dog extra panels presentation - isag · dog extra panels presentation.pptx author: sofia mikko...
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Extra STR panels for dog parentage
Applied Gene;cs of Companion Animals Workshop
20 July 2017
ISAG 22 markers
• AHT121, AHTh130, AHT137, AHTh171, AHTk211, AHTk253, AHTh260
• AMEL • CXX279 • FH2054, FH2848 • INRA21 • INU005, INU030, INU055 • REN54P11, REN64E19, REN105LO3, REN162C04, REN169D01, REN169O18, REN247M23
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ISAG 22 markers • AHT121, AHTh130, AHT137, AHTh171, AHTk211, AHTk253, AHTh260
• AMEL • CXX279 • FH2054, FH2848 • INRA21 • INU005, INU030, INU055 • REN54P11, REN64E19, REN105LO3, REN162C04, REN169D01, REN169O18, REN247M23
Canine Genotypes Panel 1.1 (ThermoFisher/Finnzymes)
19 other markers reported in ISAG CTs
• FH2001, FH2328 • LEI004 • RPE65 • VGL0760, VGL0910, VGL1063, VGL1165, VGL1541, VGL1606, VGL1828, VGL2009, VGL2136, VGL2409, VGL2918, VGL3008, VGL3112, VGL3235, VGL3438
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19 other markers used in ISAG CTs
• FH2001, FH2328 (Canine Panel 2.1) • LEI004 • RPE65 • VGL0760, VGL0910, VGL1063, VGL1165, VGL1541, VGL1606, VGL1828, VGL2009, VGL2136, VGL2409, VGL2918, VGL3008, VGL3112, VGL3235, VGL3438
Commercial kits • Canine Genotypes Panel 1.1 (ThermoFisher/Finnzymes)
– 19 markers: – AHT121, AHT137, AHTh171, AHTk211, AHTk253, AHTh260 – AMEL – CXX279 – FH2054, FH2848 – INRA21 – INU005, INU055, INU030 – REN54P11, REN162C04, REN169D01, REN169O18, REN247M23
• Canine Genotypes Panel 2.1 (ThermoFisher), data from 14 breeds – 19 markers: – FH2001, FH2004, FH2010, FH2017, FH2054, FH2088, FH2107, FH2309, FH2328, FH2361, FH3313,
FH3377 – PEZ02, PEZ05, PEZ16, PEZ17, PEZ21 – vWF.X, and ZFX/Y
• StockMarks Kit for Dogs (ThermoFisher) – 10 markers: – FHC2010, FHC2054, FHC2079 – PEZ01, PEZ3, PEZ5, PEZ6, PEZ8, PEZ12, PEZ20,
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Other extra panels used • Certagen (44 breeds)
– 12 markers: – 1_9A, AHT125, AHT126, CPH3, CXX_403, CXX2137, LEI007, UK101,
UK109, UK111, UK118, UK133
• Veterinary Gene;cs Laboratory, UC Davis (13 breeds) – 25 markers: – 1-‐0014, 1-‐0053, 10-‐0959, 1-‐0123, 2-‐0168, 2-‐0176, 3-‐0309, 3-‐0323,
4-‐0441, 6-‐0608, 6-‐0669, 8-‐0799, 9-‐0914, 11-‐1055, 13-‐1257, 15-‐1404, 17-‐1562, 17-‐1577, 21-‐1878, 24-‐2086, 26-‐2207, 31-‐2469, 32-‐2519, 34-‐2597, 35-‐2642
• Laboklin (31 breeds) – 9 markers: – FHC2010, PEZ1, PEZ5, PEZ6, PEZ8, PEZ11, PEZ12, PEZ13, PEZ20
Number of alleles
0
5
10
15
20
25
30
35
1_9A
AH
T125
AHT126
CPH3
CX
X_40
3 CX
X213
7 LEI007
UK1
01
UK1
09
UK1
11
UK1
18
UK1
33
1-‐00
14
1-‐00
53
10-‐0959
1-‐01
23
2-‐01
68
2-‐01
76
3-‐03
09
3-‐03
23
4-‐04
41
6-‐06
08
6-‐06
69
8-‐07
99
9-‐09
14
11-‐1055
13-‐1257
15-‐1404
17-‐1562
17-‐1577
21-‐1878
24-‐208
6 26
-‐2207
31-‐2469
32-‐2519
34-‐2597
35-‐264
2 PEZ1
PEZ5
PEZ6
PEZ8
PEZ12
PEZ20
FHC2
010
PEZ11
PEZ13
Certagen (44) VGL, UC Davis (13) Laboklin (31)
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Marker heterozygosity
0,0000
0,1000
0,2000
0,3000
0,4000
0,5000
0,6000
0,7000
0,8000
0,9000
1,0000
HO
HE
Certagen VGL, UC Davis Laboklin Canine 2.1
VGL heterozygosity by breed
0,00
0,10
0,20
0,30
0,40
0,50
0,60
0,70
VGL HO
VGL HE
VGL PIC
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Laboklin heterozygosity by breed
0,00
0,10
0,20
0,30
0,40
0,50
0,60
0,70
0,80
Laboklin HO
Laboklin HE
Canine 2.1 heterozygosity by breed
0,00
0,10
0,20
0,30
0,40
0,50
0,60
0,70
0,80
0,90
Canine 2.1 HO
Canine 2.1 HE
Data from Kanthaswamy et al. 2009
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0,00
0,10
0,20
0,30
0,40
0,50
0,60
0,70
0,80
0,90
Certagen HO
Certagen HE
Canine 2.1 HO
Canine 2.1 HE
Laboklin HO
Laboklin HE
VGL HO
VGL HE
Heterozygosity of breeds across panels
Boxer Yorkshire terrier
Dachshund
Golden retriever
Conclusions
• Most of the Laboklin markers are included in the Canine Stockmarks kit
• Canine Genotyping Panel 2.1 performs well • Differences between panels may reflect popula;on stra;fica;on
• What extra panel would we go for?