Engelsk

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).

6 Formulär  
  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).
pht006830
Beskrivning

pht006830

De-identified patient ID
Beskrivning

patient_id

Datatyp

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C2348585
McDonnell Genome Institute subject ID
Beskrivning

SubjID

Datatyp

string

Alias
UMLS CUI [1,1]
C2348585
UMLS CUI [1,2]
C1272753
Baseline Ki67 level
Beskrivning

baseline_ki67

Datatyp

string

Måttenheter
  • percentage
Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C1442488
percentage
End of treatment ki67 level
Beskrivning

EOT ki67

Datatyp

string

Måttenheter
  • percentage
Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C3173313
percentage
Ki67 level at surgery
Beskrivning

Surgical ki67

Datatyp

string

Måttenheter
  • percentage
Alias
UMLS CUI [1,1]
C4049944
UMLS CUI [1,2]
C0543467
percentage
Baseline Allred ER score
Beskrivning

Baseline_Allred_ER

Datatyp

text

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C4289982
End of treatment Allred ER score
Beskrivning

EOT_Allred_ER

Datatyp

text

Alias
UMLS CUI [1,1]
C4289982
UMLS CUI [1,2]
C3173313
Allred ER score at surgery
Beskrivning

Surgical_Allred_ER

Datatyp

text

Alias
UMLS CUI [1,1]
C4289982
UMLS CUI [1,2]
C0543467
PEPI RFS score based on Matthew Ellis JNCI 2008 paper; PMID: 18812550 (https://www.ncbi.nlm.nih.gov/pubmed/18812550)
Beskrivning

PEPI_Score

Datatyp

text

Alias
UMLS CUI [1,1]
C4041462
UMLS CUI [1,2]
C0449820
UMLS CUI [1,3]
C0242793
Indicator for a PEPI value of 0
Beskrivning

pepizero

Datatyp

text

Alias
UMLS CUI [1,1]
C4041462
UMLS CUI [1,2]
C1522609
Number of positive nodes
Beskrivning

posnodes

Datatyp

text

Alias
UMLS CUI [1,1]
C4086646
Pathological Node stage
Beskrivning

pathN

Datatyp

text

Alias
UMLS CUI [1,1]
C1272833
Size of tumor maximum dimension
Beskrivning

maxsxdim

Datatyp

text

Måttenheter
  • cm
Alias
UMLS CUI [1,1]
C0475440
UMLS CUI [1,2]
C0806909
cm
Pathological Tumor stage
Beskrivning

pathT

Datatyp

text

Alias
UMLS CUI [1,1]
C1300072
Was surgery performed?
Beskrivning

sxperf

Datatyp

string

Alias
UMLS CUI [1,1]
C0543467
Was there a post-surgical evaluation?
Beskrivning

post_sx_evaluation

Datatyp

string

Alias
UMLS CUI [1,1]
C0241311
UMLS CUI [1,2]
C0220825
Description of recurrence event
Beskrivning

type_of_event

Datatyp

text

Alias
UMLS CUI [1,1]
C0678257
UMLS CUI [1,2]
C0679254
Site of recurrence
Beskrivning

event_site

Datatyp

text

Alias
UMLS CUI [1,1]
C0679254
UMLS CUI [1,2]
C1545955
Binary variable for adverse event occurrence
Beskrivning

adevent

Datatyp

text

Alias
UMLS CUI [1,1]
C2827064
UMLS CUI [1,2]
C2697887
Patient follow-up time
Beskrivning

fu_time

Datatyp

text

Måttenheter
  • days
Alias
UMLS CUI [1,1]
C1522577
UMLS CUI [1,2]
C0040223
days
Cause of death
Beskrivning

cause_of_death

Datatyp

text

Alias
UMLS CUI [1,1]
C0007465
Baseline tumor type
Beskrivning

Baseline_Lobular_Ductal

Datatyp

string

Alias
UMLS CUI [1,1]
C1442488
UMLS CUI [1,2]
C4263544
I vs. II vs. III by WHO criterion
Beskrivning

Baseline_Grade

Datatyp

string

Alias
UMLS CUI [1,1]
C0043237
UMLS CUI [1,2]
C0243161
Age in years
Beskrivning

Age

Datatyp

text

Måttenheter
  • years
Alias
UMLS CUI [1,1]
C0001779
years
Disease-free survival status
Beskrivning

dfs_stat

Datatyp

text

Alias
UMLS CUI [1,1]
C0242793
UMLS CUI [1,2]
C0449438
Recurrence event interrupting disease-free status
Beskrivning

dfsevent

Datatyp

string

Alias
UMLS CUI [1,1]
C0679254
UMLS CUI [1,2]
C0443239
UMLS CUI [1,3]
C5401422
Description of recurrence event
Beskrivning

dfstxt

Datatyp

string

Alias
UMLS CUI [1,1]
C0678257
UMLS CUI [1,2]
C0679254
Full cause of death
Beskrivning

cdeathf

Datatyp

string

Alias
UMLS CUI [1,1]
C0007465
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Similar models

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).

6 Formulär
  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
Typ
Description | Question | Decode (Coded Value)
Datatyp
Alias
Item Group
pht006830
patient_id
Item
De-identified patient ID
string
C4684638 (UMLS CUI [1,1])
C2348585 (UMLS CUI [1,2])
SubjID
Item
McDonnell Genome Institute subject ID
string
C2348585 (UMLS CUI [1,1])
C1272753 (UMLS CUI [1,2])
baseline_ki67
Item
Baseline Ki67 level
string
C4049944 (UMLS CUI [1,1])
C1442488 (UMLS CUI [1,2])
EOT ki67
Item
End of treatment ki67 level
string
C4049944 (UMLS CUI [1,1])
C3173313 (UMLS CUI [1,2])
Surgical ki67
Item
Ki67 level at surgery
string
C4049944 (UMLS CUI [1,1])
C0543467 (UMLS CUI [1,2])
Baseline_Allred_ER
Item
Baseline Allred ER score
text
C1442488 (UMLS CUI [1,1])
C4289982 (UMLS CUI [1,2])
EOT_Allred_ER
Item
End of treatment Allred ER score
text
C4289982 (UMLS CUI [1,1])
C3173313 (UMLS CUI [1,2])
Surgical_Allred_ER
Item
Allred ER score at surgery
text
C4289982 (UMLS CUI [1,1])
C0543467 (UMLS CUI [1,2])
PEPI_Score
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])
C0449820 (UMLS CUI [1,2])
C0242793 (UMLS CUI [1,3])
pepizero
Item
Indicator for a PEPI value of 0
text
C4041462 (UMLS CUI [1,1])
C1522609 (UMLS CUI [1,2])
posnodes
Item
Number of positive nodes
text
C4086646 (UMLS CUI [1,1])
pathN
Item
Pathological Node stage
text
C1272833 (UMLS CUI [1,1])
maxsxdim
Item
Size of tumor maximum dimension
text
C0475440 (UMLS CUI [1,1])
C0806909 (UMLS CUI [1,2])
pathT
Item
Pathological Tumor stage
text
C1300072 (UMLS CUI [1,1])
sxperf
Item
Was surgery performed?
string
C0543467 (UMLS CUI [1,1])
post_sx_evaluation
Item
Was there a post-surgical evaluation?
string
C0241311 (UMLS CUI [1,1])
C0220825 (UMLS CUI [1,2])
type_of_event
Item
Description of recurrence event
text
C0678257 (UMLS CUI [1,1])
C0679254 (UMLS CUI [1,2])
event_site
Item
Site of recurrence
text
C0679254 (UMLS CUI [1,1])
C1545955 (UMLS CUI [1,2])
Item
Binary variable for adverse event occurrence
text
C2827064 (UMLS CUI [1,1])
C2697887 (UMLS CUI [1,2])
adevent
Code List
Binary variable for adverse event occurrence
CL Item
no (0)
CL Item
yes (1)
fu_time
Item
Patient follow-up time
text
C1522577 (UMLS CUI [1,1])
C0040223 (UMLS CUI [1,2])
cause_of_death
Item
Cause of death
text
C0007465 (UMLS CUI [1,1])
Baseline_Lobular_Ductal
Item
Baseline tumor type
string
C1442488 (UMLS CUI [1,1])
C4263544 (UMLS CUI [1,2])
Baseline_Grade
Item
I vs. II vs. III by WHO criterion
string
C0043237 (UMLS CUI [1,1])
C0243161 (UMLS CUI [1,2])
Age
Item
Age in years
text
C0001779 (UMLS CUI [1,1])
Item
Disease-free survival status
text
C0242793 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
dfs_stat
Code List
Disease-free survival status
CL Item
disease free (0)
CL Item
recurring disease (1)
dfsevent
Item
Recurrence event interrupting disease-free status
string
C0679254 (UMLS CUI [1,1])
C0443239 (UMLS CUI [1,2])
C5401422 (UMLS CUI [1,3])
dfstxt
Item
Description of recurrence event
string
C0678257 (UMLS CUI [1,1])
C0679254 (UMLS CUI [1,2])
cdeathf
Item
Full cause of death
string
C0007465 (UMLS CUI [1,1])
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