Formatting Pedigrees for My Variant Analysis

File names may only contain numbers, letters, and dashes. Spaces and other special characters in the file name may cause an error.

The file can be uploaded as a plain text file or an excel file using the example pedigree file as a template. For the plain text file, the format of the pedigree file consists of 9 columns separated by a single space along with a header. Note that the header, or first line, can be anything as the webtool ignores it completely. An easy way to format pedigrees is to use Microsoft Excel and save the file as a tab delimited text file. For both formats the 9 columns in order are:

  1. Individual ID - This column gives the unique number assigned to the current individual. Numbers are not assigned in any particular order.
  2. Father - This column gives the Individual ID of the current individual's biological father or 0 if the individual’s father is not in the pedigree. Note that both parents should be known or both should be unknown. Also, all individuals in the pedigree should be connected (i.e. If a pedigree has the proband’s grandfather then the proband’s father and mother need to be listed in the pedigree even if no other information about them is known. Likewise, siblings need to have their parents included in the file as that is how they are identified as siblings.).
  3. Mother - This column gives the Individual ID of the current individual’s biological mother or 0 if the individual’s mother is not in the pedigree. Note that both parents should be known or both should be unknown. Also, all individuals in the pedigree should be connected (i.e. If a pedigree has the proband’s grandfather then the proband’s father and mother need to be listed in the pedigree even if no other information about them is known.)
  4. Sex - This column represents the individual's sex where 1 stands for male and 2 stands for female.
  5. Affection Status - This column shows the individual’s affection status where 0 stands for unknown, 1 stands for unaffected, and 2 stands for affected. Individuals should be marked as affected for a particular gene if they have any of the phenotypes listed below. Please visit the gene-specific penetrance information pages for more information.
    • ATM - Breast cancer only
    • BRCA1 - Breast cancer or ovarian cancer
    • strong>BRCA2 - Breast cancer or ovarian cancer
    • CHEK2 - Breast cancer or colorectal cancer
    • MEN1 - Primary hyperparathyroidism (HPTH), pituitary adenoma, pancreatic neuroendocrine tumor (PNET) including carcinoids, or adrenocortical carcinoma
    • MLH1, MSH2, MSH6, or PMS2 - Colon cancer, endometrial cancer, grouped small bowel cancer, stomach or gastric cancer, ovarian cancer, or urinary tract cancers (excluding bladder)
    • PALB2 - TBD
    • RAD51C - TBD
  6. Age - This column represents one of 3 possible ages rounded to the nearest whole number. If the individual is affected, it should be the age of onset of the disease. If the individual is unaffected, it should be the current age of the individual if alive or age at death if deceased. For more help, refer to the flow chart below. If the age is unknown, it is okay to estimate it based on a sibling's or parent’s age. A good rule of thumb is that the individual is the same age as their siblings and approximately 25 years younger than their parents.
  7. Allele1 - This column gives the status of the first allele of the genotype in question where 0 is unknown, 1 is normal (negative for the VUS), and 2 is the variant (positive for the VUS). Note that Alelle1 and Allele2 are interchangeable. Also, both alleles should be known or unknown. (Normally we assume the individual has only one copy of the VUS as having two would be extremely rare.)
  8. Allele2 - This column gives the status of the second allele of the genotype in question where 0 is unknown, 1 is normal (negative for the VUS), and 2 is the variant (positive for the VUS). Note that Alelle1 and Allele2 are interchangeable. Also, both alleles should be known or unknown. (Normally we assume the individual has only one copy of the VUS as having two would be extremely rare.)
  9. Proband - This column should be 0 for all members except the proband. Note that there should only be a single proband and that they should be a carrier of the variant and affected.
Formatting Pedigrees for My Variant Analysis - Analyze My Variant