Page 1 of 2 12 LastLast
Results 1 to 10 of 12

Thread: Big Y (NGS) rollout, updates, concepts and Q&A

  1. #1
    Registered Users
    Posts
    4,074
    Sex
    Y-DNA (P)
    R1b
    mtDNA (M)
    H

    Lightbulb Big Y (NGS) rollout, updates, concepts and Q&A

    There are plenty of discussions on competitive analysis but I thought I would open a thread to focus a more on just plain providing information and trying to understand Big Y and related capabilities.

    FTDNA founder Bennett Greenspan recently presented at the So. Cal. 2014 Genealogical Society Jamboree. The first 25 minutes or so of this recorded video covers general DNA with particular emphasis on Y DNA SNP mutations and Big Y.
    http://new.livestream.com/wab/scgs-e...ideos/53183447

    He goes on to talk about autosomal DNA too so you might be interested in the whole presentation.

    Here is basic information on Big Y, including ordering information. It is a Next Generation Sequencing (NGS) offering.
    https://www.familytreedna.com/learn/...testing/big-y/

    I was a little queezy (mainly $) on Next Generation Sequencing but now that I understand it I'm a strong advocate, even if you have to pool resources with relatives or surname groups to do it. This test has the potential to identify stable SNP mutations that uniquely identify your surname within your genetic cluster or even branches within your surname. It can also help fit your overall cluster underneath ancient haplogroups.
    Last edited by TigerMW; 06-13-2014 at 01:54 PM.

  2. The Following 3 Users Say Thank You to TigerMW For This Useful Post:

     Geolocke (06-13-2014),  R.Rocca (06-13-2014),  rms2 (06-13-2014)

  3. #2
    Registered Users
    Posts
    532
    Sex
    Location
    England
    Y-DNA (P)
    J1
    mtDNA (M)
    K1a10a

    United States of America England
    What is your opinion of the concept of "junk SNPs"? Specifically, if the BigY Results page shows two matches, one with 200 Shared Novel Variants and the other with 190, should you assume you are more closely related to the first person than to the second?

  4. #3
    Registered Users
    Posts
    4,074
    Sex
    Y-DNA (P)
    R1b
    mtDNA (M)
    H

    Quote Originally Posted by J1 DYS388=13 View Post
    What is your opinion of the concept of "junk SNPs"? Specifically, if the BigY Results page shows two matches, one with 200 Shared Novel Variants and the other with 190, should you assume you are more closely related to the first person than to the second?
    I'm not sure what the terminology is but there are many SNPs that need to be weeded out or treated with caution. I certainly would not make a judgement on who was most closely related to who by small differences in SNP results presented. I view this kind of matching system just like I do for STR (genetic distance) matching. These are primarily useful for finding people and having people "pop out of the woodwork" and find you. Once you've identified a potential match, further investigation is required. This means reviewing the raw results in depth and possibly some Sanger Sequencing (advanced order FTDNA or YSEQ) testing for validation and clarification.
    Last edited by TigerMW; 06-13-2014 at 02:01 PM.

  5. The Following 2 Users Say Thank You to TigerMW For This Useful Post:

     Geolocke (06-13-2014),  Joe B (06-13-2014)

  6. #4
    Gold Class Member
    Posts
    2,718
    Sex

    Quote Originally Posted by Mikewww View Post
    This means reviewing the raw results in depth and possibly some Sanger Sequencing (advanced order FTDNA or YSEQ) testing for validation and clarification.
    I myself heartily encourage my project members to submit their BAM files to YFull ("reviewing the raw results in depth"), but I would not even bring up the notion of further Y-DNA tests (for the Big Y customer himself). For most practical purposes, the Big Y (and even more so FGC) should be the last Y chromosome test any man will ever need, especially when YFull's analysis of SNPs is combined with their extraction of over 400 STRs. I'm sure that among the many people who have superabundant disposable income, a few may wish to spend it on an unending series of Y chromosome tests, but I will not be the one to encourage that.

    Of course, STR matches who cannot afford the Big Y must order individual SNP tests instead; and indeed, that is exactly how SNPs are fully validated (e.g., for incorporation into the ISOGG haplotree without italics).
    Last edited by lgmayka; 06-13-2014 at 02:27 PM.

  7. The Following 3 Users Say Thank You to lgmayka For This Useful Post:

     parasar (06-13-2014),  rivergirl (06-14-2014),  Táltos (06-13-2014)

  8. #5
    Registered Users
    Posts
    532
    Sex
    Location
    England
    Y-DNA (P)
    J1
    mtDNA (M)
    K1a10a

    United States of America England
    OK, so what are we supposed to learn from the new BigY comparison page?

  9. #6
    Gold Class Member
    Posts
    2,718
    Sex

    Quote Originally Posted by J1 DYS388=13 View Post
    OK, so what are we supposed to learn from the new BigY comparison page?
    At the very least, it gives us the email addresses of Big Y customers in the same (or a nearby) clade. I would not take the specific SNP difference counts too seriously, because those SNPs have not been "weeded" (Ken Nordtvedt's term for discarding unreliable or highly recurrent SNPs).

    Here's a suggestion: Send an email to your Big Y matches, suggesting that they submit their BAM files to YFull.

  10. The Following 3 Users Say Thank You to lgmayka For This Useful Post:

     Calamus (06-14-2014),  J1 DYS388=13 (06-13-2014),  TigerMW (06-13-2014)

  11. #7
    Member
    Posts
    73
    Sex
    Y-DNA (P)
    R1b-CTS4299+
    mtDNA (M)
    H2a2a1

    How many of you have Big Y matches whose terminal SNPs differ - in some cases, considerably - from your terminal SNP?

    Stephen
    Administrator, Parrish/Parish, Maxfield, and Wrigley DNA projects (hosted by Family Tree DNA unless otherwise noted)
    Administrator, Maryland regional DNA project and British Quakers DNA project
    Administrator, Early New England Colonists DNA project
    Co-administrator, DF27+ and Subclades and SRY2627+/L176.2+/Z198+ haplogroup DNA projects
    Administrator, Facebook R1b-P312+ haplogroup group

  12. #8
    Registered Users
    Posts
    532
    Sex
    Location
    England
    Y-DNA (P)
    J1
    mtDNA (M)
    K1a10a

    United States of America England
    I have two matches, and they both have different terminal SNPs than mine. Different by one step, one of them officially on the FTDNA tree, the other unofficially by what the project director discovered some time ago.

  13. #9
    Registered Users
    Posts
    4,074
    Sex
    Y-DNA (P)
    R1b
    mtDNA (M)
    H

    Quote Originally Posted by lgmayka View Post
    I myself heartily encourage my project members to submit their BAM files to YFull ("reviewing the raw results in depth"), but I would not even bring up the notion of further Y-DNA tests (for the Big Y customer himself). For most practical purposes, the Big Y (and even more so FGC) should be the last Y chromosome test any man will ever need, especially when YFull's analysis of SNPs is combined with their extraction of over 400 STRs. I'm sure that among the many people who have superabundant disposable income, a few may wish to spend it on an unending series of Y chromosome tests, but I will not be the one to encourage that.

    Of course, STR matches who cannot afford the Big Y must order individual SNP tests instead; and indeed, that is exactly how SNPs are fully validated (e.g., for incorporation into the ISOGG haplotree without italics).
    I've never felt there is was "one and done" benefit from this kind of test. I guess I just believe in new technology and the almost infinite nature of our architecture (DNA). There will always be something "better". Beyond that though, this is all about testing potential distant relatives, clusters, neighboring clusters, distant origin locations, etc. It's a group thing, not an individual thing.

  14. #10
    Registered Users
    Posts
    532
    Sex
    Location
    England
    Y-DNA (P)
    J1
    mtDNA (M)
    K1a10a

    United States of America England
    post deleted
    Last edited by J1 DYS388=13; 06-13-2014 at 07:07 PM.

Page 1 of 2 12 LastLast

Similar Threads

  1. Concepts – Imputation
    By firemonkey in forum Autosomal (auDNA)
    Replies: 22
    Last Post: 04-13-2018, 04:16 AM
  2. V13 updates
    By rafc in forum E1b-M215
    Replies: 1
    Last Post: 11-08-2017, 06:53 PM
  3. Future Updates?
    By mwauthy in forum Geno 2.0
    Replies: 6
    Last Post: 09-22-2017, 03:42 AM
  4. NEW UPDATES
    By Barellalee in forum Ancient (aDNA)
    Replies: 2
    Last Post: 07-31-2017, 11:23 PM
  5. Exciting new updates?
    By firemonkey in forum FTDNA
    Replies: 33
    Last Post: 02-19-2017, 04:42 AM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •