PMID- 28503844
OWN - NLM
STAT- MEDLINE
DCOM- 20180319
LR  - 20180821
IS  - 2059-2310 (Electronic)
IS  - 2059-2302 (Linking)
VI  - 90
IP  - 1
DP  - 2017 Jul
TI  - TypeLoader: A fast and efficient automated workflow for the annotation and 
      submission of novel full-length HLA alleles.
PG  - 25-31
LID - 10.1111/tan.13055 [doi]
AB  - Recent years have seen a rapid increase in the discovery of novel allelic 
      variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons 
      encoding the peptide binding domains of novel HLA alleles are submitted. As a 
      result, the IPD-IMGT/HLA Database lacks sequence information outside those 
      regions for the majority of known alleles. This has implications for the 
      application of the new sequencing technologies, which deliver sequence data often 
      covering the complete gene. As these technologies simplify the characterization 
      of the complete gene regions, it is desirable for novel alleles to be submitted 
      as full-length sequences to the database. However, the manual annotation of 
      full-length alleles and the generation of specific formats required by the 
      sequence repositories is prone to error and time consuming. We have developed 
      TypeLoader to address both these facets. With only the full-length sequence as a 
      starting point, Typeloader performs automatic sequence annotation and 
      subsequently handles all steps involved in preparing the specific formats for 
      submission with very little manual intervention. TypeLoader is routinely used at 
      the DKMS Life Science Lab and has aided in the successful submission of more than 
      900 novel HLA alleles as full-length sequences to the European Nucleotide Archive 
      repository and the IPD-IMGT/HLA Database with a 95% reduction in the time spent 
      on annotation and submission when compared with handling these processes 
      manually. TypeLoader is implemented as a web application and can be easily 
      installed and used on a standalone Linux desktop system or within a Linux 
      client/server architecture. TypeLoader is downloadable from 
      http://www.github.com/DKMS-LSL/typeloader.
CI  - (c) 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
FAU - Surendranath, V
AU  - Surendranath V
AUID- ORCID: 0000-0003-1593-6461
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Albrecht, V
AU  - Albrecht V
AUID- ORCID: 0000-0001-6304-3989
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Hayhurst, J D
AU  - Hayhurst JD
AD  - Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
FAU - Schone, B
AU  - Schone B
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Robinson, J
AU  - Robinson J
AD  - Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
AD  - UCL Cancer Institute, University College London, London, UK.
FAU - Marsh, S G E
AU  - Marsh SGE
AUID- ORCID: 0000-0003-2855-4120
AD  - Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
AD  - UCL Cancer Institute, University College London, London, UK.
FAU - Schmidt, A H
AU  - Schmidt AH
AD  - DKMS Life Science Lab, Dresden, Germany.
AD  - DKMS, Tubingen, Germany.
FAU - Lange, V
AU  - Lange V
AD  - DKMS Life Science Lab, Dresden, Germany.
LA  - eng
PT  - Journal Article
DEP - 20170514
PL  - England
TA  - HLA
JT  - HLA
JID - 101675570
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - *Automation, Laboratory
MH  - Base Sequence
MH  - Databases, Factual
MH  - Gene Expression
MH  - Genotype
MH  - HLA Antigens/*classification/*genetics/immunology
MH  - Humans
MH  - Internet
MH  - Molecular Sequence Annotation/*methods
MH  - *Software
MH  - Workflow
OTO - NOTNLM
OT  - HLA
OT  - annotation
OT  - full-length
OT  - genotyping
OT  - novel allele
OT  - submission
EDAT- 2017/05/16 06:00
MHDA- 2018/03/20 06:00
CRDT- 2017/05/16 06:00
PHST- 2016/12/05 00:00 [received]
PHST- 2017/03/17 00:00 [revised]
PHST- 2017/04/19 00:00 [accepted]
PHST- 2017/05/16 06:00 [pubmed]
PHST- 2018/03/20 06:00 [medline]
PHST- 2017/05/16 06:00 [entrez]
AID - 10.1111/tan.13055 [doi]
PST - ppublish
SO  - HLA. 2017 Jul;90(1):25-31. doi: 10.1111/tan.13055. Epub 2017 May 14.