Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival

Bioinformatics

Volumn 31, Issue 16, 2015, Pages 2607-2613

  Suo, Chen ^a,b   Hrydziuszko, Olga ^b   Lee, Donghwan ^c   Pramana, Setia ^b,d   Saputra, Dhany ^b   Joshi, Himanshu ^b   Calza, Stefano ^b,e   Pawitan, Yudi ^b  

^a PEKING UNIVERSITY   (China)

^b KAROLINSKA INSTITUTE   (Sweden)

^c Ewha Womans University   (South Korea)

^d Institute of Statistics   (Indonesia)

^e UNIVERSITY OF BRESCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ADULT; AGED; BIOLOGY; BREAST; BREAST TUMOR; CANCER STAGING; CASE CONTROL STUDY; EXOME; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC PREDISPOSITION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; MIDDLE AGED; MORTALITY; MUTATION; PAGET NIPPLE DISEASE; PATHOLOGY; PROCEDURES; PROGNOSIS; SURVIVAL RATE; TUMOR INVASION; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; BIOMARKERS, TUMOR; BREAST; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; EXOME; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MIDDLE AGED; MUTATION; NEOPLASM INVASIVENESS; NEOPLASM STAGING; PROGNOSIS; SURVIVAL RATE;

EID: 84939503725     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv164     Document Type: Article

References (31)

1. Akavia, U. D. et al. (2010) An integrated approach to uncover drivers of cancer. Cell, 143, 1005-1017.
2. Alexeyenko, A. and Sonnhammer, E. (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genomes Res. , 19, 1109-1116.
3. Alexeyenko, A. et al. (2012) Network enrichment analysis: extension of geneset enrichment analysis to gene networks. BMC Bioinformatics, 13, 226.
4. Cancer Genome Atlas Network. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
5. Castella, M. et al. (2011) Origin, functional role, and clinical impact of Fanconi anemia FANCA mutations. Blood, 117, 3759-3769.
6. Cingolani, P. et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly(Austin) , 6, 80-92.
7. Ciriello, G. et al. (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. , 22, 398-406.
8. Cooke, S. L. and Brenton, J. D. (2011) Evolution of platinum resistance in highgrade serous ovarian cancer. Lancet Oncol. , 12, 1169-1174.
9. Flacke, J. P. et al. (2013) Type 10 soluble adenylyl cyclase is overexpressed in prostate carcinoma and controls proliferation of prostate cancer cells. J. Biol. Chem. , 288, 3126-3135.
10. Futreal, P. A. et al. (2004) A cencus of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
11. Goodwin, P. J. et al. (2012) Breast cancer prognosis in BRCA1 and BRCA2 mutation carriers: An international prospective breast cancer family registry population based cohort study. J. Clin. Oncol. , 30, 19-26.
12. Haibe-Kains, B. et al. (2012) genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. R package version 1. 6. 1. http://compbio. dfci. harvard. edu.
13. Hou, J. P. and Ma, J. (2014) DawnRank: discovering personalized driver genes in caner. Genome Med. , 6, 56.
14. Lazar, V. et al. (2013) Integrated molecular portrait of non-small cell lung cancers. BMC Med. Genomics, 6, 53.
15. Loeb, K. R. and Loeb, K. A. (2000) Significance of multiple mutations in cancer. Carcinogensis, 21, 379-385.
16. McKenna, A. et al. (2010) The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. , 20, 1297-1303.
17. Mukhopadhyay, P. et al. (2013) MUC4 overexpression augments cell migration and metastasis through EGFR family proteins in triple negativebreast cancer cells. PLoS One, 8, e54455.
18. Nagao, K. et al. (2005) Detecting tissue-specific alternative splicing and disease-associated aberrant splicing of the PTCH gene with exon junction microarrays. Hum. Mol. Genet. , 14, 3379-3388.
19. Nishimiya, H. et al. (2014) Prognostic significance of Ki-67 in chemotherapy-naive breast cancer patients with 10-year follow-up. Anticancer Res. , 34, 259-268.
20. Parker, J. S. et al. (2009) Supervised predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol. , 27, 1160-1167.
21. Pines, A. et al. (2012) PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1. J. Cell. Biol. , 199, 235-249.
22. Salomon, A. V. et al. (2013) Genome instability: A stronger prognostic marker than proliferation for early stage luminal breast carcinomas. PLoS One, 8, e76496.
23. Sanchez-Garcia, F. et al. (2014) Integration of genomic data enables selective discovery of breast cancer drivers. Cell, 159, 1461-1475.
24. Suo, C. et al. (2014) Joint estimation of isoform expression and isoformspecific read distribution using multi-sample RNA-seq data. Bioinformatics, 30, 506-513.
25. Tang, M. K. et al. (2014) BRCA1 deficiency induces protective autophagy to mitigate stress and provides a mechanism for BRCA1 haploinsufficiency in tumorigenesis. Cancer Lett. , 346, 139-147.
26. van 't Veer, L. J. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
27. Weissmueller, S. et al. (2014) Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor b signalling. Cell, 157, 382-394.
28. Youn, A. and Simon, R. (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics, 27, 175-181.
29. Zhang, K. X. and Ouellette, F. (2011) CAERUS: Predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput. Biol. , 7, e1001114.
30. Zhang, J. et al. (2011) International Cancer Genome Consortium Data Portal-a one-stop shop for cancer genomics data. Database, doi:10. 1093/database/ bar026.
31. Zhang, D. et al. (2012) Exome sequencing identifies compound heterozygous PKHD1 mutations as a cause of autosomal recessive polycystic kidney disease. Chin. Med. J. , 125, 2482-2486.