Hi, Ian. The PNAS early-release paper yesterday regarding detected biparental inheritance of mtDNA (http://www.pnas.org/content/early/2018/11/21/1810946115) made me think back a few weeks to a post of yours that indicated only about one mtDNA sequence in 500 that comes into GenBank is recognizable by its having any special feature. I looked at GenBank's statistics but I'm not certain I can differentiate the number of fully-sequenced mtDNA results on file. Do you have that number on the top of your head? Don't look it up, please; just a very informal guesstimate for personal curiosity, and I won't quote you on it. :-) Just wondering, really, about Taosheng Huang's estimate that biparental mtDNA may be present in as many as 1 in every 5,000 people. With the huge spike that began in 2003 of WGS tests cataloged at GenBank (from what I gather: 593,801 in Aug 2003 to 722,438,528 as of last 15 Oct), it just seems like such significant heteroplasmy would have been detected by now if 1:5,000 was a possible ratio. Thanks, Ian! -----Original Message----- Date: Tue, 27 Nov 2018 10:55:55 +0000 From: Ian Logan <ianlogan22@btinternet.com> Subject: [DNA] New mtDNA sequences from Viet Nam on the GenBank database (1 of 25) List A set of over 600 mtDNA sequences from Viet Nam has appeared on the GenBank database. They accompany the paper: Sci Rep. 2018 Aug 3;8(1):11651. 'Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia' Duong NT, Macholdt E, et al. ...

GenBank has many records apart from mtDNA whole genome sequences. About 46,000 of those are mtDNA. What we would expect to see is an unusually high number of heteroplasmic sites (coded with a letter other than A, C, G, or T. I'll ponder a method to detect this in my personal database of sequences if Ian hasn't already checked this. Ann Turner On Tue, Nov 27, 2018 at 8:40 AM H W <hughes_williams@hotmail.com> wrote: > Hi, Ian. The PNAS early-release paper yesterday regarding detected > biparental inheritance of mtDNA ( > http://www.pnas.org/content/early/2018/11/21/1810946115) made me think > back a few weeks to a post of yours that indicated only about one mtDNA > sequence in 500 that comes into GenBank is recognizable by its having any > special feature. > > I looked at GenBank's statistics but I'm not certain I can differentiate > the number of fully-sequenced mtDNA results on file. Do you have that > number on the top of your head? Don't look it up, please; just a very > informal guesstimate for personal curiosity, and I won't quote you on it. > :-) > > Just wondering, really, about Taosheng Huang's estimate that biparental > mtDNA may be present in as many as 1 in every 5,000 people. With the huge > spike that began in 2003 of WGS tests cataloged at GenBank (from what I > gather: 593,801 in Aug 2003 to 722,438,528 as of last 15 Oct), it just > seems like such significant heteroplasmy would have been detected by now if > 1:5,000 was a possible ratio. > > Thanks, Ian! > > -----Original Message----- > Date: Tue, 27 Nov 2018 10:55:55 +0000 > From: Ian Logan <ianlogan22@btinternet.com> > Subject: [DNA] New mtDNA sequences from Viet Nam on the GenBank > database (1 of 25) > > List > > A set of over 600 mtDNA sequences from Viet Nam has appeared on the > GenBank database. They accompany the paper: > > Sci Rep. 2018 Aug 3;8(1):11651. 'Complete human mtDNA genome sequences > from Vietnam and the phylogeography of Mainland Southeast Asia' Duong NT, > Macholdt E, et al. > ... > > > _______________________________________________ > Email preferences: http://bit.ly/rootswebpref > Unsubscribe > https://lists.rootsweb.com/postorius/lists/genealogy-dna@rootsweb.com > Privacy Statement: https://ancstry.me/2JWBOdY Terms and Conditions: > https://ancstry.me/2HDBym9 > Rootsweb Blog: http://rootsweb.blog > RootsWeb is funded and supported by Ancestry.com and our loyal RootsWeb > community >

I believe there was an article using chickens a few years ago that looked into this. http://rsbl.royalsocietypublishing.org/content/11/10/20150561 On Tue, Nov 27, 2018 at 10:55 AM Ann Turner <dnacousins@gmail.com> wrote: > GenBank has many records apart from mtDNA whole genome sequences. About > 46,000 of those are mtDNA. What we would expect to see is an unusually high > number of heteroplasmic sites (coded with a letter other than A, C, G, or > T. I'll ponder a method to detect this in my personal database of sequences > if Ian hasn't already checked this. > > Ann Turner > > On Tue, Nov 27, 2018 at 8:40 AM H W <hughes_williams@hotmail.com> wrote: > > > Hi, Ian. The PNAS early-release paper yesterday regarding detected > > biparental inheritance of mtDNA ( > > http://www.pnas.org/content/early/2018/11/21/1810946115) made me think > > back a few weeks to a post of yours that indicated only about one mtDNA > > sequence in 500 that comes into GenBank is recognizable by its having any > > special feature. > > > > I looked at GenBank's statistics but I'm not certain I can differentiate > > the number of fully-sequenced mtDNA results on file. Do you have that > > number on the top of your head? Don't look it up, please; just a very > > informal guesstimate for personal curiosity, and I won't quote you on it. > > :-) > > > > Just wondering, really, about Taosheng Huang's estimate that biparental > > mtDNA may be present in as many as 1 in every 5,000 people. With the huge > > spike that began in 2003 of WGS tests cataloged at GenBank (from what I > > gather: 593,801 in Aug 2003 to 722,438,528 as of last 15 Oct), it just > > seems like such significant heteroplasmy would have been detected by now > if > > 1:5,000 was a possible ratio. > > > > Thanks, Ian! > > > > -----Original Message----- > > Date: Tue, 27 Nov 2018 10:55:55 +0000 > > From: Ian Logan <ianlogan22@btinternet.com> > > Subject: [DNA] New mtDNA sequences from Viet Nam on the GenBank > > database (1 of 25) > > > > List > > > > A set of over 600 mtDNA sequences from Viet Nam has appeared on the > > GenBank database. They accompany the paper: > > > > Sci Rep. 2018 Aug 3;8(1):11651. 'Complete human mtDNA genome sequences > > from Vietnam and the phylogeography of Mainland Southeast Asia' Duong NT, > > Macholdt E, et al. > > ... > > > > > > _______________________________________________ > > Email preferences: http://bit.ly/rootswebpref > > Unsubscribe > > https://lists.rootsweb.com/postorius/lists/genealogy-dna@rootsweb.com > > Privacy Statement: https://ancstry.me/2JWBOdY Terms and Conditions: > > https://ancstry.me/2HDBym9 > > Rootsweb Blog: http://rootsweb.blog > > RootsWeb is funded and supported by Ancestry.com and our loyal RootsWeb > > community > > > > _______________________________________________ > Email preferences: http://bit.ly/rootswebpref > Unsubscribe > https://lists.rootsweb.com/postorius/lists/genealogy-dna@rootsweb.com > Privacy Statement: https://ancstry.me/2JWBOdY Terms and Conditions: > https://ancstry.me/2HDBym9 > Rootsweb Blog: http://rootsweb.blog > RootsWeb is funded and supported by Ancestry.com and our loyal RootsWeb > community > -- --- Regards, Rebekah A. Canada Volunteer Administrator, Family Tree DNA <https://affiliate.familytreedna.com/idevaffiliate.php?id=598> Author, Haplogroup <https://haplogroup.org> -- PRIVILEGED & CONFIDENTIAL COMMUNICATION -- This communication is privileged and contains confidential information. If it has been sent to you in error, please disregard, reply to the sender that you received it in error, and delete it. Any distribution or other reproduction is strictly prohibited.

I figured out a way to count heteroplasmic sequences in my spreadsheet of GenBank sequences. The overall rate is about 5%, mostly at one site with a few at two or three sites. Four sequences were clearly outliers in the number of heteroplasmic sites EF446784: 21 EF488201: 23 KX467286: 13 KX467324: 20 If you want to look these up, follow this model for a query: https://www.ncbi.nlm.nih.gov/nuccore/EF446784 The first two were the only sequences submitted by a group in Indonesia and are clearly contaminated, as many of the same sites were heteroplasmic. The second two were part of a large number of sequences from India. They did not accompany a publication, so it's unknown whether they addressed the issue. So two out of 46,000 are candidates for further investigation. Ann Turner On Tue, Nov 27, 2018 at 8:55 AM Ann Turner <dnacousins@gmail.com> wrote: > GenBank has many records apart from mtDNA whole genome sequences. About > 46,000 of those are mtDNA. What we would expect to see is an unusually high > number of heteroplasmic sites (coded with a letter other than A, C, G, or > T. I'll ponder a method to detect this in my personal database of sequences > if Ian hasn't already checked this. > > Ann Turner > > On Tue, Nov 27, 2018 at 8:40 AM H W <hughes_williams@hotmail.com> wrote: > >> Hi, Ian. The PNAS early-release paper yesterday regarding detected >> biparental inheritance of mtDNA ( >> http://www.pnas.org/content/early/2018/11/21/1810946115) made me think >> back a few weeks to a post of yours that indicated only about one mtDNA >> sequence in 500 that comes into GenBank is recognizable by its having any >> special feature. >> >> I looked at GenBank's statistics but I'm not certain I can differentiate >> the number of fully-sequenced mtDNA results on file. Do you have that >> number on the top of your head? Don't look it up, please; just a very >> informal guesstimate for personal curiosity, and I won't quote you on it. >> :-) >> >> Just wondering, really, about Taosheng Huang's estimate that biparental >> mtDNA may be present in as many as 1 in every 5,000 people. With the huge >> spike that began in 2003 of WGS tests cataloged at GenBank (from what I >> gather: 593,801 in Aug 2003 to 722,438,528 as of last 15 Oct), it just >> seems like such significant heteroplasmy would have been detected by now if >> 1:5,000 was a possible ratio. >> >> Thanks, Ian! >> >> -----Original Message----- >> Date: Tue, 27 Nov 2018 10:55:55 +0000 >> From: Ian Logan <ianlogan22@btinternet.com> >> Subject: [DNA] New mtDNA sequences from Viet Nam on the GenBank >> database (1 of 25) >> >> List >> >> A set of over 600 mtDNA sequences from Viet Nam has appeared on the >> GenBank database. They accompany the paper: >> >> Sci Rep. 2018 Aug 3;8(1):11651. 'Complete human mtDNA genome sequences >> from Vietnam and the phylogeography of Mainland Southeast Asia' Duong NT, >> Macholdt E, et al. >> ... >> >> >> _______________________________________________ >> Email preferences: http://bit.ly/rootswebpref >> Unsubscribe >> https://lists.rootsweb.com/postorius/lists/genealogy-dna@rootsweb.com >> Privacy Statement: https://ancstry.me/2JWBOdY Terms and Conditions: >> https://ancstry.me/2HDBym9 >> Rootsweb Blog: http://rootsweb.blog >> RootsWeb is funded and supported by Ancestry.com and our loyal RootsWeb >> community >> >

Ann I haven't seen the actual paper - so I cannot comment fully. But here are my thoughts about a couple of the points. There are 46,234 complete mtDNA seqences on the GenBank database using the search  - "homo sapiens" [organism] "complete genome" mitochondrion (of which about 1,000 are duplicates). Heteroplasmy occurs in very few sequences - and most times when it occurs it is in very predictable places. For example: T152Y is reported 54 times and T16093Y is reported 154 times. And when heteroplasmy is found in a coding region bases, it is often seen to be preamble to a full mutation appearing in the next generation. So overall, when heteroplasmy is reported, there does not appear to be any real significance to the finding. Ann mentions 4 particular sequences; and these are clearly the results of poor sequencing. What therefore is being reported by the Chinese researchers in their paper ? Especially when the paper appears to have the approval of Douglas C. Wallace. Is this paternal transmission ? Or is it transgenerational transmission ? I am actually not against 'transgenerational transmission' as I have been trying to collect data about 'polycythemia vera'; and in this disease I think there might be unusual features in the mtDNA. It would be interesting to know if FTDNA has ever found any 'mixed' sequences. Their tally today is 154,965 FGS tests ! Ian ------------------------------------------------------------------------------------------------------------------------------- On 28/11/2018 04:01, Ann Turner wrote: > I figured out a way to count heteroplasmic sequences in my spreadsheet of > GenBank sequences. The overall rate is about 5%, mostly at one site with a > few at two or three sites. Four sequences were clearly outliers in the > number of heteroplasmic sites > > EF446784: 21 > EF488201: 23 > KX467286: 13 > KX467324: 20 > > If you want to look these up, follow this model for a query: > > https://www.ncbi.nlm.nih.gov/nuccore/EF446784 > > The first two were the only sequences submitted by a group in Indonesia and > are clearly contaminated, as many of the same sites were heteroplasmic. > > The second two were part of a large number of sequences from India. They > did not accompany a publication, so it's unknown whether they addressed the > issue. > > So two out of 46,000 are candidates for further investigation. > > Ann Turner > > On Tue, Nov 27, 2018 at 8:55 AM Ann Turner <dnacousins@gmail.com> wrote: > >> GenBank has many records apart from mtDNA whole genome sequences. About >> 46,000 of those are mtDNA. What we would expect to see is an unusually high >> number of heteroplasmic sites (coded with a letter other than A, C, G, or >> T. I'll ponder a method to detect this in my personal database of sequences >> if Ian hasn't already checked this. >> >> Ann Turner >> >> On Tue, Nov 27, 2018 at 8:40 AM H W <hughes_williams@hotmail.com> wrote: >> >>> Hi, Ian. The PNAS early-release paper yesterday regarding detected >>> biparental inheritance of mtDNA ( >>> http://www.pnas.org/content/early/2018/11/21/1810946115) made me think >>> back a few weeks to a post of yours that indicated only about one mtDNA >>> sequence in 500 that comes into GenBank is recognizable by its having any >>> special feature.