کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
6116645 | 1216358 | 2015 | 25 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
HLA-genotyping of clinical specimens using Ion Torrent-based NGS
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کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری
ایمنی شناسی و میکروب شناسی
ایمونولوژی
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چکیده انگلیسی
We have evaluated and validated the NXType⢠workflow (One Lambda, Inc.) and the accompanying TypeStream⢠software on the Ion Torrent Next Generation Sequencing (NGS) platform using a comprehensive testing panel. The panel consisted of 285 genomic DNA (gDNA) samples derived from four major ethnic populations and contained 59 PT samples and 226 clinical specimens. The total number of alleles from the six loci interrogated by NGS was 3420. This validation panel provided a wide range of HLA sequence variations including many rare alleles, new variants and homozygous alleles. The NXType⢠system (reagents and software) was able to correctly genotype the vast majority of these specimens. The concordance rate between SBT-derived genotypes and those generated by TypeStream⢠auto-analysis ranged from 99.5% to 99.8% for the HLA-A, B, C, DRB1 and DQB1 loci, and was 98.9% for HLA-DPB1. A strategy for data review was developed that would allow correction of most of the few remaining typing errors. The entire NGS workflow from gDNA amplification to genotype assignment could be completed within 3 working days. Through this validation study, the limitations and shortcomings of the platform, specific assay system, and software algorithm were also revealed for further evaluation and improvement.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Human Immunology - Volume 76, Issue 12, December 2015, Pages 903-909
Journal: Human Immunology - Volume 76, Issue 12, December 2015, Pages 903-909
نویسندگان
Jonathan C. Barone, Katsuyuki Saito, Karl Beutner, Maria Campo, Wei Dong, Chirayu P. Goswami, Erica S. Johnson, Zi-Xuan Wang, Susan Hsu,