CanRisk Pedigree Data v3 File Format Specification
- Tim Carver
Description
CanRisk Pedigree Data v3 Files contain the target individual's risk factors (optional) in the header followed by pedigree data (mandatory) as a series of pedigree data records, one for each family member. The following sections describe the format of the File Header and the Pedigree Data records.
File Header
The File Header can optionally include the following breast and/or ovarian cancer risk factors for the target individual:
VARIABLE NAME |
| RISK FACTOR DESCRIPTION | ALLOWED VALUES |
|---|---|---|---|
Ethnicity | †‡ | UK based ethnic groups, The ethnicity categories here are based on those recommended by the Office for National Statisitcs for the UK. See table below. | ethnic group;ethnic background |
Menarche | † | Age at menarche | NA=unspecified, integer=age at menarche |
Parity | †‡ | Parity | NA=unspecified, integer=number of children |
First_live_birth | † | Age at first live birth | NA=unspecified, integer=age at first live birth |
OC_use | †‡ | Use of oral contraception | NA=unspecified, N=Never, F:Years=Former use, C:Years=Current use; F and C are followed by integer=number of years taken e.g. F:4 means former use of 4 years |
MHT_use | †‡ | Use of menopause hormone therapy | NA=unspecified, N=Never used, F=Former use, E=Current E-type use, C=Current other/unknown type (including combined type) use |
BMI | † | Body mass index | NA=unspecified, real number=body mass index |
Alcohol | † | Daily alcohol intake in grams per day | NA=unspecified, real number=daily alcohol intake in grams |
Menopause | † | Age at menopause | NA=unspecified, integer=age at menopause or 'N' if pre-menopause |
BIRADS | † | Mammographic density measured by BI-RADS | NA=unspecified, BI-RADS classification (a, b, c, d or 1, 2, 3, 4) |
Stratus | † | Continuous mammographic density measured by Stratus | NA=unspecified, percentage density |
Volpara | † | Continuous mammographic density measured by Volpara | NA=unspecified, percentage density |
Height | †‡ | Height in cm | NA=unspecified, real number=height in cm |
TL | ‡ | Tubal ligation procedure | NA=unspecified, N=No, Y=Yes |
Endo | ‡ | Endometriosis | NA=unspecified, N=No, Y=Yes |
PRS_BC | † | Polygenic Risk Score (Breast Cancer) | e.g. alpha=real number, zscore=real number |
PRS_OC | ‡ | Polygenic Risk Score (Ovarian Cancer) | e.g. alpha=real number, zscore=real number |
† Breast Cancer Risk Factor ‡ Ovarian Cancer Risk Factor
The PRS_BC and PRS_OC values are:
alpha - the square root of the proportion of the overall polygenic variance explained by the PRS. A real number between 0 and 1.
zscore – the standard normal PRS.
UK based Ethnic Groups and Background
Ethnic group | Ethnic background |
|---|---|
White | English/Welsh/Scottish/Northern Irish/British |
Mixed/Multiple ethnic groups | White and Black Caribbean |
Asian or Asian British | Indian |
Black or Black British | African |
Other ethnic group | Arab |
Unknown |
|
All header lines begin with '##'. Any missing risk factor variables are taken as unspecified. The risk factors are given as one per line, the variable names can be any case and in any order in the header. The following example header shows the first mandatory header record ##CanRisk 3.0 followed by some of the optional risk factors for the target in the pedigree. The last line in the header is the second mandatory pedigree data column header record beginning ##FamID Name….
Example CanRisk File Header
##CanRisk 3.0
##ethnicity=Black or Black British;African
##Menarche=13
##Parity=1
##First_live_birth=24
##OC_use=C:2
##BMI=27.1
##height=170
##alcohol=5.1
##PRS_BC=alpha=0.45, zscore=1.8
##FamID Name Target IndivID FathID MothID Sex MZtwin Dead Age Yob BC1 ….......
Pedigree Data
The CanRisk Pedigree Data Format is a simple TAB-delimited text format. CanRisk pedigree data files consist of the two mandatory header records followed by a series of pedigree data records, one for each family member. The pedigree data records include 27 parameters (data columns) separated by a single TAB (or whitespace) character.
Parameters 1-27 on the pedigree data records are defined as follows:
FamID Family/pedigree ID, character string (maximum 13 characters)
Name First name/ID of the family member, character string (maximum 8 characters)
Target The family member for whom the CanRisk risk calculation is made, 1 = target for risk calculation, 0 = other family members.
IndivID Unique ID of the family member, character string (maximum 7 characters)
FathID Unique ID of their father, 0 = no father, or character string (maximum 7 characters. Each family member must have either: (1) no parents specified (e.g. see family member '103' in the pedigree 'Example without risk factors' in the accompanying FAQ CanRisk Pedigree Data File Examples), or (2) both parents specified (e.g. see family member '201' in the same pedigree).
MothID Unique ID of their mother, 0 = unspecified, or character string (maximum 7 characters)
Sex M or F
MZtwin Identical twins, 0 = not an identical twin, Use one of these characters to identify MZ twins: 1 2 3 4 5 6 7 8 9 A
Dead The current status of the family member, 0 = alive, 1 = dead
Age Age at last follow up, 0 = unspecified, integer = age at last follow up
Yob Year of birth, 0 = unspecified, or integer (consistent with Age if the person is alive)
BC1 Age at first breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
BC2 Age at second (contralateral) breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
OC Age at ovarian cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
PRO Age at prostate cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
PAN Age at pancreatic cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
Ashkn Ashkenazi status, 0 = not Ashkenazi, 1 = Ashkenazi
BRCA1 BRCA1 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
BRCA2 BRCA2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
PALB2 PALB2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
ATM ATM genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
CHEK2 CHEK2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
BARD1 BARD1 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
RAD51D RAD51D genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
RAD51C RAD51C genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
BRIP1 BRIP1 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
ER:PR:HER2:CK14:CK56 Colon separated Estrogen receptor, Progestrogen receptor, Human epidermal growth factor receptor 2, Cytokeratin 14, Cytokeratin 56 status, 0 = unspecified, N = negative, P = positive