P262 Dna sequencing with Scisco genetics next generation sequencing HLA typing version 5 kit

Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight® HLA v2 kit, Illumina MiSeqDx platform system, and Assign™ for TruSight™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.

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Next-Generation Sequencing: From Basic Research to Diagnostics

Clinical Chemistry ◽

10.1373/clinchem.2008.112789 ◽

2009 ◽

Vol 55 (4) ◽

pp. 641-658 ◽

Cited By ~ 459

Author(s):

Karl V Voelkerding ◽

Shale A Dames ◽

Jacob D Durtschi

Keyword(s):

Next Generation Sequencing ◽

Dna Sequencing ◽

Single Molecule ◽

Basic Research ◽

Clinical Diagnostics ◽

Massively Parallel ◽

Next Generation ◽

New Paradigm ◽

The Impact ◽

Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

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Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis

Frontiers in Genetics ◽

10.3389/fgene.2018.00503 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 16

Author(s):

Amit Kishore ◽

Martin Petrek

Keyword(s):

Next Generation Sequencing ◽

Hla Typing ◽

Next Generation ◽

Generation Sequencing

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HLA‐A , ‐B, ‐C, ‐ DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next‐generation sequencing

HLA ◽

10.1111/tan.14167 ◽

2020 ◽

Author(s):

Dong Wook Jekarl ◽

Gun Dong Lee ◽

Jae Bin Yoo ◽

Jung Rok Kim ◽

Haein Yu ◽

...

Keyword(s):

Next Generation Sequencing ◽

Performance Characteristics ◽

Hla Typing ◽

Korean Population ◽

Next Generation ◽

Drb1 Allele ◽

Haplotype Frequencies ◽

And Performance ◽

Generation Sequencing

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P034 Next generation sequencing - the ultimate tool for confirmatory HLA typing in cadaveric donors? A case report

Human Immunology ◽

10.1016/j.humimm.2019.07.086 ◽

2019 ◽

Vol 80 ◽

pp. 80

Author(s):

Ibis T. Hernandez ◽

Jennifer McCue ◽

Ana Hernandez ◽

Ozzarah Ferrer ◽

Maria Reiger ◽

...

Keyword(s):

Case Report ◽

Next Generation Sequencing ◽

Hla Typing ◽

Next Generation ◽

Cadaveric Donors ◽

Generation Sequencing

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Establishing a Next Generation Sequencing laboratory for high resolution HLA typing

Human Immunology ◽

10.1016/j.humimm.2015.07.146 ◽

2015 ◽

Vol 76 ◽

pp. 101

Author(s):

Kim McGowan ◽

Laurine Bow

Keyword(s):

Next Generation Sequencing ◽

High Resolution ◽

Hla Typing ◽

Next Generation ◽

Generation Sequencing

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HLA Genotyping using Next Generation Sequencing

Romanian Journal of Internal Medicine ◽

10.1515/rjim-2016-0019 ◽

2016 ◽

Vol 54 (2) ◽

pp. 98-104

Author(s):

C. Lucan ◽

Laura-Ancuta Pop ◽

A. Florian ◽

Valentina Pileczki ◽

B. Petrushev ◽

...

Keyword(s):

Stem Cell ◽

Next Generation Sequencing ◽

Brain Tumors ◽

Stem Cell Transplantation ◽

Cell Transplantation ◽

Disease Recurrence ◽

Hla Typing ◽

Next Generation ◽

Poor Outcomes ◽

Generation Sequencing

Abstract From an oncological perspective, the second most common malignancies in children are brain tumors. Despite the recent therapeutic breakthroughs in this field, concerning surgery, radiotherapy and chemotherapy alike, some cases still have poor outcomes in curability. This is especially the case in patients with high-risk histological types of tumors, and those suffering from residual, remitting and disseminated diseases. Due to the unique neuroanatomical emplacement of brain tumors and their aggressive infiltrative behavior, their total removal remains a demanding task. This can be perceived in the high rates of failure treatment and disease recurrence. Furthermore, the adjacent healthy brain tissue is inevitably damaged in the surgical process of effectively removing these tumors. Thus, stem cell transplantation may be a viable solution for the clinical management of these malignancies, as proven by various recent breakthroughs. In the current concise review, we present the role of next generation sequencing in HLA typing for stem cell transplantation in primary CNS pediatric malignancies.

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