PMID- 26119888
OWN - NLM
STAT- MEDLINE
DCOM- 20160530
LR  - 20150825
IS  - 1744-313X (Electronic)
IS  - 1744-3121 (Linking)
VI  - 42
IP  - 5
DP  - 2015 Oct
TI  - Towards allele-level human leucocyte antigens genotyping - assessing two 
      next-generation sequencing platforms: Ion Torrent Personal Genome Machine and 
      Illumina MiSeq.
PG  - 346-58
LID - 10.1111/iji.12213 [doi]
AB  - Human leucocyte antigens (HLA) typing has been a challenge due to extreme 
      polymorphism of the HLA genes and limitations of the current technologies and 
      protocols used for their characterization. Recently, next-generation sequencing 
      techniques have been shown to be a well-suited technology for the complete 
      characterization of the HLA genes. However, a comprehensive assessment of the 
      different platforms for HLA typing, describing the limitations and advantages of 
      each of them, has not been presented. We have compared the Ion Torrent Personal 
      Genome Machine (PGM) and Illumina MiSeq, currently the two most frequently used 
      platforms for diagnostic applications, for a number of metrics including total 
      output, quality score per position across the reads and error rates after 
      alignment which can all affect the accuracy of HLA genotyping. For this purpose, 
      we have used one homozygous and three heterozygous well-characterized samples, at 
      HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1. The total output of bases produced by 
      the MiSeq was higher, and they have higher quality scores and a lower overall 
      error rate than the PGM. The MiSeq also has a higher fidelity when sequencing 
      through homopolymer regions up to 9 bp in length. The need to set phase between 
      distant polymorphic sites was more readily achieved with MiSeq using paired-end 
      sequencing of fragments that are longer than those obtained with PGM. 
      Additionally, we have assessed the workflows of the different platforms for 
      complexity of sample preparation, sequencer operation and turnaround time. The 
      effects of data quality and quantity can impact the genotyping results; having an 
      adequate amount of good quality data to analyse will be imperative for confident 
      HLA genotyping. The overall turnaround time can be very comparable between the 
      two platforms; however, the complexity of sample preparation is higher with PGM, 
      while the actual sequencing time is longer with MiSeq.
CI  - (c) 2015 John Wiley & Sons Ltd.
FAU - Duke, J L
AU  - Duke JL
AUID- ORCID: 0000-0002-4768-0846
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Lind, C
AU  - Lind C
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Mackiewicz, K
AU  - Mackiewicz K
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Ferriola, D
AU  - Ferriola D
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Papazoglou, A
AU  - Papazoglou A
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Derbeneva, O
AU  - Derbeneva O
AD  - Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Wallace, D
AU  - Wallace D
AD  - Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
AD  - Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 
      University of Pennsylvania, Philadelphia, PA, USA.
FAU - Monos, D S
AU  - Monos DS
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
AD  - Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 
      University of Pennsylvania, Philadelphia, PA, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150627
PL  - England
TA  - Int J Immunogenet
JT  - International journal of immunogenetics
JID - 101232337
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - Base Sequence
MH  - Cell Line
MH  - Genetic Loci
MH  - *Genome, Human
MH  - Genotyping Techniques/*methods
MH  - HLA Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Homozygote
MH  - Humans
MH  - Sequence Alignment
EDAT- 2015/06/30 06:00
MHDA- 2016/05/31 06:00
CRDT- 2015/06/30 06:00
PHST- 2015/02/03 00:00 [received]
PHST- 2015/04/29 00:00 [revised]
PHST- 2015/05/25 00:00 [accepted]
PHST- 2015/06/30 06:00 [entrez]
PHST- 2015/06/30 06:00 [pubmed]
PHST- 2016/05/31 06:00 [medline]
AID - 10.1111/iji.12213 [doi]
PST - ppublish
SO  - Int J Immunogenet. 2015 Oct;42(5):346-58. doi: 10.1111/iji.12213. Epub 2015 Jun 
      27.