Erratum: Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers (BMC Medical Genomics (2014) 7: 32 DOI: 10.1186/1755-8794-7-32);Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers

BMC Medical Genomics

Volumn 7, Issue 1, 2014, Pages 1-

  Sun, Zhifu ^a   Wang, Liang ^b   Eckloff, Bruce W ^a   Deng, Bo ^a,c   Wang, Yi ^a,d   Wampfler, Jason A ^a   Jang, Jinsung ^a   Wieben, Eric D ^a   Jen, Jin ^a   You, Ming ^b   Yang, Ping ^a  

^a MAYO CLINIC   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

^c THIRD MILITARY MEDICAL UNIVERSITY   (China)

^d WENZHOU MEDICAL UNIVERSITY   (China)

Author keywords

Lung adenocarcinoma of never smoker; Pathway deregulation; Patient survival; Somatic mutations

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; MESSENGER RNA;

ADULT; AGED; ARTICLE; ATAXIN 2 GENE; CANCER PROGNOSIS; CANCER SURVIVAL; CLINICAL ARTICLE; CONTROLLED STUDY; DHX9 GENE; EPIDERMAL GROWTH FACTOR RECEPTOR GENE; EXOME; FEMALE; GENE FREQUENCY; GENE MUTATION; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; MALE; MIDDLE AGED; MYOFERLIN GENE; ONCOGENE K RAS; PRIORITY JOURNAL; PTPN13 GENE; RIBOSOMAL PROTEIN S6 KINASE BETA 2 GENE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; SOMATIC MUTATION; SP1 GENE; SPECTRIN ALPHA NONERYTHROCYTIC 1 GENE; TUMOR SUPPRESSOR GENE; VERY ELDERLY;

ADENOCARCINOMA; CONSERVED SEQUENCE; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; EXOME; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; KAPLAN-MEIER ESTIMATE; LUNG NEOPLASMS; MALE; MIDDLE AGED; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SIGNAL TRANSDUCTION; SMOKING; TREATMENT OUTCOME;

EID: 84902810152     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-016-0237-y     Document Type: Erratum

References (28)

1. Lung cancer in never smokers-a review. Couraud S, Zalcman G, Milleron B, Morin F, Souquet PJ, Eur J Cancer 2012 48 9 1299 1311 10.1016/j.ejca.2012.03.007 22464348
2. Lung cancer in never smokers: a review. Subramanian J, Govindan R, J Clin Oncol 2007 25 5 561 570 10.1200/JCO.2006.06.8015 17290066 (Pubitemid 350002964)
3. Frequency of driver mutations in lung adenocarcinoma from female never-smokers varies with histologic subtypes and age at diagnosis. Zhang Y, Sun Y, Pan Y, Li C, Shen L, Li Y, Luo X, Ye T, Wang R, Hu H, Li H, Wang L, Pao W, Chen H, Clin Cancer Res 2012 18 7 1947 1953 10.1158/1078-0432.CCR-11-2511 22317764
4. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansen S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, et al. Cell 2012 150 6 1107 1120 10.1016/j.cell.2012.08.029 22980975
5. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortes ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, et al. Nature 2013 499 7457 214 218 10.1038/nature12213 23770567
6. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, Ha C, Johnson S, Kennemer MI, Mohan S, Nazarenko I, Watanabe C, Sparks AB, Shames DS, Gentleman R, de Sauvage FJ, Stern H, Pandita A, Ballinger DG, Drmanac R, Modrusan Z, Seshagiri S, Zhang Z, Nature 2010 465 7297 473 477 10.1038/nature09004 20505728
7. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK, Cell 2012 150 6 1121 1134 10.1016/j.cell.2012.08.024 22980976
8. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP, Bioinformatics (Oxford, England) 2012 28 2 277 278 10.1093/bioinformatics/btr612
9. Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics (Oxford, England) 2009 25 14 1754 1760 10.1093/bioinformatics/btp324
10. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA, Genome Res 2010 20 9 1297 1303 10.1101/gr.107524.110 20644199
11. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP, Bioinformatics (Oxford, England) 2010 26 6 730 736 10.1093/bioinformatics/btq040
12. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK, Genome Res 2012 22 3 568 576 10.1101/gr.129684.111 22300766
13. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Wang K, Li M, Hakonarson H, Nucleic Acids Res 2010 38 16 164 10.1093/nar/gkq603 20601685
14. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Kumar P, Henikoff S, Ng PC, Nat Protoc 2009 4 7 1073 1081 19561590
15. A method and server for predicting damaging missense mutations. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR, Nat Methods 2010 7 4 248 249 10.1038/nmeth0410-248 20354512
16. TopHat: discovering splice junctions with RNA-Seq. Trapnell C, Pachter L, Salzberg SL, Bioinformatics (Oxford, England) 2009 25 9 1105 1111 10.1093/bioinformatics/btp120
17. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead B, Trapnell C, Pop M, Salzberg SL, Genome Biol 2009 10 3 25 10.1186/gb-2009-10-3-r25 19261174
18. BEDTools: a flexible suite of utilities for comparing genomic features. Quinlan AR, Hall IM, Bioinformatics (Oxford, England) 2010 26 6 841 842 10.1093/bioinformatics/btq033
19. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Robinson MD, McCarthy DJ, Smyth GK, Bioinformatics (Oxford, England) 2010 26 1 139 140 10.1093/bioinformatics/btp616
20. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, Nat Methods 2008 5 7 621 628 10.1038/nmeth.1226 18516045 (Pubitemid 351911867)
21. Pathway-based personalized analysis of cancer. Drier Y, Sheffer M, Domany E, Proc Natl Acad Sci U S A 2013 110 16 6388 6393 10.1073/pnas.1219651110 23547110
22. Myoferlin depletion in breast cancer cells promotes mesenchymal to epithelial shape change and stalls invasion. Li R, Ackerman WE, Mihai C, Volakis LI, Ghadiali S, Kniss DA, PLoS One 2012 7 6 39766 10.1371/journal.pone.0039766 22761893
23. The nonreceptor-type tyrosine phosphatase PTPN13 is a tumor suppressor gene in non-small cell lung cancer. Scrima M, De Marco C, De Vita F, Fabiani F, Franco R, Pirozzi G, Rocco G, Malanga D, Viglietto G, Am J Pathol 2012 180 3 1202 1214 10.1016/j.ajpath.2011.11.038 22245727
24. Mutational analysis of the tyrosine phosphatome in colorectal cancers. Wang Z, Shen D, Parsons DW, Bardelli A, Sager J, Szabo S, Ptak J, Silliman N, Peters BA, van der Heijden MS, Parmigiani G, Yan H, Wang TL, Riggins G, Powell SM, Willson JK, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE, Science (New York, NY) 2004 304 5674 1164 1166 10.1126/science.1096096 (Pubitemid 38661854)
25. Clinical potential of the mTOR targets S6K1 and S6K2 in breast cancer. Perez-Tenorio G, Karlsson E, Waltersson MA, Olsson B, Holmlund B, Nordenskjold B, Fornander T, Skoog L, Stal O, Breast Cancer Res Treat 2011 128 3 713 723 10.1007/s10549-010-1058-x 20953835
26. Genetic variation in RPS6KA1, RPS6KA2, RPS6KB1, RPS6KB2, and PDK1 and risk of colon or rectal cancer. Slattery ML, Lundgreen A, Herrick JS, Wolff RK, Mutat Res 2011 706 1-2 13 20 21035469
27. Targeting Sp1 transcription factors in prostate cancer therapy. Sankpal UT, Goodison S, Abdelrahim M, Basha R, Med Chem 2011 7 5 518 525 10.2174/157340611796799203 22022994
28. Mechanistic modeling of the effects of myoferlin on tumor cell invasion. Eisenberg MC, Kim Y, Li R, Ackerman WE, Kniss DA, Friedman A, Proc Natl Acad Sci U S A 2011 108 50 20078 20083 10.1073/pnas.1116327108 22135466