Data instructions
In order to be included for the IMRC study on penetrance, data is needed on family history of cancer and who is and is not a mutation carrier. The preferred format for sending data is an excel file, or database containing the data listed below. Alternatively, if this is not possible, pedigrees containing as much of this data as possible is required.
Note: do not provide identifying information including names, address, or contact details.
Before sending data please email the study coordinator, Jeanette Reece (This email address is being protected from spambots. You need JavaScript enabled to view it. ), for instructions.
Progress of submission of Lynch syndrome families
Data submissions as at 1st July, 2017:
CONSORTIUMS No. submitted |
TOTAL No. families submitted |
TARGET No. families |
57 | 6054 | 8800 |
(136,900 individuals) |
Data dictionary:
"Comprehensive"
- consists of 3 tables; Demographics, Cancer and CRC_Treatment
(see below for "Minimum requirements")
Demographics data table (one row per person; multiple rows per family)
Variable | Description | Data type | Allowable values | ||||||||||||||||||||||||||||||||||||||||||
CENTER_NAME | What is the name of your center or clinic? | Text | |||||||||||||||||||||||||||||||||||||||||||
GENETIC_MMR_TEST_FAM_HX
|
Ascertainment: Was the MMR mutation testing done on the first person identified as the MMR mutation carrier (proband) because of a family history of cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
DATE_MMR_TEST_PERSON |
What is the known or approximate date of the person's MMR genetic test (if tested)? (9999=unknown year; 99=unknown month; 99=unknown date)
|
String | Format: YYYYMMDD | ||||||||||||||||||||||||||||||||||||||||||
FAMILY_ID | What is the ID number of the family? | String | |||||||||||||||||||||||||||||||||||||||||||
PERSON_ID | What is the ID number of the person? This must be an ID that is unique to your data. | String | |||||||||||||||||||||||||||||||||||||||||||
MOTHER_ID | What is the ID number of the mother? | String | |||||||||||||||||||||||||||||||||||||||||||
FATHER_ID | What is the ID number of the father? | String | |||||||||||||||||||||||||||||||||||||||||||
TWIN_ID |
If the person has a twin, what is their twin’s ID number? Leave blank if they do not have a twin. |
String | |||||||||||||||||||||||||||||||||||||||||||
TWIN_TYPE |
What type of twin are they? Leave blank if they do not have a twin.
|
Number |
Range:
1-2 or 9
|
||||||||||||||||||||||||||||||||||||||||||
PROBAND_FLAG |
Was this person the first in the family identified as a MMR mutation carrier?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
SEX |
What is the gender of the person?
|
Number |
Range:
1-2 or 9
|
||||||||||||||||||||||||||||||||||||||||||
DOB |
What is their known or approximate date of birth?
(9999=unknown year; 99=unknown month; 99=unknown date)
|
String | Format: YYYYMMDD | ||||||||||||||||||||||||||||||||||||||||||
*BASELINE_AGE | At what age was the person recruited to the study? | Number | Range: 0-130 or 999 | ||||||||||||||||||||||||||||||||||||||||||
VS |
Is the person known to be alive?
|
Number |
Range:
1-2 or 9
|
||||||||||||||||||||||||||||||||||||||||||
LIVE_AGE |
If alive, what is the person's last known age?
(999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
LIVEDATE |
What is the most recent date a subject is known to be living? (9999=unknown year; 99=unknown month; 99=unknown date)
|
String | Format: YYYYMMDD | ||||||||||||||||||||||||||||||||||||||||||
AGE_DEATH |
If deceased, at what age were they when they died?
(999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
DTHDATE | What is their date of death? (9999=unknown year; 99=unknown month; 99=unknown date) | String | Format: YYYYMMDD | ||||||||||||||||||||||||||||||||||||||||||
RACE |
What is their race/ethnicity?
|
Number |
Range:
1-19 or 99
|
||||||||||||||||||||||||||||||||||||||||||
RACE_OTHER_TXT |
Other race (text)? |
Text | |||||||||||||||||||||||||||||||||||||||||||
COB |
In which country were they born? http://seer.cancer.gov/archive/manuals/AppendB.pdf |
String |
Range:
000-750 or 999
|
||||||||||||||||||||||||||||||||||||||||||
COB_TXT |
In which country were they born (text)? |
Text | |||||||||||||||||||||||||||||||||||||||||||
MMR_GENE |
Which MMR gene is mutated in the family?
|
Number |
Range:
1-6 or 9
|
||||||||||||||||||||||||||||||||||||||||||
MMR_STATUS |
What is their mutation status?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
MMR_VARIANT_NAME | What is the description of the mutation (use LOVD nomenclature where possible)? | Text | |||||||||||||||||||||||||||||||||||||||||||
*COLONOSCOPY |
Has the person ever had a colonoscopy?
|
Number |
Range:
0-1 or 8-9
|
||||||||||||||||||||||||||||||||||||||||||
*AGE_FIRST_COLONOSCOPY
|
How old was the person when they first had a colonoscopy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
*AGE_LAST_COLONOSCOPY
|
How many separate colonoscopies has the person had? (999=unknown)
|
Number |
Range:
0-130 or 999 |
||||||||||||||||||||||||||||||||||||||||||
*COLONOSCOPY_NO
|
How old was the person when they last had a colonoscopy?(999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
POLYPECTOMY |
Has the person ever had a polypectomy?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
POLYP_TYPE1 |
Type of isolated first polyp #1 ?
|
Number |
Range:
1-9
|
||||||||||||||||||||||||||||||||||||||||||
AGE_FIRST_POLYPECTOMY |
If yes, what was their age when they had their first polypectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
HYSTERECTOMY |
Has the person ever had their uterus removed (hysterectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
AGE_HYSTERECTOMY
|
If yes, what was their age when they had their hysterectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
OOPHORECTOMY |
Has the person ever had both their ovaries removed (oophorectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
AGE_OOPHORECTOMY |
If yes, what was their age when they had their oophorectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
MASTECTOMY |
Has the person ever had one of their breasts removed (mastectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||||||||||||||||||||
AGE_MASTECTOMY |
If yes, what was their age when they had their oophorectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||||||||||||||||||||||||||||||||
AFFECTED |
Is the person affected with cancer?
|
Number |
Range:
0-1 or 9
|
*Additional variables added on 3rd March, 2016
Cancer data table (one row per primary cancer: multiple rows per person)
Variable | Description | Data type | Allowable values | ||||||||||||||||
CENTER_NAME | What is the name of your center or clinic? | Text | |||||||||||||||||
FAMILY_ID | What is the ID of the family? | String | |||||||||||||||||
PERSON_ID | What is the ID of the person? This must be an ID that is unique to your data. | String | |||||||||||||||||
TUMOR_NO |
What is the ID of the primary cancer? This must be an ID that is unique to the individual. |
Number |
|||||||||||||||||
TUMOR_SITE | What is the site of the primary cancer? Use ICD-0 where possible. http://apps.who.int/classifications/icd10/browse/2010/en#/II | Text |
Range: C00.0-C97.0 |
||||||||||||||||
HISTOLOGY |
First four digits of the ICD-0-3 morphology code which designates the histologic type of this tumor.
|
Number |
Range: 8000-9989 or 72860 | ||||||||||||||||
BEHAVIOR |
ICD-0-3 fifth digit behavior code (Coding based on SEER, NAACCR and AcoS guidelines.
|
Number |
Range: 0-3 | ||||||||||||||||
DXAGE |
What is the age at diagnosis? (999=unknown) |
Number |
Range:
0-130 or 999
|
||||||||||||||||
DXDATE |
What is the known or approximate date of diagnosis? (9999=unknown year; 99=unknown month; 99=unknown date)
|
String
|
Format: YYYYMMDD | ||||||||||||||||
DXSRC |
What is the source of information on the cancer diagnosis?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||
DXSRC_OTHER |
Other source, specify (eg. specialized genealogy) |
Text |
Treatment data table (one row per primary cancer: multiple rows per person)
Variable | Description | Data type | Allowable values | ||||||||||||||||||||||||
CENTER_NAME | What is the name of your center or clinic? | Text | |||||||||||||||||||||||||
FAMILY_ID | What is the ID of the family? | String | |||||||||||||||||||||||||
PERSON_ID | What is the ID of the person? This must be an ID that is unique to your data. | String | |||||||||||||||||||||||||
TUMOR_NO |
What is the ID of the primary cancer? This must be an ID that is unique to the individual. |
Number | |||||||||||||||||||||||||
CRC_T |
Tumor stage at baseline (0-4)
|
Number |
Range:
0-4 or 9
|
||||||||||||||||||||||||
CRC_N |
Nodal stage at baseline (0-2)
|
Number |
Range:
0-2 or 9
|
||||||||||||||||||||||||
CRC_M |
Metastasis stage at baseline (0-1)
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||
CRC_TNM |
TNM stage of tumor
|
Number |
Range:
0-4 or 9
|
||||||||||||||||||||||||
CRC_SURG |
Was surgical treatment performed for the primary colorectal cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||
CRC_SURG_DATE |
What is the date of the first resection? (9999=unknown year; 99=unknown month; 99=unknown date) |
String | Format: YYYYMMDD | ||||||||||||||||||||||||
CRC_SURG_TYPE |
Type of surgical treatment
|
Number | Range:
2-12 or 77
|
||||||||||||||||||||||||
CRC_SURG_OTHER |
Surgery performed (other), specify |
Text | |||||||||||||||||||||||||
CRC_CHEMO |
Was chemotherapy treatment performed for the primary colorectal cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||
CRC_CHEMO_METHOD |
Method of chemotherapy applied for treatment of the primary colorectal cancer:
|
Number |
Range:
1-4 or 9
|
||||||||||||||||||||||||
CRC_RAD |
Was radiation treatment performed for the primary colorectal cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||||||||||||||
CRC_RAD_METHOD |
Method of radiotherapy for the primary colorectal cancer:
|
Number |
Range:
1-4 or 9
|
-----------------------------------------------------------------------------------------------------
Data dictionary: "Minimum requirements"; 1 table
(add additional columns for second and subsequent cancers)
Variable | Description | Data type | Allowable values | ||||||||||||
CENTER_NAME | What is the name of your center or clinic? | Text | |||||||||||||
GENETIC_MMR_TEST_FAM_HX
|
Ascertainment: Was the MMR mutation testing done on the first person identified as the MMR mutation carrier (proband) because of a family history of cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||
FAMILY_ID | What is the ID number of the family? | String | |||||||||||||
PERSON_ID | What is the ID number of the person? This must be an ID that is unique to your data. | String | |||||||||||||
MOTHER_ID | What is the ID number of the mother? | String | |||||||||||||
FATHER_ID | What is the ID number of the father? | String | |||||||||||||
*TWIN_ID |
If the person has a twin, what is their twin’s ID number? Leave blank if they do not have a twin. |
String | |||||||||||||
*TWIN_TYPE |
What type of twin are they? Leave blank if they do not have a twin.
|
Number |
Range:
1-2 or 9
|
||||||||||||
PROBAND_FLAG |
Was this person the first in the family identified as a MMR mutation carrier?
|
Number |
Range:
0-1 or 9
|
||||||||||||
SEX |
What is the gender of the person?
|
Number |
Range:
1-2 or 9
|
||||||||||||
BASELINE_AGE | At what age was the person recruited to the study? | Number | Range: 0-130 or 999 | ||||||||||||
LAST_AGE |
If alive, what is the person's last known age? If deceased, what was the person's age at death (999=unknown)?
|
Number |
Range:
0-130 or 999
|
||||||||||||
MMR_GENE |
Which MMR gene is mutated in the family?
|
Number |
Range:
1-6 or 9
|
||||||||||||
MMR_STATUS |
What is their mutation status?
|
Number |
Range:
0-1 or 9
|
||||||||||||
MMR_VARIANT_NAME | What is the description of the mutation (use LOVD nomenclature where possible)? | Text | |||||||||||||
AFFECTED |
Is the person affected with cancer?
|
Number |
Range:
0-1 or 9
|
||||||||||||
TUMOR_NO
|
What is the ID of the primary cancer?
|
Number |
|
||||||||||||
TUMOR_SITE
|
What is the location of the primary cancer? Use ICD-O nomenclature where possible http://seer.cancer.gov/icd-o-3/sitetype.icdo3.d20150918.pdf
|
Text |
Range:
C00.0-C97.0 |
||||||||||||
BEHAVIOR |
ICD-0-3 fifth digit behavior code (Coding based on SEER, NAACCR and AcoS guidelines.
|
Number |
Range: 0-3 | ||||||||||||
DXAGE |
What is the age at diagnosis? (999=unknown) |
Number |
Range:
0-130 or 999
|
||||||||||||
*POLYPECTOMY |
Has the person ever had a polypectomy?
|
Number |
Range:
0-1 or 9
|
||||||||||||
*AGE_FIRST_POLYPECTOMY |
If yes, what was their age when they had their first polypectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||
*HYSTERECTOMY |
Has the person ever had their uterus removed (hysterectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||
*AGE_HYSTERECTOMY
|
If yes, what was their age when they had their hysterectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||
*OOPHORECTOMY |
Has the person ever had both their ovaries removed (oophorectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||
*AGE_OOPHORECTOMY |
If yes, what was their age when they had their oophorectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
||||||||||||
*MASTECTOMY |
Has the person ever had one of their breasts removed (mastectomy)?
|
Number |
Range:
0-1 or 9
|
||||||||||||
*AGE_MASTECTOMY |
If yes, what was their age when they had their oophorectomy? (999=unknown)
|
Number |
Range:
0-130 or 999
|
*Not essential