Y-DNA SNP testing chart
From ISOGG Wiki
This Y-DNA SNP testing chart provides comparative information on the Y chromosome SNP tests offered by the major DNA testing companies. For information on the Y-STR tests used for genealogical DNA matching purposes within surname DNA projects see the Y-DNA STR testing chart.
For background information on purchasing a DNA test see Before You Buy and and Choosing a DNA testing company.
For guidelines on DNA testing see the Genetic genealogy standards.
SNP testing for the Y chromosome advances knowledge about one's detailed haplogroup assignment and deep ancestry.
Currently the chief utility for genetic genealogy lies in ruling out false positive matches for similar Y-STR haplotypes, particularly if the haplotype is close to the modal haplotype for the haplogroup subclade.
Rapid strides in SNP discovery have the potential to bring the deep ancestry time frame forward considerably, perhaps even to the familial level, with more specificity for geographic origins. These have in the past happened through the Walk Through the Y sequencing program at Family Tree DNA under Thomas Krahn. They are currently moving forward through next generation sequencing tests.
Note that in addition to the chip genotyping and next generation sequencing tests listed below single SNPs and custom SNP panels can be ordered from Thomas Krahn's new company YSEQ.
This chart is provided for informational purposes only. Additions made upon ISOGG member request. Please submit additions, corrections/updates to .
Company and product name | 23andMe Version 4 [1]) |
Family Tree DNA[2] Big Y |
Full Genomes Corporation Y Elite |
Genographic Project Geno 2.0 Next Generation[3] |
Living DNA | YSEQ |
---|---|---|---|---|---|---|
Date when product first went on sale | November 2010 | November 2013 | Late 2012 | August 2015 | September 2016 | November 2013 |
Cost [4] | $199 for the lifetime of the platform in the U.S., CAD $249 in Canada, €169 in Denmark, Finland, Ireland, Sweden and the Netherlands, and £149 in the UK for both the medical and ancestry features. The test is also available as an ancestry-only test in the U. S. for $99 and in some other countries for $149. | $575 | $645 (v2.1) $775 (v2.0), $850 (v1.0) [5] | $199.95 | $159 US; £120 UK; €159.00 Europe; $199 Australia | panels $88-99; SNPs $18 |
International product availability | 56 countries | Worldwide | Worldwide. As of 9th March 2018 orders are not being accepted from countries in the European Union including the UK | Worldwide | Worldwide | Worldwide |
Analyzed DNA | Autosomal DNA, X-DNA, Y-DNA, mtDNA | Y-DNA | Y-DNA, mtDNA | Autosomal DNA, X-DNA, Y-DNA, mtDNA | Autosomal DNA, Y-DNA, mtDNA | Y-DNA |
Main purpose of test | Health and traits (reports not available in all countries). Ancestry: DNA Relatives, biogeographical ancestry, patrilineal and matrilineal haplogroups |
Y-SNP discovery; patrilineal haplogroup | Y-SNP discovery; patrilineal and matrilineal haplogroups; Y-STR markers | Anthropological testing: patrilineal and matrilineal haplogroups; biogeographical ancestry | Biogeographical ancestry; patrilineal and matrilineal haplogroups | detailed haplogroup; NGS SNP confirmation |
Level of Y-haplogroup resolution | Basic[6] | High | Highest available | Medium | Medium | High |
Method | Chip-based genotyping Illumina OmniExpress Plus customized chip |
Next generation sequencing Illumina HiSeq2000[7] Mappable regions: 11-13 million base pairs[8] Total sequence length: ca. 14 mbp Read length: 100 base pairs 55-80x coverage[8] library insert size: 140.4±88.6 bp [9] |
Next generation sequencing Illumina HiSeq Mappable regions: 12-16 million base pairs[10] Total sequence length: ca. 23 million base pairs. Read length: 100 base pairs ~80x coverage library insert size: 228.3±91.3 bp [11] |
Chip-based genotyping Illumina OmniExpress with 10% customised content |
Chip-based genotyping Illumina Global Screening Array with customised content |
Sanger |
Method Analysis by YFull [12] | - | Median depth coverage 47 Length coverage 13,925,100 96 of the 111 STR-panel with good quality |
Median depth coverage 39 Length coverage 22,731,890 98 of the 111 STR-panel with good quality |
- | - | - |
Results for currently known Y-SNPs | 2,329 variants covered; many are no calls | 76% of 55,000 known SNPs covered [12] | 97% of 55,000 known SNPs covered [12] | Full details not yet available but expected to cover around 20,000 SNPs[13] | 22,500 Y-SNPs on chip but no data yet available on no calls | > 50,000 as of Aug 2017 |
Results for private Y-SNPs (novel Y-variants) | Not possible with chip-genotyping | Average count 54 [12] | Average count 66 [12] | Not possible with chip-genotyping | Not possible with chip-genotyping | Not possible (see WGS product) |
Format of results | A zip .txt file with a list of all the SNPs tested and the genotype for each position. The genome reference positions are included. A raw data browser is also provided. | VCF, BED, and BAM files | A rar archive of 9 files which can be converted into a spreadsheet format. The files include a list of results for all the Y-SNPs tested, a list of private SNPs, a haplogroup compare file and a variant compare file, Y-STR and mtDNA. The raw data (in the form of a BAM file) is available on request. See the guest blog post by Itaï Perez for sample reports. | A .CSV file containing a complete listing of all the Y-SNPs tested and the genotype for each allele. The genome reference positions are not given. | Y-SNP raw data is not yet available | Online allele table |
Availability of single Y-SNPs | No | Select from catalog of approx 3,600 SNPs at $39 per SNP. Group administrators can submit requests for new SNPs to be considered for inclusion in the catalog[14] | No | Yes, if free transfer to FTDNA is used, so you can order there. | No | Yes |
Availability of SNP panels | No | A limited selection of SNP panels is currently available. There are many subhapologroup-specific SNP panels in development. | No | No | No | Yes |
Non Y-SNP results and reports included in the test | 577,382 autosomal SNPs, 19,487 X chromosome SNPs, 3154 mt SNPs health and ancestry reports included |
Y-STRs included in BAM files but results are not reported though can be obtained by purchasing a third-party analysis. Up to April 3, 2015 also the mtDNA sequence was included (later removed) | Over 300 Y-STRs (a list of alleles for all the Y-STRs tested), and mtDNA sequence included provided in two separate files showing differences from the CRS and the RSRS. | Full details not yet available but the new chip covers 750,000 markers in total. It will be possible to transfer results to Family Tree DNA to participate in the Family Finder matching database. [15] Ancestry reports included |
638,000 autosomal SNPs, 17,800 X-chromosome SNPs, 4,700 mtDNA SNPs | All tests are discrete |
Shipping charges | $14.95 for the first kit and $5 per kit for additional kits in the US; $79.95 for the UK; price for other countries varies, but tends to range between $66.95 and $94.95. See shipping DNA kits for further info. | $12.95 for USA and international orders (prepaid return postage is included for US kits)[16] | $25 for the US; $39 for international orders | None for the US; $10 for Canada; $20 for Europe and Australia; $50 for all other countries | Included in the cost of the test | $5 |
Time from receiving the kit to release of results | 6-8 weeks | 8 weeks[8] | Because of forwarding to the external laboratory and delays at the lab, sometimes several months | Up to 10 weeks | Not known | 6-8 weeks for panels, 3-4 weeks for single SNPs |
DNA sample storage | Yes, indefinitely | Yes, for a minimum of 25 years | No, but the option might be added in the future | Yes, for 25 years if the free transfer to FTDNA is used | Free for a minimum of 10 years | Yes |
Projects supported | No | Yes | Not at this time but reportedly in development | Yes. if the free transfer to FTDNA is used | No | Limited |
Project/crowd funding | No | Yes (Contact customer service for help with group project orders.) | No | No (was announced to be made available for FTDNA project order) | No | No |
Online community or forum | Active online community for 23andMe members, including demo accounts | Public FTDNA forums | Results can be discussed in the private Full Genomes Facebook group | No, but stories about one's Y patrilineal and matrilineal ancestry can be posted on the website for others to view, so add your contact information to them. | No | Facebook group |
Sponsored public database | No | Partial[17] | No | No | No | Public results group |
Additional DNA testing options available from this company | Yes, available as optional add ons at an additional charge: mtDNA haplogroup testing, biogeographical ancestry, chromosome painting, principal component analysis, and red hair test | Yes, multiple options for Y chromosome STR testing, complete or partial mitochondrial DNA testing, and autosomal genome wide scans | No | No | No | WGS; Y-STRs; mtDNA |
Lead scientists in the company | Joanna Mountain, Steve Lemon | Connie Bormans | Miguel Vilar | Martin Blythe | Thomas Krahn | |
Advisory board and consultants for the company | Itsik Pe’er, Peter Underhill, Serafim Batzoglou, George Church, Michael Eisen, Marcus Feldman, Daphne Koller, Stanley Nelson, Jonathan Pritchard | Michael Hammer, Bruce Walsh, Doron Behar, Spencer Wells[18] | Greg Magoon | Connie Bormans, Elliott Greenspan | - | - |
Ownership | Privately held by various investors, particularly Anne Wojcicki, Johnson & Johnson Development Corp., The Roche Venture Fund, Google Ventures, and New Enterprise Associates | Gene by Gene Managing partners Bennett Greenspan and Max Blankfeld | Privately held | National Geographic is a non-profit scientific and educational society |
DNA Worldwide. Directors: David Nicholson and Hannah Morden | Privately held |
Lab(s) used | National Genetics Institute (a subsidiary of LabCorp), Los Angeles, California |
Family Tree DNA Genomics Center, Houston, Texas | Family Tree DNA Genomics Center, Houston, Texas | Eurofins | YSEQ | |
Method for collecting the sample | Saliva sample (about 1 cc) | Cheek swab | Saliva sample or cheek swab | Cheek swab | Cheek swab | Cheek swab |
Payment methods | VISA, Mastercard, Discover, American Express | Credit Cards, Paypal, checks | Credit Cards, Paypal, checks | Credit Cards, Paypal | Visa, Mastercard, American Express, Paypal | Paypal; bank transfer |
Address | 23andMe 899 W Evelyn Ave Mountain View CA 94041 USA |
Family Tree DNA 1445 North Loop West Suite 820 Houston TX 77008 USA |
Full Genomes Corporation Inc 2275 Research Blvd Suite 500 Rockville MD 20850 USA |
The Genographic Project 1145 17th St. N.W. Washington, D. C. 20036-4688 USA |
Living DNA K10 The Courtyard Jenson Avenue Commerce Park Frome Somerset BA11 2FG England |
YSEQ Eiswaldtstrasse 31 12249 Berlin Germany |
Phone number | Enter a ticket online at customer care for a call-back | 713-868-1438 | All communications are via e-mail | 888-557-4450 (in the US or Canada) or 713-868-1807 | 0203 424 3482 | (+1) 281-627-8139 |
E-mail address | |
FTDNA Contact Form | |
|
| |
Year founded | 2006 | 2000 | 2012 | 2005 | 2004 (DNA Worldwide); 2016 (Living DNA) | 2013 |
Reviews
- 23andMe reviews
- Family Tree DNA Big Y reviews
- Full Genomes reviews
- Genographic Project Geno 2.0 reviews
- Living DNA reviews
Resources
- ISOGG phylogenetic tree
- ISOGG SNP Compendium Spreadsheet compiled by Dave Reynolds
- The minimal reference phylogeny for the human Y-chromosome from Phylotree
- ISOGG Ybrowse Human Y-chromosome browser
- Y-Tree An interactive version of the current Y Chromosome Consortium's phylogenetic tree and the Family Tree DNA draft Y-chromosome tree
- The YFull version of the Y-SNP tree
Further reading
- Which NGS test to take? by Jim Kane, Irish Type 2 Kane blog, 12 November 2015.
- A confusion of SNPs by Debbie Kennett, Cruwys News blog, 16 November 2013.
- The future of comprehensive Y testing is here by Kelly Wheaton. Lesson 15: Beginners' Guide to Genetic Genealogy
- Full Genomes launches Y Prime - a new Y chromosome sequencing product by Debbie Kennett, Cruwys News blog, 26 July 2014
- Introduction to the BigY A white paper from Family Tree DNA, 29 August 2014.
See also
- Before You Buy
- Choosing a DNA testing company
- Free DNA tests
- List of Y-DNA haplogroup projects
- Privacy
- SNP testing
- Surname DNA projects
- Y chromosome DNA tests
- Y-DNA next generation sequencing
- Y-DNA STR testing chart
- Y-DNA tools
- YFull
- YSEQ
Notes
- ↑ v4 includes SNPs that our researchers use to assign genetic ancestry using autosomal DNA markers as well as variants in both mitochondrial DNA and in the Y chromosome. "We will likely start using the chip in the next few weeks." November 18, 2013: http://blog.23andme.com/news/23andmes-new-custom-chip/
- ↑ Family Tree DNA also processes tests for a number of affiliate companies: African DNA, iGENEA, DNA Ancestry & Family Origin and DNA Worldwide. Participants who join Family Tree DNA's database from these companies will have kit numbers that begin with 'A' from African DNA, 'E' from iGENEA, 'M' from DNA Ancestry & Family Origin, and 'U' from DNA Worldwide. National Geographic Genographic kit transfers begin with 'N'. Family Tree DNA acquired DNA Heritage in April 2011. DNA Heritage customers were given the option of transferring their results to the FTDNA database. DNA Heritage kit numbers begin with the letter 'H'.
- ↑ Geno 2.0 Next Generation replaces Geno 2.0 which first went on sale in July 2012.
- ↑ Prices checked 31 July 2017; check company websites for current prices.
- ↑ The information in this table refers to Y Elite 1.0. See information on the Full Genomes Corporation page.
- ↑ For a list of the Y-SNPs on the 23andMe chips (v2, v3, v4 and v5) see the spreadsheet provided by Tim Janzen which can be downloaded from this link.
- ↑ Petrone J. Family Tree DNA Expands beyond Array-based Offerings with New Y Chromosome Sequencing Service ($) GenomeWeb BioArray News, 12 November 2013
- ↑ 8.0 8.1 8.2 Petrone J. Family Tree DNA's NGS-Based 'BigY' Service to Inform Future Generations of Ancestry Testing Chips ($) GenomeWeb BioArray News, 18 March 2014. Retrieved 23 March 2014.
- ↑ FGC vs BigY, FGC_Advantage_January2014_release rev2.pdf, by FGC.
- ↑ Magoon G. Facebook message 2013-10-18: "The 12-16 mbp figure is a rough estimate of the number of sites where we can confidently (>~95%) identify novel SNP variants that are free from various issues that give rise to false positives."
- ↑ FGC vs BigY, FGC_Advantage_January2014_release rev2.pdf, by FGC.
- ↑ 12.0 12.1 12.2 12.3 12.4 Vadim Urasin, 17 Sep. 2014 in the YFull Facebook group
- ↑ Geno 2.0 covered 12,065 variants with some no calls.
- ↑ A form is now available in the FTDNA GAP (under Genetic reports/Y-DNA SNP) where admins can submit their requests. Alternatively this link can be used (admins must be logged in): https://gap.familytreedna.com/ydna-snp-report.aspx
- ↑ The Geno 2.0 test covered 126,307 autosomal SNPs, 3803 X chromosome SNPs, 3281 mt SNPs
- ↑ Editorial Staff. "Shipping DNA tests worldwide". Family Tree DNA Learning Center. Gene by Gene. https://www.familytreedna.com/learn/ftdna/shipping-dna-tests-to-international-destinations/. Retrieved 2016-05-24.
- ↑ Some surname and haplogroup projects list SNP results for participants.
- ↑ Editorial Staff. "Who's Who At Family Tree DNA". Family Tree DNA. Gene by Gene. http://www.familytreedna.com/about.aspx.
Disclaimer
23andMe, BritainsDNA, DNA Ancestry & Family Origin, Family Tree DNA, Full Genomes Corporation, iGENEA, IrelandsDNA, National Geographic Genographic, ScotlandsDNA and YorkshiresDNA are registered, trademarked, and/or copyrighted names of companies, websites and organizations, not affiliated with ISOGG.