Teaching session Views on allelic diversity

Transkript

1 Teaching session Views on allelic diversity Wolfgang Helmberg UBT GRAZ Taking Owls to Athens...

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3 How did allele nomenclature evolve How did HLA evolve Where do polymorphisms map What are P and G groups What are sequence features What are serological equivalents What are common and well defined alleles What are GL-strings How did allele nomenclature evolve HLA-view SNP-view Polymorphism Polymorphism Allele Gene sequence Allele Haplotype Multiple gene sequences Haplotype Haplotype

4 How did allele nomenclature evolve Bull World Health Organ. 1968;39(3): How did allele nomenclature evolve

5 How did allele nomenclature evolve HL-A1 HL-A2 HL-A3 HL-A4 HL-A5 HL-A6 HL-A7 HL-A8 How did allele nomenclature evolve

6 How did allele nomenclature evolve How did allele nomenclature evolve

7 How did allele nomenclature evolve How did allele nomenclature evolve Evolution of nomenclature HL-A1 HL-A2 HL-A3 HL-A4 HL-A5 HL-A6 HL-A7 HL-A8 HLA-A1 HLA-A2 HLA-A3 HLA-B4 Bw4 HLA-B5 HLA-B6 Bw6 HLA-B7 HLA-B8

8 How did allele nomenclature evolve A1 A2 A203 A210 A3 A9 A10 A11 A19 A23(9) A24(9) A2403 A25(10) A26(10) A28 A29(19) A30(19) A31(19) A32(19) A33(19) A34(10) A36 A43 A66(28) A68(28) A69(28) A74(19) A80 B5 B7 B703 B8 B12 B13 B14 B15 B16 B17 B18 B21 B22 B27 B2708 B35 B37 B38(16) B39(16) B3901 B3902 B40 B4005 B41 B42 B44(12) B45(12) B46 B47 B48 B49(21) B50(21) B51(5) B5102 B5103 B52(5) B53 B54(22) B55(22) B56(22) B57(17) B58(17) B59 B60(40) B61(40) B62(15) B63(15) B64(14) B65(14) B67 B70 B71(70) B72(70) B73 B75(15) B76(15) B78 B81 Bw4 Bw6 How did allele nomenclature evolve Cross REactive GroupS (CREGS), shared epitopes Bw4 Bw6 A9 A23(9) A24(9) A2403 A25(10) A32(19) B5 B13 B17 B18 B21 B22 B27 B2708 B35 B37 B38(16).. B7 B703 B8 B12 B14 B15 B16...

9 How did allele nomenclature evolve How did allele nomenclature evolve

10 How did allele nomenclature evolve How did allele nomenclature evolve A1 A*01 A2 A*02 A203 A*0203 A210 A*0210 A3 A*03 A9 (A*23, A*24) A10 (A*25, A*26) A11 A*11 A19 A23(9) A*23 A24(9) A*24 A2403 A*2403 A25(10) A*25 (A*29, A*30, A31, ) A26(10) A*26 A28 (A*66, A*68, A*69)

11 How did allele nomenclature evolve HL-A7 HLA-B7 B*0701 B*07011 B* worst allele right now: A*02:01:86 : 86 silent variations B* N/L/S/Q (/C/A) Null allele, low expression, questionable : Serological equivalent 2: Different protein 3: Silent/synonymous mutation 4: non coding region How did allele nomenclature evolve Suffixes: N: Null allele HLA-A*24:09N L: Low expression HLA-A*30:14L S: Secreted HLA-B*44:02:01:02S Q: Questionable HLA-B*13:08Q A: Aberrant? C: Cytoplasmic?

12 How did allele nomenclature evolve Problem: A*0299 A*9201,... B*1599 B*9501,... Solution: 2010: B*07:02:01:01 A*9201: A*02:101 worst allele now: A*02:417 B*9501: B*15:101 How did HLA evolve Abi Rached et al Evolution of the MHC region Immunological Reviews 1999 Vol. 167:33-45

13 How did HLA evolve ClassI- PBD Abi Rached et al Evolution of the MHC region Immunological Reviews 1999 Vol. 167:33-45 How did HLA evolve Abi Rached et al Evolution of the MHC region Immunological Reviews 1999 Vol. 167:33-45

14 Immunoglobulin domain How did HLA evolve Abi Rached et al Evolution of the MHC region Immunological Reviews 1999 Vol. 167:33-45 IgG ClassI- KIR ClassII How did HLA evolve ClassI- KIR Immunoglobulin like domain ClassII IgG

15 How did HLA evolve

16 How did HLA evolve How did HLA evolve DRA-DPA1: DRA-DQA1 DPA1-DQA1

17 How did HLA evolve DRB1-DPB1 DRB1-DQB1 DRB1 homo sapiens SLA-DRB1 sus scrofa How did HLA evolve HLA-A HLA-B HLA-A HLA-C HLA-B HLA-C HLA-A SLA-1 (sus scrofa)

18 How did HLA evolve DRB1*01:02:01 DRB1*04:03:01 Exons Genomic Where do polymorphisms map Janeway, Travers: Immunobiology Class I HLA A mapped polymorphism

19 Where do polymorphisms map Class I HLA A mapped polymorphism of one allele per main group What are P and G groups The level of resolution achieved by many of the HLA typing technologies employed today, does not always allow for a single HLA allele to be unambiguously assigned. Often it is only possible to resolve the presence of a number of closely related alleles. This is referred to as an ambiguous string of alleles. In addition typing strategies are frequently aimed at resolving alleles that encode differences within the peptide binding domains, but fail to exclude those that differ elsewhere. For some purposes it is helpful to provide codes that aid the reporting of certain ambiguous alleles strings. The decision was taken to introduce codes to allow for the easy reporting of:

20 What are P groups HLA alleles that encode for identical peptide binding domains HLA alleles having nucleotide sequences that encode the same protein sequence for the peptide binding domains (exon 2 and 3 for HLA class I and exon 2 only for HLA class II alleles) will be designated by an upper case P which follows the allele designation of the lowest numbered allele in the group. A*02:01:01:01/02:01:01:02L/02:01:01:03/02:01:02/02:01:03/02:01:04/02:01 :05/02:01:06/02:01:07/02:01:08/02:01:09/02:01:10/02:01:11/02:01:12/02:01 :13/02:01:14/02:01:15/02:01:17/02:01:18/02:01:19/02:01:21/02:01:22/02:09 /02:66/02:75/02:89/02:97/02:132/02:134/02:140 This string can be reduced to A*02:01P What are G groups HLA alleles that share identical nucleotide sequences for the exons encoding the peptide binding domains HLA alleles that have identical nucleotide sequences across the exons encoding the peptide binding domains (exon 2 and 3 for HLA class I and exon 2 only for HLA class II alleles) will be designated by an upper case G which follows the allele designation of the lowest numbered allele in the group. A*02:01:01:01/02:01:01:02L/02:01:01:03/02:01:08/02:01:11/02:01:14/02:0 1:15/02:01:21/02:09/02:43N/02:66/02:75/02:83N/02:89/02:97/02:132/02:1 34/02:140 This string can be reduced to A*02:01:01G

21 What are P and G groups What are P and G groups

22 What are sequence features Thesis: Combinations of variable amino acid sites shared by several HLA alleles (shared epitopes) are most likely better descriptors of the actual causative genetic variants. What are sequence features Hum Mol Genet Feb 15;19(4): Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH.

23 What are sequence features What are sequence features MEDZINISCHE

24 What are sequence features Hum Mol Genet February 15; 19(4): What are serological equivalents

25 What are serological equivalents Serological equivalent information based on various sources WHO-assigned International cell exchange NMDP Neural Network. What are serological equivalents The World Health Organization (WHO) serological assignment is taken from the Nomenclature report 2004 (6) and from data submitted to the WHO Nomenclature Committee for Factors of the HLA System when a new allele is submitted for consideration.

26 What are serological equivalents International Cell Exchange, UCLA The International Cell Exchange, UCLA provided data showing serologic equivalents for these alleles: 49 HLA-A 128 HLA-B 35 HLA-C 88 HLA-DRB1 8 HLA-DRB3 3 HLA-DRB4 5 HLA-DRB5 19 HLA-DQB1 What are serological equivalents NMDP Data set includes only typings from US volunteer donors where both serologic and allele-level results have been reported for the HLA-A, -B, -C, - DRB1, or DQB1loci. An expectation maximization (EM) algorithm was used to obtain the correlation between alleles and serologic assignments. The information for 454 alleles, including 122 HLA-A, 200 -B, 50 -C, 73 -DRB1, and 9 -DQB1, was reviewed and updated.

27 What are serological equivalents Neural Network An artificial NN was used to predict serologic assignments for alleles lacking this information and to support serologic assignments from other sources. Aset of alleles used in previous iterations was used to train the NN. 10 NN were run instead of the five previously run to increase accuracy of the predictions. What are serological equivalents Expert assigned type The expert assigned type for HLA-A, -B, -C, -DRB1, -DRB 3/4/5, and -DQB1 alleles is the combination of all serologic equivalents information. This may help identify serologic equivalents when there are differences with the WHO HLA designated serologic assignments (e.g. B*4005), or where multiple assignments are possible such as hybrid molecules, or where more antigen assignments are given (e.g. A* 3204, Table 1 and B*1303, B*1304, Table 2). Occasionally, the expert assigned type is based on the NN assignment; however, while this should be considered with caution, the NN may be the only information available.

28 What are common and well defined alleles Common and Well-Documented HLA Alleles: Report of the Ad-Hoc Committee of the American Society for Histocompatiblity and Immunogenetics Pedro Cano a, William Klitz b, Steven J. Mack c, Martin Maiers d, Steven G.E. Marsh e, Harriet Noreen f, Elaine F. Reed g, David Senitzer h, Michelle Setterholm d, Anajane Smith i, Marcelo Fernández-Viña a, a University of Texas M. D. Anderson Cancer Center, HLA Typing Laboratory, Houston, Texas b Public Health Institute, Oakland, and University of California Berkeley, Berkeley, California c Children s Hospital Oakland Research Institute, Oakland, California, and Roche Molecular Systems Department of Human Genetics, Alameda, California d National Marrow Donor Program, Minneapolis, Minnesota e Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom f Fairview University of Minnesota Medical Center, Immunology Laboratory, Minneapolis, Minnesota g UCLA Immunogenetics Center, Department of Pathology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California h City of Hope National Medical Center, Duarte, California i Seattle Cancer Care Alliance, Clinical Immunogenetics Laboratory, Seattle, Washington What are common and well defined alleles Common alleles appear with gene frequencies greater than in any reference population. Accurate frequency estimations can be made for alleles observed three or more times; therefore, population studies with a sample size of 1,500 unrelated subjects (2n = 3,000 chromosomes) could detect with accuracy only allele frequencies of or greater.

29 What are common and well defined alleles Well-documented alleles have been observed in at least three independent unrelated individuals gene frequencies have not been estimated accurately. Alleles that are found only in isolated populations may have low frequency in any outbred population their frequencies are likely to be lower overall than those of most common alleles. What are common and well defined alleles Rare Alleles The remaining alleles are considered rare alleles. These alleles have extremely low frequencies and are not likely to be found again in a significant number of unrelated subjects.

30 What are common and well defined alleles What are common and well defined alleles 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT HLA Database release being CWD

31 What are common and well defined alleles Tissue Antigens, 2013, 81,

32 What are common and well defined alleles 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, - DQA1, -DQB1, -DPA1 and -DPB1 loci as CWD, 14.3% of the HLA alleles in IMGT/HLA Database release of these alleles as common (having known frequencies) 707 as being well-documented basis of 140,000 sequence-based typing observations and available HLA haplotype data assigned CWD status to specific G and P designations. 147/151 G groups as CWD 290/415 P groups as CWD What are common and well defined alleles Well-documented alleles observed five times in unrelated individuals through the use of a SBT method that assessed the pertinent exon(s) or detected three times via SBT and observed in a specific haplotype in unrelated individuals. The A*23:17 allele has been identified in three unrelated individuals in the same ethnic group via exon 5 sequencing, and is associated with a B*45:01 DRB1*13:01 haplotype. Because this allele was identified in multiple individuals, persists in a population in a specific haplotype, but is not observed in numerous populations at high frequency, it was included in the Well-Documented category.

33 What are common and well defined alleles A*24:06 - A*24:02 Differ by an amino acid Q156W, exon 3. A*24:06 reported 39 times in 10 studies, all used SSOP and SSP methods complete exon 3 sequence of this allele appeared to have been identified in only one cell. C*12:02:01 - C*12:02:02 differs by a nucleotide change (A873G) in exon 4. C*12:02:01 had been reported 89 times in 16 studies genotyping performed in these studies assessed exons 2 and 3 data C*12:02:01 was reported because it is the lowest numbered allele in an ambiguity C*12:02:01 appeared to have only been identified in one cell. What are common and well defined alleles

34 What are GL-strings Allele ambiguity results when the polymorphisms that distinguish alleles fall outside of the regions assessed by the genotyping system. A*02:07/A*02:15N/A*02:265 Genotype Ambiguity Genotype ambiguity results from an inability to establish chromosomal phase between identified polymorphisms. DRB1*04:01:01+DRB1*13:01:01 or DRB1*04:13+DRB1*13:02:01 or DRB1*04:14+DRB1*14:21 or DRB1*04:35+DRB1*13:40 or DRB1*04:38+DRB1*13:20 have identical heterozygous DRB1 exon 2

35 GLString Delimiters & Precedence Order Delimiter Description 1 ^ Gene/Locus 2 Genotype list 3 + Genotype 4 ~ Haplotype 5 / Alleles Allelic ambiguity delimiter Allele list A*23:26/A*23:39 / allele allele Possible alleles at locus A

36 ~ Haplotype delimiter cis used to group haplotype DRB5*01:02~DRB1*15:04 allele at locus DRB5 allele at locus DRB1 same chromosome + Genotype delimiter Usually interpret being on different chromosomes, genotype (trans), delimits haplotype But may be gene duplication (ambiguous cis) A*02:302+A*23:26/A*23:39 allele allele allele allelic ambiguity at A genotype

37 Genotype list delimiter A*02:69+A*23:30 A*02:302+A*23:26/A*23:39 allele allele allele allele list genotype genotype ^ Locus delimiter A*02:69+A*23:30 A*02:302+A*23:26/A*23:39^B*44:02:13+B*49:08 allele allele allele allele list allele allele possible genotype for A possible genotype for A genotype list for A genotype for B

38 Future state glstring HLA LAB URI: QRcode Print Lab Report A B C DRB1 DQB1 Sca n URI BMT Clinic URI glstring Registry 75