HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel

Wang, Yen-Yen; Mimori, Tsuneyo; Khor, Seik‐Soon; Gervais, Olivier; Kawai, Yosuke; Hitomi, Yuki; Tokunaga, Katsushi; Nagasaki, Masao

doi:10.1038/s41439-019-0061-y

Cited by 13 publications

(8 citation statements)

References 12 publications

(15 reference statements)

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“…NGS tests are currently actively being conducted by focusing on targeted genes related to cancer and are used for patient treatment, leading to the increased availability of HLA typing using NGS data. Computational software tools to predict HLA type based on NGS data have increasingly been reported (6)(7)(8)(9)(10)(11)(12)(13)(14)(15). However, there is no standard method to provide the perfect assignment for all HLA types given the difficulty of overcoming polymorphisms and the A B FIGURE 3 | The number of "true calls" and "false call" of concordant calls according to the number of the concordant calls (A).…”

Section: Discussionmentioning

confidence: 99%

“…However, HLA genotyping by NGS still fails to meet expectations due to focusing on numerous similar genes and pseudogenes, genetic complexity, difficulty in finding a reference genome, and the presence of segmental duplications. Various HLA genotype predicting tools based on NGS data have been developed to resolve these issues as follows: HLA MINER , ATHLATES (5), HLA REPORTER (6), OptiType (7), HLA-HD (8), PHLAT, seq2HLA (9), arcasHLA (10), HLAscan (11), HLA*LA (12), Kourami (13), HLA-VBSeq (14), HLA-VBSeq.V2 (15), PolySolver, HLAforest, xHLA (16), and HLAProfiler (17). These tools are based on broadly two methods, including alignment-based and assembly-based methods.…”

Section: Introductionmentioning

confidence: 99%

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A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

Lee

Seo

Song³

et al. 2021

Front. Immunol.

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BackgroundHigh-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate.Materials and MethodsWe compared availability, accuracy, correction score, and complementary ratio of eight HLA genotyping tools (OptiType, HLA-HD, PHLAT, seq2HLA, arcasHLA, HLAscan, HLA*LA, and Kourami) using 1,005 cases from the 1000 Genomes Project data. We created a new HLA-genotyping algorithm combining tools based on the precision and the accuracy of tools’ combinations. Then, we assessed the new algorithm’s performance in 39 in-house samples with normal whole-exome sequencing (WES) data and polymerase chain reaction–sequencing-based typing (PCR-SBT) results.ResultsRegardless of the type of tool, the calls presented by more than six tools concordantly showed high accuracy and precision. The accuracy of the group with at least six concordant calls was 100% (97/97) in HLA-A, 98.2% (112/114) in HLA-B, 97.3% (142/146) in HLA-C. The precision of the group with at least six concordant calls was over 98% in HLA-ABC. We additionally calculated the accuracy of the combination tools considering the complementary ratio of each tool and the accuracy of each tool, and the accuracy was over 98% in all groups with six or more concordant calls. We created a new algorithm that matches the above results. It was to select the HLA type if more than six out of eight tools presented a matched type. Otherwise, determine the HLA type experimentally through PCR-SBT. When we applied the new algorithm to 39 in-house cases, there were more than six matching calls in all HLA-A, B, and C, and the accuracy of these concordant calls was 100%.ConclusionsHLA genotyping accuracy using NGS data could be increased by combining the current HLA genotyping tools. This new algorithm could also be useful for preliminary screening to decide whether to perform an additional PCR-based experimental method instead of using tools with NGS data.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

Lee

Seo

Song³

et al. 2021

Front. Immunol.

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“…The accuracy of phasing was high, with both switch error rates and Hamming error rates lower than 1% (Supplementary Table 1 ). We estimated the HLA types with HLA-VBSeq 23 (Supplementary Fig. 3a ) for six major HLA genes, which have been found to be strongly associated with many human diseases 24 , 25 .…”

Section: Resultsmentioning

confidence: 99%

CRISPR-based targeted haplotype-resolved assembly of a megabase region

Zhang

et al. 2023

Nat Commun

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Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

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“…The accuracy of phasing was high, with both switch error rates and Hamming error rates lower than 2% (Supplementary Table 1). We estimated the HLA types with HLA-VBSeq 22 (Supplementary Fig. 3) for six major HLA genes, which have been found to be strongly associated with many human diseases 23, 24 .…”

Section: Resultsmentioning

confidence: 99%

CRISPR-based targeted haplotype-resolved assemblies of a megabase region

Zhang

et al. 2022

Preprint

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Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved de novo assemblies of targeted genomic regions with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assemblies, our targeted approach achieved comparable completeness and accuracy with greatly reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

show abstract

HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel

Cited by 13 publications

References 12 publications

A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

CRISPR-based targeted haplotype-resolved assembly of a megabase region

CRISPR-based targeted haplotype-resolved assemblies of a megabase region

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