{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002498","ANALYSIS_ID":"AN004656","VERSION":"1","CREATED_ON":"September 1, 2023, 7:44 am"},

"PROJECT":{"PROJECT_TITLE":"Plasma Metabolomics Profiling of 580 Patients from the Weill Cornell Medicine Early Detection Research Network Prostate Cancer Cohort","PROJECT_SUMMARY":"Metabolomics profiling of 580 patients who underwent prostate biopsy from plasma samples taken at the time of biopsy.","INSTITUTE":"Weill Cornell Medicine","LAST_NAME":"Krumsiek","FIRST_NAME":"Jan","ADDRESS":"1305 York Avenue, New York, NY 10021","EMAIL":"jak2043@med.cornell.edu","PHONE":"646-962-4152"},

"STUDY":{"STUDY_TITLE":"Plasma Metabolomics Profiling of 580 Patients from the Weill Cornell Medicine Early Detection Research Network Prostate Cancer Cohort","STUDY_SUMMARY":"Prostate cancer is the second most common cancer in men and affects 1 in 9 men in the United States. Early screening for prostate cancer often involves monitoring levels of prostate-specific antigen (PSA) and performing digital rectal exams. However, a prostate biopsy is always required for definitive cancer diagnosis. The Early Detection Research Network (EDRN) is a consortium within the National Cancer Institute aimed at improving screening approaches and early detection of cancers. As part of this effort, the Weill Cornell EDRN Prostate Cancer has collected and biobanked specimens from men undergoing a prostate biopsy between 2008 and 2017. In this report, we describe blood metabolomics measurements for a subset of this population. The dataset includes detailed clinical and prospective records for 580 patients who underwent prostate biopsy, 287 of which were subsequentially diagnosed with prostate cancer, combined with profiling of 1,482 metabolites from plasma samples collected at the time of biopsy. We expect this dataset to provide a valuable resource for scientists investigating prostate cancer metabolism.","INSTITUTE":"Weill Cornell Medicine","LAST_NAME":"Krumsiek","FIRST_NAME":"Jan","ADDRESS":"1305 York Avenue, New York, NY 10021","EMAIL":"jak2043@med.cornell.edu","TOTAL_SUBJECTS":"580","NUM_MALES":"580","PHONE":"646-962-4152"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
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"Subject ID":"-",
"Sample ID":"C00013",
"Factors":{"Diagnosis":"0"},
"Additional sample data":{"PreBioPSA":"2.6","PreviousPositiveBiopsy":"0","Age":"69","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"72","Weight":"180","AUAscore":"99","AUAqol":"8","RisingPSA":"0","ElevatedPSA":"0","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"1","HGPIN":"1","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"1","Prostatitis":"1","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"1","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"1","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C00013_P1","PARENT SAMPLE ID":"6875478","SAMPLE NAME":"SH-WEIL-00171","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"6","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"A6"}
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"Subject ID":"-",
"Sample ID":"C00015",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"4.44","PreviousPositiveBiopsy":"0","Age":"64","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"1","FamilyHistoryPrCa":"1","PreviousCancer":"0","Arthritis":"1","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"1","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"71","Weight":"199","AUAscore":"13","AUAqol":"5","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"1","PrDrug5":"1","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C00015_P1","PARENT SAMPLE ID":"6875479","SAMPLE NAME":"SH-WEIL-00172","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"7","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"A7"}
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"Subject ID":"-",
"Sample ID":"C00017",
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"Additional sample data":{"PreBioPSA":"9.75","PreviousPositiveBiopsy":"0","Age":"66","EthnicityLatino":"0","Ethnicity":"1","Employment":"2","Education":"5","SmokingEver":"1","FamilyHistoryPrCa":"1","PreviousCancer":"0","Arthritis":"0","Diabetes":"1","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"60","Weight":"180","AUAscore":"7","AUAqol":"3","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"1","HGPIN":"1","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00017_P1","PARENT SAMPLE ID":"6875481","SAMPLE NAME":"SH-WEIL-00174","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"9","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"A9"}
},
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"Subject ID":"-",
"Sample ID":"C00020",
"Factors":{"Diagnosis":"0"},
"Additional sample data":{"PreBioPSA":"15.3","PreviousPositiveBiopsy":"0","Age":"49","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"1","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"69","Weight":"195","AUAscore":"13","AUAqol":"4","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"1","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C00020_P28","PARENT SAMPLE ID":"6875482","SAMPLE NAME":"SH-WEIL-00175","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"10","SAMPLE AMOUNT":"200","VOLUME EXTRACTED":"80","GROUP":"B1"}
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},
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"Additional sample data":{"PreBioPSA":"12","PreviousPositiveBiopsy":"0","Age":"65","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"1","HeartAttack":"1","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"68","Weight":"193","AUAscore":"7","AUAqol":"1","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"1","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"1","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00023_P29","PARENT SAMPLE ID":"6875485","SAMPLE NAME":"SH-WEIL-00178","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"13","SAMPLE AMOUNT":"200","VOLUME EXTRACTED":"80","GROUP":"B4"}
},
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"Subject ID":"-",
"Sample ID":"C00024",
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"Additional sample data":{"PreBioPSA":"4.5","PreviousPositiveBiopsy":"0","Age":"65","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"1","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"72","Weight":"198","AUAscore":"11","AUAqol":"4","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"0","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00024_P29","PARENT SAMPLE ID":"6875486","SAMPLE NAME":"SH-WEIL-00179","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"14","SAMPLE AMOUNT":"200","VOLUME EXTRACTED":"80","GROUP":"B5"}
},
{
"Subject ID":"-",
"Sample ID":"C00025",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"7.95","PreviousPositiveBiopsy":"0","Age":"66","EthnicityLatino":"0","Ethnicity":"1","Employment":"6","Education":"6","SmokingEver":"1","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"1","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"68.5","Weight":"178","AUAscore":"11","AUAqol":"4","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"1","Urethritis":"0","UrinaryInfection":"1","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00025_P1","PARENT SAMPLE ID":"6875487","SAMPLE NAME":"SH-WEIL-00180","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"15","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B6"}
},
{
"Subject ID":"-",
"Sample ID":"C00028",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"1.25","PreviousPositiveBiopsy":"0","Age":"65","EthnicityLatino":"0","Ethnicity":"1","Employment":"6","Education":"6","SmokingEver":"1","FamilyHistoryPrCa":"0","PreviousCancer":"1","Arthritis":"1","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"68","Weight":"187","AUAscore":"26","AUAqol":"3","RisingPSA":"0","ElevatedPSA":"0","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"1","DREresults":"1","BPH":"0","Prostatitis":"1","Urethritis":"1","UrinaryInfection":"1","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"0","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00028_P1","PARENT SAMPLE ID":"6875488","SAMPLE NAME":"SH-WEIL-00181","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"16","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B8"}
},
{
"Subject ID":"-",
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"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"7.5","PreviousPositiveBiopsy":"0","Age":"53","EthnicityLatino":"0","Ethnicity":"2","Employment":"1","Education":"5","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"69","Weight":"155","AUAscore":"1","AUAqol":"2","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"0","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C00030_P1","PARENT SAMPLE ID":"6875489","SAMPLE NAME":"SH-WEIL-00182","BOX NUMBER":"Box1","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"17","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B9"}
},
{
"Subject ID":"-",
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{
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{
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{
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{
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{
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},
{
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},
{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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},
{
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},
{
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{
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},
{
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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{
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{
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{
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{
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},
{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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{
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},
{
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},
{
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{
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{
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{
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{
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},
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},
{
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},
{
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},
{
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{
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},
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
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},
{
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},
{
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{
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{
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{
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"Sample ID":"C00921",
"Factors":{"Diagnosis":"0"},
"Additional sample data":{"PreBioPSA":"4.53","PreviousPositiveBiopsy":"0","Age":"62","EthnicityLatino":"0","Ethnicity":"32","Employment":"2","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"1","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"65","Weight":"194","AUAscore":"99","AUAqol":"8","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"2","BPH":"1","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C921 P1","PARENT SAMPLE ID":"6876048","SAMPLE NAME":"SH-WEIL-00741","BOX NUMBER":"Box8","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"576","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B2"}
},
{
"Subject ID":"-",
"Sample ID":"C00923",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"6","PreviousPositiveBiopsy":"0","Age":"70","EthnicityLatino":"0","Ethnicity":"1","Employment":"6","Education":"5","SmokingEver":"1","FamilyHistoryPrCa":"0","PreviousCancer":"1","Arthritis":"1","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"71","Weight":"170","AUAscore":"7","AUAqol":"5","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"1","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"1","DREresults":"4","BPH":"1","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"0","Hematuria":"1","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"0","PrDrug2":"1","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C923 P1","PARENT SAMPLE ID":"6876049","SAMPLE NAME":"SH-WEIL-00742","BOX NUMBER":"Box8","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"577","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B3"}
},
{
"Subject ID":"-",
"Sample ID":"C00924",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"38.11","PreviousPositiveBiopsy":"0","Age":"82","EthnicityLatino":"0","Ethnicity":"1","Employment":"6","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"1","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"69","Weight":"143","AUAscore":"16","AUAqol":"4","RisingPSA":"1","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"2","BPH":"1","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"1","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"0","PrDrug1":"0","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"1","CLIENT IDENTIFIER":"C924 P1","PARENT SAMPLE ID":"6876050","SAMPLE NAME":"SH-WEIL-00743","BOX NUMBER":"Box8","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"578","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B4"}
},
{
"Subject ID":"-",
"Sample ID":"C00927",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"5.52","PreviousPositiveBiopsy":"0","Age":"70","EthnicityLatino":"0","Ethnicity":"1","Employment":"1","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"1","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"68","Weight":"155","AUAscore":"3","AUAqol":"1","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"0","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"1","BPH":"1","Prostatitis":"1","Urethritis":"0","UrinaryInfection":"0","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"1","PrDrug1":"1","PrDrug2":"0","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C927 P1","PARENT SAMPLE ID":"6876051","SAMPLE NAME":"SH-WEIL-00744","BOX NUMBER":"Box8","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"579","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B5"}
},
{
"Subject ID":"-",
"Sample ID":"C00928",
"Factors":{"Diagnosis":"1"},
"Additional sample data":{"PreBioPSA":"5.26","PreviousPositiveBiopsy":"0","Age":"66","EthnicityLatino":"0","Ethnicity":"1","Employment":"2","Education":"6","SmokingEver":"0","FamilyHistoryPrCa":"0","PreviousCancer":"0","Arthritis":"0","Diabetes":"0","IBD":"0","Ulcer":"0","ChronicLungDisease":"0","HeartFailure":"0","Stroke":"0","Hypertension":"0","HeartAttack":"0","Angina":"0","Cirrhosis":"0","Depression":"0","Height":"75","Weight":"168","AUAscore":"12","AUAqol":"4","RisingPSA":"0","ElevatedPSA":"1","PercFreePSA":"0","AbnormDRE":"1","AbnormBiopsy":"0","HGPIN":"0","Atypia":"0","ASAP":"0","FamilyHistory":"0","IndexOther":"0","DREresults":"4","BPH":"0","Prostatitis":"0","Urethritis":"0","UrinaryInfection":"1","Hematuria":"0","PrProcedure":"0","PrevBiopsy":"0","PrDrug1":"0","PrDrug2":"1","PrDrug3":"0","PrDrug4":"0","PrDrug5":"0","PrDrug6":"0","PrDrugNone":"0","CLIENT IDENTIFIER":"C928 P1","PARENT SAMPLE ID":"6876052","SAMPLE NAME":"SH-WEIL-00745","BOX NUMBER":"Box8","CLIENT MATRIX":"EDTA plasma","CLIENT SAMPLE NUMBER":"580","SAMPLE AMOUNT":"100","VOLUME EXTRACTED":"80","GROUP":"B6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The Weill Cornell EDRN Prostate Cancer Cohort consented and recruited 1,144 patients (518 cases and 626 controls) over 9 years (from 2008 to 2017). In order to be eligible for the study, patients needed to be adult males, have no prior history of prostate cancer or prostate biopsies, and be scheduled to undergo prostate biopsy at Weill Cornell Medicine in New York City. Need of prostate biopsy was determined based on suspicion of prostate cancer, which primarily included elevated PSA levels, abnormal digital rectal exam (DRE) results, or suspicious findings based on imaging. Prostate biopsies included at least 10 cores taken in a laterally directed fashion, and a fasting blood sample was collected prior to prostate biopsy from all recruited patients. Biopsy tissue, together with urine and blood samples were processed and biobanked at Weill Cornell Medicine. For each patient, extensive clinical parameters were collected, including biopsy results, prostate cancer diagnosis and 2-year follow-up clinical information. EDTA-plasma samples for metabolomics profiling were selected to include patients with complete 12- and 24-months follow-up information available (see Data Records section for more details). This subset included a total of 580 patients, with 267 men diagnosed with PCa and 313 controls.","SAMPLE_TYPE":"Blood (plasma)"},

"TREATMENT":{"TREATMENT_SUMMARY":"Fasting blood was collected prior to biopsy in 6ml BD Vacutainer® EDTA tubes. Immediately after blood draw, the tube was inverted 8-10 times to mix the additive with the blood and placed immediately on ice. Tubes were centrifuged at 2,500 rpm for 15 minutes at 4°C within two hours of blood collection. Plasma aliquots of 100ul or 200ul were extracted from the top layer, transferred into 0.5ml polypropylene micro tubes and stored at -80C until shipment for metabolomic profiling."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Following receipt, samples were inventoried and immediately stored and maintained at -80oC until processed. Each received sample was assigned a unique identifier, which was used to track all sample handling, tasks, and results. The samples and all derived aliquots were tracked throughout the process via an automated system. On the day of extraction, frozen samples were thawed on ice. Samples were prepared using the automated MicroLab STAR® system (Hamilton Company, Reno, NV). 100 µl of each sample was transferred into a well in a deepwell plate. Prior to extraction, several isotopically labelled standards were added to each sample to ensure accurate extraction of the samples. To remove proteins or dissociate small molecules bound to proteins or trapped in the precipitated protein matrix, proteins were precipitated with 500 µl of methanol under vigorous shaking for 2 minutes in a GenoGrinder 2000 (Glen Mills, Inc, Clifton, NJ) followed by centrifugation for 10 minutes at 680g."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)","SOLVENT_A":"6.5 mM ammonium bicarbonate in water, pH 8","SOLVENT_B":"6.5 mM ammonium bicarbonate in 95% methanol / 5% water","FLOW_GRADIENT":"Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"40-50"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"preprocessing_workflow.docx"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Metabolon (LC/MS Neg). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill."},

"MS_METABOLITE_DATA":{
"Units":"peak area",

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}

}