Inglese

The subject phenotype data table includes age of enrollment (n=1 variable), tumor pathology (n=10 variables; baseline breast cancer luminal subtype, tumor shape, grade, maximum dimension, number of positive nodes, pathological tumor and node stage, and general comments), PEPI RFS score (n=2 variables), WHO clinical response (n=1 variable) and breast cancer biomarkers (n=15 variables; ER+, Ki-67, and Her2).

6 moduli  
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent data table contains subject IDs, consent group information, and affection status for estrogen receptor positive (ER+) breast cancer.
    3. The subject sample mapping data table includes 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 use.
    4. The subject phenotype data table includes age of enrollment (n=1 variable), tumor pathology (n=10 variables; baseline breast cancer luminal subtype, tumor shape, grade, maximum dimension, number of positive nodes, pathological tumor and node stage, and general comments), PEPI RFS score (n=2 variables), WHO clinical response (n=1 variable) and breast cancer biomarkers (n=15 variables; ER+, Ki-67, and Her2).
    5. The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type, histological type, and time of tumor sample collection.
    6. The pre- and post-subject phenotype data table includes age, sequence of events (n=9 variables; event and recurrence of event, adverse event, follow-up time, survival status, and cause of death), surgical status (n=2 variables), tumor pathology (n=6 variables; baseline tumor type and grade, number of positive nodes, node and tumor stage, and tumor dimension), PEPI RFS score (n=2 variables), and breast cancer biomarkers (n=6 variables; Allred ER+ score and Ki-67).
pht002595
Descrizione

pht002595

POL / Z1031 A or B
Descrizione

cohort

Tipo di dati

text

Alias
UMLS CUI [1,1]
C3846158
Gene expression array ID
Descrizione

gex_id

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4284067
UMLS CUI [1,2]
C0600091
ACGH ID
Descrizione

aCGH_id

Tipo di dati

text

Alias
UMLS CUI [1,1]
C2931151
UMLS CUI [1,2]
C0600091
General comments from pathology report
Descrizione

comment

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0947611
UMLS CUI [1,2]
C0807321
Age at enrollment to study
Descrizione

Age

Tipo di dati

text

Unità di misura
  • years
Alias
UMLS CUI [1,1]
C5236162
Breast cancer luminal A/B subtype
Descrizione

Baseline_Luminal_Type

Tipo di dati

text

Alias
UMLS CUI [1,1]
C3642345
UMLS CUI [1,2]
C3642346
Size of tumor maximum dimension
Descrizione

maxsxdim

Tipo di dati

text

Unità di misura
  • cm
Alias
UMLS CUI [1,1]
C0475440
UMLS CUI [1,2]
C0806909
Number of positive nodes
Descrizione

posnodes

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4086646
Pathological Tumor stage
Descrizione

pathT

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1300072
UMLS CUI [1,2]
C1521733
Pathological Node stage
Descrizione

pathN

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1272833
Baseline Her2 level
Descrizione

Baseline_HER2_level

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C1512413
Tumor shape
Descrizione

Baseline_Lobular_Ductal

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0700329
UMLS CUI [1,2]
C3273930
Baseline Grade
Descrizione

Baseline_Grade

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C0919553
Baseline Grade (transformed)
Descrizione

Baseline_Grade2

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C0919553
Baseline Grade (transformed)
Descrizione

Baseline_Grade3

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C0919553
Baseline ER level
Descrizione

Baseline_ER

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C0034804
UMLS CUI [1,3]
C0441889
Baseline Ki67 level
Descrizione

Baseline_Ki67

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C4049944
Ki67 level at 2 Week
Descrizione

Ki67_2wk

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C4484139
Ki67 level at 4 Week
Descrizione

Ki67_4wk

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C1442465
Ki67 level at Surgery
Descrizione

Ki67_Surg

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C0543467
Ki67 level at end of treatment (latest among 2 week 4 week or at Surgery)
Descrizione

Ki67_End.of.Treatment

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C5239247
Ki67 arithmetic change between end of treatment and baseline
Descrizione

Ki67_Change

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C0871653
UMLS CUI [1,3]
C1705241
UMLS CUI [1,4]
C5239247
UMLS CUI [1,5]
C1442488
Ki67 percentage change between end of treatment and baseline
Descrizione

Ki67_PercentageChange

Tipo di dati

text

Unità di misura
  • %
Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C0439165
UMLS CUI [1,3]
C1705241
UMLS CUI [1,4]
C5239247
UMLS CUI [1,5]
C1442488
Responder based on Ki67 at end of treatment
Descrizione

Responder_Ki67

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0919876
UMLS CUI [1,2]
C4049944
UMLS CUI [1,3]
C5239247
ER level at 2 Week
Descrizione

ER_2wk

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0034804
UMLS CUI [1,2]
C0441889
UMLS CUI [1,3]
C4484139
ER level at 4 Week
Descrizione

ER_4wk

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0034804
UMLS CUI [1,2]
C0441889
UMLS CUI [1,3]
C1442465
ER level at Surgery
Descrizione

ER_Surg

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0034804
UMLS CUI [1,2]
C0543467
ER level at end of treatment (latest among 2 week 4 week or at Surgery)
Descrizione

ER_End.of.Treatment

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0034804
UMLS CUI [1,2]
C5239247
ER arithmetic change between end of treatment and baseline
Descrizione

ER_Change

Tipo di dati

text

Alias
UMLS CUI [1,1]
C0034804
UMLS CUI [1,2]
C0871653
UMLS CUI [1,3]
C1705241
UMLS CUI [1,4]
C5239247
UMLS CUI [1,5]
C1442488
PEPI RFS score based on Matthew Ellis JNCI 2008 paper; PMID: 18812550 (https://www.ncbi.nlm.nih.gov/pubmed/18812550)
Descrizione

PEPI_Score

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4041462
UMLS CUI [1,2]
C0242793
Indicator for PEPI being 0
Descrizione

PEPI_Zero

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4041462
UMLS CUI [1,2]
C0220901
WHO clinical response
Descrizione

Clinical_Response

Tipo di dati

text

Alias
UMLS CUI [1,1]
C1298650
UMLS CUI [1,2]
C4055223
Deidentified Patient ID
Descrizione

SubjID

Tipo di dati

text

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C2348585
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Similar models

The subject phenotype data table includes age of enrollment (n=1 variable), tumor pathology (n=10 variables; baseline breast cancer luminal subtype, tumor shape, grade, maximum dimension, number of positive nodes, pathological tumor and node stage, and general comments), PEPI RFS score (n=2 variables), WHO clinical response (n=1 variable) and breast cancer biomarkers (n=15 variables; ER+, Ki-67, and Her2).

6 moduli
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent data table contains subject IDs, consent group information, and affection status for estrogen receptor positive (ER+) breast cancer.
    3. The subject sample mapping data table includes 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 use.
    4. The subject phenotype data table includes age of enrollment (n=1 variable), tumor pathology (n=10 variables; baseline breast cancer luminal subtype, tumor shape, grade, maximum dimension, number of positive nodes, pathological tumor and node stage, and general comments), PEPI RFS score (n=2 variables), WHO clinical response (n=1 variable) and breast cancer biomarkers (n=15 variables; ER+, Ki-67, and Her2).
    5. The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type, histological type, and time of tumor sample collection.
    6. The pre- and post-subject phenotype data table includes age, sequence of events (n=9 variables; event and recurrence of event, adverse event, follow-up time, survival status, and cause of death), surgical status (n=2 variables), tumor pathology (n=6 variables; baseline tumor type and grade, number of positive nodes, node and tumor stage, and tumor dimension), PEPI RFS score (n=2 variables), and breast cancer biomarkers (n=6 variables; Allred ER+ score and Ki-67).
Name
genere
Description | Question | Decode (Coded Value)
Tipo di dati
Alias
Item Group
pht002595
Item
POL / Z1031 A or B
text
C3846158 (UMLS CUI [1,1])
cohort
Code List
POL / Z1031 A or B
CL Item
missing value (NA)
Item
Gene expression array ID
text
C4284067 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
gex_id
Code List
Gene expression array ID
CL Item
missing value (NA)
Item
ACGH ID
text
C2931151 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
aCGH_id
Code List
ACGH ID
CL Item
missing value (NA)
Item
General comments from pathology report
text
C0947611 (UMLS CUI [1,1])
C0807321 (UMLS CUI [1,2])
comment
Code List
General comments from pathology report
CL Item
missing value (NA)
Item
Age at enrollment to study
text
C5236162 (UMLS CUI [1,1])
Age
Code List
Age at enrollment to study
CL Item
missing value (NA)
Item
Breast cancer luminal A/B subtype
text
C3642345 (UMLS CUI [1,1])
C3642346 (UMLS CUI [1,2])
Baseline_Luminal_Type
Code List
Breast cancer luminal A/B subtype
CL Item
missing value (NA)
Item
Size of tumor maximum dimension
text
C0475440 (UMLS CUI [1,1])
C0806909 (UMLS CUI [1,2])
maxsxdim
Code List
Size of tumor maximum dimension
CL Item
missing value (NA)
Item
Number of positive nodes
text
C4086646 (UMLS CUI [1,1])
posnodes
Code List
Number of positive nodes
CL Item
missing value (NA)
Item
Pathological Tumor stage
text
C1300072 (UMLS CUI [1,1])
C1521733 (UMLS CUI [1,2])
pathT
Code List
Pathological Tumor stage
CL Item
missing value (NA)
Item
Pathological Node stage
text
C1272833 (UMLS CUI [1,1])
pathN
Code List
Pathological Node stage
CL Item
missing value (NA)
Item
Baseline Her2 level
text
C1442488 (UMLS CUI [1,1])
C1512413 (UMLS CUI [1,2])
Baseline_HER2_level
Code List
Baseline Her2 level
CL Item
missing value (NA)
Item
Tumor shape
text
C0700329 (UMLS CUI [1,1])
C3273930 (UMLS CUI [1,2])
Baseline_Lobular_Ductal
Code List
Tumor shape
CL Item
missing value (NA)
Item
Baseline Grade
text
C1442488 (UMLS CUI [1,1])
C0919553 (UMLS CUI [1,2])
Baseline_Grade
Code List
Baseline Grade
CL Item
missing value (NA)
Item
Baseline Grade (transformed)
text
C1442488 (UMLS CUI [1,1])
C0919553 (UMLS CUI [1,2])
Baseline_Grade2
Code List
Baseline Grade (transformed)
CL Item
missing value (NA)
Item
Baseline Grade (transformed)
text
C1442488 (UMLS CUI [1,1])
C0919553 (UMLS CUI [1,2])
Baseline_Grade3
Code List
Baseline Grade (transformed)
CL Item
missing value (NA)
Item
Baseline ER level
text
C1442488 (UMLS CUI [1,1])
C0034804 (UMLS CUI [1,2])
C0441889 (UMLS CUI [1,3])
Baseline_ER
Code List
Baseline ER level
CL Item
missing value (NA)
Item
Baseline Ki67 level
text
C1442488 (UMLS CUI [1,1])
C4049944 (UMLS CUI [1,2])
Baseline_Ki67
Code List
Baseline Ki67 level
CL Item
missing value (NA)
Item
Ki67 level at 2 Week
text
C4049944 (UMLS CUI [1,1])
C4484139 (UMLS CUI [1,2])
Ki67_2wk
Code List
Ki67 level at 2 Week
CL Item
missing value (NA)
Item
Ki67 level at 4 Week
text
C4049944 (UMLS CUI [1,1])
C1442465 (UMLS CUI [1,2])
Ki67_4wk
Code List
Ki67 level at 4 Week
CL Item
missing value (NA)
Item
Ki67 level at Surgery
text
C4049944 (UMLS CUI [1,1])
C0543467 (UMLS CUI [1,2])
Ki67_Surg
Code List
Ki67 level at Surgery
CL Item
missing value (NA)
Item
Ki67 level at end of treatment (latest among 2 week 4 week or at Surgery)
text
C4049944 (UMLS CUI [1,1])
C5239247 (UMLS CUI [1,2])
Ki67_End.of.Treatment
Code List
Ki67 level at end of treatment (latest among 2 week 4 week or at Surgery)
CL Item
missing value (NA)
Item
Ki67 arithmetic change between end of treatment and baseline
text
C4049944 (UMLS CUI [1,1])
C0871653 (UMLS CUI [1,2])
C1705241 (UMLS CUI [1,3])
C5239247 (UMLS CUI [1,4])
C1442488 (UMLS CUI [1,5])
Ki67_Change
Code List
Ki67 arithmetic change between end of treatment and baseline
CL Item
missing value (NA)
Item
Ki67 percentage change between end of treatment and baseline
text
C4049944 (UMLS CUI [1,1])
C0439165 (UMLS CUI [1,2])
C1705241 (UMLS CUI [1,3])
C5239247 (UMLS CUI [1,4])
C1442488 (UMLS CUI [1,5])
Ki67_PercentageChange
Code List
Ki67 percentage change between end of treatment and baseline
CL Item
missing value (NA)
Item
Responder based on Ki67 at end of treatment
text
C0919876 (UMLS CUI [1,1])
C4049944 (UMLS CUI [1,2])
C5239247 (UMLS CUI [1,3])
Responder_Ki67
Code List
Responder based on Ki67 at end of treatment
CL Item
missing value (NA)
Item
ER level at 2 Week
text
C0034804 (UMLS CUI [1,1])
C0441889 (UMLS CUI [1,2])
C4484139 (UMLS CUI [1,3])
ER_2wk
Code List
ER level at 2 Week
CL Item
missing value (NA)
Item
ER level at 4 Week
text
C0034804 (UMLS CUI [1,1])
C0441889 (UMLS CUI [1,2])
C1442465 (UMLS CUI [1,3])
ER_4wk
Code List
ER level at 4 Week
CL Item
missing value (NA)
Item
ER level at Surgery
text
C0034804 (UMLS CUI [1,1])
C0543467 (UMLS CUI [1,2])
ER_Surg
Code List
ER level at Surgery
CL Item
missing value (NA)
Item
ER level at end of treatment (latest among 2 week 4 week or at Surgery)
text
C0034804 (UMLS CUI [1,1])
C5239247 (UMLS CUI [1,2])
ER_End.of.Treatment
Code List
ER level at end of treatment (latest among 2 week 4 week or at Surgery)
CL Item
missing value (NA)
Item
ER arithmetic change between end of treatment and baseline
text
C0034804 (UMLS CUI [1,1])
C0871653 (UMLS CUI [1,2])
C1705241 (UMLS CUI [1,3])
C5239247 (UMLS CUI [1,4])
C1442488 (UMLS CUI [1,5])
ER_Change
Code List
ER arithmetic change between end of treatment and baseline
CL Item
missing value (NA)
Item
PEPI RFS score based on Matthew Ellis JNCI 2008 paper; PMID: 18812550 (https://www.ncbi.nlm.nih.gov/pubmed/18812550)
text
C4041462 (UMLS CUI [1,1])
C0242793 (UMLS CUI [1,2])
PEPI_Score
Code List
PEPI RFS score based on Matthew Ellis JNCI 2008 paper; PMID: 18812550 (https://www.ncbi.nlm.nih.gov/pubmed/18812550)
CL Item
missing value (NA)
Item
Indicator for PEPI being 0
text
C4041462 (UMLS CUI [1,1])
C0220901 (UMLS CUI [1,2])
PEPI_Zero
Code List
Indicator for PEPI being 0
CL Item
missing value (NA)
Item
WHO clinical response
text
C1298650 (UMLS CUI [1,1])
C4055223 (UMLS CUI [1,2])
Clinical_Response
Code List
WHO clinical response
CL Item
no clinical response (SD or PD) (0)
CL Item
Clinical Response (CR or PR) (1)
CL Item
missing value (NA)
Item
Deidentified Patient ID
text
C4684638 (UMLS CUI [1,1])
C2348585 (UMLS CUI [1,2])
SubjID
Code List
Deidentified Patient ID
CL Item
missing value (NA)
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