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.This email address is being protected from spambots. You need JavaScript enabled to view it. 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? 
  0  No  (population-based)
  1  Yes (clinic-based)
  9  Unknown
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.
 
  1  Monozygous (identical)
  2  Dizygous (non-identical)
  9  Unknown
Number
Range:
1-2 or 9
 PROBAND_FLAG
Was this person the first in the family identified as a MMR mutation carrier?
 
  0  No
  1  Yes
  9  Unknown
Number
Range:
0-1 or 9
 
 SEX
What is the gender of the person?
 
  1  Male
  2  Female
  9  Unknown
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?
  1  Alive
  2  Dead
  9  Unknown
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?

Caucasian
2

African American/Black (except African; except Caribbean)

3

Latino, Hispanic, Mexican American, Mexican, Cuban, Puerto Rican

4 Japanese
5 Chinese
6 Filipino/Malay/Indonesian
7 Korean
8

South East Asian (except Chinese) (such as Vietnamese, Laotian, Thai, Hmong, Kampuchean)

9 South Asian (such as Indian, Pakistani, Sri Lankan)
10 Native American, Inuit, Aleutian, First Nations Person
11

Polynesian (such as Hawaiian, Maor, Samoan, Tongan, Tahitian, Cook Islander)

12 Micronesian
13 Australian Aboriginal
14 Melanesian (such as Fijian, New Guinean)
15

Caribbean Black (such as Jamaican, Trinidadian, Tobagonian)

16

Central/South American (such as Costa Rican, Salvadorian, Columbian,  Brazilian, Black African)

17 Black African
18 North African (such as Egyptian, Algerian, Moroccan)
19 Middle Eastern (such as Iranian, Lebanese, Kuwaiti, Saudi)
98 Other
99 Unknown
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?

  1   MLH1
  2   MSH2
  3   MSH6
  4   PMS2
  5   EPCAM
  9   Unknown
Number
Range:
1-6 or 9
 MMR_STATUS
What is their mutation status?
 
 -1  Not tested
  0  Non-carrier
  1  Carrier - heterozygous
  2  Carrier - homozygous
  9  Test result - inconclusive
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?
 
  0  No
  1  Yes
  8  Not asked
  9  Unknown
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?
 
  0  No
  1  Yes
  9  Unknown
Number
Range:
0-1 or 9
 POLYP_TYPE1

Type of isolated first polyp #1 ?

  1  TA (tubular adenoma)
  2  TV (tubulovillous)
  3  VA (villous)
  4  SA (serrated adenoma)
  5  HP (hyperplastic polyp)
  6  Other
  7  Adenomatous, type unspecified
  8  Mixed Polyp
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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?
 
  0  No
  1  Yes
  9  Unknown
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.

  8000   No specific histologic type information
  8001 to 9989    Range
  72680   Keratocanthoma

Number

Range: 8000-9989 or 72860

 BEHAVIOR

ICD-0-3 fifth digit behavior code (Coding based on SEER, NAACCR and AcoS guidelines.

   0   Benign
1   Uncertain; Low malignant potential; borderline
2   Carcinoma in situ
3   Malignant (invasive)
6   Malignant (metastatic site)
9   Malignant (uncertain whether primary or metastatic)

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?

 1  Pathology review or pathology report 
 2  Hospital or clinic record
 3  Cancer registry
 4  Death certificate
 5  Report by the person
 6  Report by a relative or spouse of the person
 7  Other
 9  Unknown

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)

  0 Carcinoma in situ/TIS
  1 Tumor invades submucosa
  2 Tumor invades muscularis propria
  3

Tumor invades through muscularis propria into submucosa or into non peritonealised pericolic or perirectal tissues

  4

Tumor directly invades other organs/structures/perforates visceral peritoneum

  9 Unknown
Number
Range:
0-4 or 9
 CRC_N

Nodal stage at baseline (0-2)

  0 No regional lymph node metastasis
  1 Metastasis in 1 to 3 regional lymph nodes
  2 Metastasis in 4 or more regional lymph nodes
  9 Unknown
Number
Range:
0-2 or 9
 CRC_M

Metastasis stage at baseline (0-1)

  0 No distant metastasis
  1 Distant metastasis is present
  9 Unknown
Number
Range:
0-1 or 9
 CRC_TNM

TNM stage of tumor

 1 I
2 II
3 III
4 IV
0 In-situ lesions
9 Unknown
Number
Range:
0-4 or 9
 CRC_SURG

Was surgical treatment performed for the primary colorectal cancer?

  0 No    
  1 Yes    
  9 Unknown    

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

 2   Local tumor destruction, i.e. laser, electrocautery
 3

  Local surgical excision with specimen - i.e. trans anal excision, polypectomy, snare

 4   Right Hemi colectomy
 5   Left Hemi colectomy
 6   Hemi colectomy side not specified: not total
 7   Low Anterior resection
 8   Total Colectomy
 9   Total Proctectomy
10   Total Proctocolectomy
11   Abdominoperineal resection
12   Segmental / Wedge / Partial Resection NOS
77   Other surgery
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?

  0   No
  1   Yes
  9   Unknown
Number
Range:
0-1 or 9
 
 CRC_CHEMO_METHOD

Method of chemotherapy applied for treatment of the primary colorectal cancer:

  1 Adjuvant
  2 Palliative
  3 Psuedo Adjuvant
  4 Neo Adjuvant (pre-operative)
  9 Unknown
Number
Range:
1-4 or 9
 CRC_RAD

Was radiation treatment performed for the primary colorectal cancer?

  0 No  
  1 Yes  
  9 Unknown  

Number

Range:
0-1 or 9
 CRC_RAD_METHOD

Method of radiotherapy for the primary colorectal cancer:

  1 Adjuvant  
  2 Palliative  
  3 Psuedo Adjuvant  
  4 Neo Adjuvant  
  9 Unknown  

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? 
  0  No  (population-based)
  1  Yes (clinic-based)
  9  Unknown
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.
 
  1  Monozygous (identical)
  2  Dizygous (non-identical)
  9  Unknown
Number
Range:
1-2 or 9
 PROBAND_FLAG
Was this person the first in the family identified as a MMR mutation carrier?
 
  0  No
  1  Yes
  9  Unknown
Number
Range:
0-1 or 9
 
 SEX
What is the gender of the person?
 
  1  Male
  2  Female
  9  Unknown
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?

  1   MLH1
  2   MSH2
  3   MSH6
  4   PMS2
  5   EPCAM
  9   Unknown
Number
Range:
1-6 or 9
 MMR_STATUS
What is their mutation status?
 
 -1  Not tested
  0  Non-carrier
  1  Carrier - heterozygous
  2  Carrier - homozygous
  9  Test result - inconclusive
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?
 
  0  No
  1  Yes
  9  Unknown
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.

   0   Benign
1   Uncertain; Low malignant potential; borderline
2   Carcinoma in situ
3   Malignant (invasive)
6   Malignant (metastatic site)
9   Malignant (uncertain whether primary or metastatic)

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?
 
  0  No
  1  Yes
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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)?
 
  0  No
  1  Yes
  9  Unknown
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