PMID- 32124312
OWN - NLM
STAT- MEDLINE
DCOM- 20210208
LR  - 20210208
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2120
DP  - 2020
TI  - HLA Typing from RNA Sequencing and Applications to Cancer.
PG  - 71-92
LID - 10.1007/978-1-0716-0327-7_5 [doi]
AB  - The human leukocyte antigen (HLA) complex is necessary for antigen presentation 
      and regulates both innate and adaptive immune responses. In the context of cancer 
      and treatment therapies, the HLA locus plays a critical role in tumor recognition 
      and tolerance mechanisms. In silico HLA class I and class II typing, as well as 
      expression quantification from next-generation RNA sequencing, can therefore have 
      great potential clinical applications. However, HLA typing from short-read data 
      is a challenging task given the high polymorphism and homology at the HLA locus. 
      In this chapter, we present our highly accurate HLA typing solution, arcasHLA. We 
      provide a detailed outline for practitioners using our protocol to perform HLA 
      typing and demonstrate the applicability of arcasHLA in several clinical samples 
      from tumors.
FAU - Orenbuch, Rose
AU  - Orenbuch R
AD  - Department of Systems Biology, Columbia University Irving Cancer Research Center, 
      New York, NY, USA.
FAU - Filip, Ioan
AU  - Filip I
AD  - Department of Systems Biology, Columbia University Irving Cancer Research Center, 
      New York, NY, USA. if2179@cumc.columbia.edu.
AD  - Program for Mathematical Genomics, Columbia University Irving Medical Center, New 
      York, NY, USA. if2179@cumc.columbia.edu.
FAU - Rabadan, Raul
AU  - Rabadan R
AD  - Department of Systems Biology, Columbia University Irving Cancer Research Center, 
      New York, NY, USA.
AD  - Program for Mathematical Genomics, Columbia University Irving Medical Center, New 
      York, NY, USA.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Gene Frequency
MH  - HLA Antigens/*genetics
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Neoplasms/*genetics
MH  - Polymorphism, Genetic
MH  - Sequence Analysis, RNA/*methods
MH  - Software
OTO - NOTNLM
OT  - Cancer
OT  - Expression
OT  - Genotyping
OT  - Human leukocyte antigens
OT  - Major histocompatibility complex
OT  - RNA sequencing
EDAT- 2020/03/04 06:00
MHDA- 2021/02/09 06:00
CRDT- 2020/03/04 06:00
PHST- 2020/03/04 06:00 [entrez]
PHST- 2020/03/04 06:00 [pubmed]
PHST- 2021/02/09 06:00 [medline]
AID - 10.1007/978-1-0716-0327-7_5 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2020;2120:71-92. doi: 10.1007/978-1-0716-0327-7_5.