Virtual DNA analysis — a new tool for combination and standardised evaluation of SSO, SSP and sequencing‐based typing results

Abstract

In order to obtain reliable information on HLA types, DNA typing with sequence-specific oligonucleotide/primer (SSO/SSP) typing sets or sequencing-based typing (SBT) is increasingly performed. The quality of the evaluation depends on the presence of a complete listing of all typed alleles as well as on the ability of detecting all corresponding alleles/allele pairs. We have developed the concept of virtual DNA analysis (VDA), which is able to combine all types of SSO/SSP/SBT results and evaluate this typing in combination according to the latest published allele sequence lists. The concept is based on the target DNA recognised by the respective typing techniques. All SSO/SSP or SBT results are transformed to a virtual sample DNA, which subsequently is analysed. Evaluation of generic or allele-specific DNA typing or the combination of both is supported. Due to this flexible approach, all kinds of SSO/SSP sets, as far as the respective SSO/SSP sequences are available, can be entered and evaluated immediately. The combination of collected data of different typing sets and procedures leads to the highest possible typing resolution. If more than one possible allele combination persists, the program reduces the result to the most specific common denominator in a stepwise manner. VDA offers the possibility of re-evaluation of former SSO/SSP/SBT results, alone or in combination. No solutions are omitted. This might be a first step towards standardisation of evaluating DNA-based HLA typing results or transfer of the respective typing data for later evaluation.

HLA-A*02 is associated with a reduced risk and HLA-A*01 with an increased risk of developing EBV+ Hodgkin lymphoma

“…10,26 In this study, the HLA-A gene was analyzed for association with EBV ϩ HL. The results confirmed an association; HLA-A*02 was underrepresented in patients with EBV ϩ HL (15%), and HLA-A*01 was overrepresented in patients with EBV ϩ HL (37.1%).…”

“…Differences in frequencies per haplotype and genotype were calculated by 2 or Fisher exact tests. HLA-A alleles of the most frequent haplotypes on a level of 2 digits were determined using the SCORE program (version 2.13) 26 . This program can distinguish between all different HLA-A alleles and indicates if a given sequence is specific for only 1 HLA-A allele or not.…”

Multiple HLA class I and II associations in classical Hodgkin lymphoma and EBV status defined subgroups

“…The HLA alleles were defined by specific hybridization patterns of multiple probes. HLA genotype was ascertained according to the manufacturer's instructions using the manufacturer's software and additionally by the SCORE 4.0204F software, 19 enabling the exclusion of probes with borderline hybridization signals. The presumed antigen or T-cell receptor binding function of the SNPs was identified according to Bjorkman and Parham.…”

Identification of a New HLA-B Allele (B*1576) by Haplotype Specific Extraction

“…All conventional typing assays failed to give conclusive results and suggested the likely presence of a new allele. When considering Helmberg-SCORE analysis [2] of exons 2 and 3 and allowing for up to three mismatches, the closest typing of the sample appeared to be of a low-resolution type B*15 and B*56.…”