Testing

Consumer genotyping

Note: There are currently 94978 SNPs in SNPedia.

DNA testing services usable with SNPedia and Promethease:

• Ancestry.com uses Illumina OmniExpress Plus, reporting all SNP's on that chip for $99. Current users will receive data for about ~47,000 of the SNPs in SNPedia. ~25,000 of these are in ClinVar. Prior to May 2016, Ancestry customers received data for around 13,000 of the SNPs in SNPedia with only a few hundred from ClinVar.. This test is available in the USA, UK, Ireland, Australia/New Zealand, and Canada, as well as 29 additional more recently added countries throughout Asia and Europe. (Note that Promethease reports from Ancestry data will not return ApoE status, because Ancestry files lack data for rs7412.)
• 23andMe $99 "ancestry only" product, is sufficient for Promethease, or the $199 "ancestry + health" product, which also includes carrier status reports. One time payment, lifetime membership. Both products use the (same) customized Illumina chip which covers 25695 of the 94978 SNPs in SNPedia. Less than 2,000 of these are known to be in ClinVar; presumably some of the proprietarily named "i-SNPs" correspond to ClinVar/SNPedia entries as well but 23andMe does not reveal which publicly or to its non-corporate users.
• FamilyTreeDNA Family Finder uses an Illumina OmniExpress for autosomal ancestry testing for $79, including partial raw data download. It covers 13,193 of the SNPs in SNPedia, with ~2,000 of those being known to ClinVar.
  • The STR-based Y DNA tests such as the Y37, Y67 and Y111 tests, cannot be used with Promethease as they produce no SNP data.
  • The "Big Y" Y DNA test produces SNP data (more than 10,000,000 base pairs) that is accepted by Promethease (only the VCF format results, not the much larger BAM file). The "Big Y" test is only available to those who have already done STR-based Y DNA testing with FamilyTreeDNA.
  • Mitochondrial DNA test results (FASTA format) are not accepted by Promethease.
• MyHeritage seems very similar to FamilyTreeDNA, reports have ~12,000 genotypes.
• Genes for Good $0 after answering surveys. As of Feb 2017 Promethease reports for Genes for Good have ~16,700 genotypes reported, with ~2,700 of them being from ClinVar.
• WeGene Chinese company with an East Asian population focus, but some data quality issues currently make it unreliable for use with Promethease.

Genome sequencing based services usable with SNPedia and Promethease:

• Full Genomes Corp offers full human genome sequencing. The highest tier has 30x coverage for $1425 and currently (as of November 30th, 2015) provides data for 60,326 SNPs (based on one sample) in SNPedia. Lower depth of coverage (2x, 4x, 10x, 20x) are available for lower prices.
• Veritas presumed promethease compatible, but use of VCF 4.1 means that promethease reports contain only ~16,000 genotypes.
• Illumina https://www.understandyourgenome.com/ or http://everygenome.com must be ordered by your physician
• Genos Research offered exome sequencing, but as of April 2017, following an acquisition, is "temporarily holding off on accepting new orders". Was offering 75x coverage for $499. An option to download a Promethease-compatible file was available. See linked page for more details including Promethease stats and download instructions. As of Dec 2016 Promethease reports for Genos exomes have ~40k SNPs reported, with ~32k of them being from ClinVar.

(See also links listed on Ancestry page for genetic genealogical testing.)

http://www.isogg.org/wiki/Autosomal_DNA_testing_comparison_chart

Not usable:

• VeriYou from Good Start Genetics: as far as we know, they won't release raw data and so this test is of no use with Promethease
• Pathway Genomics offers various kits for Ancestry and Health, but will not allow data to be downloaded by owner so can't be used with Promethease.
• ancestrybydna.com $199+ but the raw data is very limited, and unlikely to be of much use with SNPedia.
• Color Genomics $249 to get BRCA1 and some other genes sequenced, however, the company does not release any data back to the customer and does not even provide a list of which variants are being checked.
• ConnectMyDNA produces no data of use with SNPedia
• Helix's National Geographic Geno 2.0 Next Generation test: data is not available for downloading in any standard genomic format so it can't be transferred to Promethease. Even if it were, there is apparently very little data of interest outside of perhaps ancestry utility; 1,500 SNPs or less overlap with SNPedia.

Possibly useful but apparently impractical:

• Complete Genomics offers full human genome sequencing for $5k as a service for researchers.
• The Personal Genome Project aims to recruit 100,000 volunteers and publish their genomes and medical information
• Coriell Personalized Medicine Collaborative is free, but returns information on only 51 SNPs which meet their IRB approval

Genetics & Public Policy Center Aug 2011 list of DTC companies

• Alpha by Disease
• by disease category

See also testing experiences

NEJM sets realistic expectations. Also note that current Affymetrix and Illumina microarray chips as used by 23andMe, deCODEme and others cover less than 50% of all likely genome variation at even 50% efficacy.[PMID 17726055]

Reminder: the heritability of medical conditions varies widely, from conditions that show little inherited genetic influence to those that are almost completely genetically determined (such as cystic fibrosis). A list summarizing some published heritability estimates for various medical conditions is available. We are also summarizing some average lifetime risks for many of these same conditions on the Lifetime Risk page.

Note: Anyone who wishes genetic counseling may find a counselor directly through several means, completely independent of the gene testing companies. In the U.S., the primary sources include the National Society of Genetic Counselors, asking your doctor, and checking with your healthcare insurer. If you are a qualified physician or genetic counselor interested in helping individuals interpret their genomic test results, please email us at info@snpedia.com as we intend to release a list of such individuals in the future.

At SNPedia, we have begun to collect pages about people's testing experiences. A particularly thoughtful article (among others) has been published by psychologist Steven Pinker (My Genome, My Self) based on his pondering his own DNA chip and (partial) DNA sequence data; it's well worth reading.

In the US, some people are wary of having genetic tests performed due to concerns over the possible use of genetic information by potential employers or insurance (health or life) companies in the absence of federal legislation banning genetic discrimination. Federal legislation known as GINA, the Genetic Information Nondiscrimination Act, was signed into law on May 21, 2008. Most states, but not all, have passed legislation providing either genetic privacy protection or some degree of protection against discrimination. The NIH/NHGRI maintains webpages about genetic discrimination primarily the federal level, and the National Conference of State Legislatures maintains a webportal surveying laws related to many aspects of genetics in different states.

For an interesting discussion (and possible solution) of the ways in which SNP/disease patents may threaten you or your physician from learning things about your health, see this article.