A Novice in Genetics and DNA Testing Has Some Questions

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TertiusOrdoBellator

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So I tested my DNA with LivingDNA and got my results. Now I want to know what I can do with those results. I'm very interested in exploring my ancestry and history of my lineages. I will ask some questions and hopefully someone out there is able to answer them. Keep in mind that I am a complete novice in this field so some of the questions may appear ridiculous.

I have heard of ancient ancestry calculators, [specifically] what are they, where can I find them and how do I use them?

If and when I upload my raw data I got from the test I bought, how do I make sure nefarious people don't get their hands on it (i.e. how do I know a site is reliable)?

My Y-DNA haplogroup is N-VL29 and it seems to have a lot of subclades. Is that my definitive haplogroup or is it possible that I have some subclade of it but the test wasn't accurate enough to determine it? If the answer is yes, is it possible for me to find out a more specific subclade using the raw data I have (same questions regarding mtDNA haplogroup)?

The family matching at LivingDNA is very poor probably due to a lack of samples. What are some [reliable] sites that I can upload my raw data to for family matching/finding genetic relatives?

Where can I learn more about haplogroups and their naming system? They seem a bit confusing at times. Resources regarding population genetics in general are appreciated also.

That's it for now I think. Thank you in advance for answering to who ever bothers to do it. Some new questions may pop up so I will throw them at you later in the thread.
 
You might try loading your data up to GEDmatch dot com. I have found it much easier to associate my relatives with a family tree with names and dates on it; so I use ancestry dot com, but use my DNA information as a clue or a confirmation. My first DNA test was with familytreedna and it is a quality product to explore Y and mtDNA and relatives it alone wasn't enough to go forward. The extra help from official records convinced my to get an additional DNA test for Ancestry dot com so I could see who matched me compared to their tree. You can start a free account at ADC too but it is of limited use if you can't access their database. GEDmatch will allow you to upload for free and see everyone who matches you and there are some free tools and some more advanced tools. Don't worry about not understanding it all right away, you will eventually start seeing how it works. look for you-tube videos; some of which are excellent.
 
Unfortunately with Living DNA Raw data your only option is Gedmatch. Of course not everybody who's done a genetic test uploads there and there is certain limitations in comparing raw results from different companies (snp overlap...so a distant relative may seem closer etc.) . I am unsure whether under the new ownership one can opt-in/out of Law Enforcement matching (not that it'd change anything).


https://isogg.org/wiki/Autosomal_DNA_testing_comparison_chart


Living DNA uses chip technology (like all other companies) and the y-dna and mt-dna snps tested are "pre-selected", so to say ...and with some haplogroups they do a decent job finding the branch...and not so with others.


This is yours :
https://www.yfull.com/tree/N-VL29/


As you can see by the flags ,pretty "finnic" so no surprises there.


You may also want to check the public FTDNA y-tree for your branch :


https://www.familytreedna.com/public/y-dna-haplotree/N;name=N-CTS2929 (n-cts2929 = n-vl29 per Yfull).


But to find your exact subclade you need further testing.


Now...if you need to find more relatives on autosomal level you may want to test with FTDNA and/or Ancestry. FTDNA would be choice #1 as many folks use their services for uniparenal markers testing too and their database is pretty solid . Also Scandinavians and Eastern Europeans are better represented there in comparison to the other testing companies(at least that's my impression). Autosomal test can be had for 49 usd during campaign...Full Sequence Mt-DNA - for 149 and BigY700 (y-dna) - for about 399 usd (Father's day sale as of now).


https://www.familytreedna.com/


This will answer your questions about proper subclade placement and uploading to Yfull will calculate your most recent common ancestor date with your male line "cousins".


If you want to get everything in one pack (autosomal; Y-dna; Mt-dna; possibly health info etc.)- order a x30 WGS test at Nebula genomics (check out the relevant threads in the forum), 299 USD...


https://nebula.org/whole-genome-sequencing-dna-test/
https://dna-explained.com/category/whole-genome-sequencing-wgs/

Extracting the relevant info from the Nebula raw files may be very challenging for inexperienced users, please check before ordering. I do not know whether they (nebula) or other companies offer the service of converting the giant raw files into usable raw files that one can upload here and there (Gedmatch, Yfull etc.)
Yseq for $25 would do this with Dante file for example...not sure about Nebula.


Hope this helps a bit.
 
td120 said:
Unfortunately with Living DNA Raw data your only option is Gedmatch. Of course not everybody who's done a genetic test uploads there and there is certain limitations in comparing raw results from different companies (snp overlap...so a distant relative may seem closer etc.) . I am unsure whether under the new ownership one can opt-in/out of Law Enforcement matching (not that it'd change anything).


Living DNA uses chip technology (like all other companies) and the y-dna and mt-dna snps tested are "pre-selected", so to say ...and with some haplogroups they do a decent job finding the branch...and not so with others.


This is yours :


As you can see by the flags ,pretty "finnic" so no surprises there.


You may also want to check the public FTDNA y-tree for your branch :


(n-cts2929 = n-vl29 per Yfull).


But to find your exact subclade you need further testing.


Now...if you need to find more relatives on autosomal level you may want to test with FTDNA and/or Ancestry. FTDNA would be choice #1 as many folks use their services for uniparenal markers testing too and their database is pretty solid . Also Scandinavians and Eastern Europeans are better represented there in comparison to the other testing companies(at least that's my impression). Autosomal test can be had for 49 usd during campaign...Full Sequence Mt-DNA - for 149 and BigY700 (y-dna) - for about 399 usd (Father's day sale as of now).





This will answer your questions about proper subclade placement and uploading to Yfull will calculate your most recent common ancestor date with your male line "cousins".


If you want to get everything in one pack (autosomal; Y-dna; Mt-dna; possibly health info etc.)- order a x30 WGS test at Nebula genomics (check out the relevant threads in the forum), 299 USD...





Extracting the relevant info from the Nebula raw files may be very challenging for inexperienced users, please check before ordering. I do not know whether they (nebula) or other companies offer the service of converting the giant raw files into usable raw files that one can upload here and there (Gedmatch, Yfull etc.)
Yseq for $25 would do this with Dante file for example...not sure about Nebula.


Hope this helps a bit.
Click to expand...


Thanks! Helps a lot. I used LivingDNA because a friend recommended it to me. I mainly wanted to know about my haplogroups and he said that the LivingDNA one is the best for the cheapest price when it comes to haplogroups. Now that I have the results, I yearn more specific information of my hg subclades and want to find genetic relatives, for which the LivingDNA test is quite poor unfortunately. So I planned to do an Ancestry test some day in the future but first I want to focus on researching my family tree through documents and other historical sources.

I uploaded my raw data I got from LivingDNA to GEDmatch and played around with the calculators. Turns out I'm a mix between Eastern and Western Finns leaning a bit more to the Western side. No surprises there. I haven't checked if there are any matches yet.

I have a problem with FTDNA. I read that they won't destroy your sample and refuse to delete all your data if you ask. Not that privacy is the biggest concern to me since I have already sent my DNA around the world but being able to have a company tell me they don't have my data anymore if I ask for them to destroy it at least makes me sleep like a baby at night. Do you happen to have any experience with them? That Nebula genomics pack seems interesting but other companies don't seem to accept their raw data for matching. If I took the Ancestry autosomal I could access their database, MyHeritage database (which a very popular DNA testing company here) and possibly FTDNA database. That Ancestry Y-DNA test seems quite expensive.
 
Yes, I have tested with all major companies (save for MyHeritage) . I never regretted doing any of these (all of the testing companies revealed something interesting).
As for "we're going to destroy your sample and results" corporate promise-well, I won't hold my breath .Some of them would trade with your results ...Too late to worry anyway. Nebula (used to...not sure about these days ) send the samples for testing at BGI labs in Hong Kong which would be a "no-no" for many folks...some testers would never send their results to Yfull for example...all kind of stuff...meanwhile ,with the speed the technology is evolving one would be "sequenced" while they were watching their favorite musician perform on stage. If one checks who owns and runs these companies they'll probably never test, so...yeah, what can you do...Some of the companies allow the user to modify the privacy settings (opt in/out LE matching or research consent etc...right..) .
Some companies would not perform the test unless you agree on the fact that your sample will be used for clinical research for example (whatever that means)...
Anyway, if you really want to explore further- go ahead ,but wait for the sale campaigns for the respective companies.
Living has a very limited matching database, Ancestry has the biggest. Ancestry however needs a subscription (that one could cancel)to be able to dig in the paper archives (pretty extensive) or observe the family trees of the participants.
FTDNA accepts (normally) raw files from Ancestry and 23andme ...thing is, your matches will be limited to your immediate and close "cousins" (without the "speculative" ones) and they charge a fee (was it 19..or 29 usd? I forgot.). So if you plan to test anything else with FTDNA , get yourself a $45 autosomal test along with the other stuff. FTDNA has the biggest Y-;Mt-DNA database and is host for many DNA projects (family; national,regional etc.).

https://www.familytreedna.com/groups/finland/about


https://www.familytreedna.com/autosomal-transfer

https://www.familytreedna.com/

You may want to test your relatives too (GP's, parents, cousins) , if funds are available.

As for representation with the companies and regarding your Finn ancestry
-23andme does not serve Russia, Ukraine and Belarus (very limited number of participants, mostly from the diaspora...folks need to go thru hoops and loops to get the desired kit).

https://int.customercare.23andme.com/hc/en-us/articles/214806628-What-Countries-Do-You-Ship-To-

AFAIK the same with AncestryDNA :

https://support.ancestry.com/s/article/Countries-Where-AncestryDNA-is-Available?language=en_US

-I might be wrong on this, but Ancestry is not Scandinavians' most popular choice (although the most interesting connection might pop up precisely there, considering their enormous database and the US immigration).
-Other groups of interest -Germans, Brits, Western and South Slavs are kind of equally distributed in my opinion.
 
Yeah the companies probably have enough samples from my countrymen (maybe even relatives) already to sequence my DNA anyway so the privacy concern is not the biggest issue. As for Ancestry's database, I'm supposed to have relatives in the US to whom we lost connection a generation or so ago, so not too long ago.
Those FTDNA limitations are a bummer. So what would you recommend me as my next test if I want to primarily find relatives but also learn my specific Y-DNA haplogroup subclade? As far as I as I know I don't have any other ancestry other than Finnish (possible Swedish speaking Finnish; very unlikely Swedish) ancestry for many generations back.
My uncle didn't want to take a DNA test a while back probably because of security concerns (he's interested in our family history) but since I have already taken one I kind of ruined the privacy part for him too so I will have to try and get him interested in taking a test.
 
I just checked my GEDmatch matches and I had couple. I just can't interpret what all the data about the matches means. Any help is appreciated but I will try to search around myself.
 
You see, if you want to find your y- terminal haplogroup, you need to do a WGS test or a dedicated Y-chromosome full seq.
Your options for WGS are :

-Nebula Genomics (gaining momentum, $199 on sale)

-Dante Labs (lots of complaints since 2020 ,I used them once, got lucky)

-YSEQ WGS++ (Mixed reviews on WGS400, so get the higher priced option. Germans, they test in a local lab, planning soon to do everything in-house, great service, great folks).
https://www.yseq.net/index.php?cPath=29

All these three will give you an autosomal result, your terminal y- and mt- haplogroup and with Dante and Nebula- health info, if you care about that. Yseq will have your results broken in readily usable smaller files that you can upload to Gedmatch, possibly to FTDNA (as they do it in 23andme format) and to Yfull (.bam file for the Y-result and FASTA file for the mt-result).YSEQ did this with a DANTE Lab result for me for 25 usd saving me a lot of headache, God bless them ( https://www.yseq.net/product_info.php?products_id=107732 )

...and with the Y-chr. tests we got:

-FTDNA BigY-700 (pricy but worth the money imo...will put you on the FT tree in the biggest database so far...you need to pay another $100 for the generation of a .bam file if you need to upload to Yfull though).

-a dedicated snp panel at YSEQ ( https://www.yseq.net/product_info.php?cPath=27&products_id=18382 ). This would find your position on the tree and may or may not pinpoint your terminal snp (you can order additional snps to be tested after consulting with more experienced users).You cannon upload this for matching and age calculation at Yfull.

As for mt-dna result, it will come "for free" with the WGS result from Nebula or Dante or Yseq WGS++...of if you want to do a dedicated Full Squence mt-dna test :
-FTDNA , $149 (will put you on their mt-tree and matching database, you can participate in the respective project)

-YSEQ , $149 ( https://www.yseq.net/index.php?cPath=28 )

Both these will give you a small FASTA file that you can upload to Yfull for free along with your Y-dna result (the .bam file) or to GenBank .

Unfortunately FTDNA do not accept Y-chr or mt-results for upload to their database, so there is no other option to sneak in there.

So, what we've got :

-Nebula $199,need to find an option to convert and break the gigantic raw files info usable small ones (free program exist, one need a... hm, decent comp with enough free space and some experience. Does not work every time...or use YSEQ service to do it for you).There might be some more charges concerning Nebula, I have not used them, check carefully users' experience, anthrogenica has subforums for the different companies).

-Dante Labs ,pass as of now

-FTDNA ..well, sooner or later you'll knock on their door...$399(BigY) + $100(eventually for a .bam file) + $49(autosomal) + $149(mt-Full sequence). No need to do it at once, the sample is kept there, enough for all these without sending a new one, they test in-house.

-YSEQ WGS++ $699 (I am unaware of any sale campaigns there, price is firm). You get all of the above in one pack. Test in Germany(or in-house already, these were the plans). The autosomal file will be WGS, may or may upload it to Gedmatch (idk as of now),the smaller 23andme-format autosomal file can be uploaded to Gedmatch and possibly to FTDNA...possibly.

As for the other autosomal testing companies, like I mentioned, I've used them all with good results (and many of my matches too...keep on bumping on same "cousins" among the different companies...yep). I have not used MyHeritage, but I think they allow for transfers.

At the moment Ancestry is on sale for $59, FTDNA for $49 and 23andme has $50 off an Ancestry+Health package ($149).
There will be like three more sale campaigns till the end of the year so no rush ...

P.S. about the Gedmatch... back then with the old ownership there used to be a "Tier1 section" with interesting tools and for $10 monthly fee one could use them...like "segment matching" , triangulation etc..one could set the desired parameters for matching too... give it a try if it still exists.
Also, there are great resources online concerning the questions a novice would have. Do yourself a favor and get this book:
https://www.amazon.com/Family-Guide...r&qid=1655428471&sprefix=betti,aps,957&sr=8-2
..available in kindle format too.

As for matching segment size/relationship, have a look at :
https://thegeneticgenealogist.com/2020/03/27/version-4-0-march-2020-update-to-the-shared-cm-project/

Finns however differ in this respect so finding such specific info concerning your folks (there should be some published already I guess) will be of help (for example a given segment size among Finns will usually mean more distant relationship as compared to a "german and germans" or "a german and slavs" or "a slav and and americans" matching)... meaning a third cousin among Finns(per the chart above) may be an actual fifth or very distant etc.
 
That's a lot of useful information and I will be visiting this thread for reference. I appreciate you for taking the time to instruct me.

"Finns however differ in this respect so finding such specific info concerning your folks (there should be some published already I guess) will be of help (for example a given segment size among Finns will usually mean more distant relationship as compared to a "german and germans" or "a german and slavs" or "a slav and and americans" matching)... meaning a third cousin among Finns(per the chart above) may be an actual fifth or very distant etc. "

Could you elaborate a bit on this? Why is it so?
 
Don't quote me on this as I am just a mere user and several years ago I had exactly your questions...for whatever reason I was left with the impression that Finland had a relatively "closed" population ... and for ex. the same phenomenon described above can be observed (even more pronounced) with other endogamous populations like the Ashkenazi Jews (although for different reasons).

Glad to be of help !Ask away whatever you need!
 
Oh yeah, Finland tends to form a cluster of our own in the greater European cluster, genetically (though Eastern and Western Finns can be quite far apart from each other). Kind of between Sweden and Estonia. Happened probably due to a population bottleneck(s) in the past. I will ask if any questions arise.
 
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