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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 Family Tree DNA's BIG Y test under Dr. David Mittelman and through the Full Genomes Corporation.

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]) 		BritainsDNA ScotlandsDNA IrelandsDNA YorkshiresDNA CymruDNAWales[2]
Chromo2 Raw YDNA 		Family Tree DNA[3]
Big Y 		Full Genomes Corporation
Y Elite 		Genographic Project
Geno 2.0 Next Generation[4]
Date when product first went on sale November 2010 June 2013 November 2013 Late 2012 August 2015
Cost [5] $99 for the lifetime of the platform in the U.S. (ancestry only; health reports discontinued in November 2013); CAD $199 or £125 for health and ancestry reports (Canada, Britain and Ireland only at this time) $199 (£129)[6] $575 $775 (v2.0), $850 (v1.0) [7] $199.95 (£127)
International product availability 56 countries Worldwide Worldwide Worldwide Worldwide
Analyzed DNA Autosomal DNA, X-DNA, Y-DNA, mtDNA Y-DNA [8] Y-DNA Y-DNA, mtDNA Autosomal DNA, X-DNA, Y-DNA, mtDNA
Main purpose of test Ancestry: DNA Relatives, global origins, ancestral haplogroups
Health: carrier status, disease risks, drug response (the health reports were suspended in November 2013 by the FDA) 		Patrilineal haplogroup Y-SNP discovery; patrilineal haplogroup Y-SNP discovery; patrilineal and matrilineal haplogroups; Y-STR markers Anthropological testing: patrilineal and matrilineal haplogroups; biogeographical ancestry analysis
Level of Y-haplogroup resolution Basic[9] Medium High Highest available Medium
Method Chip-based genotyping
Illumina OmniExpress Plus customized chip (v3) 		Chip-based genotyping
Illumina Core customized chip 		Next generation sequencing
Illumina HiSeq2000[10]
Mappable regions: 11-13 million base pairs[11]
Total sequence length: ca. 14 mbp
Read length: 100 base pairs
55-80x coverage[11]
library insert size: 140.4±88.6 bp [12] 		Next generation sequencing
Illumina HiSeq
Mappable regions: 12-16 million base pairs[13]
Total sequence length: ca. 23 million base pairs.
Read length: 100 base pairs
50x coverage
library insert size: 228.3±91.3 bp [14] 		Chip-based genotyping
Illumina OmniExpress with 10% customised content
Method Analysis by YFull [15] - - 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 14,497 variants covered 76% of 55,000 known SNPs covered [15] 97% of 55,000 known SNPs covered [15] Full details not yet available but expected to cover around 20,000 SNPs[16]
Results for private Y-SNPs (novel Y-variants) Not possible with chip-genotyping Not possible with chip-genotyping Average count 54 [15] Average count 66 [15] Not possible with chip-genotyping
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. A Word file with a list of all the SNPs for which the customer has tested positive. A .CSV file containing a complete listing of all the Y-SNPs tested and the genotype for each allele is also provided. The genome reference positions are not given. 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.
Availability of single Y-SNPs No 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[17] Not at this time. Custom SNPs can be ordered from YSEQ at $17.50 per SNP. Yes, if free transfer to FTDNA is used, so you can order there.
Availability of SNP panels No No A limited selection of SNP panels is currently available. There are many subhapologroup-specific SNP panels in development. No No
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 		No 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. [18]
Ancestry reports included
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. Included in the cost of the kit in the UK; £13 for the Republic of Ireland (includes return courier service) $12.95 for USA and international orders (prepaid return postage is included for US kits)[19] $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
International product availability 56 countries Worldwide Worldwide Worldwide Worldwide
Time from receiving the kit to release of results 6-8 weeks 6-8 weeks 8 weeks[11] Because of forwarding to the external laboratory and delays at the lab, sometimes several months Up to 10 weeks
DNA sample storage Yes, indefinitely 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
Projects supported No No Yes Not at this time but reportedly in development Yes. if the free transfer to FTDNA is used
Project/crowd funding No No Yes (Contact customer service for help with group project orders.) No No (was announced to be made available for FTDNA project order)
Online community or forum Active online community for 23andMe members, including demo accounts No 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.
Sponsored public database No No Partial[20] No No
Additional DNA testing options available from this company No 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
Lead scientists in the company Joanna Mountain, Brian Naughton, Steve Lemon James Wilson, Angelika Kritz, Katie Barnes Connie Bormans Spencer Wells
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 Not applicable Michael Hammer, Bruce Walsh, Doron Behar, Spencer Wells[21] Greg Magoon Connie Bormans, Eran Elhaik, Thomas Krahn, 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 The Moffat Partnership Gene by Gene Managing partners Bennett Greenspan and Max Blankfeld Privately held National Geographic
is a non-profit scientific and educational society
Lab(s) used National Genetics Institute
(a subsidiary of LabCorp), Los Angeles, California 		Source Bioscience, Nottingham, England Family Tree DNA Genomics Center, Houston, Texas BGI Hongkong[22] Family Tree DNA Genomics Center, Houston, Texas
Method for collecting the sample Saliva sample (about 1 cc) Saliva sample Cheek swab Saliva sample or cheek swab Cheek swab
Payment methods VISA, Mastercard, Discover, American Express VISA, Mastercard, American Express Credit Cards, Paypal, checks Credit Cards, Paypal, checks Credit Cards, Paypal
Address 23andMe
1390 Shorebird Way
Mountain View
CA 94043
USA 		The Moffat Partnership Limited
Capella
60 York Street
Glasgow G2 8JX
Scotland 		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
Phone number Enter a ticket online at customer care for a call-back 0845 872 7634 713-868-1438 All communications are via e-mail 888-557-4450 (in the US or Canada) or 713-868-1807
E-mail address FTDNA Contact Form
Year founded 2006 2011 (2004)[23] 2000 2012 2005

Notes

  1. ↑ 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/
  2. ↑ The companies now trading as BritainsDNA, ScotlandsDNA, IrelandsDNA, CymruDNAWales and YorkshiresDNA were formerly known as Ethnoancestry.
  3. ↑ 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'.
  4. ↑ Geno 2.0 Next Generation replaces Geno 2.0 which first went on sale in July 2012.
  5. ↑ Prices checked 21 August 2015; check company websites for current prices.
  6. ↑ $399 (£250) when ordered with Chromo2 Complete which includes autosomal and mtDNA SNPs with interpretation and narrative reports.
  7. ↑ The information in this table refers to Y Elite 1.0. See informations in the Full Genomes Corporation page.
  8. ↑ mtDNA and autosomal DNA available at additional cost as part of the Chromo2 Complete test
  9. ↑ 23andMe users can find their terminal SNP with the Haplogroup Mutation Mapper tool, then go to the ISOGG tree and search for it on the appropriate page for the major branch.
  10. ↑ Petrone J. Family Tree DNA Expands beyond Array-based Offerings with New Y Chromosome Sequencing Service ($) GenomeWeb BioArray News, 12 November 2013
  11. ↑ 11.0 11.1 11.2 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.
  12. ↑ FGC vs BigY, FGC_Advantage_January2014_release rev2.pdf, by FGC.
  13. ↑ 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."
  14. ↑ FGC vs BigY, FGC_Advantage_January2014_release rev2.pdf, by FGC.
  15. ↑ 15.0 15.1 15.2 15.3 15.4 Vadim Urasin, 17 Sep. 2014 in the YFull Facebook group
  16. ↑ Geno 2.0 covered 12,065 variants with some no calls.
  17. ↑ 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
  18. ↑ The Geno 2.0 test covered 126,307 autosomal SNPs, 3803 X chromosome SNPs, 3281 mt SNPs
  19. ↑ 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. 
  20. ↑ Some surname and haplogroup projects list SNP results for participants.
  21. ↑ Editorial Staff. "Who's Who At Family Tree DNA". Family Tree DNA. Gene by Gene. http://www.familytreedna.com/about.aspx. 
  22. ↑ Beta-testing is also being done at UCLA (University of California, Los Angeles) but they have not as yet been confirmed as a sequencing provider.
  23. ↑ The company was founded in 2004 as Ethnoancestry, and relaunched as ScotlandsDNA in 2011. The trade names BritainsDNA, IrelandsDNA and YorkshiresDNA were added in 2012.

Reviews

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Resources

Further reading

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.

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