GENESIS from GEDmatch: the new chip

Technology never stands still. The latest change affecting all of us who love using DNA for genealogy is a new chip from Illumina. The past six or so years of autosomal DNA testing have shown that the current chip is great for testers with European ancestry, but does not have enough SNP coverage to figure out the details of the ethnic make up for people from other parts of the world. Many more and different SNPs are tested in this new GSA chip.

All the 23andMe tests done since this past July use that chip, as does Living DNA (highly recommended if you have British ancestry since it does local regional breakdowns). I imagine eventually the others will follow along. The bad news is that there is not that much overlap between this chip and the previous ones, which affects cousin matching.

Debbie Kennet wrote a blog post describing the new chip at https://cruwys.blogspot.com/2017/08/23andme-launch-new-v5-chip-and-revise.html

Because the SNPs are so different the DNA results from these kits cannot be uploaded to GEDmatch, however our friends there have built another site to handle these new kits called GENESIS. They have come up with a whole new algorithm for relative matching that works with lower SNP counts.

At the recent i4GG.org conference (videos coming in February), I gave a presentation on what’s new at GEDmatch, the second part of it went into much detail about GENESIS, starting with this slide:
http://slides.com/kittycooper/gedmatch-10-13-23#/38

The functions available at GEDmatch are being gradually implemented at GENESIS. Most of the key ones are there now. Plus there is some new functionality. One major addition is the showing of the number of SNPs actually overlapping between kits. Very important to know since the overlaps can be as small as 108,000 SNPs or as large as 580.000.

The thing I like best is the new multi kit analysis selection page which lets you add kits easily, including dropdowns of your own kits, to the ones that you already checked at the one-to-many or kits that match two kits. But I miss the tag groups.

The other new feature that is great is the ability to look just at the FIRs (fully identical regions) on the one to one comparisons. Only full siblings and other close doubly related people share long blocks of FIRs. It also gives the total number of cMs in those FIR blocks, which is very helpful for figuring those ¾ relationships. UPDATE 16-Dec-2017: I have received emails asking about the statement they see under a one to one match like “80.8 Pct SNPs are full identical” – these are individual SNPs, normal when you come from similar population groups. This is not the long shared regions of double relatives.

Also new is the addition of more colors for validity on the one-to-one images including a color for too large a gap between SNPs.

Missing is the connection to trees from the one-to-many but that will come. The current one-to-many is not the final version I am told.

I recommend you look through the screenshots from my presentation or upload a kit or two and take a look around. In a few months the GEDmatch database will be moved over but why wait?

One to Many as of December 2017

26 thoughts on “GENESIS from GEDmatch: the new chip

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  1. In general, I rested at the two major companies two years ago. Will I need to retest in order to take advantage of these new technologies?
    Thank you

    • You don’t need to, but everything is on sale so you might get a kit that uses the new chip, particularly if you have ancestry from the British Isles try LivingDNA.. They also give your haplogroups

      • Is the LivingDNA useful if one’s heritage is from the Connemara region of Galway, Ireland? My ethnic breakdowns from Ancestry and FTDNA indicate that I have “British Isles” in addition to Irish/Scottish.

        • Barbara –
          Ask them but yes it might well be. One thing is that when you get your results, you have to click the plus sign next to regional to see the sub regions which many people miss.
          Also it gives you your mtDNA haplogroup
          Kitty

  2. Thanks for the tip on Living DNA (during a sale no less)! Roughly half my ancestry is British. Very interested to see this breakdown.

  3. “Only full siblings and other close doubly related people have these. [FIRs]” — Just to be clear for newcomers – you are addressing very large FIRs.

    We all have smaller regions of FIRs with other humans, it’s why false-positives are so common in half-identical matching.

    As for Genesis itself – I don’t know how successful they will be able to overcome the low commonality some genotype files will have with others, especially as newer genotyping products come and go and use different SNP sets. When we get down to only say 100k shared SNPs over all 23 chromosomes.

    I guess time will tell.

    • Dan –
      Thank you for pointing out that my wording was not clear. I have fixed that, I hope, and also added an explanation for another point of confusion from several readers (see the update in the FIR paragraph).

  4. I am concerned. I’m scheduled to give a few talks on gedmatch in early 2018, including one at the Ohio Genealogical Society conference in mid-April. The syllabus for printing is due by mid-January. Now I’m getting that sick feeling that everything I’ve prepared will no longer be valid. Advice?

    • Kathleen,
      If the conference uses an app, you can upload a new version of your syllabus … by mid April I would expect that GEDMatch will have migrated to the full GENESIS functionality … se be prepared? Email gedmatch at gmail for the expected timeline. Meanwhile get familiar with GENESIS and be ready with some of those screenshots!

  5. I have learned much by reading your blog, it has been a huge learning tool. That said, I was on Gedmatch and I have a match to a Kitty Cooper @ 6.8 mrca. If this is your kit, I am honored and a little giddy to be related (and I did double check the match one on one)

    Happy new year and thank you for the excellent tutorials.

    Beatrice

  6. Both GEDMatch and Genesis don’t allow segment matching at the level of 3-4 cM and with less than 500 SNP. I am attempting to triangulate among known cousins and a potential 8th cousin to establish a common ancestor from early 1700’s. We have a matching segment among three cousins and this potential 8th cousin, but I’d like to determine a probability of the relationship. I hope to recruit more verified cousins to see if we all match on the same segment, and also that at say a 1/100 probability, a random kit will not match. Suggestions? Thank you.

  7. Please don’t use such small segments. They are just not a reliable indicator of relatedness. You can find 3cM matches to almost anyone with North European ancestry.
    I do drop down to 5cM and 400 SNPs for KNOWN RELATIVES only but take any small segments with a grain of salt uness they triangulate.
    You will only match half your 4th cousins and maybe 15% of your 5ths. See https://isogg.org/wiki/Cousin_statistics
    So for deeper ancestry, Y DNA matching is the best tool

  8. Any prediction of when GEDmatch will merge their main database with Genesis? I have a new kit but no clear matches on Genesis, but know that I should be getting a lot of hits on the main database, so am chomping at the bit for when they will be merged. There’s no information at all on the GEDmatch site.

    • Daniel – I asked them and they hope for soon but cannot commit to a date yet, sorry! I will blog it out and add to the comments here when that happens.

  9. I have no idea what to do. I know I have Native American blood on my father’s side, but it didn’t show up. Was told to upload to Gedmatch. I tried, but not sure if I was successful. I don’t know where or how to look. Technically challenged is an understatement!!

  10. I tested with ancestry, uploaded dna to myheritage, ftdna, dnaland, gedmatch, and gedmatch genesis.
    My question is, I had a search angel help find my family. I have been in touch with a half-sister, I assume. We figre there are at least 10 sibling in the family, so I thought, to cover all bases, she should test with 23andme. So I bought the kit and had it sent to her. So, to see if we are indeed siblings, will she have to upload her raw dna to gedmatch genesis also?

  11. Kitty,
    Is there any way to upload Y-DNA to Genesis? I am getting conflicting reports from useres. If not are there any plans to add Y-DNA functionality in the fiuture?

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