Christian Gabriel, Linz Is next generation sequencing mature for medical diagnostics? Applications from immunogenetics to virology by 454 Sequencing  Christian Gabriel, Linz

Red Cross Transfusion Service Linz Die neue Blutzentrale Linz: ganz rechts das allgemeine Krankenhaus. Blutzentrale Linz

Jumping out of biology Medical applications

A very brief introduction IMMUNOGENETICS

MHC 3 classes Important for: MHC I – bind TCR´s of CD8 The distinction of “non-self and self” Antigen presentation 3 classes MHC I – bind TCR´s of CD8 MHC II – bind TCR´s of CD4 MHC III - complement C2, C4, TNF Many other functional proteins, which resemble the structure of MHC Different levels of expression in different tissues.

Figure 5-16

new alleles Last lecture Spring 2008 in Switzerland IMGT/HLA Database ImMunoGeneTics http://www.ebi.ac.uk/imgt/hla/index.html 7

Numbers of HLA Alleles HLA Class I alleles 4,383 HLA Class II alleles 1,291 HLA Alleles 5,674 Other non-HLA Alleles 114 8

HLA- A*02I101I01I02IL HLA nomenclature Shows differences in the non-coding region Shows synonymous subsitition in the coding region Silent substitution Locus HLA- A*02I101I01I02IL Allele group – broad specificity serologic equivalent HLA-protein Suffix : L, S, C, A, Q, N N= null allele L = Low cell surface expression S = Secreted molecule but not present on the cell surface C = In the cytoplasm but not on the cell surface. A = indicates aberrant expression Q = allele is questionable 9

MEDICAL USE

Medical significance of HLA Transplantation Bone marrow and stem cell transplantation Solid organs: esp. kidney-transplantation Association of HLA-antigens with diseases and predispositions: Autoimmune diseases (Mb Bechterew) Pharmacogenetics Infectious diseases

Mismatch Stem cell transplantation Donor Allele Mismatch Donor Antigen Mismatch Patient MHC I HLA-A*0201,3101 HLA-B*4402,5601 HLA-C*0102,0501 MHC II DRB1*0101,0401 DQB1*0301,0501 MHC I HLA-A*0205,3101 HLA-B*4402,5601 HLA-C*0102,0501 MHC II DRB1*0101,0401 DQB1*0301,0501 MHC I HLA-A*2401,3101 HLA-B*4402,5601 HLA-C*0102,0501 MHC II DRB1*0101,0401 DQB1*0301,0501 12

The more mismatches you have, the worse is the outcome Survival is more dependent on HLA-match the earlier you have your treatment. Lee et al: Blood 2007 Dec 15;110(13):4576-83.

Methods and Variations Complex labs produce complex solutions Methods and Variations

HLA Typing Methods: Resolution Serology: Molecular: Low = 2 digits (complement-dependent-cytotoxity-assay) Molecular: PCR-SSO (sequence-specific oligonucleotides) PCR-SSP (sequence-specific primers) Sequencing (sequencing-based typing, SBT) Resolution Low = 2 digits High = 4 digits Ultra-high = all digits

Sequencing (sequencing-based typing, SBT) R M Atria HLA B (generic sequencing)

Regions of interest class I class II

Time, work-load and ambiguities PROBLEMS

Sequencing (sequencing-based typing, SBT) vs. B*1801,5502

Allele ambiguity example: HLA-B B*0702, 4402 B*0702, 4419N outlier mutations: allele ambiguitiy results when polymorphisms that distinguish alleles fall outside of the regions examined by the typing system Exon 3 Exon 2 Exon 1 Exon 4 example: HLA-B B*0702, 4402 B*0702, 4419N Polymorphic positions Core heterozygous sequence data

Genotype ambiguities A+B=D+E Results from an inability to establish phase between closely linked polymorphisms identified by the typing system example: HLA-B B*0702, 4402 B*0720, 4416 B*0724, 4421 A+B=D+E

cis/trans Problems M = A und T S = G und C TGGAGGGCSMGTGCGTGGA S = G und C M = A und T -------------SM------------- -------------GA-------------- -------------CT-------------- -------------GT-------------- -------------CA--------------   TGGAGGGCSMGTGCGTGGA Number of possible linkages = 2n n=2; 4 combinations n=4; 16 combinations

Workflow stem cell Transplantation Diagnosis Registration 1-6 m No sibling SBT Patient Family typing SSP, Serology Donor requests, typing 3-6 wks selection Selection and donation HLA- Typing For confirmation Collection Conditioning Transplantation Transplantation

Ergebnisse: Es wurden 32 Proben mit ambiguities ausgewählt Ergebnisse: Es wurden 32 Proben mit ambiguities ausgewählt. Alle Proben sind durch Familientypisierung und Sequenzierung bestätigt worden. Mit der MID-Technologie konnten sie gleichzeitig typisiert werden. Dabei sind auch zusätzliche Nukleotidaustausche gefunden worden, die als stille Mutationen beschrieben werden können.

Selected use for the 454 system in immunogenetics Registry Typing Low resolution 4 digit (intermediate resolution) A,B,C,DRB1 und DQB1 9-10 Amplicons 100-200pts. Price: US 50-100Euros, Linz 30 - 70 HSCT Typing High resolution 4 digits Ambiguity-free A,B,C,DRB1 und DQB1 16-18 Amplicons 50-100pts. Price: 600Euros, Linz 240Euros

HLA Alpha Site Study Goal Technical performance study to compare high resolution 454 sequencing with state of the art high resolution typing (Sanger) of relevant HLA loci Investigators 8 experienced and new 454 users Samples Samples submitted by the participants, 20 chosen, blinded Primers 14 primer sets labeled with 11 MIDs for amplicon generation (1 set consists of 2 MTPs with total 319 oligonucleotides dried in micro titer plates) Software GS Flx SW plus Conexio Genomics ATF

HLA Study Workflow Steps for high resolution / high throughput protocol – manual workflow „MR“ - 2 plates OR „HR“ - 4 plates Amplicon Generation Samples: 20 DNA samples +2 neg. controls PCR: 308 rx (14 primers x11 MIDs x 2 plates) Purification Quantification Equimolar Pooling: 2 pools (sample 1-10; samples 11-20 plus neg. controls) GS FLX Chemistry emPCR Breaking Enrichment GS FLX Sequencing PTP: 1 run; 2-regions; 10 samples (MIDs) / region GS FLX SW: v2.0.01 Conexio ATF Software Read length: 250 bp Read depth: 670 reads/amplicon acc. to standard 454 protocols

Genotype Assignment Assignment for 95% of the 2240 genotypes examined Causes for Failure to Assign Genotype 3% 4/8 sites had no genotypes omitted due to procedural/technical issues

Summary of Agreement and Concordance Agreement = Identical ambiguity string obtained Concordance = Reported genotype/allele in a limited ambiguity string matched submitted

Conclusions Improvements recommended by participants Workflow Simplification (Titanium) Automation Additional ambiguity resolution esp. for null alleles (Ti UHR) Conexio ATF software (will be addressed in next version) Sequence insertions in new variants should be visible Allow easier manipulation of less abundant sequences sometimes needed for genotyping Allow program to automatically correct for specifically identified systematic sequencing errors in homopolymer run/end of sequence of a given amplicon

Acknowledgements

Haplotyping

Team Genomics Johannes Pröll, Christa Hackl, Katja Hofer, Steffi Stabentheiner, Martin Danzer, Norbert Niklas