure codes, vital signs, and free text clinical notes, were used to identify cases for eight cancers among all patients aged 18 or greater in the SD with DNA samples using the following algorithms:

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C1706256
    UMLS CUI [1,2]
    C0009932
    UMLS CUI [1,3]
    C0205396
    UMLS CUI [1,4]
    C2707520
    UMLS CUI [1,5]
    C0805443
    UMLS CUI [1,6]
    C0449695
    UMLS CUI [1,7]
    C4048239
    UMLS CUI [1,8]
    C2826024
    UMLS CUI [1,9]
    C1136256
    UMLS CUI [1,10]
    C0518766
    UMLS CUI [1,11]
    C2066349
    UMLS CUI [1,12]
    C0001779
    Breast cancer: Three or more mentions of ICD-9 primary code for malignant neoplasm of the female breast and all sub-codes on separate clinic visits OR a tumor registry entry for breast cancer AND female;
    Description

    Breast cancer: Three or more mentions of ICD-9 primary code for malignant neoplasm of the female breast and all sub-codes on separate clinic visits OR a tumor registry entry for breast cancer AND female;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0006142
    UMLS CUI [1,2]
    C1304708
    UMLS CUI [1,3]
    C1137111
    UMLS CUI [1,4]
    C0008952
    UMLS CUI [1,5]
    C0086287
    Colorectal cancer: Tumor registry entry for colorectal cancer;
    Description

    Colorectal cancer: Tumor registry entry for colorectal cancer;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0009402
    UMLS CUI [1,2]
    C0805443
    Endometrial cancer: Tumor registry entry for endometrial cancer AND histology AND female;
    Description

    Endometrial cancer: Tumor registry entry for endometrial cancer AND histology AND female;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0476089
    UMLS CUI [1,3]
    C0019638
    UMLS CUI [1,4]
    C0086287
    Lung cancer: Tumor registry entry for lung cancer, any location and any type;
    Description

    Lung cancer: Tumor registry entry for lung cancer, any location and any type;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0684249
    UMLS CUI [1,3]
    C0450429
    UMLS CUI [1,4]
    C0030193
    UMLS CUI [1,5]
    C1552551
    UMLS CUI [1,6]
    C0332307
    Melanoma: Three or more mentions of ICD-9 codes for malignant melanoma of skin OR tumor registry entry for melanoma;
    Description

    Melanoma: Three or more mentions of ICD-9 codes for malignant melanoma of skin OR tumor registry entry for melanoma;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0025202
    UMLS CUI [1,3]
    C1137111
    Non-Hodgkin's lymphoma: Tumor registry entry for non-Hodgkin's lymphoma with histology;
    Description

    Non-Hodgkin's lymphoma: Tumor registry entry for non-Hodgkin's lymphoma with histology;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0024305
    UMLS CUI [1,3]
    C0019638
    Ovarian cancer: Tumor registry entry for ovarian cancer AND female;
    Description

    Ovarian cancer: Tumor registry entry for ovarian cancer AND female;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0029925
    UMLS CUI [1,3]
    C0086287
    Prostate cancer: Three or more mentions of ICD-9 codes for malignant neoplasm of prostate OR tumor registry entry for prostate cancer.
    Description

    Prostate cancer: Three or more mentions of ICD-9 codes for malignant neoplasm of prostate OR tumor registry entry for prostate cancer.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0805443
    UMLS CUI [1,2]
    C0600139
    UMLS CUI [1,3]
    C1137111
    Approximately two control samples were identified per case. Controls were matched by sex, race/ethnicity (administratively assigned), and age (within five years of the cases). Controls were required to have at least two clinical narratives, with preference given to records with at least one fully documented history and physical. Exclusion criteria included records with one or more codes for neoplasms, records with a tumor registry entry, and records that had one or more cancer related keywords in the problem list.
    Description

    Approximately two control samples were identified per case. Controls were matched by sex, race/ethnicity (administratively assigned), and age (within five years of the cases). Controls were required to have at least two clinical narratives, with preference given to records with at least one fully documented history and physical. Exclusion criteria included records with one or more codes for neoplasms, records with a tumor registry entry, and records that had one or more cancer related keywords in the problem list.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C1512693
    UMLS CUI [1,2]
    C1706256
    UMLS CUI [1,3]
    C0009932
    UMLS CUI [1,4]
    C0150103
    UMLS CUI [1,5]
    C0015031
    UMLS CUI [1,6]
    C1522384
    UMLS CUI [1,7]
    C0001779
    UMLS CUI [2,1]
    C1512693
    UMLS CUI [2,2]
    C4553389
    UMLS CUI [2,3]
    C0205210
    UMLS CUI [2,4]
    C0600664
    UMLS CUI [2,5]
    C0443225
    UMLS CUI [2,6]
    C0262926
    UMLS CUI [3,1]
    C0680251
    UMLS CUI [3,2]
    C0034869
    UMLS CUI [3,3]
    C0346429
    UMLS CUI [3,4]
    C0805443
    UMLS CUI [3,5]
    C1708608
    UMLS CUI [3,6]
    C0332281
    UMLS CUI [3,7]
    C0006826
    Additional control criteria are as follows:
    Description

    Additional control criteria are as follows:

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0243148
    UMLS CUI [1,2]
    C0243161
    Breast cancer controls are female only. For women over 40 years of age, we required that records contain at least one mammography Bi-Rad score as 1 (negative) or 2 (benign);
    Description

    Breast cancer controls are female only. For women over 40 years of age, we required that records contain at least one mammography Bi-Rad score as 1 (negative) or 2 (benign);

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0006142
    UMLS CUI [1,2]
    C0086287
    UMLS CUI [1,3]
    C0001779
    UMLS CUI [1,4]
    C1514873
    UMLS CUI [1,5]
    C0025102
    UMLS CUI [1,6]
    C0024671
    UMLS CUI [1,7]
    C4480026
    Endometrial cancer controls are female only;
    Description

    Endometrial cancer controls are female only;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0476089
    UMLS CUI [1,2]
    C0086287
    Ovarian cancer controls are female only;
    Description

    Ovarian cancer controls are female only;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0029925
    UMLS CUI [1,2]
    C0086287
    For colorectal cancer controls, we required for patients over 50 years of age the keyword "colonoscopy" in the problem list OR a procedure code for colonoscopy;
    Description

    For colorectal cancer controls, we required for patients over 50 years of age the keyword "colonoscopy" in the problem list OR a procedure code for colonoscopy;

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0009402
    UMLS CUI [1,2]
    C4553389
    UMLS CUI [1,3]
    C0001779
    UMLS CUI [1,4]
    C1514873
    UMLS CUI [1,5]
    C1708608
    UMLS CUI [1,6]
    C0009378
    UMLS CUI [1,7]
    C0552582
    UMLS CUI [1,8]
    C1550373
    Prostate cancer controls are male only. For male controls aged 40 years and greater to have at least one prostate specific antigen (PSA) level <4 and that the most recent PSA level is within the normal range.
    Description

    Prostate cancer controls are male only. For male controls aged 40 years and greater to have at least one prostate specific antigen (PSA) level <4 and that the most recent PSA level is within the normal range.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0600139
    UMLS CUI [1,2]
    C0086582
    UMLS CUI [1,3]
    C0001779
    UMLS CUI [1,4]
    C0201544
    UMLS CUI [1,5]
    C1513491
    UMLS CUI [1,6]
    C0086715
    A total of 7,348 cases of cancer were identified in BioVU for targeted genotyping in EAGLE (Table).
    Description

    A total of 7,348 cases of cancer were identified in BioVU for targeted genotyping in EAGLE (Table).

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C1853237
    UMLS CUI [1,2]
    C3854164
    UMLS CUI [1,3]
    C0205396
    *Table. Case counts by cancer and race/ethnicity.* Cases of specific cancers were determined in the de-identified electronic medical records within BioVU using algorithms implemented in late 2010/early 2011 as described in the text. Race/ethnicity was administratively assigned. *Cancer* *EA* *AA* *H* *A* *AI/NA* *O* *U* *Total* Breast 1,052 163 7 17 2 10 66 1,317 Colorectal 797 75 6 5 1 5 23 912 Endometrial 203 19 1 1 0 1 8 233 Lung 782 66 2 3 1 4 43 901 Melanoma 1,225 23 2 0 0 3 95 1,348 Non-Hodgkin's lymphoma 276 17 1 0 0 2 46 342 Ovarian 161 7 3 2 0 0 10 183 Prostate 1,895 172 4 2 0 7 32 2,112 Total 6,391 542 26 30 4 32 323 7,348
    Description

    *Table. Case counts by cancer and race/ethnicity.* Cases of specific cancers were determined in the de-identified electronic medical records within BioVU using algorithms implemented in late 2010/early 2011 as described in the text. Race/ethnicity was administratively assigned. *Cancer* *EA* *AA* *H* *A* *AI/NA* *O* *U* *Total* Breast 1,052 163 7 17 2 10 66 1,317 Colorectal 797 75 6 5 1 5 23 912 Endometrial 203 19 1 1 0 1 8 233 Lung 782 66 2 3 1 4 43 901 Melanoma 1,225 23 2 0 0 3 95 1,348 Non-Hodgkin's lymphoma 276 17 1 0 0 2 46 342 Ovarian 161 7 3 2 0 0 10 183 Prostate 1,895 172 4 2 0 7 32 2,112 Total 6,391 542 26 30 4 32 323 7,348

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C1706074
    UMLS CUI [1,2]
    C1706256
    UMLS CUI [1,3]
    C0750480
    UMLS CUI [1,4]
    C0034510
    Abbreviations: European American (EA), African American (AA), Hispanic (H), Asian (A), American Indian/Native Alaskan (AI/NA), Other (O), Unknown (U).
    Description

    Abbreviations: European American (EA), African American (AA), Hispanic (H), Asian (A), American Indian/Native Alaskan (AI/NA), Other (O), Unknown (U).

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0000723
    UMLS CUI [1,2]
    C0085756
    UMLS CUI [1,3]
    C0683983
    UMLS CUI [1,4]
    C0086528
    UMLS CUI [1,5]
    C1515945
    UMLS CUI [1,6]
    C0078988
    UMLS CUI [1,7]
    C0205394
    UMLS CUI [1,8]
    C0439673
    For the first five cancers defined in BioVU (breast, colorectal, melanoma, ovarian, and prostate cancers), we identified approximately two controls per case for genotyping as defined in the inclusion/exclusion criteria. A total of 8,996 controls were targeted for genotyping. Two controls per case of endometrial cancer, lung cancer, and non-Hodgkin's lymphoma were defined from among the genotyped control samples.
    Description

    For the first five cancers defined in BioVU (breast, colorectal, melanoma, ovarian, and prostate cancers), we identified approximately two controls per case for genotyping as defined in the inclusion/exclusion criteria. A total of 8,996 controls were targeted for genotyping. Two controls per case of endometrial cancer, lung cancer, and non-Hodgkin's lymphoma were defined from among the genotyped control samples.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0006826
    UMLS CUI [1,2]
    C1706256
    UMLS CUI [1,3]
    C0009932
    UMLS CUI [1,4]
    C0150103
    UMLS CUI [1,5]
    C0796344
    UMLS CUI [1,6]
    C0006142
    UMLS CUI [1,7]
    C0009402
    UMLS CUI [1,8]
    C0025202
    UMLS CUI [1,9]
    C1140680
    UMLS CUI [1,10]
    C0376358
    UMLS CUI [2,1]
    C0796344
    UMLS CUI [2,2]
    C0009932
    UMLS CUI [2,3]
    C2347026
    UMLS CUI [2,4]
    C0476089
    UMLS CUI [2,5]
    C0024305
    UMLS CUI [2,6]
    C0242379
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    Eligibility Criteria

    5 forms
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. Subject ID and consent group of participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      3. Subject ID, sample ID and sample use variable obtained from participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      4. Subject ID, age, sex, race, ethnicity, smoking status, smoking ICD9 code, CEU population, follow-up time of cancer participant visit, cancer status, cancer diagnosis, cancer site, CEU population, total population, smoking status, year of diagnosis, cancer type, cancer stage, breast cancer, colorectal cancer, lung cancer, melanoma, non-Hodgkin's lymphoma, ovarian cancer, prostate cancer, endometrial cancer, multiply cancer and follow-up time of cancer participant's visit of subjects with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
      5. Sample ID, body site where sample was collected [blood], analyte type, tumor status, and histological type of sample obtained from participants with or without cancer and involved in the "Population Architecture Using Genomics and Epidemiology (PAGE): Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project" project.
    Name
    Type
    Description | Question | Decode (Coded Value)
    Data type
    Alias
    Item Group
    Inclusion and exclusion criteria
    Cancer cases and controls were identified using a combination of in-patient and out-patient data as well as tumor registry entries. These data include primary site designations and histology information collected for clinical reporting purposes for the North America Association of Central Cancer Registries. A combination of the tumor registry data, along with ICD-9 billing codes, procedure codes, vital signs, and free text clinical notes, were used to identify cases for eight cancers among all patients aged 18 or greater in the SD with DNA samples using the following algorithms:
    Item
    Cancer cases and controls were identified using a combination of in-patient and out-patient data as well as tumor registry entries. These data include primary site designations and histology information collected for clinical reporting purposes for the North America Association of Central Cancer Registries. A combination of the tumor registry data, along with ICD-9 billing codes, procedure codes, vital signs, and free text clinical notes, were used to identify cases for eight cancers among all patients aged 18 or greater in the SD with DNA samples using the following algorithms:
    boolean
    C1706256 (UMLS CUI [1,1])
    C0009932 (UMLS CUI [1,2])
    C0205396 (UMLS CUI [1,3])
    C2707520 (UMLS CUI [1,4])
    C0805443 (UMLS CUI [1,5])
    C0449695 (UMLS CUI [1,6])
    C4048239 (UMLS CUI [1,7])
    C2826024 (UMLS CUI [1,8])
    C1136256 (UMLS CUI [1,9])
    C0518766 (UMLS CUI [1,10])
    C2066349 (UMLS CUI [1,11])
    C0001779 (UMLS CUI [1,12])
    Breast cancer: Three or more mentions of ICD-9 primary code for malignant neoplasm of the female breast and all sub-codes on separate clinic visits OR a tumor registry entry for breast cancer AND female;
    Item
    Breast cancer: Three or more mentions of ICD-9 primary code for malignant neoplasm of the female breast and all sub-codes on separate clinic visits OR a tumor registry entry for breast cancer AND female;
    boolean
    C0006142 (UMLS CUI [1,1])
    C1304708 (UMLS CUI [1,2])
    C1137111 (UMLS CUI [1,3])
    C0008952 (UMLS CUI [1,4])
    C0086287 (UMLS CUI [1,5])
    Colorectal cancer: Tumor registry entry for colorectal cancer;
    Item
    Colorectal cancer: Tumor registry entry for colorectal cancer;
    boolean
    C0009402 (UMLS CUI [1,1])
    C0805443 (UMLS CUI [1,2])
    Endometrial cancer: Tumor registry entry for endometrial cancer AND histology AND female;
    Item
    Endometrial cancer: Tumor registry entry for endometrial cancer AND histology AND female;
    boolean
    C0805443 (UMLS CUI [1,1])
    C0476089 (UMLS CUI [1,2])
    C0019638 (UMLS CUI [1,3])
    C0086287 (UMLS CUI [1,4])
    Lung cancer: Tumor registry entry for lung cancer, any location and any type;
    Item
    Lung cancer: Tumor registry entry for lung cancer, any location and any type;
    boolean
    C0805443 (UMLS CUI [1,1])
    C0684249 (UMLS CUI [1,2])
    C0450429 (UMLS CUI [1,3])
    C0030193 (UMLS CUI [1,4])
    C1552551 (UMLS CUI [1,5])
    C0332307 (UMLS CUI [1,6])
    Melanoma: Three or more mentions of ICD-9 codes for malignant melanoma of skin OR tumor registry entry for melanoma;
    Item
    Melanoma: Three or more mentions of ICD-9 codes for malignant melanoma of skin OR tumor registry entry for melanoma;
    boolean
    C0805443 (UMLS CUI [1,1])
    C0025202 (UMLS CUI [1,2])
    C1137111 (UMLS CUI [1,3])
    Non-Hodgkin's lymphoma: Tumor registry entry for non-Hodgkin's lymphoma with histology;
    Item
    Non-Hodgkin's lymphoma: Tumor registry entry for non-Hodgkin's lymphoma with histology;
    boolean
    C0805443 (UMLS CUI [1,1])
    C0024305 (UMLS CUI [1,2])
    C0019638 (UMLS CUI [1,3])
    Ovarian cancer: Tumor registry entry for ovarian cancer AND female;
    Item
    Ovarian cancer: Tumor registry entry for ovarian cancer AND female;
    boolean
    C0805443 (UMLS CUI [1,1])
    C0029925 (UMLS CUI [1,2])
    C0086287 (UMLS CUI [1,3])
    Prostate cancer: Three or more mentions of ICD-9 codes for malignant neoplasm of prostate OR tumor registry entry for prostate cancer.
    Item
    Prostate cancer: Three or more mentions of ICD-9 codes for malignant neoplasm of prostate OR tumor registry entry for prostate cancer.
    boolean
    C0805443 (UMLS CUI [1,1])
    C0600139 (UMLS CUI [1,2])
    C1137111 (UMLS CUI [1,3])
    Approximately two control samples were identified per case. Controls were matched by sex, race/ethnicity (administratively assigned), and age (within five years of the cases). Controls were required to have at least two clinical narratives, with preference given to records with at least one fully documented history and physical. Exclusion criteria included records with one or more codes for neoplasms, records with a tumor registry entry, and records that had one or more cancer related keywords in the problem list.
    Item
    Approximately two control samples were identified per case. Controls were matched by sex, race/ethnicity (administratively assigned), and age (within five years of the cases). Controls were required to have at least two clinical narratives, with preference given to records with at least one fully documented history and physical. Exclusion criteria included records with one or more codes for neoplasms, records with a tumor registry entry, and records that had one or more cancer related keywords in the problem list.
    boolean
    C1512693 (UMLS CUI [1,1])
    C1706256 (UMLS CUI [1,2])
    C0009932 (UMLS CUI [1,3])
    C0150103 (UMLS CUI [1,4])
    C0015031 (UMLS CUI [1,5])
    C1522384 (UMLS CUI [1,6])
    C0001779 (UMLS CUI [1,7])
    C1512693 (UMLS CUI [2,1])
    C4553389 (UMLS CUI [2,2])
    C0205210 (UMLS CUI [2,3])
    C0600664 (UMLS CUI [2,4])
    C0443225 (UMLS CUI [2,5])
    C0262926 (UMLS CUI [2,6])
    C0680251 (UMLS CUI [3,1])
    C0034869 (UMLS CUI [3,2])
    C0346429 (UMLS CUI [3,3])
    C0805443 (UMLS CUI [3,4])
    C1708608 (UMLS CUI [3,5])
    C0332281 (UMLS CUI [3,6])
    C0006826 (UMLS CUI [3,7])
    Additional control criteria are as follows:
    Item
    Additional control criteria are as follows:
    boolean
    C0243148 (UMLS CUI [1,1])
    C0243161 (UMLS CUI [1,2])
    Breast cancer controls are female only. For women over 40 years of age, we required that records contain at least one mammography Bi-Rad score as 1 (negative) or 2 (benign);
    Item
    Breast cancer controls are female only. For women over 40 years of age, we required that records contain at least one mammography Bi-Rad score as 1 (negative) or 2 (benign);
    boolean
    C0006142 (UMLS CUI [1,1])
    C0086287 (UMLS CUI [1,2])
    C0001779 (UMLS CUI [1,3])
    C1514873 (UMLS CUI [1,4])
    C0025102 (UMLS CUI [1,5])
    C0024671 (UMLS CUI [1,6])
    C4480026 (UMLS CUI [1,7])
    Endometrial cancer controls are female only;
    Item
    Endometrial cancer controls are female only;
    boolean
    C0476089 (UMLS CUI [1,1])
    C0086287 (UMLS CUI [1,2])
    Ovarian cancer controls are female only;
    Item
    Ovarian cancer controls are female only;
    boolean
    C0029925 (UMLS CUI [1,1])
    C0086287 (UMLS CUI [1,2])
    For colorectal cancer controls, we required for patients over 50 years of age the keyword "colonoscopy" in the problem list OR a procedure code for colonoscopy;
    Item
    For colorectal cancer controls, we required for patients over 50 years of age the keyword "colonoscopy" in the problem list OR a procedure code for colonoscopy;
    boolean
    C0009402 (UMLS CUI [1,1])
    C4553389 (UMLS CUI [1,2])
    C0001779 (UMLS CUI [1,3])
    C1514873 (UMLS CUI [1,4])
    C1708608 (UMLS CUI [1,5])
    C0009378 (UMLS CUI [1,6])
    C0552582 (UMLS CUI [1,7])
    C1550373 (UMLS CUI [1,8])
    Prostate cancer controls are male only. For male controls aged 40 years and greater to have at least one prostate specific antigen (PSA) level <4 and that the most recent PSA level is within the normal range.
    Item
    Prostate cancer controls are male only. For male controls aged 40 years and greater to have at least one prostate specific antigen (PSA) level <4 and that the most recent PSA level is within the normal range.
    boolean
    C0600139 (UMLS CUI [1,1])
    C0086582 (UMLS CUI [1,2])
    C0001779 (UMLS CUI [1,3])
    C0201544 (UMLS CUI [1,4])
    C1513491 (UMLS CUI [1,5])
    C0086715 (UMLS CUI [1,6])
    A total of 7,348 cases of cancer were identified in BioVU for targeted genotyping in EAGLE (Table).
    Item
    A total of 7,348 cases of cancer were identified in BioVU for targeted genotyping in EAGLE (Table).
    boolean
    C1853237 (UMLS CUI [1,1])
    C3854164 (UMLS CUI [1,2])
    C0205396 (UMLS CUI [1,3])
    *Table. Case counts by cancer and race/ethnicity.* Cases of specific cancers were determined in the de-identified electronic medical records within BioVU using algorithms implemented in late 2010/early 2011 as described in the text. Race/ethnicity was administratively assigned. *Cancer* *EA* *AA* *H* *A* *AI/NA* *O* *U* *Total* Breast 1,052 163 7 17 2 10 66 1,317 Colorectal 797 75 6 5 1 5 23 912 Endometrial 203 19 1 1 0 1 8 233 Lung 782 66 2 3 1 4 43 901 Melanoma 1,225 23 2 0 0 3 95 1,348 Non-Hodgkin's lymphoma 276 17 1 0 0 2 46 342 Ovarian 161 7 3 2 0 0 10 183 Prostate 1,895 172 4 2 0 7 32 2,112 Total 6,391 542 26 30 4 32 323 7,348
    Item
    *Table. Case counts by cancer and race/ethnicity.* Cases of specific cancers were determined in the de-identified electronic medical records within BioVU using algorithms implemented in late 2010/early 2011 as described in the text. Race/ethnicity was administratively assigned. *Cancer* *EA* *AA* *H* *A* *AI/NA* *O* *U* *Total* Breast 1,052 163 7 17 2 10 66 1,317 Colorectal 797 75 6 5 1 5 23 912 Endometrial 203 19 1 1 0 1 8 233 Lung 782 66 2 3 1 4 43 901 Melanoma 1,225 23 2 0 0 3 95 1,348 Non-Hodgkin's lymphoma 276 17 1 0 0 2 46 342 Ovarian 161 7 3 2 0 0 10 183 Prostate 1,895 172 4 2 0 7 32 2,112 Total 6,391 542 26 30 4 32 323 7,348
    boolean
    C1706074 (UMLS CUI [1,1])
    C1706256 (UMLS CUI [1,2])
    C0750480 (UMLS CUI [1,3])
    C0034510 (UMLS CUI [1,4])
    Abbreviations: European American (EA), African American (AA), Hispanic (H), Asian (A), American Indian/Native Alaskan (AI/NA), Other (O), Unknown (U).
    Item
    Abbreviations: European American (EA), African American (AA), Hispanic (H), Asian (A), American Indian/Native Alaskan (AI/NA), Other (O), Unknown (U).
    boolean
    C0000723 (UMLS CUI [1,1])
    C0085756 (UMLS CUI [1,2])
    C0683983 (UMLS CUI [1,3])
    C0086528 (UMLS CUI [1,4])
    C1515945 (UMLS CUI [1,5])
    C0078988 (UMLS CUI [1,6])
    C0205394 (UMLS CUI [1,7])
    C0439673 (UMLS CUI [1,8])
    For the first five cancers defined in BioVU (breast, colorectal, melanoma, ovarian, and prostate cancers), we identified approximately two controls per case for genotyping as defined in the inclusion/exclusion criteria. A total of 8,996 controls were targeted for genotyping. Two controls per case of endometrial cancer, lung cancer, and non-Hodgkin's lymphoma were defined from among the genotyped control samples.
    Item
    For the first five cancers defined in BioVU (breast, colorectal, melanoma, ovarian, and prostate cancers), we identified approximately two controls per case for genotyping as defined in the inclusion/exclusion criteria. A total of 8,996 controls were targeted for genotyping. Two controls per case of endometrial cancer, lung cancer, and non-Hodgkin's lymphoma were defined from among the genotyped control samples.
    boolean
    C0006826 (UMLS CUI [1,1])
    C1706256 (UMLS CUI [1,2])
    C0009932 (UMLS CUI [1,3])
    C0150103 (UMLS CUI [1,4])
    C0796344 (UMLS CUI [1,5])
    C0006142 (UMLS CUI [1,6])
    C0009402 (UMLS CUI [1,7])
    C0025202 (UMLS CUI [1,8])
    C1140680 (UMLS CUI [1,9])
    C0376358 (UMLS CUI [1,10])
    C0796344 (UMLS CUI [2,1])
    C0009932 (UMLS CUI [2,2])
    C2347026 (UMLS CUI [2,3])
    C0476089 (UMLS CUI [2,4])
    C0024305 (UMLS CUI [2,5])
    C0242379 (UMLS CUI [2,6])
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