Genomic profile analysis of diffuse-type gastric cancers

Genome Biology

Volumn 15, Issue 4, 2014, Pages

  Lee, Yeon Su ^a   Cho, Yun Sung ^b   Lee, Geon Kook ^a   Lee, Sunghoon ^b   Kim, Young Woo ^a   Jho, Sungwoong ^b   Kim, Hak Min ^b   Hong, Seung Hyun ^a   Hwang, Jung Ah ^a   Kim, Sook young ^a   Hong, Dongwan ^a   Choi, Il Ju ^a   Kim, Byung Chul ^b,c   Kim, Byoung Chul ^b   Kim, Chul Hong ^c   Choi, Hansol ^b   Kim, Youngju ^a   Kim, Kyung Wook ^a   Kong, Gu ^d   Kim, Hyung Lae ^e   Bhak, Jong ^b,c,f,g   Lee, Seung Hoon ^a   Lee, Jin Soo ^a   more..

^a National Cancer Center   (South Korea)

^b Personal Genomics Institute   (South Korea)

^c Theragen BiO Institute   (South Korea)

^d Hanyang University   (South Korea)

^e Ewha Womans University School of Medicine   (South Korea)

^f Seoul National University   (South Korea)

^g Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; DNA; PROTEIN MDM2; UVOMORULIN; CADHERIN; CDH1 PROTEIN, HUMAN; MDM2 PROTEIN, HUMAN; RNF216 PROTEIN, HUMAN; TUBERIN; TUMOR SUPPRESSOR PROTEIN; UBIQUITIN PROTEIN LIGASE;

ARTICLE; BINDING SITE; CALCIUM BINDING; CANCER INHIBITION; CARCINOGENESIS; CDH1 GENE; CHROMOSOMAL INSTABILITY; CHROMOSOME DELETION; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA EXTRACTION; EXOME; FROZEN SECTION; FUSION GENE; GASTRECTOMY; GENE AMPLIFICATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIATION; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MDM2 GENE; ONCOGENE; PROTEIN STRUCTURE; RNF216 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; STOMACH; STOMACH CANCER; THREE DIMENSIONAL IMAGING; TSC2 GENE; TUMOR SUPPRESSOR GENE; ADULT; AMINO ACID SEQUENCE; CASE CONTROL STUDY; CHEMISTRY; FEMALE; GENE FUSION; GENETICS; HUMAN GENOME; MALE; METABOLISM; MOLECULAR GENETICS; MUTATION; STOMACH NEOPLASMS;

ADULT; AMINO ACID SEQUENCE; CADHERINS; CASE-CONTROL STUDIES; FEMALE; GENE AMPLIFICATION; GENE FUSION; GENOME, HUMAN; HUMANS; MALE; MOLECULAR SEQUENCE DATA; MUTATION; PROTO-ONCOGENE PROTEINS C-MDM2; STOMACH NEOPLASMS; TUMOR SUPPRESSOR PROTEINS; UBIQUITIN-PROTEIN LIGASES;

EID: 84922373636     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-4-r55     Document Type: Article

References (79)

1. Ferlay J, Soerjomataram I, Ervik M, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray F: GLOBOCAN. 2012, http://globocan.iarc.fr , : Estimated Cancer Incidence, Mortality and Prevalence Worldwide in 2012,
2. Lauren P: The Two histological main types of gastric carcinoma: diffuse and so-called intestinal-type carcinoma. An attempt at a histo-clinical classification. Acta Pathol Microbiol Scand. 1965, 64: 31-49.
3. Crew KD, Neugut AI: Epidemiology of gastric cancer. World J Gastroenterol. 2006, 12: 354-362.
4. Parkin DM, Bray F, Ferlay J, Pisani P: Estimating the world cancer burden: Globocan 2000. Int J Cancer. 2001, 94: 153-156. 10.1002/ijc.1440.
5. Ushijima T, Sasako M: Focus on gastric cancer. Cancer Cell. 2004, 5: 121-125. 10.1016/S1535-6108(04)00033-9.
6. Vauhkonen M, Vauhkonen H, Sipponen P: Pathology and molecular biology of gastric cancer. Best Pract Res Clin Gastroenterol. 2006, 20: 651-674. 10.1016/j.bpg.2006.03.016.
7. Rosai J, Ackerman LV: Rosai and Ackerman's Surgical Pathology. 2004, St. Louis, Mo. London: Mosby, 9
8. Henson DE, Dittus C, Younes M, Nguyen H, Albores-Saavedra J: Differential trends in the intestinal and diffuse types of gastric carcinoma in the United States, 1973-2000: increase in the signet ring cell type. Arch Pathol Lab Med. 2004, 128: 765-770.
9. Compare D, Rocco A, Nardone G: Risk factors in gastric cancer. Eur Rev Med Pharmacol Sci. 2010, 14: 302-308.
10. Wu H, Rusiecki JA, Zhu K, Potter J, Devesa SS: Stomach carcinoma incidence patterns in the United States by histologic type and anatomic site. Cancer Epidemiol Biomarkers Prev. 2009, 18: 1945-1952. 10.1158/1055-9965.EPI-09-0250.
11. Tahara E: Genetic pathways of two types of gastric cancer. IARC Sci Publ. 2004, 157: 327-349.
12. Nobili S, Bruno L, Landini I, Napoli C, Bechi P, Tonelli F, Rubio CA, Mini E, Nesi G: Genomic and genetic alterations influence the progression of gastric cancer. World J Gastroenterol. 2011, 17: 290-299. 10.3748/wjg.v17.i3.290.
13. Guilford P, Humar B, Blair V: Hereditary diffuse gastric cancer: translation of CDH1 germline mutations into clinical practice. Gastric Cancer. 2010, 13: 1-10. 10.1007/s10120-009-0531-x.
14. Chen Y, Kingham K, Ford JM, Rosing J, Van Dam J, Jeffrey RB, Longacre TA, Chun N, Kurian A, Norton JA: A prospective study of total gastrectomy for CDH1-positive hereditary diffuse gastric cancer. Ann Surg Oncol. 2011, 18: 2594-2598. 10.1245/s10434-011-1648-9.
15. Suriano G, Oliveira C, Ferreira P, Machado JC, Bordin MC, De Wever O, Bruyneel EA, Moguilevsky N, Grehan N, Porter TR, Richards FM, Hruban RH, Roviello F, Huntsman D, Mareel M, Carneiro F, Caldas C, Seruca R: Identification of CDH1 germline missense mutations associated with functional inactivation of the E-cadherin protein in young gastric cancer probands. Hum Mol Genet. 2003, 12: 575-582. 10.1093/hmg/ddg048.
16. Oliveira C, Senz J, Kaurah P, Pinheiro H, Sanges R, Haegert A, Corso G, Schouten J, Fitzgerald R, Vogelsang H, Keller G, Dwerryhouse S, Grimmer D, Chin SF, Yang HK, Jackson CE, Seruca R, Roviello F, Stupka E, Caldas C, Huntsman D: Germline CDH1 deletions in hereditary diffuse gastric cancer families. Hum Mol Genet. 2009, 18: 1545-1555. 10.1093/hmg/ddp046.
17. Corso G, Pedrazzani C, Pinheiro H, Fernandes E, Marrelli D, Rinnovati A, Pascale V, Seruca R, Oliveira C, Roviello F: E-cadherin genetic screening and clinico-pathologic characteristics of early onset gastric cancer. Eur J Cancer. 2011, 47: 631-639. 10.1016/j.ejca.2010.10.011.
18. Carneiro P, Figueiredo J, Bordeira-Carriço R, Fernandes MS, Carvalho J, Oliveira C, Seruca R: Therapeutic targets associated to E-cadherin dysfunction in gastric cancer. Expert Opin Ther Targets. 2013, 17: 1187-1201. 10.1517/14728222.2013.827174.
19. Carvalho J, van Grieken NC, Pereira PM, Sousa S, Tijssen M, Buffart TE, Diosdado B, Grabsch H, Santos MA, Meijer G, Seruca R, Carvalho B, Oliveira C: Lack of microRNA-101 causes E-cadherin functional deregulation through EZH2 up-regulation in intestinal gastric cancer. J Pathol. 2012, 228: 31-44.
20. Carneiro F, Oliveira C, Leite M, Seruca R: Molecular targets and biological modifiers in gastric cancer. Semin Diagn Pathol. 2008, 25: 274-287. 10.1053/j.semdp.2008.07.004.
21. Sakamoto H, Yoshimura K, Saeki N, Katai H, Shimoda T, Matsuno Y, Saito D, Sugimura H, Tanioka F, Kato S, Matsukura N, Matsuda N, Nakamura T, Hyodo I, Nishina T, Yasui W, Hirose H, Hayashi M, Toshiro E, Ohnami S, Sekine A, Sato Y, Totsuka H, Ando M, Takemura R, Takahashi Y, Ohdaira M, Aoki K, Honmyo I, Study Group of Millennium Genome Project for Cancer, et al: Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer. Nat Genet. 2008, 40: 730-740. 10.1038/ng.152.
22. Wang K, Kan J, Yuen ST, Shi ST, Chu KM, Law S, Chan TL, Kan Z, Chan AS, Tsui WY, Lee SP, Ho SL, Chan AK, Cheng GH, Roberts PC, Rejto PA, Gibson NW, Pocalyko DJ, Mao M, Xu J, Leung SY: Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet. 2011, 43: 1219-1223. 10.1038/ng.982.
23. Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A, Lim KH, Ong CK, Huang D, Chin SY, Tan IB, Ng CC, Yu W, Wu Y, Lee M, Wu J, Poh D, Wan WK, Rha SY, So J, Salto-Tellez M, Yeoh KG, Wong WK, Zhu YJ, Futreal PA, Pang B, et al: Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet. 2012, 44: 570-574. 10.1038/ng.2246.
24. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J: Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009, 461: 272-276. 10.1038/nature08250.
25. 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, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, et al: Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 2012, 150: 1107-1120. 10.1016/j.cell.2012.08.029.
26. Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, et al: The genetic landscape of high-risk neuroblastoma. Nat Genet. 2013, 45: 279-284. 10.1038/ng.2529.
27. Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodriguez-Cuevas S, Romero-Cordoba SL, Schumacher SE, Stransky N, et al: Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012, 486: 405-409. 10.1038/nature11154.
28. Chang VY, Federman N, Martinez-Agosto J, Tatishchev SF, Nelson SF: Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li-Fraumeni syndrome. Pediatr Blood Cancer. 2013, 60: 570-574. 10.1002/pbc.24316.
29. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, et al: The genomic complexity of primary human prostate cancer. Nature. 2011, 470: 214-220. 10.1038/nature09744.
30. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, et al: Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol. 2012, 13: R115-10.1186/gb-2012-13-12-r115.
31. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ: Cancer Genome Atlas Research Network: landscape of somatic retrotransposition in human cancers. Science. 2012, 337: 967-971. 10.1126/science.1222077.
32. Tsukamoto Y, Uchida T, Karnan S, Noguchi T, Nguyen LT, Tanigawa M, Takeuchi I, Matsuura K, Hijiya N, Nakada C, Kishida T, Kawahara K, Ito H, Murakami K, Fujioka T, Seto M, Moriyama M: Genome-wide analysis of DNA copy number alterations and gene expression in gastric cancer. J Pathol. 2008, 216: 471-482. 10.1002/path.2424.
33. Li M, Zhao H, Zhang X, Wood LD, Anders RA, Choti MA, Pawlik TM, Daniel HD, Kannangai R, Offerhaus GJ, Velculescu VE, Wang L, Zhou S, Vogelstein B, Hruban RH, Papadopoulos N, Cai J, Torbenson MS, Kinzler KW: Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet. 2011, 43: 828-829. 10.1038/ng.903.
34. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, et al: Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008, 321: 1801-1806. 10.1126/science.1164368.
35. Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, et al: The genetic landscape of the childhood cancer medulloblastoma. Science. 2011, 331: 435-439. 10.1126/science.1198056.
36. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW: Cancer genome landscapes. Science. 2013, 339: 1546-1558. 10.1126/science.1235122.
37. Becker KF, Atkinson MJ, Reich U, Becker I, Nekarda H, Siewert JR, Höfler H: E-cadherin gene mutations provide clues to diffuse type gastric carcinomas. Cancer Res. 1994, 54: 3845-3852.
38. Berx G, Becker KF, Höfler H, van Roy F: Mutations of the human E-cadherin (CDH1) gene. Hum Mutat. 1998, 12: 226-237. 10.1002/(SICI)1098-1004(1998)12:4<226::AID-HUMU2>3.0.CO;2-D.
39. Machado JC, Soares P, Carneiro F, Rocha A, Beck S, Blin N, Berx G, Sobrinho-Simões M: E-cadherin gene mutations provide a genetic basis for the phenotypic divergence of mixed gastric carcinomas. Lab Invest. 1999, 79: 459-465.
40. Corso G, Carvalho J, Marrelli D, Vindigni C, Carvalho B, Seruca R, Roviello F, Oliveira C: Somatic mutations and deletions of the E-cadherin gene predict poor survival of patients with gastric cancer. J Clin Oncol. 2013, 31: 868-875. 10.1200/JCO.2012.44.4612.
41. Carneiro F, Oliveira C, Suriano G, Seruca R: Molecular pathology of familial gastric cancer, with an emphasis on hereditary diffuse gastric cancer. J Clin Pathol. 2008, 61: 25-30.
42. Oliveira C, Pinheiro H, Figueiredo J, Seruca R, Carneiro F: E-cadherin alterations in hereditary disorders with emphasis on hereditary diffuse gastric cancer. Prog Mol Biol Transl Sci. 2013, 116: 337-359.
43. Kim HC, Wheeler JM, Kim JC, Ilyas M, Beck NE, Kim BS, Park KC, Bodmer WF: The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Korea. Gut. 2000, 47: 262-267. 10.1136/gut.47.2.262.
44. Barbi S, Cataldo I, De Manzoni G, Bersani S, Lamba S, Mattuzzi S, Bardelli A, Scarpa A: The analysis of PIK3CA mutations in gastric carcinoma and metanalysis of literature suggest that exon-selectivity is a signature of cancer type. J Exp Clin Cancer Res. 2010, 29: 32-10.1186/1756-9966-29-32.
45. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, et al: Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008, 455: 1069-1075. 10.1038/nature07423.
46. Yang CY, Cheng MF, Tsai SS, Hsieh YL: Calcium, magnesium, and nitrate in drinking water and gastric cancer mortality. Jpn J Cancer Res. 1998, 89: 124-130. 10.1111/j.1349-7006.1998.tb00539.x.
47. Pećina-Slaus N: Tumor suppressor gene E-cadherin and its role in normal and malignant cells. Cancer Cell Int. 2003, 3: 17-
48. Ma L, Chen Z, Erdjument-Bromage H, Tempst P, Pandolfi PP: Phosphorylation and functional inactivation of TSC2 by Erk implications for tuberous sclerosis and cancer pathogenesis. Cell. 2005, 121: 179-193. 10.1016/j.cell.2005.02.031.
49. Kang YJ, Lu MK, Guan KL: The TSC1 and TSC2 tumor suppressors are required for proper ER stress response and protect cells from ER stress-induced apoptosis. Cell Death Differ. 2011, 18: 133-144. 10.1038/cdd.2010.82.
50. Miah SM, Purdy AK, Rodin NB, MacFarlane AW, Oshinsky J, Alvarez-Arias DA, Campbell KS: Ubiquitylation of an internalized killer cell Ig-like receptor by Triad3A disrupts sustained NF-kappaB signaling. J Immunol. 2011, 186: 2959-2969. 10.4049/jimmunol.1000112.
51. Tamura G, Yin J, Wang S, Fleisher AS, Zou T, Abraham JM, Kong D, Smolinski KN, Wilson KT, James SP, Silverberg SG, Nishizuka S, Terashima M, Motoyama T, Meltzer SJ: E-Cadherin gene promoter hypermethylation in primary human gastric carcinomas. J Natl Cancer Inst. 2000, 92: 569-573. 10.1093/jnci/92.7.569.
52. Machado JC, Oliveira C, Carvalho R, Soares P, Berx G, Caldas C, Seruca R, Carneiro F, Sobrinho-Simöes M: E-cadherin gene (CDH1) promoter methylation as the second hit in sporadic diffuse gastric carcinoma. Oncogene. 2001, 20: 1525-1528. 10.1038/sj.onc.1204234.
53. Seruca R, Suijkerbuijk RF, Gärtner F, Criado B, Veiga I, Olde-Weghuis D, David L, Castedo S, Sobrinho-Simões M: Increasing levels of MYC and MET co-amplification during tumor progression of a case of gastric cancer. Cancer Genet Cytogenet. 1995, 82: 140-145. 10.1016/0165-4608(95)00033-L.
54. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, et al: ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010, 363: 1532-1543. 10.1056/NEJMoa1008433.
55. Jones S, Wang TL, Shih IM, Mao TL, Nakayama K, Roden R, Glas R, Slamon D, Diaz LA, Vogelstein B, Kinzler KW, Velculescu VE, Papadopoulos N: Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science. 2010, 330: 228-231. 10.1126/science.1196333.
56. Günther T, Schneider-Stock R, Häckel C, Kasper HU, Pross M, Hackelsberger A, Lippert H, Roessner A: Mdm2 gene amplification in gastric cancer correlation with expression of Mdm2 protein and p53 alterations. Mod Pathol. 2000, 13: 621-626. 10.1038/modpathol.3880107.
57. Wade M, Li YC, Wahl GM: MDM2, MDMX and p53 in oncogenesis and cancer therapy. Nat Rev Cancer. 2013, 13: 83-96. 10.1038/nrc3430.
58. Nagar B, Overduin M, Ikura M, Rini JM: Structural basis of calcium-induced E-cadherin rigidification and dimerization. Nature. 1996, 380: 360-364. 10.1038/380360a0.
59. Handschuh G, Luber B, Hutzler P, Hofler H, Becker KF: Single amino acid substitutions in conserved extracellular domains of E-cadherin differ in their functional consequences. J Mol Biol. 2001, 314: 445-454. 10.1006/jmbi.2001.5143.
60. Brooks-Wilson AR, Kaurah P, Suriano G, Leach S, Senz J, Grehan N, Butterfield YS, Jeyes J, Schinas J, Bacani J, Kelsey M, Ferreira P, MacGillivray B, MacLeod P, Micek M, Ford J, Foulkes W, Australie K, Greenberg C, LaPointe M, Gilpin C, Nikkel S, Gilchrist D, Hughes R, Jackson CE, Monaghan KG, Oliveira MJ, Seruca R, Gallinger S, Caldas C, et al: Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria. J Med Genet. 2004, 41: 508-517. 10.1136/jmg.2004.018275.
61. Ozawa M, Engel J, Kemler R: Single amino acid substitutions in one Ca2+ binding site of uvomorulin abolish the adhesive function. Cell. 1990, 63: 1033-1038. 10.1016/0092-8674(90)90506-A.
62. Leckband D, Prakasam A: Mechanism and dynamics of cadherin adhesion. Annu Rev Biomed Eng. 2006, 8: 259-287. 10.1146/annurev.bioeng.8.061505.095753.
63. Garziera M, De Re V, Geremia S, Seruca R, Figueiredo J, Melo S, Simões-Correia J, Caggiari L, De Zorzi M, Canzonieri V, Cannizzaro R, Toffoli G: A novel CDH1 germline missense mutation in a sporadic gastric cancer patient in north-east of Italy. Clin Exp Med. 2013, 13: 149-157. 10.1007/s10238-012-0184-7.
64. Simões-Correia J, Figueiredo J, Lopes R, Stricher F, Oliveira C, Serrano L, Seruca R: E-cadherin destabilization accounts for the pathogenicity of missense mutations in hereditary diffuse gastric cancer. PLoS One. 2012, 7: e33783-10.1371/journal.pone.0033783.
65. Suriano G, Mulholland D, de Wever O, Ferreira P, Mateus AR, Bruyneel E, Nelson CC, Mareel MM, Yokota J, Huntsman D, Seruca R: The intracellular E-cadherin germline mutation V832 M lacks the ability to mediate cell-cell adhesion and to suppress invasion. Oncogene. 2003, 22: 5716-5719. 10.1038/sj.onc.1206672.
66. Oliveira C, Suriano G, Ferreira P, Canedo P, Kaurah P, Mateus R, Ferreira A, Ferreira AC, Oliveira MJ, Figueiredo C, Carneiro F, Keller G, Huntsman D, Machado JC, Seruca R: Genetic screening for familial gastric cancer. Hered Cancer Clin Pract. 2004, 2: 51-64. 10.1186/1897-4287-2-2-51.
67. Becker KF, Höfler H: Frequent somatic allelic inactivation of the E-cadherin gene in gastric carcinomas. J Natl Cancer Inst. 1995, 87: 1082-1084. 10.1093/jnci/87.14.1082.
68. Shibata D: Cancer. Heterogeneity and tumor history. Science. 2012, 336: 304-305. 10.1126/science.1222361.
69. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.
70. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: 1000 Genome Project Data Processing Subgroup: the sequence alignment/map format and SAMtools. Bioinformatics. 2009, 25: 2078-2079. 10.1093/bioinformatics/btp352.
71. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.
72. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol. 1981, 147: 195-197. 10.1016/0022-2836(81)90087-5.
73. Kanehisa M: The KEGG database. Novartis Found Symp. 2002, 247: 91-101. discussion 101-103, 119-128, 244-252
74. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004, 91: 355-358.
75. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009, 6: 677-681. 10.1038/nmeth.1363.
76. Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ: Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011, 108: E1128-E1136. 10.1073/pnas.1110574108.
77. Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B: The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure. 2011, 19: 244-256. 10.1016/j.str.2010.11.016.
78. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M: Evaluation of comparative protein modeling by MODELLER. Proteins. 1995, 23: 318-326. 10.1002/prot.340230306.
79. The sequence read archive. http://www.ncbi.nlm.nih.gov/sra ,