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Klotho – a gene for longevity and better brain function as you age

A recent discovery in the news is the Klotho gene which seems boost brain function and adds to longevity. About one in five people have the good variant.

KLsnpIf you tested at 23andme, you can find out if you have it by checking the SNP at rs9536314, the protective variant is the heterozygous one, GT, while the normal variant is TT. The homozygous version, GG, appears to be deleterious.

So log into your 23andme account and then click this URL to see if you have the GT  version is
https://you.23andme.com/tools/data/?query=rs9536314&filter_by_platforms=true

Here are a few informative news articles explaining this discovery:
http://www.ucsf.edu/news/2014/05/114196/better-cognition-seen-gene-variant
http://www.medicalnewstoday.com/articles/276665.php

Now to get more technical.

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A Web Site with Tools for Y and other DNA analysis

There is a wonderful site at http://www.y-str.org with many good tools for Y DNA and autosomal DNA that run as programs on your PC plus a cool ISOGG Y tree add-on for the Chrome browser. My specific interest at the moment is figuring out which Y SNPs are already tested by 23andme so as not to test them again at FamilyTreeDNA since my Dad has kits at both places. I blogged about how to do that manually back in February, but now there is a program that will do that for you. However it took me a while to figure out how to do what I wanted from the instructions given, so I will do a step-by-step tutorial in this post in order to remember what I did.

BrowseMenuFirst download your raw data from 23andme by going to the “Browse Raw Data” Page which is listed in the menu that appears under your name on the top right. Then on the raw data page click on “Download” in the second top bar on the right hand side. This takes you to a page with various warnings and requires that you reenter your password as well as the answer to your secret question before it starts the download.

Save the download file somewhere that makes sense for you. I have a folder called RawData in the folder DNA that I use. Once the raw data file is downloaded, you will need to unzip it before using it with the various tools. To unzip in windows all you need to do is open a file explorer window (a manila envelope is the icon) and then right click on the file name to get a little menu that includes “extract all” which is the one to click.

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Figuring out a DNA relative’s shared DNA with 23andme’s “Countries of Ancestry”

Maybe you have had great luck with people responding to your shares on 23andme but most of us have at best 30% of our share requests accepted (of 1800 DNA relatives my Dad has 338 shares and 40 introduction accepted so just under a 20% acceptance rate). This is especially frustrating when someone is clearly a close relative and does not respond. Of course some of the reason for the lack of response is that the default setting on 23andme is to not send emails when there are messages in the inbox. Fortunately the occasional email from 23andme about new relatives or news does get some of them to log in and see the invites. I always get several acceptances from old shares after one of those broadcast emails.

Yes I can hear those of you who have tested at familytree DNA laughing and say well we can see the shared DNA. But you also may never hear back from some of the most promising leads who do not have much of a tree posted and more importantly you cannot compare people you match with each other which we can do with our shares. There are pluses and minuses to each testing company.

Below are a few of my closest non accepting DNA relatives. S M is public and accepted contact but not sharing. G S is public and responded to a message asking if he was related to my S family from Etne with a no, but has not shared. I made an error on the 3rd introduction to one relative and now can no longer contact them, at least from this account.

Some close DNA Relatives

So for those of us using 23andme I will use these matches as a case study on how to find the DNA segments where they match my Dad using “Countries of Ancestry.” This only works if your relative has entered the countries of origin for their parents and grandparents.

First a little known trick, you can download a CSV of all your DNA relatives by clicking the Download button on the top right of the page when on the DNA relatives page.

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Getting all the in common with (ICW) matches at 23andme

The DNAgedcom website has a wonderful feature whereby you can download the overlapping segment data for one of your matches with all your other matches at 23andme. Since it will include you in the CSV file, you can quickly see if you and your share both match another person at the same spot (called triangulation by genetic genealogists).

Here is a sample of that type of match from the resulting sorted spreadsheet for an adopted close DNA relative I am working with (names of non-family removed for privacy):

Comparison Chr Start point End point Genetic distance # SNPs
Adoptee CR vs 1st cousin GP
5 113000000 124000000 11.8 2217
Adoptee CR vs me
5 114000000 121000000 7.2 1401
Adoptee CR vs Dad 5 114000000 124000000 11.2 2038
Adoptee CR vs my brother 5 114000000 124000000 11.7 2112
Adoptee CR vs SS 5 115000000 123000000 8.9 1602
Adoptee CR vs EJ 5 116000000 123000000 6.8 1391
Adoptee CR vs AH 5 116000000 123000000 7.8 1482
Adoptee CR vs AC 5 117000000 124000000 7.4 1421

The four other matches are a bit small but the one with SS is mildly promising; so to be absolutely sure it is a triangulation I have to compare SS back to my family members. Here is how that looks in the 23andme chromosome browser (which can do three at a time with any of your shares):

SSvsUs
And we see that the overlap with me is just a little bit too small to show up, less than the 23andme threshold, but my Dad and brother are a triangulation.

So read on to find out how to use this download feature at DNAgedcom.com.

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How to figure out what Y SNPs are tested at 23andme

Those of us who are tested at 23andme and have also done the Y STR test at family tree DNA may wonder when some family tree DNA project manager says “Test SNP so and so” whether that SNP is already tested by 23andme. This post explains how to figure that out. If I have already lost you, then this post may just be too technical or else not your cup of tea. To better understand Y testing read this Y lesson by Kelly Wheaton.

For a good explanation of what a STR versus a SNP is, read Roberta Estes’ post – http://dna-explained.com/2014/02/10/strs-vs-snps-multiple-dna-personalities

So to figure out which SNPs my Dad has already tested, I first created the L11 subset image below of the R1b Y haplogroup SNPs from the beautiful diagram created for R1b by Mike Walsh because I need visuals:

R1bL11

Back to the original question. My Dad is an R1b etc and 23andme uses a four year old haplogroup designator rather than the current ISOGG R haplogroup listing. A visitor to this blog suggested that we test DF100 because that is an interesting subclade we may belong to since we have these SNPs according to 23andme: L11/PF6539/S127, L52/PF6541, P310/PF6546/S129, P311/PF6545/S128.

The diagram shows that the possible downstream SNPs for Dad are U106, DF100, and P312. So how to find out if they are tested at 23andme? Since the haplogroup at 23andme shows L52 as the last SNP can I assume the others are tested?

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