PMID- 25143287
OWN - NLM
STAT- MEDLINE
DCOM- 20150221
LR  - 20220316
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 30
IP  - 23
DP  - 2014 Dec 1
TI  - OptiType: precision HLA typing from next-generation sequencing data.
PG  - 3310-6
LID - 10.1093/bioinformatics/btu548 [doi]
AB  - MOTIVATION: The human leukocyte antigen (HLA) gene cluster plays a crucial role 
      in adaptive immunity and is thus relevant in many biomedical applications. While 
      next-generation sequencing data are often available for a patient, deducing the 
      HLA genotype is difficult because of substantial sequence similarity within the 
      cluster and exceptionally high variability of the loci. Established approaches, 
      therefore, rely on specific HLA enrichment and sequencing techniques, coming at 
      an additional cost and extra turnaround time. RESULT: We present OptiType, a 
      novel HLA genotyping algorithm based on integer linear programming, capable of 
      producing accurate predictions from NGS data not specifically enriched for the 
      HLA cluster. We also present a comprehensive benchmark dataset consisting of RNA, 
      exome and whole-genome sequencing data. OptiType significantly outperformed 
      previously published in silico approaches with an overall accuracy of 97% 
      enabling its use in a broad range of applications.
CI  - (c) The Author 2014. Published by Oxford University Press.
FAU - Szolek, Andras
AU  - Szolek A
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany.
FAU - Schubert, Benjamin
AU  - Schubert B
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany Applied Bioinformatics, Center for Bioinformatics, Quantitative 
      Biology Center, and Department of Computer Science, University of Tubingen, 
      Institute of Medical Genetics and Applied Genomics, University of Tubingen, and 
      CeGaT GmbH, 72076 Tubingen, Germany.
FAU - Mohr, Christopher
AU  - Mohr C
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany Applied Bioinformatics, Center for Bioinformatics, Quantitative 
      Biology Center, and Department of Computer Science, University of Tubingen, 
      Institute of Medical Genetics and Applied Genomics, University of Tubingen, and 
      CeGaT GmbH, 72076 Tubingen, Germany.
FAU - Sturm, Marc
AU  - Sturm M
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany.
FAU - Feldhahn, Magdalena
AU  - Feldhahn M
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany.
FAU - Kohlbacher, Oliver
AU  - Kohlbacher O
AD  - Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, 
      and Department of Computer Science, University of Tubingen, Institute of Medical 
      Genetics and Applied Genomics, University of Tubingen, and CeGaT GmbH, 72076 
      Tubingen, Germany.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140820
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Algorithms
MH  - Exome
MH  - Genotyping Techniques
MH  - HLA Antigens/genetics
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Introns
MH  - Sequence Analysis, DNA/*methods
PMC - PMC4441069
EDAT- 2014/08/22 06:00
MHDA- 2015/02/24 06:00
PMCR- 2014/08/20
CRDT- 2014/08/22 06:00
PHST- 2014/08/22 06:00 [entrez]
PHST- 2014/08/22 06:00 [pubmed]
PHST- 2015/02/24 06:00 [medline]
PHST- 2014/08/20 00:00 [pmc-release]
AID - btu548 [pii]
AID - 10.1093/bioinformatics/btu548 [doi]
PST - ppublish
SO  - Bioinformatics. 2014 Dec 1;30(23):3310-6. doi: 10.1093/bioinformatics/btu548. 
      Epub 2014 Aug 20.