Geno 2.0 Y-SNPs

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Posts: 77
Joined: Sat Sep 22, 2012 8:06 pm
Location: Nuevo México
YDNA:
N-L1034
MtDNA:
H4a1*
PostPosted: Thu Nov 22, 2012 5:53 am
In case anyone is interested, I looked through the data from here and found which SNPs from haplogroups N, NO, K(xLT), K, and IJK are and aren't included on the chip.

On the chip
L15, L16, L178, L380, L392, L395, L549, L550, L551, L591, L648, L665, L708, L709, L710, L711, L727, L728, L731, L732, L733, M178, M214, M231, M526, P119, P128, P131, P132, P188, P192, P193, P194, P195, P21_1, P298, P63, P67_1, PAGES00056, Tat

Not on the chip
L1022, L1023, L1025, L1026, L1027, L1032, L1033, L1034, L149.2, L220.2, L224, L225, L248, L316, L548, L58, L593_1, L593_2, L646, L666, L729, L730, L839, LLY22g.1_1, LLY22g.1_2, LLy22g.2_1, LLy22g.2_2, M128, M9, P105, P189.2, P21_2, P21_3, P43, P67_2, P67_3, V161, VL29, VL32, VL33, Z1925, Z1935, Z1936, Z1940, Z1941
963RX: N-L1034 | H4a1*
AEYC6: I-M423 | U5b2b2
¡A la máquina!

N-Z1936 Project
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Posts: 69
Joined: Wed Mar 14, 2012 1:39 pm
PostPosted: Thu Nov 22, 2012 11:05 am
Y SNP class / amount
-----------------------------
CTS 3326
DF 5
F 3016
IMS 3
L 571
M 276
N 3
P 207
PAGE 61
PF 4064
PK 4
s 4
SRY 1
TAT 1
U 18
V 132
YSC 188
Z 563
Last edited by napobo3 on Thu Nov 22, 2012 2:06 pm, edited 3 times in total.
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Posts: 96
Joined: Wed Mar 14, 2012 5:39 pm

YDNA:
N1c1-L1022
MtDNA:
T2b7a1
PostPosted: Thu Nov 22, 2012 11:11 am
Not that entertaining reading, at least L550 is on the list . To bad with the exclusion of L666, L729 and L839.

We have put our hopes to the Chinese. I think this is the abstract that brought the F-serie of SNPs. Probably not that intresting for us L1026+, though.

Paleolithic human migrations in East Eurasia by sequencing Y chromosomes. S. Yan1,2, C. C. Wang1, L. Jin1,2 1) MOE Key Lab of Contemporary Anthorpology, Fudan University, Shanghai, China; 2) Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.

Paleolithic human migrations in East Eurasia remains largely unknown due to the lack of sufficient markers derived from the mutations that occurred during that time frame. To tackle this problem, using the sequence capturing, barcoding technology and next-generation sequencing, we identified more than 4,000 new SNPs encompassing most single copy non-recombining region of human Y chromosome. New clades for haplogroups O, C, N, D, and Q could be geographically located. Especially, a few star-like expansions were unveiled, showing strong population growth. The phylogeny of Haplogroup N was radically rearranged, and all the N individuals could now be categorized into either a northern clade N1 or southern clade N2, revealing a Paleolithic migratory routes of the ancestors of Uralic speaking populations. Haplogroup C, especially the East Eurasia-dominant clade C3, could also be separated into at least two ancient clades, suggesting Paleolithic migrations in East Asia. Three major clades under O, M117+, M134xM117, and 002611+, each could be now further classified into several subclades. With these new findings, we proposed the modified the routes and dates for human populations’ migration, especially those in Paleolithic time. A few Y-chromosomal expansions could now be linked to certain prehistoric cultures or ancestors of language families.

You may contact the first author (during and after the meeting) at yanshi@picb.ac.cn

Posts: 43
Joined: Fri Apr 20, 2012 10:24 pm

MtDNA:
H24
PostPosted: Thu Nov 22, 2012 11:49 am
napobo3 wrote:Y SNP class / amount
-----------------------------
CTS 3326
DF 5
F 3016
IMS 3
L 571
M 279
N 3
P 4336
PAGE 51
PF 4064
PK 4
s 4
SRY 1
TAT 1
U 18
V 132
YSC 188
Z 563

I recognize some but not all of the prefixes. Can anyone flesh out this list?
User avatar
Posts: 77
Joined: Sat Sep 22, 2012 8:06 pm
Location: Nuevo México
YDNA:
N-L1034
MtDNA:
H4a1*
PostPosted: Thu Nov 22, 2012 5:16 pm
• 3326 CTS :?:
• 5 DF (Anonymous researcher)
• 3011 F (Fudan University, Shanghai) :?:
• 3 IMS-JST Institute of Medical Science, Tokyo; Japan Science and Technology Agency
• 571 L (Thomas Krahn)
• 274 M (Stanford)
• 2 MEH (microsomal epoxide hydrolase) :?:
• 3 N (Institute of Biophysics, Beijing)
• 207 P (U of A)
• 61 PAGE (Whitehead Institute, MIT)
• 4064 PF :?:
• 4 PK (Biomedical and Genetic Engineering Laboratories, Islamabad)
• 4 s (Edinburgh University) :?:
• 1 SRY (sex-determining region Y)
• 1 TAT (No idea where the name "Tat" comes from, but of course this is also called M46 and Page70.) :?:
• 18 U (UCF)
• 132 V (Sapienza, Rome)
• 188 YSC :?:
• 563 Z (G. Magoon, Richard Rocca, David F. Reynolds, Bonnie Schrack, Peter M. Op den Velde Boots, Ray H. Banks, Thomas Krahn, and various anonymous and independent researchers)

12438 total
963RX: N-L1034 | H4a1*
AEYC6: I-M423 | U5b2b2
¡A la máquina!

N-Z1936 Project

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Thu Nov 22, 2012 11:45 pm
CTS is believed to be Chris Tyler-Smith, associate of Spencer Wells, who trawled the 1K genome project for SNPs.

PF are believed to be the initials of Paolo Francalacci, the guy who provided Sardinian SNPs.
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.
User avatar
Posts: 77
Joined: Sat Sep 22, 2012 8:06 pm
Location: Nuevo México
YDNA:
N-L1034
MtDNA:
H4a1*
PostPosted: Fri Nov 23, 2012 8:13 pm
I'm curious if any of these CTS, F, and PF markers will be useful to us. They comprise 83.6 percent of the total Y-SNPs tested, so I would hope that at least some of them are specific to haplogroup N.
963RX: N-L1034 | H4a1*
AEYC6: I-M423 | U5b2b2
¡A la máquina!

N-Z1936 Project

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Sat Nov 24, 2012 7:09 am
AJRLegits wrote:I'm curious if any of these CTS, F, and PF markers will be useful to us. They comprise 83.6 percent of the total Y-SNPs tested, so I would hope that at least some of them are specific to haplogroup N.


We won't know much about any of these "new" SNPs until they are placed on the haplotree.

The CTS series is believed to be a second mining of the 1000 Genomes Project DNA. Information about the sample populations can be found here:

http://www.1000genomes.org/about

The F series is believed to be a set of East Asian SNPs, and PF Sardinian SNPs. They are probably too far south for N?
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.

Posts: 228
Joined: Wed Mar 14, 2012 4:16 pm
Location: Kangastan
YDNA:
N-L1034
MtDNA:
B5a1a
PostPosted: Sat Nov 24, 2012 1:11 pm
GTC wrote:The F series is believed to be a set of East Asian SNPs... ...They are probably too far south for N?

In private conversation Chinese researcher says that Chinese N1c1 are a way far of any other N1c1. And estimated number of N1c1 in China is a few tens of millions people.
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Posts: 71
Joined: Tue Jun 12, 2012 5:57 pm

YDNA:
R-L627
PostPosted: Sat Nov 24, 2012 4:07 pm
1386 of the 2159 SNP names listed in the ISOGG SNP Index are in the Geno 2.0 Y-SNP list.
https://dl.dropbox.com/u/92587284/ISOGG ... no_2.0.xls

‎924 SNPs (L, M, P, PAGES, V, YSC, and Z) listed in Geno 2.0 that are not in the ISOGG SNP Index.
https://dl.dropbox.com/u/92587284/Geno- ... _ISOGG.xls

No information available at this point on 10000+ of the 12438 SNPs listed in Geno 2.0.
https://dl.dropbox.com/u/92587284/Geno-Y-SNPs.txt

Regards,
david
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