C3c haplogroup


Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Sun Mar 18, 2012 7:33 am
SNP mutation M48 is ancestral to M86 and M77 mutations. So M77 defines haplogroup C3c1 as well as M86.
See paper in RJGG (in Russian):
http://rjgg.org/index.php/RJGGRE/article/view/117

Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Thu Jul 19, 2012 9:50 am
The C3c haplogroup Tree should be revised.

On the Y-chromosome haplogroup C3c classification.
Boris A Malyarchuk, Miroslava Derenko and Galina Denisova.

Abstract
As there are ambiguities in classification of the Y-chromosome haplogroup C3c, relatively frequent in populations of Northern Asia, we analyzed all three haplogroup-defining markers M48, M77 and M86 in C3-M217-individuals from Siberia, Eastern Asia and Eastern Europe. We have found that haplogroup C3c is characterized by the derived state at M48, whereas mutations at both M77 and M86 define subhaplogroup C3c1. The branch defined by M48 alone would belong to subhaplogroup C3c*, characteristic for some populations of Central and Eastern Siberia, such as Koryaks, Evens, Evenks and Yukaghirs. Subhaplogroup C3c* individuals could be considered as remnants of the Neolithic population of Siberia, based on the age of C3c*-short tandem repeat variation amounting to 4.5±2.4 thousand years.

http://www.nature.com/jhg/journal/vaop/ ... 1293a.html

Posts: 7
Joined: Sun Jul 22, 2012 8:57 pm
PostPosted: Sun Jul 22, 2012 9:55 pm
nimissin wrote:The C3c haplogroup Tree should be revised.

On the Y-chromosome haplogroup C3c classification.
Boris A Malyarchuk, Miroslava Derenko and Galina Denisova.

Abstract
As there are ambiguities in classification of the Y-chromosome haplogroup C3c, relatively frequent in populations of Northern Asia, we analyzed all three haplogroup-defining markers M48, M77 and M86 in C3-M217-individuals from Siberia, Eastern Asia and Eastern Europe. We have found that haplogroup C3c is characterized by the derived state at M48, whereas mutations at both M77 and M86 define subhaplogroup C3c1. The branch defined by M48 alone would belong to subhaplogroup C3c*, characteristic for some populations of Central and Eastern Siberia, such as Koryaks, Evens, Evenks and Yukaghirs. Subhaplogroup C3c* individuals could be considered as remnants of the Neolithic population of Siberia, based on the age of C3c*-short tandem repeat variation amounting to 4.5±2.4 thousand years.

http://www.nature.com/jhg/journal/vaop/ ... 1293a.html


Thanks for this article. The Supplementary Material helped me to identify the probable SNPs that define some common Mongol haplotypes I extracted from SMGF.org that I entered to Ysearch under User ID XGVGJ and 43XUD. The first is most likely C3c1 and the second is likely C3*.
Kathy

Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Tue Jul 24, 2012 8:54 am
Kathy Johnston wrote:Thanks for this article. The Supplementary Material helped me to identify the probable SNPs that define some common Mongol haplotypes I extracted from SMGF.org that I entered to Ysearch under User ID XGVGJ and 43XUD. The first is most likely C3c1 and the second is likely C3*.
Kathy

You are right.
The XGVGJ with duplication 16/17 in DYS19 is obviously C3c1-M77,M86.
The 43XUD sample belongs to C3* starcluster.

Posts: 7
Joined: Sun Jul 22, 2012 8:57 pm
PostPosted: Wed Jul 25, 2012 5:37 am
Someone needs to add all these C Haplogroup haplotypes to the haplogroup predictors. Those with limited STR results from Central Asia often are classified incorrectly when they enter their STR results at Whit Athey's predictor or the predictor here at this web site. Maybe that is because we have had limited data from Central Asia to work with until now.

Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Thu Jan 31, 2013 7:58 am
Preliminary WTY results from Kazakh DNA Project participant (С3с-M48, kit 206676). Seven novel snips detected:

L1367 5646590 T -> C
L1368 12178192 A -> C
L1369 12178195 A -> C
L1370 13534634 A -> G
L1371 13689497-13689499 GTT -> del
L1372 14177318 G -> T
L1373 21120980 A -> G

Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Wed Jan 29, 2014 9:46 am
New snips are detected in Lippold et al (2014) Bam files (GRCh37/hg19):

8 395 838 C -> T
8 480 384 G -> A
8 592 725 A -> G
15 043 282 A -> T
17 673 490 A -> G
21 053 145 A -> T
21 760 973 A -> T

Derived states are in all the C3c1-M77,M86 samples HGDP 01204, 01206, 01208, 01247, 01250, 01302.
Ancestral alleles are in two C3-starcluster samples HGDP 01205, 01230.

Posts: 59
Joined: Fri Mar 16, 2012 12:14 pm
PostPosted: Sat Feb 22, 2014 4:22 am
nimissin wrote:New snips are detected in Lippold et al (2014) Bam files (GRCh37/hg19):

8 395 838 C -> T
8 480 384 G -> A
8 592 725 A -> G
15 043 282 A -> T
17 673 490 A -> G
21 053 145 A -> T
21 760 973 A -> T

Derived states are in all the C3c1-M77,M86 samples HGDP 01204, 01206, 01208, 01247, 01250, 01302.
Ancestral alleles are in two C3-starcluster samples HGDP 01205, 01230.

hi nimissin,where can find the Bam files?

Posts: 34
Joined: Thu Mar 15, 2012 3:54 am
PostPosted: Sun Feb 23, 2014 12:09 am
Look at
http://www.ebi.ac.uk/ena/

From Lippold et al (2014):
The NRY raw data are in the European Nucleotide Archive
(ENA) (http://www.ebi.ac.uk/ena/ home) with the study accession number
PRJEB4417 (sample accession numbers ERS333252-ERS333873).

Posts: 59
Joined: Fri Mar 16, 2012 12:14 pm
PostPosted: Sun Feb 23, 2014 3:38 pm
Thank you.

Return to C Haplogroup (Y-DNA)

Who is online

Users browsing this forum: No registered users and 2 guests