PMID- 33222728
OWN - NLM
STAT- MEDLINE
DCOM- 20210621
LR  - 20210621
IS  - 1681-7168 (Electronic)
IS  - 1022-386X (Linking)
VI  - 30
IP  - 11
DP  - 2020 Nov
TI  - Comparison of Sequence Specific Primers in the Next Generation Sequencing in 
      Human Leukocyte Antigen Typing for Transplant Recipients.
PG  - 1138-1142
LID - 10.29271/jcpsp.2020.11.1138 [doi]
AB  - OBJECTIVE: To compare two human leukocyte antigen (HLA) typing methods, namely 
      sequence specific primers (SSP) and next generation sequencing (NGS) for alleles 
      concordance Study Design: Descriptive study. PLACE AND DURATION OF STUDY: 
      Immunology department, Armed Forces Institute of Pathology, Rawalpindi, Pakistan, 
      from December 2019 to May 2020. METHODOLOGY: A total of 48 subjects, including 30 
      males and 18 females, were typed by NGS at 7 loci, making a total of 672 types 
      loci. SSP typing was done for 276 loci among these. Comparison was made at SSP 
      level of low resolution. NGS typing was done with Illumina's MiSeq instrument 
      using Omixon HLA holotype 7 loci kit and analysis done with HLA twin software. 
      SSP typing was done with micro SSP kit from onelambda. Statistical analysis was 
      done using statistical package for social sciences (SPSS) version 24.0. RESULTS: 
      Among the 672 NGS types loci and 276 SSP types loci, there were mismatches at one 
      B locus and one C locus, whereby NGS computed HLA-B*58:01 and HLA-C*12:02 while 
      SSP detected HLA-B*57 and HLA-C*05, respectively. At remaining 274 loci, HLA 
      typing fully matched at low resolution, making concordance rate 99.3%. Commonest 
      alleles detected by NGS were HLA-A*02:01, B*51:01, C*07:02, DPB1*04:01, 
      DQA1*01:03, DQB1*02:01 and DRB1*13:01. CONCLUSION: Batch testing, high 
      throughput, improved accuracy, more loci coverage, maximum gene coverage 
      including all exons and introns and high-resolution typing confer significant 
      advantages to next generation sequencing over old methods of HLA typing. This 
      technique is suitable for high throughput laboratories. High running cost hampers 
      its routine implementation in 3rd world countries. Key Words: Human leukocyte 
      antigen, Next generation sequencing, High resolution.
FAU - Tipu, Hamid Nawaz
AU  - Tipu HN
AD  - Department of Immunology, Armed Forces Institute of Pathology, Rawalpindi, 
      Pakistan.
LA  - eng
PT  - Journal Article
PL  - Pakistan
TA  - J Coll Physicians Surg Pak
JT  - Journal of the College of Physicians and Surgeons--Pakistan : JCPSP
JID - 9606447
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Female
MH  - Genotype
MH  - HLA Antigens/genetics
MH  - *High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Testing
MH  - Humans
MH  - Male
MH  - Pakistan
MH  - Sequence Analysis, DNA
MH  - *Transplant Recipients
EDAT- 2020/11/24 06:00
MHDA- 2021/06/22 06:00
CRDT- 2020/11/23 05:24
PHST- 2020/06/20 00:00 [received]
PHST- 2020/10/21 00:00 [accepted]
PHST- 2020/11/23 05:24 [entrez]
PHST- 2020/11/24 06:00 [pubmed]
PHST- 2021/06/22 06:00 [medline]
AID - 040579197 [pii]
AID - 10.29271/jcpsp.2020.11.1138 [doi]
PST - ppublish
SO  - J Coll Physicians Surg Pak. 2020 Nov;30(11):1138-1142. doi: 
      10.29271/jcpsp.2020.11.1138.