Improved HLA typing of Class I and Class II alleles from next‐generation sequencing data

HLA ◽  
2019 ◽  
Vol 94 (6) ◽  
pp. 504-513 ◽  
Author(s):  
Angelina Sverchkova ◽  
Irantzu Anzar ◽  
Richard Stratford ◽  
Trevor Clancy
Keyword(s):  
Next Generation Sequencing ◽  
Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data

2018 ◽  
pp. 225-233 ◽  
Author(s):  
Shuji Kawaguchi ◽  
Koichiro Higasa ◽  
Ryo Yamada ◽  
Fumihiko Matsuda
Keyword(s):  
Next Generation Sequencing ◽  
Hla Typing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing ◽  
A Current

scholarly journals HLA‐HD: An accurate HLA typing algorithm for next‐generation sequencing data

2017 ◽  
Vol 38 (7) ◽  
pp. 788-797 ◽  
Author(s):  
Shuji Kawaguchi ◽  
Koichiro Higasa ◽  
Masakazu Shimizu ◽  
Ryo Yamada ◽  
Fumihiko Matsuda
Keyword(s):  
Next Generation Sequencing ◽  
Hla Typing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals Next generation sequencing HLA-typing of recipients and donors of allogeneic haematopoietic stem cells

2021 ◽  
Vol 66 (2) ◽  
pp. 206-217
Author(s):  
E. G. Khamaganova ◽  
A. R. Abdrakhimova ◽  
E. A. Leonov ◽  
S. P. Khizhinskiy ◽  
T. V. Gaponova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Next Generation ◽  
Coding Regions ◽  
Hla Genes ◽  
Generation Sequencing

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.

scholarly journals OptiType: precision HLA typing from next-generation sequencing data

2014 ◽  
Vol 30 (23) ◽  
pp. 3310-3316 ◽  
Author(s):  
András Szolek ◽  
Benjamin Schubert ◽  
Christopher Mohr ◽  
Marc Sturm ◽  
Magdalena Feldhahn ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hla Typing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals HLAreporter: a tool for HLA typing from next generation sequencing data

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Yazhi Huang ◽  
Jing Yang ◽  
Dingge Ying ◽  
Yan Zhang ◽  
Vorasuk Shotelersuk ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hla Typing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

2021 ◽  
Author(s):  
Anne Krogh Nøhr ◽  
Kristian Hanghøj ◽  
Genis Garcia Erill ◽  
Zilong Li ◽  
Ida Moltke ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Software Tool ◽  
Estimation Methods ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C ++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

scholarly journals recoup: flexible and versatile signal visualization from next generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Panagiotis Moulos
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Special Focus ◽  
Next Generation ◽  
Sequencing Data ◽  
User Friendliness ◽  
Computational Environment ◽  
Level Data ◽  
Data Signal ◽  
Generation Sequencing

Abstract Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.

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