Genome Testing & Analysis

This page contains educational material about genome testing. This information is for educational purposes only. Nothing in this text is intended to serve as medical advice. All medical decisions should be made only with the guidance of your own personal medical authority. I am doing my best to get this data up quickly and correctly. If you find errors in this data, please let me know.

For data on understanding Genome Reports and Definitions click here.

1. 23++ (http://23pp.david-web.co.uk/about/) (FREE) – An extension for the Google Chrome web browser that adds additional functionality to the 23andMe website. The extension especially adds a number of features to Relative Finder.
2. Clinical Variant Data Base (http://www.ncbi.nlm.nih.gov/clinvar) was created. The ClinVar database includes Information on variants and their associated phenotypes, interpretation of the functionality of the variant, and the evidence used to classify the variant. ClinVar is incorporated into the suite of tools NCBI provides for analyzing variation.
3. Clinvitae (http://clinvitae.invitae.com) is being developed for use by researchers and diagnostic laboratories. It is a repository of clinically interpreted variants with a user-friendly search engine. Variants are aggregated from many different source databases. Search results will provide all of the variants for a gene, where the user may type in a gene name and all of the variants are in one scroll. The variants can be sorted by protein change and reported classification. General features include an active outreach, a comment system for variant level discussion, and INVITAE interpretations of the variants. The entire database is available for download.
4. David Pike’s Utilities (http://www.math.mun.ca/~dapike/FF23utils/) (FREE) – A comprehesive suite of tools for analyzing raw data, including searching for Runs of Homozygosity (ROHs), searching for shared DNA in two files, and several advanced phasing tools.
5. DNAGedcom (http://www.dnagedcom.com) (FREE) – A suite of tools for 23andMe and Family Tree DNA customers.  Users can download their matches, shared segments, and other data into a handy spreadsheet for further analysis.
6. DNAMatch4iPad (http://www.dnamatch4ipad.com) ($) – A app for the iPad that is an “alternative to the use of conventional spreadsheets for the processing of autosomal DNA data.” Users download their match data from one of the testing companies in the form of a .CSV file and upload it to DNAMatch4iPad.
7. GEDmatch (http://gedmatch.com/) (FREE) – Tools for 23andMe, AncestryDNA, and Family Tree DNA raw data.  Users can compare their DNA to everyone else in the database or to a specific individual in the database, or perform numerous admixture analyses, phase their DNA, and much more.
8. Genes & Us (http://www.genesand.us)  (FREE) – A website for 23andMe users to “combine their genomes in order to better understand what disease risks most affect their family.”  For example, a mother and father can link their 23andMe accounts to the site and determine the possible combinations for their children’s DNA.  Appears to work with 23andMe’s new API offering.
9. Genetic Genealogy Tools (http://www.y-str.org) (FREE) – Tools for analyzing raw data, including an X-DNA Relationship Path Finder, Ancestral Cousin Marriages, Autosomal Segment Analyzer, a DNA Cleaner, a SNP look up, and many more.
10. Genetic Genie (http://geneticgenie.org/) (FREE) – A tool that analyzes your 23andMe results to perform a methylation gene analysis (“Methylation Analysis”).  The site also provides a tool for a “Detox Profile” which looks for defects in the Cytochrome P450 detox enzymes.  The site uses the 23andme API, so users can link their 23andMe account to the service.
11. G2P research program (http://www.genomes2people.org) was established to understand translational genomics and health outcomes.
12. Genetrainer (https://www.genetrainer.com/) ($) – Genetically Guided Fitness: Users of 23andMe and Family Tree DNA can link their results to the Genetrainer service, which will then provide you with training plans and exercises personalized to the user.
13. Identifying Variants associated with a Disease (http://atgu.mgh.harvard.edu/xbrowse) is a software platform designed to identify variants associated with disease. One aspect of this platform is to calculate gene-specific mutational expectations. For example, the mutability rate between genes differs, where genes under exceptional constraint may contain many synonymous mutations but few missense mutations. By estimating the mutability of each gene, one can get an expectation of how often one will see a mutation in each category and get statistics on that rate versus observed, which will allow for variant predictions. Software platforms that can identify rare but potentially functional variants will be required to identify the important mutation-associated disease, especially when large numbers of genomes are being analyzed.
14. Inborn Errors of Metabolism Database (http://www.iembase.org) was developed to provide a database of biochemical, molecular, and clinical characteristics of genetic-based inborn errors of metabolism.
15. Interpretome (http://esquilax.stanford.edu/) (FREE) – A collection of tools for analyzing 23andMe raw data using only a web browser (i.e., raw data is not uploaded).  The tools include an admixture analysis, health information, and a Neanderthal calculator.
16. Locus Reference Genomic (LRG) record (http://www.lrg-sequence.org). a reference resource for the reporting of clinically relevant sequence variants.” Why do we need another reference sequence? Created in collaboration with locus-specific experts, each manually curated LRG record contains genomic, transcript, and protein reference sequences that are not versioned, will not change, and are deemed the most appropriate to fulfill the reporting needs of that specific gene. Widespread use of this resource will reduce ambiguity over time. LRG records have two sections, a fixed section that is stable and contains identifiers, reference sequences, and an exon numbering system, and an updatable section that contains annotation of additional transcripts, legacy exon, and amino acid numbering systems and other information. Currently, over 700 LRGs have been created and the aim is to create an LRG for every clinically relevant locus. Variants reported in LRG coordinates are compatible with HGVS conventions and can be submitted to dbSNP and ClinVar through the LRG Website
17. LOVDv3 (http://databases.lovd.nl/shared/), have implemented a so-called VIP status for both variants and phenotypes from exome or genome sequencing studies that need specific attention from others because suggestive, but not yet conclusive, evidence was obtained to make a new gene-disease link. Investigators can submit both phenotype descriptions and/or gene variants with the request to assign these a VIP status. Upon request, to protect the interest of the submitters, curators of the database can make submission anonymous and/or break the connection between variant and phenotype. Early submission and VIP status provides an opportunity to find other researchers to work on variants/phenotypes of common interest. Increasing the compilation of data from a number of individuals with variants in the same gene is especially important for rare disorders.
18. Minor Allele Program (http://www.ianlogan.co.uk/23andme/23andMe_index2.htm) (FREE) – A tool to identify rare SNPs in your 23andMe or Family Tree DNA raw data. 
19. mtDNA Haplogroup Analysis (http://dna.jameslick.com/mthap/) (FREE) – A tool for predicting your maternal haplogroup using a variety of formats, including 23andMe raw data.
20. NAT2PRED (http://nat2pred.rit.albany.edu) (FREE) – a tool for inferring human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype.  In other words, a tool for predicting the function of your NAT2 enzyme (either slow, rapid, or intermediate) based on your DNA.  The NAT2 enzyme is involved in activating and deactivating arylamine and hydrazine drugs and carcinogens, among other things.
21. Nutrahacker http://nutrahacker.com I saw these folks advertising to analyze genome data and give suggestions for supplementation etc. Unsure if they are any good though. So proceed at your own risk. Let me know what you think of them.
22. PON-P2 (http://structure.bmc.lu.se/PON-P2) predicts the pathogenicity of amino acid substitutions. It is a machine learning-based approach and utilizes amino acid features, Gene Ontology (GO) annotations, evolutionary conservation, and if available, annotations of functional sites. Note that, PON-P2 is NOT a meta-predictor. PON-P2 estimates the reliability of predictions and groups the variants into pathogenic, neutral and unknown classes.Read more in article.
23. Promethease (https://promethease.com/ondemand) ($5) – Analyze your 23andMe, Family Tree DNA, or AncestryDNA raw data and build a report based on SNPedia. Reports contain information about health and ancestry as well as several other new options. 
24. Segment Mapper (http://kittymunson.com/dna/SegmentMapper.php) (FREE) – A tool to show specific DNA segments in a graphic chromosome-style chart.  This is a clever and powerful “mapping” tool.  
25. SNPTips (http://snptips.5amsolutions.com/) (FREE) – A Firefox browser extension that allows 23andMe customers to access their SNP genotype information without logging into their 23andMe account or leave the webpage they are browsing.  Users can simply hover their mouse cursor over a SNP RSID on a webpage and, if that was tested by 23andMe, the SNPTips extension will provide a popup with the user’s genotype and some relevant links.
26. SPA (http://genetics.cs.ucla.edu/spa/index.html) (FREE) – Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual’s DNA. 23andMe users can download the software and analyze their results with this admixture tool.
27. The 23andMe Gene App at Livewello (https://livewello.com/23andme) ($19.95) – a Variance Report Software analyzes 23andMe Raw Data are reports on 300 SNPs for things like “Methylation Detox, Immune Factors, IgE, IgG disorders and much more.”  Livewello is a Social Health Management Platform with customized App.