HLApers: HLA Typing and Quantification of Expression with Personalized Index.
Methods Mol Biol
; 2120: 101-112, 2020.
Article
in En
| MEDLINE
| ID: mdl-32124314
The plethora of RNA-seq data which have been generated in the recent years constitutes an attractive resource to investigate HLA variation and its relationship with normal and disease phenotypes, such as cancer. However, next generation sequencing (NGS) brings new challenges to HLA analysis because of the mapping bias introduced by aligning short reads originated from polymorphic genes to a single reference genome. Here we describe HLApers, a pipeline which adapts widely used tools for analysis of standard RNA-seq data to infer HLA genotypes and estimate expression. By generating reliable expression estimates for each HLA allele that an individual carries, HLApers allows a better understanding of the relationship between HLA alleles and phenotypes manifested by an individual.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Histocompatibility Testing
/
Sequence Analysis, RNA
/
HLA Antigens
Limits:
Humans
Language:
En
Journal:
Methods Mol Biol
Journal subject:
BIOLOGIA MOLECULAR
Year:
2020
Document type:
Article
Affiliation country:
Country of publication: