Monday, March 4, 2013

Geno 2.0 YDNA SNP Pathways.

The Geno 2.0 chip tests some 13,000 SNPs on the Y-Chromosome, by far the largest from all commercial DNA companies, in addition, a lot of these SNPs do not have a place assigned in the YDNA phylogeny, no official phylogeny has been published yet either.

However, the customers of this project get the option to transfer the SNPs to FTDNA and thereby join the numerous grouped projects under the FTDNA umbrella, which then displays the results of which SNPs they tested positive for.

Although we don't know where most of these SNPs belong on the YDNA tree, we do know where some of them belong, and by utilizing the most rudimentary operations of set mathematics (union, intersection and set difference), in addition to the positions of the known SNPs in the current YDNA phylogeny tree (ISOGG 2013) it is possible to segregate these SNPs that appear on the project pages into phylogenetic pathways.

This posting will change frequently as more and more kits appear in the FTDNA project pages.

The first thing to realize is that the following list of 101 SNPs are either erroneous or erroneously reported and need to be discarded if they appear on any of the results until FTDNA , NATGEO or whoever else is responsible fixes them,

CTS1034+ CTS10436+ CTS10713+ CTS10738+ CTS11085+ CTS11454+ CTS11844+ CTS12173+ CTS2080+ CTS2223+ CTS230+ CTS2447+ CTS295+ CTS3234+ CTS335+ CTS3647+ CTS3763+ CTS3914+ CTS4276+ CTS4623+ CTS4714+ CTS477+ CTS5458+ CTS5580+ CTS6010+ CTS6353+ CTS6384+ CTS6891+ CTS7453+ CTS7492+ CTS7859+ CTS7951+ CTS8133+ CTS8178+ CTS8244+ CTS9096+ CTS947+ CTS9512+ CTS9548+ F1173+ F1221+ F1300+ F1327+ F1369+ F1707+ F1754+ F1831+ F1833+ F1842+ F1870+ F1882+ F2000+ F2137+ F2150+ F2177+ F2223+ F2494+ F2503+ F2546+ F2631+ F2845+ F2887+ F2932+ F3035+ F3039+ F317+ F3187+ F3225+ F3394+ F3397+ F3455+ F375+ F3948+ F3965+ F4131+ F4277+ F830+ F842+ F869+ F889+ F910+ F942+ F943+ F969+ L366+ L477+ L493+ L515+ L516+ L517+ L552+ L594+ M263+ PF4208+ PF4330+ PF5061+ PF6868+ PF7392+ Z148+ Z191+ Z365+  

Notes : Unions will be listed without symbol, ex Set ABC = Set ( (A  B) ∪ C)
            Known SNP identification is all based on ISOGG 2013 only.

Pathway from root to CT-M168 (=Set # A)

Binary Operation: Set1 Set2

Number of SNPs: 77

CTS10362+ CTS109+ CTS11358+ CTS11575+ CTS125+ CTS1996+ CTS3331+ CTS3431+ CTS3662+ CTS4364+ CTS4368+ CTS4740+ CTS5318+ CTS5457+ CTS5532+ CTS6383+ CTS6800+ CTS6907+ CTS7922+ CTS7933+ CTS8243+ CTS8980+ CTS9828+ L566+ L781+ M139+ M168+ M294+ M42+ M94+ PF1016+ PF1029+ PF1031+ PF1040+ PF1046+ PF1061+ PF1092+ PF1097+ PF110+ PF1203+ PF1269+ PF1276+ PF15+ PF192+ PF210+ PF212+ PF223+ PF234+ PF258+ PF263+ PF272+ PF278+ PF292+ PF316+ PF325+ PF342+ PF500+ PF601+ PF667+ PF719+ PF720+ PF725+ PF779+ PF796+ PF803+ PF815+ PF821+ PF840+ PF844+ PF892+ PF937+ PF951+ PF954+ PF970+ V189+ V52+ V9+

Identified as same level as BT
Identified as same level as CT-M168
Identified as same level as P <---- Looks unreliable and maybe a false positive report.

Pathway from CT-M168 to DE (YAP+) (=Set # B)

Binary Operation: (Set1 ∩ Set2) \ (Set # A)

Number of SNPs: 16

CTS101+ CTS10714+ CTS3334+ F1977+ F3170+ F3195+ F986+ M145+ M203+ P144+ P153+ P165+ P183+ PF1427+ PF1442+ PF1455+

Identified as same level as DE (YAP+)

Pathway from DE (YAP+) to E-P2 (=Set # C)

Set2: Kit # N65401, E-M34+

Binary Operation: (Set1 ∩ Set2) \ (Set # A B)

Number of SNPs: 102

CTS10296+ CTS1075+ CTS119+ CTS124+ CTS1446+ CTS1545+ CTS1978+ CTS2150+ CTS3250+ CTS3262+ CTS4685+ CTS5316+ CTS5373+ CTS5404+ CTS6333+ CTS6513+ CTS6842+ CTS7913+ CTS8053+ CTS8432+ CTS8900+ CTS8947+ F1365+ L489+ L499+ L504+ L507+ L510+ L512+ L537+ L614+ M96+ P147+ P150+ P152+ P155+ P162+ P169+ P171+ P172+ P173+ P175+ P176+ P177+ P179+ P180+ P181+ P2+ P29+ PF1456+ PF1459+ PF1462+ PF1467+ PF1468+ PF1472+ PF1473+ PF1476+ PF1477+ PF1480+ PF1485+ PF1486+ PF1489+ PF1490+ PF1494+ PF1495+ PF1500+ PF1501+ PF1535+ PF1536+ PF1545+ PF1547+ PF1548+ PF1550+ PF1551+ PF1552+ PF1553+ PF1554+ PF1555+ PF1557+ PF1559+ PF1561+ PF1563+ PF1564+ PF1565+ PF1567+ PF1576+ PF1583+ PF1593+ PF1608+ PF1610+ PF1618+ PF1795+ PF1796+ PF1798+ PF1799+ PF1809+ PF1819+ PF1822+ PF1827+ PF1828+ PF1873+ PF1927+

Identified as same level as E-M96
Identified as same level as E1
Identified as same level as E1b
Identified as same level as E-P2

Pathway from E-P2 to E-M215/M35 (=Set # D)

Binary Operation: (Set1 ∩ Set2)  \  Set # ABC

Number of SNPs: 87

CTS10184+ CTS10513+ CTS10637+ CTS10679+ CTS1389+ CTS2216+ CTS225+ CTS2474+ CTS2591+ CTS2620+ CTS3512+ CTS3637+ CTS3988+ CTS4220+ CTS4856+ CTS5530+ CTS5792+ CTS6298+ CTS6809+ CTS6834+ CTS6953+ CTS7154+ CTS7677+ CTS7980+ CTS8033+ CTS8131+ CTS8479+ CTS8586+ CTS890+ CTS8945+ CTS9017+ CTS9049+ CTS9324+ CTS9956+ L117+ L336+ L538+ L545+ L676+ L796+ M215+ M243+ P170+ PF1454+ PF1457+ PF1466+ PF1471+ PF1484+ PF1487+ PF1492+ PF1499+ PF1531+ PF1532+ PF1534+ PF1537+ PF1538+ PF1540+ PF1542+ PF1543+ PF1560+ PF1566+ PF1569+ PF1570+ PF1571+ PF1572+ PF1574+ PF1575+ PF1598+ PF1619+ PF1755+ PF1793+ PF1801+ PF1807+ PF1812+ PF1813+ PF1818+ PF1820+ PF1826+ PF1830+ PF1831+ PF1832+ PF1835+ PF1836+ PF1871+ PF1909+ PF1913+ PF1929+

Identified as same level as E-M215
Identified as same level as E-M35

Pathway from E-M215/35 to E-Z827 (=Set # J)

Binary Operation: (Set1 ∩ Set2)  \  Set # ABCD

Number of SNPs: 1


Identified as same level as E-Z827

Pathway from E-M215/35 to E-M78 (=Set # K)

Binary Operation: (Set1 ∩ Set2)  \  Set # ABCD

Number of SNPs: 52

CTS10323+  CTS10617+  CTS11082+  CTS11310+  CTS2270+  CTS2661+  CTS3278+  CTS4208+  CTS5561+  CTS5697+  CTS58+  CTS675+  CTS7166+  CTS7924+  CTS8002+  CTS8899+  F1244+  L539+  L541+  L544+  L546+  L547+  M78+  PF1956+  PF2098+  PF2107+  PF2108+  PF2109+  PF2110+  PF2111+  PF2112+  PF2113+  PF2114+  PF2115+  PF2117+  PF2118+  PF2119+  PF2122+  PF2124+  PF2147+  PF2173+  PF2175+  PF2176+  PF2177+  PF2178+  PF2179+  PF2181+  PF2182+  PF2185+  PF2188+  PF2202+  V68+

Identified as same level as E-V68
Identified as same level as E-M78

Pathway from E-P2 to E-M180 (=Set # E)

Binary Operation: (Set1 ∩ Set2)  \  Set # ABC

Number of SNPs: 68

CTS1001+ CTS10066+ CTS10638+ CTS10659+ CTS10806+ CTS10914+ CTS11461+ CTS11557+ CTS11579+ CTS11729+ CTS11732+ CTS12659+ CTS1847+ CTS1878+ CTS2075+ CTS224+ CTS3105+ CTS3259+ CTS3299+ CTS3344+ CTS3425+ CTS3576+ CTS3989+ CTS4054+ CTS4350+ CTS4408+ CTS5042+ CTS5539+ CTS5572+ CTS5629+ CTS6180+ CTS6302+ CTS6319+ CTS6474+ CTS7095+ CTS7282+ CTS7454+ CTS7641+ CTS8068+ CTS8123+ CTS8443+ CTS8562+ CTS8936+ CTS9188+ CTS9338+ CTS9768+ CTS9978+ L432+ L433+ L488+ L491+ L494+ L501+ L608+ L610+ L86+ L88+ M180+ M2+ M291+ P1+ P182+ P293+ PAGES00066+ PAGES00106+ V100+ V38+ V43+

Identified as same level as E-V38
Identified as same level as E-M2
Identified as same level as E-M180

Pathway from CT-M168 to CF-P143

Binary Operation: (Set1 ∩ Set2)  \  Set # A

Number of SNPs: 0

No SNPs were found that met the criteria, P143 is also not directly tested by the geno chip, a possible explanation is that one or more of the erroneous SNPs listed above could potentially meet the criteria, will have to wait till they get fixed.

Pathway from CF-P143 to F-M89 (=Set # F)

Binary Operation: (Set1 ∩ Set2)  \  Set # A

Number of SNPs: 72

CTS11726+ CTS12632+ CTS3536+ CTS3654+ CTS3868+ CTS3996+ CTS4443+ CTS6135+ F1046+ F1209+ F1302+ F1320+ F1329+ F1704+ F1714+ F1753+ F1767+ F2048+ F2075+ F2142+ F2155+ F2402+ F2587+ F2688+ F2710+ F2837+ F2985+ F2993+ F3111+ F3136+ F3335+ F3556+ F3692+ F719+ L132+ L350+ L468+ L470+ L498+ M235+ M89+ P135+ P136+ P138+ P14+ P141+ P145+ P146+ P148+ P151+ P158+ P159+ P160+ P166+ P187+ PF2591+ PF2593+ PF2599+ PF2600+ PF2608+ PF2611+ PF2615+ PF2624+ PF2631+ PF2643+ PF2745+ PF2747+ PF2748+ PF2749+ PF2770+ V186+ V205+

Identified as same level as F-M89

Pathway from F-M89  to IJK (=Set # G)

Binary Operation: (Set1 ∩ Set2)  \  Set # AF

Number of SNPs: 2

 L15+ L16+

Identified as same level as IJK

Pathway from IJK to IJ (=Set # H)

Binary Operation: (Set1 ∩ Set2)  \  Set # AFG

Number of SNPs: 29

 CTS6932+ CTS9240+ F1450+ F1460+ F2345+ F2366+ F2794+ F3368+ F3402+ F4188+ F922+ L403+ L748+ P123+ P124+ P126+ P127+ P130+ PF3504+ PF3514+ PF3515+ PF3517+ PF3518+ PF3534+ PF3560+ PF3561+ PF3562+ YSC0000056+ YSC0000265+

Identified as same level as IJ

Pathway from IJ to J-M304 (=Set # I)

Binary Operation: (Set1 ∩ Set2)  \  Set # AFGH

Number of SNPs: 55

CTS1068+    CTS10858+ CTS11571+ CTS11765+ CTS11787+ CTS12047+ CTS2769+ CTS3936+ CTS5280+ CTS5628+ CTS7738+ CTS852+ CTS8938+ F1167+ F1181+ F1634+ F1744+ F2116+ F2174+ F2276+ F2390+ F2502+ F2746+ F2749+ F2769+ F2817+ F2839+ F2973+ F3074+ F3119+ F3347+ F3358+ F3384+ F4072+ L134+ L778+ M304+ P209+ PF4490+ PF4491+ PF4513+ PF4521+ PF4530+ PF4572+ PF4591+ PF4595+ PF4598+ PF4622+ YSC0000064+ YSC0000066+ YSC0000165+ YSC0000197+ YSC0000228+ YSC0000236+ YSC0000239+

Identified as same level as J-M304

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