P185 Next generation sequencing of HLA class II in an argentinian registry population reveals the complexity of these loci

Introduction. The patient survival after allogeneic haematopoietic stem cell transplantation (allo-HSCT) from an unrelated or related haploidentical donor is improved in a donor–recipient match resolution at the level of non-coding region identity of HLA genes. Next-generation sequencing (NGS) allows detection of point substitutions in HLA non-coding regions.Aim — assessment of the NGS-based HLA-typing performance.Materials and methods. An NGS-based HLA-typing of 1,056 DNA samples from allo-HSCT recipients, their related and registry donors was performed with AllTypekit chemistry (OneLambda, USA). A parallel HLA-typing assay of 96 samples by 8 genes (A/B/C/DRB1/DRB3/DRB4/DRB5/DQB1) was accomplished within one working week.Results. HLA class I genes were typed at a 4-field (allelic), and HLA class II genes — 2–4-field (high to allelic) resolution. An allelic-resolution typing of HLA class I genes in a Russian population (657 registry donors) was conducted for the first time. The most frequent HLA alleles have been identified: А*02:01:01:01 in HLA-A (26.9 %), B*07:02:01:01 in HLA-B (12.5 %) and C*07:02:01:03 in HLA-C (12.6 %). The most frequent HLA class II variants were DRB1*07:01:01 (14.1 %), DRB3*02:01:01 (18.0 %), DRB4*01:03:01 (18.9 %), DRB5*01:01:01 (13.5 %), DQB1*03:01P (17.4 %).Conclusion. An NGS-geared HLA-typing has yielded low-ambiguity allelic and high-level resolution results in a parallel sequencing assay with a large number of samples. The method implemented detects genetic polymorphisms also in non-exonic non-coding regions of HLA genes and facilitates typing in candidate HSCT recipients, related and unrelated donors.

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Deconstruction of HLA-DRB104:01:01 and HLA-DRB115:01:01 class II haplotypes using next-generation sequencing in European-Americans with multiple sclerosis

Multiple Sclerosis Journal ◽

10.1177/1352458518770019 ◽

2018 ◽

Vol 25 (6) ◽

pp. 772-782 ◽

Cited By ~ 5

Author(s):

Lisa E Creary ◽

Kalyan C Mallempati ◽

Sridevi Gangavarapu ◽

Stacy J Caillier ◽

Jorge R Oksenberg ◽

...

Keyword(s):

Multiple Sclerosis ◽

Next Generation Sequencing ◽

Class Ii ◽

Effect Sizes ◽

Molecular Architecture ◽

Next Generation ◽

European Americans ◽

Resolution Level ◽

Hla Dqa1 ◽

Generation Sequencing

Background: The association between HLA-DRB1*15:01 with multiple sclerosis (MS) susceptibility is well established, but the contribution of the tightly associated HLA-DRB5*01:01 allele has not yet been completely ascertained. Similarly, the effects of HLA-DRB1*04:01 alleles and haplotypes, defined at the full-gene resolution level with MS risk remains to be elucidated. Objectives: To characterize the molecular architecture of class II HLA-DR15 and HLA-DR4 haplotypes associated with MS. Methods: Next-generation sequencing was used to determine HLA-DQB1, HLA-DQA1, and HLA-DRB1/4/5 alleles in 1403 unrelated European-American patients and 1425 healthy unrelated controls. Effect sizes of HLA alleles and haplotypes on MS risk were measured by odds ratio (OR) with 95% confidence intervals. Results: HLA-DRB1*15:01:01:01SG (OR = 3.20, p < 2.2E–16), HLA-DRB5*01:01:01 (OR = 2.96, p < 2.2E–16), and HLA-DRB5*01:01:01v1_STR1 (OR = 8.18, p = 4.3E–05) alleles all occurred at significantly higher frequencies in MS patients compared to controls. The most significant predis-posing haplotypes were HLA-DQB1*06:02:01~ HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01 and HLA-DQB1*06:02:01~HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01v1_STR1 (OR = 3.19, p < 2.2E–16; OR = 9.30, p = 9.7E–05, respectively). Analyses of the HLA-DRB1*04 cohort in the absence of HLA-DRB1*15:01 haplotypes revealed that the HLA-DQB1*03:01:01:01~HLA-DQA1*03:03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was protective (OR = 0.64, p = 0.028), whereas the HLA-DQB1*03:02:01~HLA-DQA1*03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was associated with MS susceptibility (OR = 1.66, p = 4.9E–03). Conclusion: HLA-DR15 haplotypes, including genomic variants of HLA-DRB5, and HLA-DR4 haplotypes affect MS risk.

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