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Lu et al. Hepatoma Res 2018;4:21 I http://dx.doi.org/10.20517/2394-5079.2018.44 Page 9 of 10
liver cancer. Nat Genet 2016;48:500-9.
7. Schulze K, Imbeaud S, Letouzé E, Alexandrov LB, Calderaro J, Rebouissou S, Couchy G, Meiller C, Shinde J, Soysouvanh F, Calatayud
AL, Pinyol R, Pelletier L, Balabaud C, Laurent A, Blanc JF, Mazzaferro V, Calvo F, Villanueva A, Nault JC, Bioulac-Sage P, Stratton MR,
Llovet JM, Zucman-Rossi J. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic
targets. Nat Genet 2015;47:505-11.
8. Cancer Genome Atlas Research Network. Comprehensive and integrative genomic characterization of hepatocellular carcinoma. Cell
2017;169:1327-41.e23.
9. Shen FM, Lee MK, Gong HM, Cai XQ, King MC. Complex segregation analysis of primary hepatocellular carcinoma in Chinese families:
interaction of inherited susceptibility and hepatitis B viral infection. Am J Hum Genet 1991;49:88-93.
10. Yu MW, Chang HC, Liaw YF, Lin SM, Lee SD, Liu CJ, Chen PJ, Hsiao TJ, Lee PH, Chen CJ. Familial risk of hepatocellular carcinoma
among chronic hepatitis B carriers and their relatives. J Natl Cancer Inst 2000;92:1159-64.
11. Hassan MM, Spitz MR, Thomas MB, Curley SA, Patt YZ, Vauthey JN, Glover KY, Kaseb A, Lozano RD, El-Deeb AS, Nguyen NT, Wei
SH, Chan W, Abbruzzese JL, Li D. The association of family history of liver cancer with hepatocellular carcinoma: a case-control study in
the United States. J Hepatol 2009;50:334-41.
12. Dragani TA. Risk of HCC: genetic heterogeneity and complex genetics. J Hepatol 2010;52:252-7.
13. Turati F, Edefonti V, Talamini R, Ferraroni M, Malvezzi M, Bravi F, Franceschi S, Montella M, Polesel J, Zucchetto A, La Vecchia C, Negri
E, Decarli A. Family history of liver cancer and hepatocellular carcinoma. Hepatology 2012;55:1416-25.
14. Caruso S, Calderaro J, Letouzé E, Nault JC, Couchy G, Boulai A, Luciani A, Zafrani ES, Bioulac-Sage P, Seror O, Imbeaud S, Zucman-
Rossi J. Germline and somatic DICER1 mutations in familial and sporadic liver tumors. J Hepatol 2017;66:734-42.
15. Jin F, Xiong WJ, Jing JC, Feng Z, Qu LS, Shen XZ. Evaluation of the association studies of single nucleotide polymorphisms and
hepatocellular carcinoma: a systematic review. J Cancer Res Clin Oncol 2011;137:1095-104.
16. MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D,
Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. The new NHGRI-EBI Catalog of published genome-wide association studies
(GWAS Catalog). Nucleic Acids Res 2017;45:D896-901.
17. Braun R, Buetow K. Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data. PLoS Genet
2011;7:e1002101.
18. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool
set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75.
19. GTEx Consortium. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
Science 2015;348:648-60.
20. GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)-Analysis Working Group; Statistical Methods groups-
Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA;
Biospecimen Collection Source Site-NDRI; Biospecimen Collection Source Site-RPCI; Biospecimen Core Resource-VARI; Brain Bank
Repository-University of Miami Brain Endowment Bank; Leidos Biomedical-Project Management; ELSI Study; Genome Browser Data
Integration & Visualization-EBI; Genome Browser Data Integration & Visualization-UCSC Genomics Institute, University of California
Santa Cruz; Lead analysts; Laboratory, Data Analysis & Coordinating Center (LDACC); NIH program management; Biospecimen
collection; Pathology; eQTL manuscript working group; Battle A, Brown CD, Engelhardt BE, Montgomery SB. Genetic effects on gene
expression across human tissues. Nature 2017;550;204-13.
21. Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC; GTEx Consortium; Engelhardt BE, Battle A. Co-expression networks reveal the
tissue-specific regulation of transcription and splicing. Genome Res 2017;27:1843-58.
22. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015;12:357-60.
23. Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie
and Ballgown. Nat Protoc 2016;11:1650-67.
24. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Bioinformatics 2014;30:923-30.
25. Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol
2014;15:R29.
26. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and
microarray studies. Nucleic Acids Res 2015;43:e47.
27. Efroni S, Schaefer CF, Buetow KH. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS
One 2007;2:e425.
28. Efroni S, Carmel L, Schaefer CG, Buetow KH. Superposition of transcriptional behaviors determines gene state. PLoS One 2008;3:e2901.
29. Greenblum SI, Efroni S, Schaefer CF, Buetow KH. The PathOlogist: an automated tool for pathway-centric analysis. BMC Bioinformatics
2011;12:133.
30. Sharma P, Allison JP. The future of immune checkpoint therapy. Science 2015;348:56-61.
31. Garbe C, Peris K, Hauschild A, Saiag P, Middleton M, Bastholt L, Grob JJ, Malvehy J, Newton-Bishop J, Stratigos AJ, Pehamberger H;
Eggermont AM; European Dermatology Forum (EDF); European Association of Dermato-Oncology (EADO); European Organisation for
Research and Treatment of Cancer (EORTC). Diagnosis and treatment of melanoma. European consensus-based interdisciplinary guideline
- update 2016. Eur J Cancer 2016;63:201-17.
32. Garon EB, Rizvi NA, Hui R, Leighl N, Balmanoukian AS, Eder JP, Patnaik A, Aggarwal C, Gubens M, Horn L, Carcereny E, Ahn MJ,
Felip E, Lee JS, Hellmann MD, Hamid O, Goldman JW, Soria JC, Dolled-Filhart M, Rutledge RZ, Zhang J, Lunceford JK, Rangwala R,
Lubiniecki GM, Roach C, Emancipator K, Gandhi L; KEYNOTE-001 Investigators. Pembrolizumab for the treatment of non-small-cell
lung cancer. N Engl J Med 2015;372:2018-28.