Long read technologies provides novel insight into the diversity of the MHC in Africa

Transcription

1 Long read technologies provides novel insight into the diversity of the MHC in Africa a roadmap to understanding HLA diversity in Africa Martin Pollard Global Health and Populations Human Genetics, WellcomeSanger Institute Sandhu Group Department of Medicine, University of Cambridge

2 Introduction Africa -genetically most diverse region in the world Hundreds of distinct populations Evolutionary adaptation to selective pressures Different causative loci between populations

3 HLA MHC -one of the most genetically diverse regions African HLA diversity high relative to Europeans Understudied in Africa classicalsequences in IMGT Of those 575 sequences with African ethnic source tag Jan van Rood ( )

4 MHC region: relevance Immature CD4 + T cell Antigen TCR MHCII Mature helper T cell (Th1 or Th2) Antigen Presenting Cell Immature CD8 + T cell Antigen TCR MHCI CD4 + CD8 + Mature cytotoxic T Cell (Tc) Antigen Presenting Cell Infectious and noninfectious disease Autoimmunity Cancer Vaccine response Transplant medicine Picture By user:sjef- CC BY-SA 3.0 wikicommons

5 Challenges in the study of the HLA region Genetic diversity high heterozygosity High levels of homopolymerrepeats Structural variation Limited sequence data in reference resources (82.7% IMGT sequences partial ) Lack of validation in African populations of current methods Sanger based sequencing - resolution of phase Primer based amplification Capture

6 Sequencing of the HLA region MiSeq+ Pacbio N=(1706) Pacbio sequencing (n=285) Demultiplex Consensus A*01:01:01:01 B*07:02 C*33:10:01 A*01:01:01:01 B*07:02 C*33:10:01

7 Lab Process Sample Management

8 Lab Process PCR

9 Lab Process QC & EM pool

10 The workhorses

11 Long Amplicon Analysis

12 HLA Diversity in Africa panel Population Samples Population Samples Urban Entebbe, Uganda 330 Urban Banfora, Burkina Faso 167 Urban Soweto,South Africa Yoruba Ibadan, Nigeria (YRI) 110 Esan Nigeria (ESN) 99 Maasai Kinyawa, Kenya (MKK) 166 Gambian Western Division, The Gambia (GWD) 112 Mende Sierra Leone (MSL) 84 Americans of African Ancestry, SW USA (ASW) Afro Caribbean Barbados (ACB) Luhya Webuye, Kenya (LWK) 97 MorrocanExpat Netherlands 25 Igbo Nigeria 25 Kalenjin Kenya 25 Ashanti Ghana 25 Zulu South Africa 25 Egyptian Egypt 17 Fur (2 Borgu, 1 Mima, 1 Karanga) Sudan Burkinabe Gouin, Burkina Faso Maasai Kinyawa, Kenya (MKK) 25 Mandinka Gambia 25 Muganda Uganda 25 Nama South Africa 25 Phase 3 In progress 93 IAVI Protocol C later this year 600 Phase 4 later this year 50 1,831 HLA typed persons 1,322 Full length full phase 22 diverse populations

13 A workflow for accurate HLA typing in Africans: A clinical and medical genetics resources Poor disambiguation of HLA types with Sanger sequencing High concordance between SBT and PacBio sequencing (>95% at 2 digits) PacBiosequencing more accurate when discordance observed High levels of novelty

14 Novel Allele Differences

15 Novel Allele Genetic Origin

16 Novel Allele Ethnic Origin

17 Diversity of DQB1

18 HLA diversity in Africa in the global context Alexander Mentzer

19 Distribution of functionally important alleles Gambian) Mende shanti Burkina Faso Esan Ibo Luhya Kalenjin B*53:01:01 Malaria Symptom Resistance Afro Caribbean, Ashanti, Burkina Faso, Esan, Ibo, Luhya, Maasai, Yoruba Maasai Yoruba Entebbe Afro-Caribbean Zulu Malaria endemic regions World Bank/MARA/ARMA B*53:01:01G Other allele

20 HLA panel as a resource for imputation Alexander Mentzerand Alexander Dilthey

21 African HLA panels as a resource for medical research Does Human Variation influence vaccine response? 2499 Samples Multiplex Immunoassay against vaccine antigens (Total IgG) Pertussis Toxin Filamentous Haemagglutinin Pertactin Tetanus Toxin Diphtheria Toxin Haemophilusinfluenzaetype b Hepatitis B surface antigen Measles virus Alexander Mentzer

22 HLA panel facilitates fine mapping of HLA signals Alexander Mentzer

23 Conclusion HLA diversity in Africa panel- largest HLA sequence to date Informs clinical typing Use of long range sequencing platforms Novel alleles Resolving ambiguity A resource for medical genetics Substantial improvement in imputation Fine mapping High levels of genetic diversity across Africa Functional importance Impact on clinical phenotypes Availability Managed access (EGA) Imputation Server

24 Acknowledgements Our many research participants from across Africa My co-author Alex Mentzer(University of Oxford) Wellcome Sanger Institute ManjSandhu Deepti Gurdasani Cristina Pomilla Tarryn Porter Tommy Carstensen Mike Quail & the Sanger Seq R&D group Naomi Park PacBio Team University of Oxford Adrian Hill Gill McVean Kathryn Auckland Alex Dilthey PacBio Nicola Cahill Swati Ranade John Harting John Baeten Mark Thornber RikiAydeniz Samples Alison Elliot (EMaB) Brenna Henn and Eileen G. Hoal(Nama) Charles Rotimi (AADM) Charles Agyemangand KarienStronks(HELIUS) Endashaw Bekele (Amhara, Gumuz, Somali) Fraser Pirie and Ayesha Motaya(DCC) Hisham Hassan and Mihai Netea(Beja, Copts, Fulani, Fur, Mahas) Pierre Zalloua(Sara, Toubou, Egyptians) Richard Cooper (EpiTransGhana) Shabir Madhi(South African Infants GWAS) SodiomonB. Sirma(BanforaVAC050, Gouin) NHGRI repository at CoriellInstitute IHWG Histogenetics IMGT/HLA IAVI, USAID and Wellcome