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Testing

From SNPedia

Consumer genotyping

Note: There are currently 110232 SNPs in SNPedia.

DNA testing (genotyping) 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 ~53,000 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 accurate ApoE status due to lack of relevant data.)
  • 23andMe Both the $99 "ancestry only" product and the $199 "ancestry + health" product are useable with Promethease, and the raw data is identical from both products and therefore results in exactly the same Promethease report. One time payment, lifetime membership. Both products use the (same) customized Illumina chip which covers 24637 of the 110232 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 14,151 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: Promethease supports the original data format, but does not support the v2 format introduced in April 2019.
  • Genes for Good $0 after answering surveys. As of December 2017 Promethease reports for Genes for Good have ~17,100 genotypes reported, with ~2,800 of them being from ClinVar.
  • WeGene Chinese company with an East Asian population focus, works with Promethease.
  • LivingDNA Living DNA is a company focusing on ancestry, apparently with a special interest in Britain and Ireland. Autosomal raw data is available and is compatible with Promethease, covering ~22,000 of the 110232 SNPs currently in SNPedia, of which ~9,500 are known to ClinVar.


Genome sequencing based services usable with SNPedia and Promethease:

  • Genos Research exome sequencing, 125x coverage for $499. An option to download a Promethease-compatible file is 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.
  • Full Genomes offers full human genome sequencing. The highest tier has 30x coverage for $1150 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 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
  • Helix is a DNA marketplace. They sequence your exome and sell access to slices of it via apps. You pay the full price of sequencing to download the raw data.
  • Dante Labs provides Whole Genome Sequencing for $699 and Whole Exome Sequencing for $499. They provide raw data formats: VCF, BAM, FASTQ. Their data now (usually) works with Promethease.

(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.
  • ConnectMyDNA produces no data of use with SNPedia
  • Tellmegen has historically produced data that has orientation issues and that raises quality warning flags when run through Promethease.


Possibly useful:

  • 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
  • All of Us Research Program The NIH has the goal to recruit 1 million USA residents (including non-citizens) to securely share their genomes, surveys, and medical records. For each participant there will be whole genome sequencing and some sort of genotyping. Participants will receive a clinically validated health report about the ACMG-59 list of genes. Also participants will have the option to obtain their genomic data files. BAM or CRAM format files seem likely. More interpretive formats, such as VCF, will depend on FDA approval. GenomeWeb Article


Clinical Testing:

Many Promethease users would like to have specific DNA variants from their reports tested using a quick and low cost clinically validated assay, in order to know if the results are confirmed (or, will turn out to be false positives in the data from the company they got their raw data from). We continue to search for such a service, and if you are or know of a clinical lab offering to test a variant for under $100 please let us know.

In the meantime, the least expensive direct-to-consumer options for clinically validated testing are probably the products offered by companies like Color Genomics and Invitae. For roughly $250, a panel of genes is sequenced using a clinically valid method; make sure to check if the variant of interest is normally sequenced before purchasing the product, and be aware that these companies generally refuse to return raw data or to name the variants considered reportable to their customers.

Dedicated clinical testing may also be found via the Genetic Testing Registry, maintained by the NIH. A commercial registry operating in a similar manner is available through Concert Genetics.

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.

See also testing experiences

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. You may also use our Find a genetic counselor service, geared towards Promethease users seeking counselors with direct-to-consumer data. 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.

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.