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Thread: Big Y-700

  1. #61
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    U7a3a-C15433T

    England United Kingdom India India Punjab
    Quote Originally Posted by JamesKane View Post
    In comparing Dante's 30x WGS vs Y Elite the important question is do you want 150bp reads or the results of your autosomal DNA? There's no difference when it comes to SNP detection. Longer INDELs like STRs would be expected to be less accurate with Dante's shorter reads. The papers I've seen on the BGI technologies give a slight edge to Illumina machines for accuracy.

    Keep in mind Dante's results are just raw data. There isn't any analysis of note, so you'd be sending the BAM to someone to make sense of.

    As usual... check the call summary I maintain here: https://haplogroup-r.org/stats.html The Dante result set is limited and indications are they are all at least 40x coverage. This makes their coverage stats a bit more inflated compared with the Illumina based WGS samples.
    I've tested with FTDNA and MyHeritage, whose files are accurate enough for ancestry, so ancestry isn't really a priority for me in that regard. I've picked up a recent interest in WGS specifically for health reasons, so a whole genome sequence would be appreciated there, as knowledge of any bad mutations I have will allow me to adjust my lifestyle accordingly as a preventative measure. There may be better value tests for this though, so WGS for this purpose may be overkill perhaps? There are chip genotyping services out there who mainly search for medically relevant SNPs, so that's another option for me if I choose to go with FGC Y Elite. I would appreciate feedback from anyone telling me what the best option is for me, from a medical perspective?

    I'm mainly interested in Y-SNP's as oppose to Y-STR's at the moment. I'm not interesting in finding others with my surname, but I am very interested in finding subclade Y-DNA matches from different ethnic groups/castes in NW South Asia and I'm guessing SNP's are more suitable for this. I'm not looking for very close matches (<500 years).

    Nonetheless, do you have a rough idea of the difference between the number of discovered STR's between Y Elite and Dante? I know the former usually finds around 600+ Y-STR's as far as I know at least. If Dante Labs could discover at least 500 Y-STR's then that would be nice.

    Analysis isn't much of a concern for me. I intend to upload my .BAM file to YFull once I receive my results.

    I looked at the link you provided and the results from Dante look promising, until you look at the sample count! As the sample size increases, I have no idea what will happen to the CV percentage. I wouldn't write off Dante Labs based on that though. Their problems are mainly related to wait times from what I've seen, but their results appear to be the real deal.

    Sorry for dishing out yet more questions, and thank you for all the help you've given me so far! You've been very informative here!
    FATHER:

    Y-DNA (ISOGG 2019): R2a2b1b2a1a1-Y1383*
    (Y154917-)

    mtDNA: M5a1a


    MATERNAL UNCLE:

    Y-DNA (ISOGG 2019): R1b1a1b1b3a-Z2109

    mtDNA: U7a3a-C15433T


    Other Y-DNA lines:

    MATERNAL GRANDMOTHER'S MOTHER: R1a1a1b2a1a2c-Y7

  2. #62
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    Quote Originally Posted by aaronbee2010 View Post
    I've tested with FTDNA and MyHeritage, whose files are accurate enough for ancestry, so ancestry isn't really a priority for me in that regard. I've picked up a recent interest in WGS specifically for health reasons, so a whole genome sequence would be appreciated there, as knowledge of any bad mutations I have will allow me to adjust my lifestyle accordingly as a preventative measure. There may be better value tests for this though, so WGS for this purpose may be overkill perhaps? There are chip genotyping services out there who mainly search for medically relevant SNPs, so that's another option for me if I choose to go with FGC Y Elite. I would appreciate feedback from anyone telling me what the best option is for me, from a medical perspective?

    I'm mainly interested in Y-SNP's as oppose to Y-STR's at the moment. I'm not interesting in finding others with my surname, but I am very interested in finding subclade Y-DNA matches from different ethnic groups/castes in NW South Asia and I'm guessing SNP's are more suitable for this. I'm not looking for very close matches (<500 years).

    Nonetheless, do you have a rough idea of the difference between the number of discovered STR's between Y Elite and Dante? I know the former usually finds around 600+ Y-STR's as far as I know at least. If Dante Labs could discover at least 500 Y-STR's then that would be nice.

    Analysis isn't much of a concern for me. I intend to upload my .BAM file to YFull once I receive my results.

    I looked at the link you provided and the results from Dante look promising, until you look at the sample count! As the sample size increases, I have no idea what will happen to the CV percentage. I wouldn't write off Dante Labs based on that though. Their problems are mainly related to wait times from what I've seen, but their results appear to be the real deal.

    Sorry for dishing out yet more questions, and thank you for all the help you've given me so far! You've been very informative here!
    You can always run the chip based test output through Promethease and its like, if you haven't yet. You probably could argue that is better value in terms of medically informative SNPs per buck but if some breakthrough next week finds a load more useful SNPs you won't have them, whereas with a WGS you will.

    The problem I found when I started trying to analyse my first WGS test is there are just so many SNPs to look at. There was one disease I was interested and I found a research site all about it and they listed about 300 relevant SNPs. :-(
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

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     aaronbee2010 (02-07-2019)

  4. #63
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    U7a3a-C15433T

    England United Kingdom India India Punjab
    Quote Originally Posted by MacUalraig View Post
    You can always run the chip based test output through Promethease and its like, if you haven't yet. You probably could argue that is better value in terms of medically informative SNPs per buck but if some breakthrough next week finds a load more useful SNPs you won't have them, whereas with a WGS you will.
    I've run my 23andMe raw data through Promethease because I found out about Promethease shortly before upgrading my 23andMe to include health reports. Promethease is a cheaper service, and it's a lot more comprehensive, so I guess I dodged a bullet there!

    The only thing with 23andMe is that I don't feel it looks at enough health-related SNP's, which is completely understandable as it also looks at ancestry-related SNP's too. I would be open to another genotyping service that looks at medically relevant SNP's, or even a WGS if the price difference is small enough. WGS will definitely be the way to go in the future, but even now it's still a good option.

    I feel like WGS has become very prominent very recently, so the no. of medically informative SNP's per unit currency is set to skyrocket, to the point where it starts to get surprisingly close to genotyping services. Even if that wasn't the case, WGS is a lot more handy because as more medically-relevant SNP's are gradually discovered over a given amount of time, you don't have to worry one bit.

    With a genotyping service, the company would need to occasionally update their chip configurations as new medically relevant SNP's are discovered and older test users would need to get another test done, whereas a WGS user is set for life, just like you said! So you could say that the difference in no. of SNP's per buck is more than justified.

    If Dante Labs have another Black Friday offer then the price difference will be completely offset by the massive increase in genetic information you get. The only thing is was that they probably lost money on each customer because their price was so low, so I'm worried they might not do an offer like that again. The regret is real!

    Quote Originally Posted by MacUalraig View Post
    The problem I found when I started trying to analyse my first WGS test is there are just so many SNPs to look at. There was one disease I was interested and I found a research site all about it and they listed about 300 relevant SNPs. :-(
    First world problems summed up quite nicely there!
    FATHER:

    Y-DNA (ISOGG 2019): R2a2b1b2a1a1-Y1383*
    (Y154917-)

    mtDNA: M5a1a


    MATERNAL UNCLE:

    Y-DNA (ISOGG 2019): R1b1a1b1b3a-Z2109

    mtDNA: U7a3a-C15433T


    Other Y-DNA lines:

    MATERNAL GRANDMOTHER'S MOTHER: R1a1a1b2a1a2c-Y7

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     MacUalraig (02-08-2019)

  6. #64
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    Ireland England Netherlands Germany France
    Keeping these brief as we are drifting well away from the topic. Perhaps we should start something in the Other group, if more followup is needed.

    Quote Originally Posted by aaronbee2010 View Post
    I would appreciate feedback from anyone telling me what the best option is for me, from a medical perspective?
    30x WGS is the minimum recommended coverage for medical purposes that has been bandied about. For true medical diagnostics, there was a paper recommending 300x. So in those applications you'd be looking at just the exome or a very expensive test.

    Quote Originally Posted by aaronbee2010 View Post
    Nonetheless, do you have a rough idea of the difference between the number of discovered STR's between Y Elite and Dante?
    I am able to get about 5,000 STRs using HipSTR and Willem's reference BED with either of these tests, but really haven't looked at the data set enough to judge accuracy.

    Quote Originally Posted by aaronbee2010 View Post
    I looked at the link you provided and the results from Dante look promising, until you look at the sample count! As the sample size increases, I have no idea what will happen to the CV percentage. I wouldn't write off Dante Labs based on that though. Their problems are mainly related to wait times from what I've seen, but their results appear to be the real deal.
    I wouldn't expect the coefficient of variance to change dramatically unless they start running the test to advertised specifications. As noted before they are actually delivering 40x coverage. The big caveat is you need to be prepared to wait a year to see the BAM.

  7. The Following User Says Thank You to JamesKane For This Useful Post:

     aaronbee2010 (02-08-2019)

  8. #65
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    Today was supposed to be the release date of Big Y-700 kits ordered before November 1st. Anyone have any insight to share on the changes?

  9. The Following 2 Users Say Thank You to mwauthy For This Useful Post:

     aaronbee2010 (02-09-2019),  lgmayka (02-10-2019)

  10. #66
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    H20

    Portugal 1143 Portugal 1485 Portugal Order of Christ
    I was waiting for my Big Y-500 and it now says Big Y-700. Maybe it was upgraded?
    YDNA - E-Y31991>PF4428. Domingos Rodrigues, b. circa 1680 Hidden Content , Viana do Castelo, Portugal
    mtDNA - H20. Maria Josefa de Almeida, b. circa 1750 Hidden Content , Porto, Portugal

    Global25 PCA plot Hidden Content ; Western Europe-only Hidden Content
    Hidden Content

    [1] "distance%=2.2305"

    Ruderico

    Hallstatt_Bylany,43.4
    Iberia_BA,34.4
    Roman_Collegno_o1,18.4
    Iberomaurusian,3.8

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     aaronbee2010 (02-09-2019)

  12. #67
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    Quote Originally Posted by Ruderico View Post
    I was waiting for my Big Y-500 and it now says Big Y-700. Maybe it was upgraded?
    When did you order your Big Y-500 test?

  13. #68
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    Lisbon, Portugal
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    Nationality
    Portuguese
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    E-Y31991 > PF4428
    mtDNA
    H20

    Portugal 1143 Portugal 1485 Portugal Order of Christ
    Early December, like the 4th
    YDNA - E-Y31991>PF4428. Domingos Rodrigues, b. circa 1680 Hidden Content , Viana do Castelo, Portugal
    mtDNA - H20. Maria Josefa de Almeida, b. circa 1750 Hidden Content , Porto, Portugal

    Global25 PCA plot Hidden Content ; Western Europe-only Hidden Content
    Hidden Content

    [1] "distance%=2.2305"

    Ruderico

    Hallstatt_Bylany,43.4
    Iberia_BA,34.4
    Roman_Collegno_o1,18.4
    Iberomaurusian,3.8

  14. #69
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    Ireland
    Quote Originally Posted by Ruderico View Post
    Early December, like the 4th
    You'll be getting Big Y-700. FTDNA have already announced this:
    Who gets the automatic upgrade to Big Y-700?
    All customers who placed Big Y-500 orders on or after Nov 1st, 2018
    All customers who placed Big Y-500 orders prior to Nov 1st, 2018 and have not yet received results
    Ancestry: Ireland (Roscommon, Galway, Mayo)
    Paternal ancestor (Y): Kelly b. c1830 in Co. Roscommon
    Father's mtDNA: Fleming b. c1831 in Co. Roscommon (H27e)
    Maternal ancestor (mt): McDermott b. c1814 in Co. Roscommon
    Paternal great grandfather (mt): Connella b. c1798 in Co. Roscommon (T2a1a8)

  15. #70
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    I1 Z138+ A6397+
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    J1c2t

    France Italy Two Sicilies England North of England Sweden Skåne
    I think that in this moment of transition there is a bit of confusion in FTDNA.
    I ordered B Y500 on 11/15/2018 and bached 19.11.2018 (916). After several
    changes from B y500 to B y700 and delivery from 11.02.19 to 25.02.19 now
    FTDNA no longer indicates the delivery date. I contacted FTDNA to have
    information and he replied that delivery could arrive by March 6.
    I understand the situation but this confusion for changes and difficulties, I hope
    that is only momentary !

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     mattassis (02-12-2019)

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