TY - JOUR
T1 - Genomic landscape of DNA repair genes in cancer
AU - Chae, Young Kwang
AU - Anker, Jonathan F.
AU - Carneiro, Benedito A.
AU - Chandra, Sunandana
AU - Kaplan, Jason
AU - Kalyan, Aparna
AU - Santa-Maria, Cesar A.
AU - Platanias, Leonidas C.
AU - Giles, Francis J.
PY - 2016/4/26
Y1 - 2016/4/26
N2 - DNA repair genes are frequently mutated in cancer, yet limited data exist regarding the overall genomic landscape and functional implications of these alterations in their entirety. We created comprehensive lists of DNA repair genes and indirect caretakers. Mutation, copy number variation (CNV), and expression frequencies of these genes were analyzed in COSMIC. Mutation co-occurrence, clinical outcomes, and mutation burden were analyzed in TCGA. We report the 20 genes most frequently with mutations (n > 19,689 tumor samples for each gene), CNVs (n > 1,556), or up-or down-regulated (n = 7,998). Mutual exclusivity was observed as no genes displayed both high CNV gain and loss or high up-and down-regulation, and CNV gain and loss positively correlated with up-and down-regulation, respectively. Co-occurrence of mutations differed between cancers, and mutations in many DNA repair genes were associated with higher total mutation burden. Mutation and CNV frequencies offer insights into which genes may play tumor suppressive or oncogenic roles, such as NEIL2 and RRM2B, respectively. Mutual exclusivities within CNV and expression frequencies, and correlations between CNV and expression, support the functionality of these genomic alterations. This study provides comprehensive lists of candidate genes as potential biomarkers for genomic instability, novel therapeutic targets, or predictors of immunotherapy efficacy.
AB - DNA repair genes are frequently mutated in cancer, yet limited data exist regarding the overall genomic landscape and functional implications of these alterations in their entirety. We created comprehensive lists of DNA repair genes and indirect caretakers. Mutation, copy number variation (CNV), and expression frequencies of these genes were analyzed in COSMIC. Mutation co-occurrence, clinical outcomes, and mutation burden were analyzed in TCGA. We report the 20 genes most frequently with mutations (n > 19,689 tumor samples for each gene), CNVs (n > 1,556), or up-or down-regulated (n = 7,998). Mutual exclusivity was observed as no genes displayed both high CNV gain and loss or high up-and down-regulation, and CNV gain and loss positively correlated with up-and down-regulation, respectively. Co-occurrence of mutations differed between cancers, and mutations in many DNA repair genes were associated with higher total mutation burden. Mutation and CNV frequencies offer insights into which genes may play tumor suppressive or oncogenic roles, such as NEIL2 and RRM2B, respectively. Mutual exclusivities within CNV and expression frequencies, and correlations between CNV and expression, support the functionality of these genomic alterations. This study provides comprehensive lists of candidate genes as potential biomarkers for genomic instability, novel therapeutic targets, or predictors of immunotherapy efficacy.
KW - Cancer
KW - Copy number variations
KW - DNA repair
KW - Gene expression
KW - Mutations
UR - http://www.scopus.com/inward/record.url?scp=84966669663&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84966669663&partnerID=8YFLogxK
U2 - 10.18632/oncotarget.8196
DO - 10.18632/oncotarget.8196
M3 - Article
C2 - 27004405
AN - SCOPUS:84966669663
SN - 1949-2553
VL - 7
SP - 23312
EP - 23321
JO - Oncotarget
JF - Oncotarget
IS - 17
ER -