CanRisk Pedigree Data v2 File Format Specification

Owned by Tim Carver
Jan 31, 2022
4 min read


Description

CanRisk Pedigree Data v2 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 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 2.0 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 2.0
##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:

  1. FamID Family/pedigree ID, character string (maximum 13 characters)
  2. Name First name/ID of the family member, character string (maximum 8 characters)
  3. Target The family member for whom the CanRisk risk calculation is made, 1 = target for risk calculation, 0 = other family members.
  4. IndivID Unique ID of the family member, character string (maximum 7 characters)
  5. 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).
  6. MothID Unique ID of their mother, 0 = unspecified, or character string (maximum 7 characters)
  7. Sex M or F
  8. 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
  9. Dead The current status of the family member, 0 = alive, 1 = dead
  10. Age Age at last follow up, 0 = unspecified, integer = age at last follow up
  11. Yob Year of birth, 0 = unspecified, or integer (consistent with Age if the person is alive)
  12. BC1 Age at first breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  13. BC2 Age at second (contralateral) breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  14. OC Age at ovarian cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  15. PRO Age at prostate cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  16. PAN Age at pancreatic cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  17. Ashkn Ashkenazi status, 0 = not Ashkenazi, 1 = Ashkenazi
  18. BRCA1 BRCA1 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  19. BRCA2 BRCA2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  20. PALB2 PALB2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  21. ATM ATM genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  22. CHEK2 CHEK2 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  23. BARD1 BARD1  genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  24. RAD51D RAD51D genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  25. RAD51C RAD51C genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  26. BRIP1 BRIP1 genetic test type:result; type 0=untested, S=mutation search, T=direct gene test; result 0=untested, P=positive, N=negative
  27. 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