Help

Interface basics

• Add new genome
  button allows to load a new genome file to the system
• Calculate all reports
  button calculates all the traits and risks for selected genomes
• The two leftmost tabs show first and second parent. If you loaded more than one genome, you can switch them by clicking on a tab
• The two rightmost tabs show results of selected parents' offsprings
• Depending on condition, different models will be used to calculate the results:
  1. For simple Mendelian traits (such as Bitter Taste Perception) and more complex carrier statuses the model will show the probability of each possible outcome.
  2. For more complex traits (like hair and eye color) a categorized logistic regression model will be used. It shows the most probable outcomes for both parents and their offsprings
  3. Multiplicative Risk Model is used to estimate risk ratio of different diseases. It shows the adjusted lifetime risk and risk multiplicator, in comparison to population average
  4. Additive model (used to calculate cholesterol levels) will show adjusted levels together with percent of increase, in comparison to population average
  5. Both multiplicative and additive models will show a probability-adjusted values for offsprings, together with minimal ("they got the best genes from both parents") and maximal ("they got the worst genes from both parents") possible values (in brackets)
• Parent's genotype used in each model is shown under the results, together with each SNP's effect, where possible. Missing values are marked with ?? and imputed ones are marked with *

Tutorial

1. At the Heredity Report page, press the Add new genome
   button
2. Select European Male 1 and click the Load File button
3. Now do it again, but select European Female 1 this time
4. Now we have two genomes loaded, and their names (Genome #1 and Genome #2) appear on the leftmost tabs
5. Click on the Calculate button near the Blood Type (ABO) trait. It will show that the first person has group A, the second one has group O and their offsprings have 50% probability of inheriting either group A or group O from their parents
6. Click on the Calculate button near the Eye color trait. Looks like the first person has blue eyes, the second one has brown ones and their offsprings are likely to inherit brown eyes from their parents
7. Let's check another trait - Spot Baldness. Click on the Calculate button to see the results. The average lifetime risk of getting spot baldness is 1.7%, and the first person has an increased risk (2%, x1.18 the average risk which is 18% above the average) while the second one has her risk decreased to 0.6% (x0.35 the average risk, which is 65% below the average). Their offsprings' expected risk for Spot Baldness ranges between 0.4% and 3% with the most probable value around 1.2%, so they are likely to have below than average risk for this trait.
8. Now click the Calculate all reports
   button to open all traits and conditions

Getting raw data files from personal genomics companies

23andMe

• Open https://www.23andme.com/you/download/ and log in to your account
• Enter your password and secret answer and make sure you select All DNA in Data set field
• Click on the Download Data button in the bottom right corner
• In a few moments you'll download a zipped file named like genome_Your_Name_Full_20120101024450.zip
• Extract the content of this file to get unzipped genome_Your_Name_Full_20120101024450.txt
• Use that genome_Your_Name_Full_20120101024450.txt raw data file with GHC

Family Tree DNA

• Open the Download Files section https://www.familytreedna.com/my-ftdna/download-files.aspx log in to your account
• Download Autosomal Results file and extract its content
• Use the resulting raw data file with GHC