Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Enhancing Donor Selection: Building Blocks of the New Search Algorithm NMDP Council 2005

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Selection of Suitable Donor Patient’s HLA-A,-B,-C,-DR High resolution (allele) Registry Potential donors Selected donor HLA alleles matched Low-Intermediate HLA-A,-B,-DR High resolution HLA-A,-B,-C,-DR Extensive HLA Typing >5 Million Search algorithm

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Search Report—Many Potential Matches 87 Potential Matches TC Match:  A,B,C,DRB1,DQB1  High resolution Recipient:

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Low to Intermediate Resolution Potential Matches A/B AntigensDRB1 AlleleExample of Typing Allele Potential Match A*02code,*03code, B*35code,*51code, DRB1*04code,*11code Split MatchAllele Potential MatchA2,3, B35,51, DRB1*04code,*11code Split Match A2,3, B35,51, DR4,11 Are all 87 potential donors equal? Will all turn out to be perfect matches?

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Likelihood of Allele Match Varies Based on Recipient’s HLA 87 Potential Matches Allele Matched Allele Mismatched Allele Mismatched Allele Matched Uncommon alleles or Uncommon haplotypes R Common alleles Common haplotypes R

5 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Information & Expertise Needed for Donor Selection Enhanced Search Algorithm HLA Typing Information HLA Typing Information Population Genetics of HLA Population Genetics of HLA 87 Potential Matches

6 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Incorporating DNA-Based HLA Typing Information into the Algorithm

7 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Building a Foundation Search Algorithm Population Genetics HLA Typing Quality & Resolution  Increase accuracy of HLA assignments  Help TC find allele matched donors  Provide “raw material” for population genetics studies

8 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Improving HLA Typing Replaced serology with DNA testing  DRB1 in 1992, A & B in 1997  Today, 85% new volunteers (235K/yr) tested through quality controlled contract lab network  Improved quality, <0.1% error rate  Typing of minority volunteers most dramatically improved Provided higher resolution to facilitate allele matching & to “feed” population genetics studies  Added reagents to increase resolution from XX to subsets of alleles  Upgraded computer system to collect & utilize higher resolution types

9 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Early Challenge with DNA Typing Data  Typing labs base their HLA assignments on alleles known to exist  But new HLA alleles are described every week  Challenge: Patients with newer alleles will have difficulty in finding matches Solution: Collect DNA typing data in its most basic form before it is “interpreted” by the HLA lab into HLA types

10 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Reminder: HLA Inheritance, Genes & Alleles Chromosome 6 Inheritance Father Mother Child DPDQDRBCA Genotype Homozygous=2 identical alleles at locus Heterozygous=2 different alleles Haplotype Phenotype=serologic type

11 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Transfer of HLA Information from the HLA Typing Laboratory to the Transplant Center Basic typing data (DNA sequences present or absent) Interpretation to HLA genotypes Converted to types capable of listing on NMDP Registry HLA Typing Lab Transplant Center Interpreted into HLA genotypes May not be same

12 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® DNA Sequences Differ Among Alleles DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TTC GTG CGG TTG CTG GAA AGA DRB1* GA- T-C TC- -C- -C- --G AC C --- DRB1* GA- --- G-- --A CA- --G C C --- DRB1* GA- T-C TC- -C- -C- --G C C ---  Each gene is specified by ~1000 bases (A,T,C,G)  Each locus has many alleles differing in DNA sequence  Polymorphic sequences are shared among alleles Dash, same as top line DRB1 Locus/Gene

13 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® HLA Typing Targets DNA Sequences That Differ Among Alleles GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA --C C -AC C TTG CTG GAA DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TTC GTG CGG TTG CTG GAA AGA DRB1* GA- T-C TC- -C- -C- --G AC C --- DRB1* GA- --- G-- --A CA- --G C C --- DRB1* GA- T-C TC- -C- -C- --G C C --- HLA Test Results = ?

14 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Interpreting DNA Typing Results Based on Known Alleles GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA --C C -AC C TTG CTG GAA DRB1*0101 and DRB1*0301 = DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TTC GTG CGG TTG CTG GAA AGA DRB1* GA- T-C TC- -C- -C- --G AC C --- DRB1* GA- --- G-- --A CA- --G C C --- DRB1* GA- T-C TC- -C- -C- --G C C --- Genotype HLA Test Results

15 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Another DNA Typing Result GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA -TG GGT DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TAC GGG GTT GGT GAG AGC TTC DRB1* GA- --- G-- --A CA- --G TG DRB1* GA- --- G-- --A CA- --G DRB1* GA- T-C TC- -C- -C- --G DRB1* GA- T-C TC- -C- -C- --G TG HLA Test Results = ?

16 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Alternative Genotypes GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA -TG GGT DRB1*0404 & DRB1*1101 OR DRB1*0408 & DRB1*1104 = DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TAC GGG GTT GGT GAG AGC TTC DRB1* GA- --- G-- --A CA- --G TG DRB1* GA- --- G-- --A CA- --G DRB1* GA- T-C TC- -C- -C- --G DRB1* GA- T-C TC- -C- -C- --G TG Alternative Genotype List HLA Test Results

17 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Lost in Translation Between the HLA Typing Laboratory & the Transplant Center Basic typing data (DNA sequences present or absent) Interpretation to HLA genotypes Converted to types capable of listing on NMDP Registry HLA Typing Lab Transplant Center Interpreted into HLA genotypes Information lost in translation

18 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Lost in Translation--At HLA Lab GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA -TG GGT DRB1*0404 & DRB1*1101 or DRB1*0408 & DRB1*1104 DRB1*0404 or *0408 (DRB1*04DE) and DRB1*1101 or *1104 (DRB1*11AD) Sent to NMDP Alternative Genotype List What’s Lost Alternative genotype list DNA sequences tested as present or absent

19 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Lost in Translation-- Search Report & TC Interpretation Potential donor: DRB1*04DE, DRB1*11AD What genotypes does this donor carry? DE, 04 or 08 AD, 01 or 04

20 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Lost in Translation-- Search Report & TC Interpretation Potential donor: DRB1*04DE, DRB1*11AD What genotypes does this donor carry? DE, 04 or 08 AD, 01 or 04

21 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Creation of Heterozygous Genotypes That Don’t Exist in Donor—2 nd Challenge Potential donor: DRB1*04DE, DRB1*11AD DE, 04 or 08 AD, 01 or 04 Transplant Center over-interprets donor’s HLA type Phase Mismatch

22 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Phase Mismatch Genotypes Don’t Exist GA- --- G-- --A CA- --G GA- T-C TC- -C- -C- --G TGG CAG CTT AAG TTT GAA -TG GGT DRB1*0404 & DRB1*1101 OR DRB1*0408 & DRB1*1104 = DRB1*0101 CA CGT TTC TTG TGG CAG CTT AAG TTT GAA TGT CAT TAC GGG GTT GGT GAG AGC TTC DRB1* GA- --- G-- --A CA- --G TG DRB1* GA- --- G-- --A CA- --G DRB1* GA- T-C TC- -C- -C- --G DRB1* GA- T-C TC- -C- -C- --G TG Alternative Genotype List HLA Test Results Could donor carry DRB1*0404, *1104 ? No

23 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Collecting the Most Basic DNA Typing Data Solves Two Challenges NMDP 1.Recreate genotype lists 2. Re-interpret to determine if new allele HLA Typing Lab TGGCAGCTTAAGTTTGAA + GAGTACTCTACGTCTGAG - GGT - GTG +

24 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Overview of Primary Data Project  Collected 2.3 million DRB, 1.6 million HLA-A, B  Developed electronic transfer of primary data – Proposed international standard  Instituted validation checks as data enters registry to reduce errors  Partnered with 9 vendors to store their proprietary reagent sequences in typing kit database  Developed interpretation software to standardize results & allow reinterpretation

25 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Should This Donor Be Tested as Potential Match For DRB1*0408, *1101 Recipient? Potential donor: DRB1*04DE, DRB1*11AD DE, 04 or 08; AD, 01 or 04 Search report will now indicate that this donor is not an allele match if the primary DNA data is available for this donor

26 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® New Search Report DRB1*0404 recipient Potential donor 1 DRB1*04XX+ P P - P # P Potential donor 4 DRB1*04XX Potential donor 2 DRB1*04XX Potential donor 3 DRB1*04XX Allele exists Allele does not exist Pair does not exist No DNA data P=potential allele match

27 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Building Expertise Into NMDP Search Algorithm to Aid in Donor Selection Enhanced Search Algorithm Reinterpret basic DNA typing data—id new allele or phase mismatch Reinterpret basic DNA typing data—id new allele or phase mismatch Population Genetics Population Genetics Enhance HLA typing quality & resolution, collect basic DNA typing data Enhance HLA typing quality & resolution, collect basic DNA typing data

28 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Incorporating Population Genetics into the Algorithm

29 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® What Is Population Genetics? Study of genetic information carried by human populations HLA alleles at multiple loci (A,B,C,DRB1,DQB1) Traveling together on each copy of chromosome 6 Inherited from our parents Lots of math

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Linkage Disequilibrium—Alleles Traveling Together on Chromosome 6 HLA A B C DRB1 DQB1 Chr 6 HLA A*3001 B*4201 Cw*1701 DRB1*0302 DQB1*0402 Genes Alleles on Chrom 6 Recombination reshuffles alleles on a chromosome HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602 HLA A*0101 B*0801 Cw*0701 DRB1*0301 DQB1*0201

Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Linkage Disequilibrium—Alleles Traveling Together on Chromosome 6 Specific alleles of HLA loci are commonly found together on a chromosome (haplotype) Knowing haplotypes greatly helps donor search Do patient’s alleles & haplotypes appear frequently in the population? Identification of haplotypes in populations Uses mathematical algorithms (eg EM) Requires information on HLA alleles carried by populations Challenge: Allele data is limited HLA A*0201 B*0702 Cw*0702 DRB1*1501 DQB1*0602

32 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® First Analysis of HLA Haplotypes in NMDP Registry  HLA gene & haplotype frequencies in the North American population, Mori et al, Transplantation 1997 Limitations  5 broad race/ethnic groups  HLA typing by serology  Low resolution  Accuracy questionable (minorities)  Not all HLA loci tested (HLA-DR,C)  Had to reduce HLA typing to lowest common denominator for EM analysis LatinoWhite A2,B35,DR8A1,B8,DR3 A29,B44,DR7A3,B7,DR2 A1,B8,DR3A2,B44,DR4 A2,B35,DR4A2,B7,DR2 A3,B7,DR2A29,B44,DR7 A28,B39,DR4A2,B62,DR4 A2,B39,DR4A3,B35,DR1 A24,B39,DR6A1,B57,DR7 Haplotypes by race/ethnicity

33 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Building Data & Tools for Population Studies at NMDP HLA alleles in random donors from specific populations typed & used to predict haplotypes* Strategy developed to use most basic DNA data to predict alleles Modifications to math algorithms developed & applied to population genetics predictions HLA alleles in actual donors identified & used to predict haplotypes Accuracy & resolution of HLA types of volunteer donors improved *Ongoing

34 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Applying a More Flexible Version of the Expectation Maximization (EM) Algorithm to Predict Haplotypes A*0101,B*0801,DRB1*0301 A*3001,B*4201,DRB1*0302 A*0101, B*4501, DRB1*0301 A*2301, B*0801, DRB1*0701 A*0101,B*0801, DRB1*1101 A*7401,B*1503, DRB1*0301 A*0101,B*0801,DRB1*0301 Appear to be traveling together

35 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Increasing Resolution Using New EM-- Haplotypes in Registry African American Mori A30,B42,DR3A*3001,B*4201,DRB1*0302 A1,B8,DR3A*0101,B*0801,DRB1*0301 A3,B7,DR2A*0301,B*0702,DRB1*1501 A2,B44,DR4A*0201,B*4402,DRB1*0401 A33,B53,DR8A*3303,B*5301,DRB1*0804 A28,B58,DR12A*6801,B*5802,DRB1*1201 A30,B42,DR8A*3001,B*4201,DRB1*0804 A34,B44,DR2A*3402,B*4403,DRB1*1503  A-B-DR (low resolution) to A-B-DRB (high resolution)  Ranking differs

36 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Population Genetics Information Merged into Search Algorithm Allele & haplotypes likely based on ethnicity Allele & haplotypes likely based on ethnicity Most basic DNA data to identify possible genotypes & likelihood new alleles Most basic DNA data to identify possible genotypes & likelihood new alleles Each potential donor Probability of allele match

37 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® New Search Report DRB1*0404 recipient Potential donor 1 DRB1*04XX 99% 63% 0% Potential donor 2 DRB1*04XX Potential donor 3 DRB1*04XX Very likely matched Less likely to match Will not be a match P=potential allele match

38 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Quality Control Side of the Story  Each phase overseen by experts in the field  Each phase validated & documented by peer-reviewed scientific publications Enhanced Search Algorithm HLA Typing Information HLA Typing Information Population Genetics Population Genetics

39 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® New Algorithm Will Help with Selection of Suitable Donor in Timely Fashion Patient’s HLA-A,-B,-C,-DR High resolution (allele) Registry Potential donors Selected donor HLA alleles matched Low-Intermediate HLA-A,-B,-DR High resolution HLA-A,-B,-C,-DR Extensive HLA Typing >5 Million Search algorithm

40 Creating Connections. Saving Lives. ™ NATIONAL MARROW DONOR PROGRAM ® Building Expertise Into NMDP Search Algorithm to Aid in Donor Selection Enhanced Search Algorithm HLA Typing Information HLA Typing Information Population Genetics Population Genetics 87 Potential Matches Probability of allele match Allele frequencies Haplotype predictions Genotypes present New alleles Incorrect typings HLA nomenclature Benefits Provides more expertise in finding best match Save time Save resources