A Case Study for HLA Typing in Clinics: Reproducibility and Flowspace Alignment of NGS Reads

Authors: Krisztina Rigó, György Horváth, Szilveszter Juhos, Sabine Canivet, Philippe Pellet, Abdelali Boudifa, Veronique Bertrand, Ioannis Theodorou

Long reads produced by Roche 454 sequencers are used for HLA typing for quite a while. Having long reads it is easier to determine the phase, but homopolymer errors are bringing in other difficulties. We were investigating HLA typing problems arising from these sequencing errors, focusing on accuracy and reproducibility of typing of different approaches. The three typing algorithm under our scope considered exons only, exons and introns and novel alleles respectively. Our comparison shows that it is possible to precisely and type high quality clinical samples, reproduce typing results and present QC measures for typing. Detecting novel alleles is possible only for high quality data, but samples typed as common alleles by other methods can actually contain differences in non-coding regions and these deviations can be detected in the clinics.

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