Integrating transcriptome-wide association study and copy number variation study identifies candidate genes and pathways for diffuse non-Hodgkin's lymphoma.
Adipokines
/ metabolism
B-Cell CLL-Lymphoma 10 Protein
/ genetics
DNA Copy Number Variations
Gene Expression Profiling
Genetic Predisposition to Disease
Genome-Wide Association Study
Humans
Hypoxia-Inducible Factor 1, alpha Subunit
/ metabolism
Lymphoma, Non-Hodgkin
/ genetics
Signal Transduction
/ genetics
TOR Serine-Threonine Kinases
/ metabolism
Copy number alterations
Diffuse non-Hodgkin's lymphoma
Transcriptome-wide association study
Journal
Cancer genetics
ISSN: 2210-7762
Titre abrégé: Cancer Genet
Pays: United States
ID NLM: 101539150
Informations de publication
Date de publication:
05 2020
05 2020
Historique:
received:
22
08
2019
revised:
10
02
2020
accepted:
20
02
2020
pubmed:
18
3
2020
medline:
22
9
2020
entrez:
18
3
2020
Statut:
ppublish
Résumé
The genetic basis of diffuse non-Hodgkin's lymphoma (DNHL) is largely unknown now. We conducted a large-scale transcriptome-wide association study (TWAS) of DNHL to identify novel candidates for DNHL. The GWAS summary data of DNHL was obtained from the UKBiobank, involving 685 cases and 451,579 controls. TWAS of DNHL was performed using tissue-specific gene expression weights generated from the Genotype-Tissue Expression (GTEx) data. The DNHLTWAS results were further validated by a previous published copy number alterations (CNA) study of DNHL. Gene ontology (GO) and pathway enrichment analysis of identified candidate genes were conducted by the DAVID 6.8. We identified 214 genes with TWAS P value < 0.05 for DNHL, such as MRPL19 (P Our study identified multiple DNHL associated genes and pathways, providing novel useful information for the pathogenetic studies of DNHL.
Sections du résumé
BACKGROUND
The genetic basis of diffuse non-Hodgkin's lymphoma (DNHL) is largely unknown now. We conducted a large-scale transcriptome-wide association study (TWAS) of DNHL to identify novel candidates for DNHL.
METHODS
The GWAS summary data of DNHL was obtained from the UKBiobank, involving 685 cases and 451,579 controls. TWAS of DNHL was performed using tissue-specific gene expression weights generated from the Genotype-Tissue Expression (GTEx) data. The DNHLTWAS results were further validated by a previous published copy number alterations (CNA) study of DNHL. Gene ontology (GO) and pathway enrichment analysis of identified candidate genes were conducted by the DAVID 6.8.
RESULTS
We identified 214 genes with TWAS P value < 0.05 for DNHL, such as MRPL19 (P
CONCLUSIONS
Our study identified multiple DNHL associated genes and pathways, providing novel useful information for the pathogenetic studies of DNHL.
Identifiants
pubmed: 32179489
pii: S2210-7762(20)30138-1
doi: 10.1016/j.cancergen.2020.02.005
pii:
doi:
Substances chimiques
Adipokines
0
B-Cell CLL-Lymphoma 10 Protein
0
BCL10 protein, human
0
HIF1A protein, human
0
Hypoxia-Inducible Factor 1, alpha Subunit
0
MTOR protein, human
EC 2.7.1.1
TOR Serine-Threonine Kinases
EC 2.7.11.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7-10Informations de copyright
Copyright © 2020. Published by Elsevier Inc.
Déclaration de conflit d'intérêts
Declaration of Competing Interests The authors declare that they have no competing interests.