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ContextTyping comparisonsPopulation Genetics
Conclusion
From SSO to NGS in HLA population studies:the case of Mandenka (Senegal)
Thomas Goeury, Lydie Brunet, Lisa Creary, Maeva Pasquier,Jean-Marie Tiercy, Maxime Galan, Barbara Kervaire,
Marcelo A. Fernandez Vinia, André Langaney, José Manuel Nunesand Alicia Sanchez-Mazas
Contact: [email protected]
11 May 2016
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
Materials & Methods
Genetic data & Typing methods
Genetic data
Mandenka (Niger-congo)Western Africa – Senegal
3 Class II HLA genes:HLA-DPB1 ; -DRB1 ; -DQB1
Typings
1 PCR-SSO (Geneva 1992)2 NGS:
Exon 2: 454 pyrosequencing(Geneva 2012)
Full gene: MiSeq(Stanford and Geneva, 2015-2016)
Mali
Figure : Sampling location in the Kedougou city
neighborhood, eastern Senegal
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
DifferencesCauses of differences
Comparisons of techniquesH
LA D
PB
1H
LA D
QB
1H
LA D
RB
1
Mea
n
HLA
DP
B1
HLA
DQ
B1
HLA
DR
B1
Mea
n
HLA
DP
B1
HLA
DQ
B1
HLA
DR
B1
Mea
n
454 versus MiSeq SSO versus 454 SSO versus MiSeq
0
25
50
75
100
Mat
ch p
ropo
rtio
ns
Proportions of typing matches between SSO, 454and MiSeq techniques for the 3 HLA Class II loci
Good match between NGS:DNA sequences
Correct match between454 & SSO:Exon 2
Discrepancies betweenSSO & MiSeq:
Locus-dependant
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
DifferencesCauses of differences
Years of allele reports
1980 1990 2000 2010
454MiSeq
NGS ERA
14:5401:01; 03:01; 03:02; 04:03; 04:05 07:01; 08:04; 08:06; 09:01; 10:0111:01; 11:02; 13:01; 13:02; 13:03
13:04; 16:02
SSO
NGS ERA
02:01; 02:02; 03:01; 03:0204:02; 05:01;05:02; 05:03
06:02; 06:03
06:09 03:1903:01:04
1980 1990 2000 2010NGS ERA
124:01; 131:01; 417:01430:01; 461:01
02:0103:0104:01
01:01; 10:0113:01; 17:01
01:01:02 85:01 104:01105:01107:01
1980 1990 2000 2010
HLA-DPB1HLA-DPB1
HLA-DQB1HLA-DQB1
HLA-DRB1HLA-DRB1
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
DifferencesCauses of differences
Resolutive power of Class II HLA exons
Exo
n 1
Exo
n 2
Exo
ns 2
&3
Exo
n 3
Exo
n 4
Exo
ns 5
&6
Exo
n 1
Exo
n 2
Exo
ns 2
&3
Exo
n 3
Exo
n 4
Exo
ns 5
&6
Exo
n 1
Exo
n 2
Exo
ns 2
&3
Exo
n 3
Exo
ns 4
&5
HLA−DQB1 HLA−DRB1 HLA−DPB1
−25
0
25
50
75
100
Percent of unique haplotypes (compared to max)per exon and per locus
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
HLA-DQB1: Frequencies in Mandenka
DQB1*03:02
DQB1*04:01
DQB1*06:05
DQB1*06:06
DQB1*05:03
DQB1*06:04
DQB1*04:02
DQB1*05:02
DQB1*06:03
DQB1*06:02
DQB1*05:01
DQB1*02
DQB1*03:01
0.0 0.1 0.2 0.3 0.4 0.5
Frequencyrange
>10%
5%−10%
2%−5%
1%−2%
10%
5%−10%
2%−5%
1%−2%
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
HLA-DPB1: Frequencies in Mandenka
DPB1*15:01
DPB1*39:01
DPB1*50:01
DPB1*11:01
DPB1*14:01
DPB1*40:01
DPB1*27:01
DPB1*03:01
DPB1*04:01
DPB1*13:01
DPB1*04:02
DPB1*01:01
DPB1*02:01
DPB1*17:01
0.0 0.1 0.2 0.3 0.4
Frequencyrange
>10%
5%−10%
2%−5%
1%−2%
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
HLA-DRB1: Frequencies in Mandenka
DRB1*01:01
DRB1*01:02
DRB1*04:03
DRB1*04:05
DRB1*09:01
DRB1*12:01
DRB1*08:01
DRB1*08:06
DRB1*14:01
DRB1*08:04
DRB1*16:01
DRB1*08:02
DRB1*13:03
DRB1*03:02
DRB1*13:01
DRB1*13:02
DRB1*10:01
DRB1*11:02
DRB1*07
DRB1*11:01
DRB1*03:01
DRB1*13:04
0.0 0.1 0.2 0.3
Frequencyrange
>10%
5%−10%
2%−5%
1%−2%
10%
5%−10%
2%−5%
1%−2%
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
Haplotypic and global linkage disequilibrium
Chr.6
Long
arm
Sho
rt a
rmC
ento
rom
ere
Tel
omer
eT
elom
ere
HCP5P15
PSMB9
Telomeric side
Centromeric side
HCG4P11HLA-FRPL23AP1MICEHCG9P5IFITM4P3.8-1.5HCP5P14HCG4P10HLA-75HCG4HCP5P13HLA-90
TUBB
LOC100129921
LSM2
BAT1
ATP6V1G2NFKBIL1LTATNFLTBLST1NCR3
AIF1BAT2
BAT3APOMC6orf47BAT4CSNK2BLY6G5BLY6G5CBAT5LY6G6FLY6G6ELY6G6D
C6orf25DDAH2CLIC1MSH5
C6orf27VARS
HSPA1LHSPA1AHSPA1BC6orf48
NEU1SLC44A4
EHMT2ZBTB12C2CFBRDBPSKIV2LDOM3ZSTK19C4BCYP21A1P
TNXBCREBL1FKBPLPRRT1PPT2EGFL8AGPAT1
HLA-DRAHLA-DRB9HLA-DRB5HLA-DRB6HLA-DRB1HLA-DQA1HLA-DQB1HLA-DQB3HLA-DQA2HLA-DQB2HLA-DOBTAP2PSMB8TAP1
PPP1R2P1HLA-ZHLA-DMBHLA-DMABRD2HLA-DOAHLA-DPA1
RPL32P1HLA-DPB1
HLA-DPA2HLA-DPB2HLA-DPA3COL11A2RXRBSLC39A7HSD17B8RING1VPS52RPS18B3GALT4
D6S2723EWDR46
PFDN6RGL2TAPBPZBTB22DAXXLOC646720
KIFC1LYPLA2P1
RPL7AP7MICGHCG2P8HCP5P12HCG4P8P5-11HLA-GLOC100133214
MICF3.8-1.4HCP5P10HCG4P7P5-09HLA-HP5-07HLA-16HCG2P73.8-1.3HCP5P6HCG4P6P5-05HLA-KHLA-UHCG4P5P5-04HLA-AHCP5P3HCG4P4HLA-WHCG2P6MICDHCG93.8-1.2HCP5P2HCG4P3HLA-J
ETF1P1
ZNRD1PPP1R11RNF39TRIM31TRIM40TRIM10
FLJ45422
TRIM39RPP21HLA-NHCG2P5HCG2P4MICCHCG2P3RANP1HLA-EGNL1PRR3ABCF1PPP1R10MRPS18BPTMAP1C6orf134C6orf136DHX16KIAA1949NRMRPL7APMDC1
FLOT1IER3DDR1
TCF19
GTF2H4VARS2
DPCR1MUC21
HCG22
CDSNPSORS1C1PSORS1C2
CCHCR1
POU5F1
HCG27HCG2P2HCG9P3HLA-CHCG4P2KIAA0055PRPL3PHCG2P1HLA-BHCG4P1DHFRP2HLA-SHCP5P8HCG9P2MICAHLA-XHCP53.8-1HCG9P1MICB
LOC100129065
HCG4P9
MCCD1
Cla
ss I
regi
on
Cla
ss I
regi
on
Cla
ss II
I reg
ion
Cla
ss II
reg
ion
Ext
ende
d cl
ass
II re
gion
Alp
h ab l
ock
Kap
p ab l
ock
Bet
abl
o ck
ZNFsORsGABBR1SUMO2PMOGZNP57
LOC100133303
SFTA2
LOC729792
C6orf15
LOC100129610
PSORS1C3
TRIM15
HLA-LPPIP9
SNORD117SNORD84
LOC100130756
SNORA38
LY6G6C
C6orf26
SNORD48SNORD52
LOC100128067
TNXASTK19PC4ACYP21A2
LOC100131609
RNF5AGERPBX2GPSM3NOTCH4C6orf10
BTNL2
MYL8P
HCG8
C6orf12
TRIM26
Figure 1 Gene map of the human leukocyte antigen (HLA) region. The major histocompatibility complex (MHC) gene map corresponds to the genomiccoordinates of 29677984 (GABBR1) to 33485635 (KIFC1) in the human genome build 36.3 of the National Center for Biotechnology Information (NCBI)map viewer. The regions separated by arrows show the HLA subregions such as extended class I, classical class I, class III, classical class II and extendedclass II regions from telomere (left and top side) to centromere (right and bottom side). White, gray, striped and black boxes show expressed genes, genecandidates, non-coding genes and pseudogenes, respectively. The location of the alpha, beta and kappa blocks containing the cluster of duplicated HLAclass I genes in the class I region are indicated.
A 2009 update of the HLA genomic loci mapT Shiina et al
24
Journal of Human Genetics
Figure : Adapted fromShiina et al, 2009
Haplotypes in Linkage Disequilibrium
DRB1*13:04 ∼ DQB1*03:19DRB1*11:02:01 ∼ DQB1*03:19
DRB1*03:01:01:01 ∼ DQB1*02:01:01–
Consequence of typing accuracy:DPB1*17:01-DQB1*03:01 no more in LD
(DPB1*17:01SSO = 17:01 + 131:01)
Global Linkage Disequilibrium between loci
HLA-DRB1 ∼ HLA-DQB1
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
Hypothesis of gene conversion
Hill et al (1992)
”The DRB1*1304 allele differs by only two amino acids, 57 and 58,from the DRB1*1102 allele, and it was suggested that a smallnonreciprocal genetic exchange event, perhaps with a DRB1*0803allele as the donor, led to the creation of the DRB1*1304 allele.”
AA Codon 55 60
DRB1*11:02:01 CGG CCT GAT GAG GAG TAC
DRB1*13:04 --- --- AGC -CC --- ---
Ser Ala
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
Alleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
Gene conversion – New insigths
Donor and recipient
Recipient: DRB1*11:02:01
Donor ? Not DRB1*08:03
Presence of specific Ser-Ala pattern
Absent in this study, very rare in Africa
Two potentials donors: DRB1*08:06 & DRB1*13:03:01
Ser-Ala pattern, conserved region, present in Mandenka
Role ?
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
ConclusionAcknowledgement
Highlights
Key points
Importance of accurate typing using NGS and long rangesequencing
High frequency of DRB1*13:04 and DQB1*03:19, in LD
DQB1*03:19 may be involved in Onchocerciasis resistance
Loci HLA-DRB1 and HLA-DQB1 in strong LD
DRB1*13:04: hypothesis of a gene conversion betweenDRB1*11:02:01 and either DRB1*08:06 or DRB1*13:03:01
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
ConclusionAcknowledgement
Acknowledgement
Εφςηαριστό για τιν προσοςηı́ σαςThank you for your attention
And also many thanks to. . .
The Mandenka people
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
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ContextTyping comparisonsPopulation Genetics
Conclusion
ConclusionAcknowledgement
[EFI 2016 Population Genetics Working Group] T. Goeury HLA: From SSO to NGS
ContextMaterials & Methods
Typing comparisonsDifferencesCauses of differences
Population GeneticsAlleles FrequenciesLinkage disequilibriumsHLA-DRB1*13:04
ConclusionConclusionAcknowledgement