Information:
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ID
45808
Description
Principal Investigator: Matthew Goetz, MD, Mayo Clinic, Rochester, MN, USA MeSH: Breast Neoplasms,Carcinoma, Ductal, Breast https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001050 The Breast Cancer Genome Guided Therapy Study (BEAUTY) is a prospective neoadjuvant clinical study enrolling 140 women with Stage I-III breast cancer. The goals of this study were to 1) perform comprehensive sequencing of germline and tumor tissues (exome and RNA seq), 2) identify genomic alterations and perturbed pathways associated with response/resistance to standard chemotherapy, and 3) develop patient-derived xenograft (PDX) for testing of therapeutic regimens chosen on the basis of alterations identified by genetic sequencing.
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Keywords
Versions (1)
- 6/23/23 6/23/23 - Simon Heim
Copyright Holder
Matthew Goetz, MD, Mayo Clinic, Rochester, MN, USA
Uploaded on
June 23, 2023
DOI
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License
Creative Commons BY 4.0
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dbGaP phs001050 Breast Cancer Genome Guided Therapy Study (BEAUTY)
This sample attributes table contains sample ID, body site where sample was collected, analyte type, tumor status, histologic type, primary metastatic tumor, primary tumor location, tumor stage, grade, treatment, name of the center which conducted sequencing, portion of sequencing lane, and comments.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and case control status of the subject. All subjects are patients with Stage I-III breast cancer.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample aliases and sample use.
- This subject phenotype table contains subject ID, pathological complete response in breast and nodes, clinical molecular tumor type, tumor stage, nodal stage, lab estimate of tumor percentage at baseline, Ki67 sensitivity, estrogen and progesterone receptor level, HER2 results by IHC or Fish, and patient age.
- This sample attributes table contains sample ID, body site where sample was collected, analyte type, tumor status, histologic type, primary metastatic tumor, primary tumor location, tumor stage, grade, treatment, name of the center which conducted sequencing, portion of sequencing lane, and comments.
Similar models
This sample attributes table contains sample ID, body site where sample was collected, analyte type, tumor status, histologic type, primary metastatic tumor, primary tumor location, tumor stage, grade, treatment, name of the center which conducted sequencing, portion of sequencing lane, and comments.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and case control status of the subject. All subjects are patients with Stage I-III breast cancer.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample aliases and sample use.
- This subject phenotype table contains subject ID, pathological complete response in breast and nodes, clinical molecular tumor type, tumor stage, nodal stage, lab estimate of tumor percentage at baseline, Ki67 sensitivity, estrogen and progesterone receptor level, HER2 results by IHC or Fish, and patient age.
- This sample attributes table contains sample ID, body site where sample was collected, analyte type, tumor status, histologic type, primary metastatic tumor, primary tumor location, tumor stage, grade, treatment, name of the center which conducted sequencing, portion of sequencing lane, and comments.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
SAMPLE_ID
Item
De-identified Sample ID
string
C4684638 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
C1299222 (UMLS CUI [1,2])
BODY_SITE
Item
Body site where sample was collected
string
C0449705 (UMLS CUI [1,1])
ANALYTE_TYPE
Item
Analyte Type
string
C4744818 (UMLS CUI [1,1])
CL Item
Is not a tumor (N)
C0027651 (UMLS CUI [1,1])
C1518422 (UMLS CUI [1,2])
C1518422 (UMLS CUI [1,2])
CL Item
Is Tumor (Y)
C0027651 (UMLS CUI [1,1])
HISTOLOGIC_TYPE
Item
Cell or tissue type or subtype of sample
string
C2347026 (UMLS CUI [1,1])
C0007634 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2347026 (UMLS CUI [2,1])
C0007634 (UMLS CUI [2,2])
C0449560 (UMLS CUI [2,3])
C1292533 (UMLS CUI [3,1])
C0332307 (UMLS CUI [3,2])
C1292533 (UMLS CUI [4,1])
C0449560 (UMLS CUI [4,2])
C0007634 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2347026 (UMLS CUI [2,1])
C0007634 (UMLS CUI [2,2])
C0449560 (UMLS CUI [2,3])
C1292533 (UMLS CUI [3,1])
C0332307 (UMLS CUI [3,2])
C1292533 (UMLS CUI [4,1])
C0449560 (UMLS CUI [4,2])
PRIMARY_METASTATIC_TUMOR
Item
Primary tumor, metastasis, or transformed cell line
string
C0677930 (UMLS CUI [1,1])
C0027627 (UMLS CUI [2,1])
C0007601 (UMLS CUI [3,1])
C0027627 (UMLS CUI [2,1])
C0007601 (UMLS CUI [3,1])
PRIMARY_TUMOR_LOCATION
Item
Primary tumor location
string
C0475447 (UMLS CUI [1,1])
TUMOR_STAGE
Item
Tumor stage of sample
string
C1300072 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
C0370003 (UMLS CUI [1,2])
TUMOR_GRADE
Item
Tumor grade of sample
string
C0919553 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
C0370003 (UMLS CUI [1,2])
TUMOR_TREATMENT
Item
Type of tumor treatment for sample
string
C0332307 (UMLS CUI [1,1])
C0087111 (UMLS CUI [1,2])
C0006826 (UMLS CUI [1,3])
C0370003 (UMLS CUI [1,4])
C0087111 (UMLS CUI [1,2])
C0006826 (UMLS CUI [1,3])
C0370003 (UMLS CUI [1,4])
SEQUENCING_CENTER
Item
Name of the center which conducted sequencing
string
C1301943 (UMLS CUI [1,1])
C5575037 (UMLS CUI [1,2])
C1561491 (UMLS CUI [1,3])
C5575037 (UMLS CUI [1,2])
C1561491 (UMLS CUI [1,3])
LANE_PORTION
Item
Portion of sequencing lane taken by the sample
string
C5667285 (UMLS CUI [1,1])
COMMENTS
Item
Description of sequencing preparation or alignment exceptions
string
C5667288 (UMLS CUI [1,1])
C3846158 (UMLS CUI [1,2])
C3846158 (UMLS CUI [1,2])
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