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Description
CanRisk Pedigree Data 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 | |
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 C-type 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 |
BIRADS | † | Mammographic density measured by BI-RADS | NA=unspecified, BI-RADS classification (a, b, c, d or 1, 2, 3, 4) |
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.
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 1.0 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….
| Info | ||
|---|---|---|
| ||
##CanRisk 1.0 |
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 26 parameters (data columns) separated by a single TAB (or whitespace) character.
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