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False positive hotspots to upload into Genome Mate

False positive hotspots to upload into Genome Mate

Posted: 4 Sep 2014 6:09PM GMT
Classification: Query
I really like how Genome Mate marks the centromere in yellow, and recently in the FB group Becky said she was looking at trying to pull in ethnicity info from 23andMe (by chromosome). I've already done this manually, making fake matches with the ethnicity names, just as a way to keep an eye on the non-Euro bits that stick out of my usual Brit/Irish swirl.

(Some people extract this data from 23andMe using the 529 add-on, but I prefer to do something similar to the method described here: http://dna-footprints.com/489/23andme-download-ancestry-comp... If you don't have 23andMe results, you could always eyeball the start and end points in GEDmatch's admixture tool.)

I've just been catching up on the big Ancestry thread at 23andMe, where Barbara B. has posted a chart of areas that are believed to be more likely to yield false positives. (Apologies if I've missed any discussion of it here.) Here's the paper with all the big words: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907355/

Using the data in Barbara's post, I've reformatted it below so that can be copied and pasted into a text file, edited to use your profile name, saved as a CSV, and imported into Genome Mate using the generic import. If you didn't test at every company, perhaps import it as results from somewhere else just to have the color stand out plus make it easy to flip on/off.

(You may want to call the second field aka match name something other than "WONKY." Also, the SNPs - the last field - are just made-up placeholders that I added.)

Profile Name,WONKY,1,118434520,153401108,9.95,1111
Profile Name,WONKY,2,85304243,99558013,6.53,1111
Profile Name,WONKY,2,132695025,141442636,9.16,1111
Profile Name,WONKY,2,192352906,198110229,5.04,1111
Profile Name,WONKY,8,10428647,13469693,7.96,1111
Profile Name,WONKY,9,38293483,72605261,8.15,1111
Profile Name,WONKY,10,44555093,53240188,7.58,1111
Profile Name,WONKY,15,20060673,25145260,10.46,1111
Profile Name,WONKY,15,27115823,30295750,9.29,1111
Profile Name,WONKY,16,19393906,24031556,6.18,1111
Profile Name,WONKY,17,59518083,64970531,6.23,1111
Profile Name,WONKY,17,77186666,78417478,5.66,1111
Profile Name,WONKY,21,16344186,19375168,6.91,1111
Profile Name,WONKY,22,16051881,25095451,20.82,1111

(Smart people in that 23andMe thread are still talking about their spreadsheets, but I fought the urge to once again preach from the Book of Genome Mate. Bless all our hearts.)

Re: False positive hotspots to upload into Genome Mate

Posted: 4 Sep 2014 10:41PM GMT
Classification: Query
Thanks, Shari--I just created a .csv file and tried to import it to Genome Mate, without success. I selected it under the generic import but it never loaded. Are you aware of any tricks I could try?

Jim

Re: False positive hotspots to upload into Genome Mate

Posted: 4 Sep 2014 11:05PM GMT
Classification: Query
Figured it out--On my Mac I had to save it as an MS-DOS .csv. Thanks for this. I was expecting to find a hot spot on Ch. 3 in a region where I have literally dozens of ICW matches, but it was not in this list. I think it probably is a very old IBD Irish segment.

Jim

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 4:01AM GMT
Classification: Query
Excellent - I added your MS-DOS tip when posting this to the Facebook user group. Thanks! (Group is here if anyone is interested: https://www.facebook.com/groups/1487955884768702/ )

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 12:18PM GMT
Classification: Query
Shari, this is terrific! Thanks for making this process so user friendly.

And, Jim, as always, thanks for being a beta tester for those of us who use MACs.

Of course my first matching Wonky segment is to a person who has a documented paper trail to a common ancestor and matches others on this family line. Should I assume that this is a genuine match or a coincidence? If the latter, I'll lose a nice swatch of chromosome painting! Still, it's better to be cautious than to waste time on false trails.

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 12:32PM GMT
Classification: Query
I wouldn't worry too much, Blanche. The hotspot simply means a higher probability of a false match, not a certainty, and your documented match may well be on the other strand. No reason, IMO, to discard solid research.

Jim

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 2:08PM GMT
Classification: Query
Thanks for posting the list Shari. I'll have to add it to my info in Genome Mate.

and I guess I might have to violate my personal moratorium of Twitbook since it appears that the whole world revolves around it...

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 2:32PM GMT
Classification: Query
I have a Facebook account but only use it to follow specific groups of interest. I check it once every day or two and occasionally find useful info. I am a member of Irish Family History, Irish DNA, ISOGG (International Society of Genetic Genealogists) and Gedmatch Users Group. I also check Ancestry.com and Genome Mate on facebook every couple of days.

Jim

Re: False positive hotspots to upload into Genome Mate

Posted: 5 Sep 2014 4:50PM GMT
Classification: Query
I'll have to check those groups out. I may as well get the most bang for whatever exposure I'm opening myself up to. lol
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