Application of high‐throughput next‐generation sequencing for HLA typing of DNA extracted from postprocessing cord blood units

Seshasubramanian, Vani; Venugopal, Meganathan; Kannan, Aruna D. S.; Naganathan, Chandramouleeswaran; Manisekar, N. K.; Kumar, Yogesh N.; Narayan, Saranya; Periathiruvadi, Srinivasan

doi:10.1111/tan.13565

Cited by 4 publications

(2 citation statements)

References 29 publications

(29 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Now NGS technology is increasingly used in HLA genotyping forhigh resolution [18][19][20][21][22][23][24][25][26][27],it has high throughput and can bedecreased the rate of the ambiguous allele combinations. Here weused a commercial NGS method for HLA genotyping.…”

Section: Discussionmentioning

confidence: 99%

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Wang

Dong

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background The allele and haplotype frequencies of HLA loci are various in the populations. Most of the data for HLA alleles and haplotypes were at low resolution or two fields resolution. Here, the data for HLA alleles and haplotypes at three fields resolution was reported in Chinese Han population. Methods All samples were come from the Zhejiang Cord Blood Bank, China after information consent. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing (NGS) method. The allele frequencies of HLA loci were analyzed at three fields resolution. The haplotype estimation and linkage disequilibrium analysis was used Arlequin software 3.5.2.2. Result The top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02 (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01(21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01 (12.08%); DRB4*01:03:01(25.72%), DRB3*02:02:01(20.27%), DRB5*01:01:01(10.96%) respectively. A total of 1542 distinct A-B-C-DRB1-DQB1-DRB3/4/5 haplotypes were identified. The alleles of HLA loci were showed strong linkage disequilibrium. Conclusion The data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level was obtained, which will help to analyze the HLA ploymorphism in the populations.

show abstract

Section: Discussionmentioning

confidence: 99%

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Wang

Dong

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The "long-amplicon, short-reads" approach to NGS-based HLA typing has also been implemented successfully on the Illumina platform. Several commercially available assays have achieved comparable accuracy and efficiency based on well-designed validation studies [9,10,[18][19][20]. The general workflows of these assays are similar to AllType, except for some differences in the PCR strategy, barcoding method, and sequencing chemistry.…”

Section: Plos Onementioning

confidence: 99%

Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing

et al. 2020

View full text Add to dashboard Cite

Background Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplantrelevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. Methods Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/ DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. Results The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library

show abstract

Generation of good manufacturing practice grade virus-specific T cells for the management of post-transplant CMV infections

Arunachalam

Palani

Yasar

et al. 2022

Journal of Immunological Methods

View full text Add to dashboard Cite

Application of high‐throughput next‐generation sequencing for HLA typing of DNA extracted from postprocessing cord blood units

Cited by 4 publications

References 29 publications

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing

Generation of good manufacturing practice grade virus-specific T cells for the management of post-transplant CMV infections

Contact Info

Product

Resources

About