Genes for Good Genotypes Download Version 1.

2
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Thank you for participating in Genes for Good!
Contents of this README
----------------------I.
II.
III.
IV.
V.
VI.
VII.
VIII.

What Is In Your Download

What File Formats Are Present
How To Read Your Genotypes
Data Integrity and Risk Disclaimer
Recommended Text-Based Tools For Viewing Genotypes
Graphical/Interactive Tool Options
Genotype Version History
Additional Information and Further Reading

I. What Is In Your Download

--------------------------You have just downloaded a ZIP archive containing the following 9 files:
1.
2.
3.
4.
5.
6.
7.
8.
9.

GFG_filtered_unphased_genotypes.vcf.gz
GFG_filtered_unphased_genotypes.vcf.gz.tbi
GFG_filtered_unphased_genotypes_23andMe.txt
GFG_filtered_unphased_genotypes_vcf.txt
GFG_filtered_imputed_genotypes_noY_noMT.vcf.gz
GFG_filtered_imputed_genotypes_noY_noMT.vcf.gz.tbi
GFG_filtered_imputed_genotypes_noY_noMT_23andMe.txt
GFG_filtered_imputed_genotypes_noY_noMT_vcf.txt
README.txt

Files 1-4 contain different formats of the list of about 500,000 positions in yo
ur DNA (your genotypes) directly measured by software at Genes for Good. The gen
otypes are quality-controlled but we have made no attempt to interpret your geno
types. For example, we have not attempted to figure out which genotypes may carr
y disease risk.
Files 5-8 contain your imputed genotypes. That means we estimated genotypes at a
n additional 7 million positions by comparing your directly measured genotypes t
o a set of 2,500 people whose genotypes have already been determined, and fillin
g in the best guesses for your DNA bases we did not directly measure. Because th
ese files contain imputed and not directly measured genotypes, there is a greate
r chance of errors. Also, some text editors may not be able to open these files
because of their larger size.
File 9 is this README file.
II. What File Formats Are Present
--------------------------------Files 4 and 8 are text files (.txt) in uncompressed Variant Call Format (VCF) v4
.1. These files will open in a text program, but you may not be able to understa
nd what everything says. Please see below for more details to help you understan
d how the information is displayed.
Files 1 and 5 are zipped VCF files (.vcf.gz). This is a standardized text file f
ormat used in bioinformatics and you may not be able to read it on your computer

.
Files 2 and 6 are Tabix indexes (.vcf.gz.tbi) that accompany the zipped VCF file
s and are not readable by humans, but allow some bioinformatics tools to analyze
the compressed VCF file faster.
Files 3 and 7 are text files (.txt) with your data in a more easily readable 23
andMe format.
III. How To Read Your Genotypes
------------------------------If you are viewing a VCF file using a text editor, then a typical genotype may l
ook like this:
1
0/0

798959 rs11240777

PASS

GT

The first column indicates the number of the chromosome, 1, where this genetic m
arker is found.
The second column contains "798959", which is the position or number of bases fr
om this marker to the end of the chromosome.
The third column contains "rs1124077", which is the name of this marker. We atte
mpted to use names assigned by the National Center for Biotechnology Information
and these begin with "rs". Other markers have generic names that we generated.
The fourth column contains "G", which is the first of two possible alleles that
participants can have at this marker. This G refers to the genetic base guanine.
The fifth column contains "A", which is the second possible allele that a partic
ipant can have at this marker. This A refers to the genetic base adenine.
The sixth column is required as part of the VCF format but we do not use it. In
these files, it contains a dot.
The seventh column contains the word "PASS", indicating that this marker passed
our internal quality control protocols.
The eighth column is also required as part of the VCF format but we do not use i
t. In these files, it contains a dot.
Finally, the ninth column contains "0/0", which is the genotype for this partici
pant at this marker. Specifically, "0/0" means that this participant has two cop
ies -- one on each copy of chromosome 1 -- of the reference allele, which column
four indicates is G in this case. A "0/1" genotype would mean that this partici
pant has a copy of both the reference allele, G, and the alternate allele, A. "1
/1" would mean that this participant has two copies of the alternate allele, A.
In the files with the imputed genotypes, a pipe "|" instead of a slash "/" in th
e genotype indicates that we have attempted to phase this genotype, which means
we attempt to determine which allele in each pair belongs on which chromosome. W
e estimate the alleles on the left of the pipe to all be on the same physical ch
romosome, and the alleles on the right of the pipe on the other copy of the chro
mosome.
The genotype would look like the following in the 23andMe format:

rs11240777

798959 GG

This indicates that this person has two copies of the G allele at rs11240777, wh
ich is located on chromosome 1 at position 798959.
IV. Data Integrity and Risk Disclaimer
-------------------------------------Generally speaking, we expect a small percentage of your genotypes to be wrong.
We do not know where those errors are and cannot correct them.
Although we do everything we can to ensure high quality standards in sample hand
ling and data generation, unexpected things can happen and we are not able to de
tect or correct all types of errors.
Genes for Good is a research study. The technology and protocols we use are suit
able for genetic research, not for clinical genetic testing such as you would re
ceive at a hospital or doctor s office.
Clinical genetic testing is held to higher standards. Laboratories which handle
these samples are certified by governmental regulations called CLIA.
In the United States, methods used to diagnose disease or recommend treatment mu
st be approved by the FDA. The genotypes we have generated have not been reviewe
d by the FDA.
Our genotype lab is NOT FDA-approved or CLIA-certified! This approval and certif
ication is not necessary for a research study.
For more info see: https://www.cms.gov/clia
Other risks associated with attempting to understand your genetic data include d
iscovering that a family member was adopted or their biological parents or sibli
ngs may not be who they believed them to be.
There are also risks associated with storing your genetic information on a perso
nal computer or other medium of electronic storage. Take care to protect these d
ata.
V. Recommended Text-Based Tools For Viewing Genotypes
----------------------------------------------------Many word processing programs will fail to open the text files in your download
because the files are too big and word processors are optimized to work with sma
ller, richly formatted documents.
To maximize your ability to view the very large text files in your download, con
sider using any of the following free text editors:
Windows:
* glogg - http://glogg.bonnefon.org/download.html
* Notepad++ - https://notepad-plus-plus.org/
* Vim/gVim - http://www.vim.org/download.php
Mac:
* TextWrangler http://www.barebones.com/products/textwrangler/
* Vim/gVim - http://www.vim.org/download.php

Unix/Linux:
* glogg - http://glogg.bonnefon.org/download.html
* Vim/gVim - http://www.vim.org/download.php
Whichever text editor you use, loading such large text files requires lots of me
mory (RAM), so consider also closing any other programs running when you try to
load and view your data.
VI. Graphical/Interactive Tool Options
-------------------------------------IMPORTANT NOTE
None of the options listed below are explicitly recommended by Genes For Good. T
his is merely a list of available software packages and websites for viewing and
working with raw genetic data curated to include options with wider accessibili
ty and ease of use. None of these options or the developers or companies associa
ted with them are associated with Genes For Good in any way and their inclusion
in this section does not constitute an endorsement of their software.
Use third-party software for viewing your raw genetic data at your own risk. It
is your responsibility to research any software that you install, purchase, or o
therwise load your data into.
* Integrative Genomics Viewer
Type: Software Download OR Website (Java Applet)
OS: Windows, Mac, Linux
URL: https://www.broadinstitute.org/igv/viewing_vcf_files
Free, requires registering an account with Broad Institute website
* Savant Genome Browser
Type: Software Download
OS: Windows, Mac, Linux
URL: http://genomesavant.com/p/savant/download
Free, open source, may require automatic reformatting of files
* Diploid
Type: Software Download
OS: Mac
URL: http://www.diploid.com/differ
Free, requires registering email with website
If you have used and enjoyed other websites or software to view and work with yo
ur raw genetic data then please contact Genes For Good to recommend the solution
that worked best for you. We may want to include it in this list for all partic
ipants!
VII. Genotype Version History
----------------------------The processing pipeline we use for generating participant genotype data is an ac
tive project. Periodically a new version of genotype data will be released. Typi
cally new versions may have slightly more accurate data from improved or optimiz
ed methods, or may present new data extracted from the same samples that was not
present in earlier versions.
You can determine with certainty which version you have by checking the version
number on the first line of this file. At any given time only the most current v

ersion will be available for participants to download.

Change Log:
* Version 1.2 - July 2016
More RS numbers - We now have RS numbers for 97% of the variants in the unimpu
ted files and 99.7% in the imputed.
A new imputation reference panel for X-nonPAR that has about 2,000 fewer varia
nts.
* Version 1.1 - June 2016
More RS numbers, indels added to 23andMe format files, other minor changes to
improve speed and memory usage in the generation pipeline
* Version 1.0 - September 2015
Initial release of results including ancestry pie chart, chromosome painting,
PCA plot, and downloadable genotypes
VIII. Additional Information and Further Reading
-----------------------------------------------For a brief introduction on human genetics that may be useful in attempting to u
nderstand these files, please see: https://www.genome.gov/25520880
The Variant Call Format (VCF) was developed by the 1000 Genomes Consortium and i
s maintained by the Global Alliance for Genomics and Health Data. The format spe
cification is available at: http://samtools.github.io/hts-specs/VCFv4.1.pdf
Basing health decisions on genetic data is risky. This article in The Atlantic p
rovides some further insight into such risks: http://www.theatlantic.com/science
/archive/2015/12/why-human-genetics-research-is-full-of-costly-mistakes/420693/
This README file is also available online at the address: https://genesforgood.s
ph.umich.edu/readme/readme1.2.txt
Thank you again for your participation!