Journal: Human immunology

Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

doi: 10.1016/j.humimm.2020.06.002

Figure Lengend Snippet: (A) HLA-B allele alignment of next generation sequencing data for one sample in HLA Explore software (exons 1–4). This sample resulted in a failure or “no call” for the HLA-B locus; however, by actual HLA typing was found to be HLA-B*44:02:01/*56:01:01. The top row shows the correct alignment of reads (represented by stacked grey bars) to the HLA-B*56:01:01 allele from exon 1 (left side) to exon 4 (right side of diagram), while the middle row shows reads unevenly and incorrectly mapping to the HLA-B*83:01 allele, and the bottom row shows a lack of reads mapping to the correct HLA-B*44:02:01 allele. (B) In contrast, the Optitype plots for the same sample are shown. This software produced a call concordant to the second field for each allele.

Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

Techniques: Next-Generation Sequencing, Software, Produced

Journal: Human immunology

Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

doi: 10.1016/j.humimm.2020.06.002

Figure Lengend Snippet: Summary of concordance between actual HLA typing by SSO and predicted typing by next generation sequencing by locus. Number (percentage) of alleles (for 68 samples from Data Set 1: Germline Whole Exome Sequencing of Patients with Breast Cancer) is provided. A) Using Omixon software; B) Using OptiType software; C) Using HLA-Genotyper software. Full results are available in the Supplementary materials .

Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

Techniques: Next-Generation Sequencing, Sequencing, Software

Journal: Human immunology

Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

doi: 10.1016/j.humimm.2020.06.002

Figure Lengend Snippet: Summary of concordance of HLA calls generated by actual HLA typing (SSO) and predicted typing by next generation sequencing by locus for tumor specimens of each of the 5 subjects. The tumor from subject A was typed at 4 different time points. Full data is available in the Supplementary materials .

Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

Techniques: Generated, Next-Generation Sequencing