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- W170152017 abstract "Ion Torrent Next Generation Sequencing (NGS) technology using the Personal Genomic Sequencer (PGM) provides a new platform for HLA sequence based typing. The recent assay development opens the door for unambiguous genotype with unprecedented coverage and accuracy. Interpretation from the massive data generated by PGM becomes a challenge, in addition to the issues of transferring data across networks or computers. Our approach is to leverage the existing PGM framework and infrastructure to develop HLA software tools. The PGM uses the Torrent Suite software through web browser to configure, execute and review a sample run. Other software packages can be added to the Torrent Suite through plug-ins. A plug-in is fully integrated into the Torrent Suite and can be automatically executed after a run. In addition, the plug-in can directly access raw PGM data, eliminating any data transfer from the PGM. We have developed a plug-in to read and process barcode files for a run directly on the PGM computer. It uses proprietary algorithms to map NGS reads to the HLA allele alignment library to construct consensus sequences and determine genotypes from the consensus sequences. The genotype for each barcode is reported in a tabulated form as part of the Torrent Suite run report. So far, whole gene sequences of HLA-A,B,C,DRB1, and DQB1 from 30 samples have been used to verify the typing algorithm. We are able to achieve typing concordance in the majority with average read depth in hundreds and complete coverage across target region. The challenges in HLA allele calling are mainly due to unknown HLA library sequences and insertion-deletion sequences. While the algorithm will continue to evolve by validating against deep sequencing analysis tools using a panel of well characterized HLA samples, Life Technologies HLA typing plug-in can be seamlessly integrated into the assay workflow and provides users the simplest way to produce HLA genotypes from the PGM. Shi:Life Technologies: Employee. Dinauer: Life Technologies: Employee. Radick: Life Technologies: Employee. Hunsicker: Life Technologies: Employee. Veldre: Life Technologies: Employee. Lelivelt: Life Technologies: Employee. Conradson: Life Technologies: Employee." @default.
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- W170152017 date "2013-11-01" @default.
- W170152017 modified "2023-09-25" @default.
- W170152017 title "161-P" @default.
- W170152017 doi "https://doi.org/10.1016/j.humimm.2013.08.236" @default.
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