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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 sectio= ns describe the format of the File Header and the Pedig= ree Data records.
The File Header can optionally include the following breast and/or ovari= an cancer risk factors for the target individual:
VARIABLE NAME |
|
RISK FACTOR DESCRIPTION |
ALLOWED VALUES |
Menarche |
=E2=80=A0 |
Age at menarche |
NA=3Dunspecified, integer=3Dage at menarche |
Parity |
=E2=80=A0=E2=80=A1 |
Parity |
NA=3Dunspecified, integer=3Dnumber of children |
First_live_birth |
=E2=80=A0 |
Age at first live birth |
NA=3Dunspecified, integer=3Dage at first live birth |
OC_use |
=E2=80=A0=E2=80=A1 |
Use of oral contraception |
NA=3Dunspecified, N=3DNever, F:Years=3DFormer use, C:Years=3DCurrent use= ; F and C are followed by integer=3Dnumber of years taken e.g. F:4 means fo= rmer use of 4 years |
MHT_use |
=E2=80=A0=E2=80=A1 |
Use of menopause hormone therapy |
NA=3Dunspecified, N=3DNever used, F=3DFormer use, E=3DCurrent E-type use= , C=3DCurrent other/unknown type (including combined type) use |
BMI |
=E2=80=A0 |
Body mass index |
NA=3Dunspecified, real number=3Dbody mass index |
Alcohol |
=E2=80=A0 |
Daily alcohol intake in grams per day |
NA=3Dunspecified, real number=3Ddaily alcohol intake in grams |
Menopause |
=E2=80=A0 |
Age at menopause |
NA=3Dunspecified, integer=3Dage at menopause |
BIRADS |
=E2=80=A0 |
Mammographic density measured by BI-RADS |
NA=3Dunspecified, BI-RADS classification (a, b, c, d or 1, 2, 3, 4) <= /td> |
Height |
=E2=80=A0=E2=80=A1 |
Height in cm |
NA=3Dunspecified, real number=3Dheight in cm |
TL |
=E2=80=A1 |
Tubal ligation procedure |
NA=3Dunspecified, N=3DNo, Y=3DYes |
Endo |
=E2=80=A1 |
Endometriosis |
NA=3Dunspecified, N=3DNo, Y=3DYes |
PRS_BC |
=E2=80=A0 |
Polygenic Risk Score (Breast Cancer) |
e.g. alpha=3Dreal number, zscore=3Dreal number |
PRS_OC |
=E2=80=A1 |
Polygenic Risk Score (Ovarian Cancer) |
e.g. alpha=3Dreal number, zscore=3Dreal number |
=E2=80=A0 Breast Cancer Risk Factor =E2=80=A1 Ovarian Cancer Risk Factor=
The PRS_BC and PRS_OC values are=
:
All header lines begin with '##'. Any missing risk factor variables are = taken as unspecified. The risk factors are given as one per line, the varia= ble names can be any case and in any order in the header. The following exa= mple header shows the first mandatory header record ##CanRisk 1.0= strong> 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 dat= a column header record beginning ##FamID Name=E2=80=A6.
Example CanRisk File Header
##CanRisk 1.0
##Menarche=3D13
##Parity=3D1
##First_live_birth=3D24
##OC_use=3DC:2
##BMI=3D27.1
##height=3D170
##alcohol=3D5.1
##PRS_BC=3Dalpha=3D0.45, zscore=3D1.8
##FamID Name Target IndivID FathID MothID Sex MZtwin Dead Age Yob BC1 =E2=
=80=A6.......
The CanRisk Pedigree Data Format is a simple TAB-delimited text format. = CanRisk pedigree data files consist of the two mandatory header records fol= lowed 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.
Parameters 1-26 on the pedigree data records are defined as follows: