Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma

Nature Communications

Volumn 7, Issue , 2016, Pages

  Shiraishi, Kouya ^a   Okada, Yukinori ^b,c,d   Takahashi, Atsushi ^d,e   Kamatani, Yoichiro ^d   Momozawa, Yukihide ^d   Ashikawa, Kyota ^d   Kunitoh, Hideo ^f   Matsumoto, Shingo ^a   Takano, Atsushi ^g,h   Shimizu, Kimihiro ⁱ   Goto, Akiteru ^j   Tsuta, Koji ^k,l   Watanabe, Shun Ichi ^k   Ohe, Yuichiro ^k   Watanabe, Yukio ^k   Goto, Yasushi ^k   Nokihara, Hiroshi ^k   Furuta, Koh ^k,m   Yoshida, Akihiko ^k,n   Goto, Koichi ⁿ   Hishida, Tomoyuki ⁿ   Tsuboi, Masahiro ^a   Tsuchihara, Katsuya ^m   Miyagi, Yohei ^m   Nakayama, Haruhiko ^m   Yokose, Tomoyuki ⁱ   Tanaka, Kazumi ⁱ   Nagashima, Toshiteru ⁱ   Ohtaki, Yoichi ^j   Maeda, Daichi ^j   Imai, Kazuhiro ^j   Minamiya, Yoshihiro ^a   Sakamoto, Hiromi ^o   Saito, Akira ^a   Shimada, Yoko ^a   Sunami, Kuniko ^k   Saito, Motonobu ^a   Inazawa, Johji ^b   Nakamura, Yusuke ^p   Yoshida, Teruhiko ^a   Yokota, Jun ^q   Matsuda, Fumihiko ^r   Matsuo, Keitaro ^s   Daigo, Yataro ^g,h   Kubo, Michiaki ^d   Kohno, Takashi ^a   more..

^a NATIONAL CANCER CENTER RESEARCH INSTITUTE   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^c OSAKA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^d RIKEN Center for Integrative Medical Sciences   (Japan)

^e NATIONAL CEREBRAL AND CARDIOVASCULAR CENTER   (Japan)

^f JAPANESE RED CROSS MEDICAL CENTER   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h SHIGA UNIVERSITY OF MEDICAL SCIENCE   (Japan)

ⁱ GUNMA UNIVERSITY HOSPITAL   (Japan)

^j AKITA UNIVERSITY   (Japan)

^k NATIONAL CANCER CENTER HOSPITAL   (Japan)

^l KANSAI MEDICAL UNIVERSITY   (Japan)

^m KANAGAWA CANCER CENTER   (Japan)

ⁿ NATIONAL CANCER CENTER HOSPITAL EAST   (Japan)

^o Kuramae Orashion Bldg 9F   (Japan)

^p University of Chicago   (United States)

^q Institute of Predictive and Personalized Medicine of Cancer (IMPPC)   (Spain)

^r KYOTO UNIVERSITY   (Japan)

^s AICHI CANCER CENTER HOSPITAL   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BROMODOMAIN PHD FINGER TRANSCRIPTION FACTOR; BUTYROPHILIN LIKE 2; EPIDERMAL GROWTH FACTOR RECEPTOR; FORKHEAD BOX P4 PROTEIN; HLA ANTIGEN CLASS 2; HLA DPA1 ANTIGEN; HLA DPB1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; PROTEIN; TELOMERASE REVERSE TRANSCRIPTASE; TUMOR PROTEIN; TUMOUR PROTEIN P63; UNCLASSIFIED DRUG; FORKHEAD TRANSCRIPTION FACTOR; FOXP4 PROTEIN, HUMAN;

CANCER; GENE EXPRESSION; GENETIC ANALYSIS; HEALTH RISK; MUTATION; PUBLIC HEALTH; RESPIRATORY DISEASE;

ALLELE; ARTICLE; CANCER RISK; CASE CONTROL STUDY; CONTROLLED STUDY; EAST ASIAN; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HEREDITY; HUMAN; HUMAN TISSUE; JAPANESE (PEOPLE); LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MALE; MULTIPLEX POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY; ADENOCARCINOMA; GENETIC PREDISPOSITION; GENETICS; LUNG TUMOR; MUTATION; REPRODUCIBILITY; RISK FACTOR;

EUROPE; JAPAN;

ADENOCARCINOMA; FORKHEAD TRANSCRIPTION FACTORS; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; LUNG NEOPLASMS; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTOR, EPIDERMAL GROWTH FACTOR; REPRODUCIBILITY OF RESULTS; RISK FACTORS;

EID: 84982146157     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12451     Document Type: Article

References (40)

1. Clinical Lung Cancer Genome P. & Network Genomic M. A genomics-based classification of human lung tumors. Sci. Transl. Med. 5, 209ra153 (2013)
2. Cancer Genome Atlas Research N. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511, 543-550 (2014)
3. Kohno, T. et al. KIF5B-RET fusions in lung adenocarcinoma. Nat. Med. 18, 375-377 (2012)
4. Sun, S., Schiller, J. H. & Gazdar, A. F. Lung cancer in never smokers-a different disease. Nat. Rev. Cancer 7, 778-790 (2007)
5. Kohno, T. et al. Beyond ALK-RET, ROS1 and other oncogene fusions in lung cancer. Transl. Lung Cancer Res. 4, 156-164 (2015)
6. Pallis, A. G. & Syrigos, K. N. Lung cancer in never smokers: disease characteristics and risk factors. Crit. Rev. Oncol. Hematol. 88, 494-503 (2013)
7. Matsuo, K. et al. Soy consumption reduces the risk of non-small-cell lung cancers with epidermal growth factor receptor mutations among Japanese. Cancer Sci. 99, 1202-1208 (2008)
8. Matsuo, K. et al. Risk factors differ for non-small-cell lung cancers with and without EGFR mutation: assessment of smoking and sex by a case-control study in Japanese. Cancer Sci. 98, 96-101 (2007)
9. Camidge, D. R., Pao, W. & Sequist, L. V. Acquired resistance to TKIs in solid tumours: learning from lung cancer. Nat. Rev. Clin. Oncol. 11, 473-481 (2014)
10. Wang, Y. et al. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat. Genet. 46, 736-741 (2014)
11. Landi, M. T. et al. A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am. J. Hum. Genet. 85, 679-691 (2009)
12. Amos, C. I. et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat. Genet. 40, 616-622 (2008)
13. Hung, R. J. et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 452, 633-637 (2008)
14. Shiraishi, K. et al. A genome-wide association study identifies two new susceptibility loci for lung adenocarcinoma in the Japanese population. Nat. Genet. 44, 900-903 (2012)
15. Lan, Q. et al. Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat. Genet. 44, 1330-1335 (2012)
16. Miki, D. et al. Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations. Nat. Genet. 42, 893-896 (2010)
17. Wei, R. et al. TERT polymorphism rs2736100-C is associated with EGFR mutation-positive non-small cell lung cancer. Clin. Cancer Res. 21, 5173-5180 (2015)
18. Okada, Y. et al. Construction of a population-specific HLA imputation reference panel and its application to Graves disease risk in Japanese. Nat. Genet. 47, 798-802 (2015)
19. Diaz, G. et al. Functional analysis of HLA-DP polymorphism: a crucial role for DPb residues 9, 11, 35, 55, 56, 69 and 84-87 in T cell allorecognition and peptide binding. Int. Immunol. 15, 565-576 (2003)
20. Dai, S. et al. Crystal structure of HLA-DP2 and implications for chronic beryllium disease. Proc. Natl Acad. Sci. USA 107, 7425-7430 (2010)
21. Genomes Project C et al. A global reference for human genetic variation. Nature 526, 68-74 (2015)
22. Wang, Z. et al. Meta-analysis of genome-wide association studies identifies multiple lung cancer susceptibility loci in never-smoking Asian women. Hum. Mol. Genet. 25, 620-629 (2016)
23. Nakamura, Y. The BioBank Japan Project. Clin. Adv. Hematol. Oncol. 5, 696-697 (2007)
24. Kamitsuji, S. et al. Japan PGx Data Science Consortium Database: SNPs and HLA genotype data from 2994 Japanese healthy individuals for pharmacogenomics studies. J. Hum. Genet. 60, 319-326 (2015)
25. Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006)
26. Nomoto, K. et al. Detection of EGFR mutations in archived cytologic specimens of non-small cell lung cancer using high-resolution melting analysis. Am. J. Clin. Pathol. 126, 608-615 (2006)
27. Naoki, K. et al. The PCR-invader method (structure-specific 5 nuclease-based method), a sensitive method for detecting EGFR gene mutations in lung cancer specimens; comparison with direct sequencing. Int. J. Clin. Oncol. 16, 335-344 (2011)
28. Horiike, A. et al. Detection of epidermal growth factor receptor mutation in transbronchial needle aspirates of non-small cell lung cancer. Chest 131, 1628-1634 (2007)
29. Miyamae, Y. et al. Significance of epidermal growth factor receptor gene mutations in squamous cell lung carcinoma. Oncol. Rep. 25, 921-928 (2011)
30. Lindeman, N. I. et al. Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. J. Thorac. Oncol. 8, 823-859 (2013)
31. Untergasser, A. et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012)
32. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002)
33. Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002)
34. Delaneau, O., Marchini, J. & Zagury, J. F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179-181 (2012)
35. Fuchsberger, C., Abecasis, G. R. & Hinds, D. A. minimac2: faster genotype imputation. Bioinformatics 31, 782-784 (2015)
36. Li, Y., Willer, C., Sanna, S. & Abecasis, G. Genotype imputation. Annu. Rev. Genomics Hum. Genet. 10, 387-406 (2009)
37. Pruim, R. J. et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 26, 2336-2337 (2010)
38. Ward, L. D. & Kellis, M. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res. 44, D877-D881 (2016)
39. Team RDC. A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2005)
40. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007)