Identification of germline genomic copy number variation in familial pancreatic cancer

Human Genetics

Volumn 131, Issue 9, 2012, Pages 1481-1494

  Al Sukhni, Wigdan ^a,b   Joe, Sarah ^a   Lionel, Anath C ^c,d   Zwingerman, Nora ^a   Zogopoulos, George ^a,b   Marshall, Christian R ^c   Borgida, Ayelet ^a   Holter, Spring ^a   Gropper, Aaron ^a   Moore, Sara ^a   Bondy, Melissa ^e   Klein, Alison P ^f   Petersen, Gloria M ^g   Rabe, Kari G ^g   Schwartz, Ann G ^h   Syngal, Sapna ⁱ   Scherer, Stephen W ^c,d   Gallinger, Steven ^a,b,j  

^a MOUNT SINAI HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^f JOHNS HOPKINS UNIVERSITY   (United States)

^g Mayo Clinic   (United States)

^h WAYNE STATE UNIVERSITY   (United States)

ⁱ DANA FARBER CANCER INSTITUTE   (United States)

^j TORONTO GENERAL HOSPITAL   (Canada)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ALGORITHM; ARTICLE; CANCER RISK; COMPUTER PROGRAM; CONTROLLED STUDY; COPY NUMBER VARIATION; FAMILIAL CANCER; GENETIC ANALYSIS; GENETIC PREDISPOSITION; GENOMICS; GENOTYPE; HIGH RISK PATIENT; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; PANCREAS CANCER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ADENOCARCINOMA; CASE-CONTROL STUDIES; GENE DOSAGE; GERM CELLS; HUMANS; PANCREATIC NEOPLASMS; POLYMERASE CHAIN REACTION;

EID: 84866738096     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-012-1183-1     Document Type: Article

References (52)

1. Alaerts M, Del-Favero J (2009) Searching genetic risk factors for schizophrenia and bipolar disorder: learn from the past and back to the future. Hum Mutat 30:1139-1152
2. Brune KA, Lau B, Palmisano E, Canto M, Goggins MG, Hruban RH, Klein AP (2010) Importance of age of onset in pancreatic cancer kindreds. J Natl Cancer Inst 102:119-126
3. Buchholz M, Braun M, Heidenblut A, Kestler HA, Klöppel G, Schmiegel W, Hahn SA, Lüttges J, Gress TM (2005) Transcriptome analysis of microdissected pancreatic intraepithelial neoplastic lesions. Oncogene 24:6626-6636
4. Cotterchio M, Manno M, Klar N, McLaughlin J, Gallinger S (2005) Colorectal screening is associated with reduced colorectal cancer risk: a case-control study within the population-based Ontario Familial Colorectal Cancer Registry. Cancer Causes Control 16:865-875
5. Cutts RJ, Gadaleta E, Hahn SA, Crnogorac-Jurcevic T, Lemoine NR, Chelala C (2011) The Pancreatic Expression database: 2011 update. Nucleic Acids Res 39 (Database issue):D1023-1028
6. Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, Cole K, Mossé YP, Wood A, Lynch JE, Pecor K, Diamond M, Winter C, Wang K, Kim C, Geiger EA, McGrady PW, Blakemore AI, London WB, Shaikh TH, Bradfield J, Grant SF, Li H, Devoto M, Rappaport ER, Hakonarson H, Maris JM (2009) Copy number variation at 1q21.1 associated with neuroblastoma. Nature 459:987-991
7. Engert S, Wappenschmidt B, Betz B, Kast K, Kutsche M, Hellebrand H, Goecke TO, Kiechle M, Niederacher D, Schmutzler RK, Meindl A (2008) MLPA screening in the BRCA1 gene from 1, 506 German hereditary breast cancer cases: novel deletions, frequent involvement of exon 17, and occurrence in single earlyonset cases. Hum Mutat 29:948-958
8. Gu W, Lupski JR (2008) CNV and nervous system diseases-what's new? Cytogenet Genome Res 123:54-64
9. Higgins ME, Claremont M, Major JE, Sander C, Lash AE (2007) CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res 35 (Database issue):D721-D726
10. Hruban RH, Canto MI, Goggins M, Schulick R, Klein AP (2010) Update on familial pancreatic cancer. Adv Surg 44:293-311
11. Huang L, Yu D, Wu C, Zhai K, Jiang G, Cao G, Wang C, Liu Y, Sun M, Li Z, Tan W, Lin D (2012) Copy number variation at 6q13 functions as a long-range regulator and is associated with pancreatic cancer risk. Carcinogenesis 33(1):94-100
12. Jiang J, Yu L, Huang X, Chen X, Li D, Zhang Y, Tang L, Zhao S (2001) Identification of two novel human dynein light chain genes, DNLC2A and DNLC2B, and their expression changes in hepatocellular carcinoma tissues from 68 Chinese patients. Gene 281:103-113
13. Jin Q, Gao G, Mulder KM (2009) Requirement of a dynein light chain in TGFbeta/Smad3 signaling. J Cell Physiol 221:707-715
14. Jin G, Sun J, Liu W, Zhang Z, Chu LW, Kim ST, Sun J, Feng J, Duggan D, Carpten JD, Wiklund F, Grönberg H, Isaacs WB, Zheng SL, Xu J (2011) Genome-wide copy-number variation analysis identifies common genetic variants at 20p13 associated with aggressiveness of prostate cancer. Carcinogenesis 32:1057-1062
15. Karageorgi S, Prescott J, Wong JY, Lee IM, Buring JE, De Vivo I (2011) GSTM1 and GSTT1 copy number variation in population-based studies of endometrial cancer risk. Cancer Epidemiol Biomarkers Prev 20:1447-1452
16. Kim YH, Lee HC, Kim SY, Yeom YI, Ryu KJ, Min BH, Kim DH, Son HJ, Rhee PL, Kim JJ, Rhee JC, Kim HC, Chun HK, Grady WM, Kim YS (2011) Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol 18:2338-2347
17. Klein AP, Beaty TH, Bailey-Wilson JE, Brune KA, Hruban RH, Petersen GM (2002) Evidence for a major gene influencing risk of pancreatic cancer. Genet Epidemiol 23:133-149
18. Klein AP, Brune KA, Petersen GM, Goggins M, Tersmette AC, Offerhaus GJ, Griffin C, Cameron JL, Yeo CJ, Kern S, Hruban RH (2004) Prospective risk of pancreatic cancer in familial pancreatic cancer kindreds. Cancer Res 64:2634-2638
19. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 40:1253-1260
20. Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, Schreiber S (2006) PopGen: population-based recruitment of patients and controls for the analysis of complex genotypephenotype relationships. Community Genet 9:55-61
21. Kuiper RP, Vissers LE, Venkatachalam R, Bodmer D, Hoenselaar E, Goossens M, Haufe A, Kamping E, Niessen RC, Hogervorst FB, Gille JJ, Redeker B, Tops CM, van Gijn ME, van den Ouweland AM, Rahner N, Steinke V, Kahl P, Holinski-Feder E, Morak M, Kloor M, Stemmler S, Betz B, Hutter P, Bunyan DJ, Syngal S, Culver JO, Graham T, Chan TL, Nagtegaal ID, van Krieken JH, Schackert HK, Hoogerbrugge N, van Kessel AG, Ligtenberg MJ (2011) Recurrence and variability of germline EPCAM deletions in Lynch syndrome. Hum Mutat 32:407-414
22. Lanktree M, Hegele RA (2008) Copy number variation in metabolic phenotypes. Cytogenet Genome Res 123:169-175
23. Li C, Hung Wong W (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2(8): RESEARCH0032
24. Liu W, Sun J, Li G, Zhu Y, Zhang S, Kim ST, Sun J, Wiklund F, Wiley K, Isaacs SD, Stattin P, Xu J, Duggan D, Carpten JD, Isaacs WB, Grönberg H, Zheng SL, Chang BL (2009) Association of a germ-line copy number variation at 2p24.3 and risk for aggressive prostate cancer. Cancer Res 69:2176-2179
25. Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH (2007) Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biol Ther 6:1592-1599
26. Madlensky L, Berk TC, Bapat BV, McLeod RS, Couture J, Baron D, Hiruki T, Redston M, Cohen Z, Gallinger S (1995) A preventive registry for hereditary nonpolyposis colorectal cancer. Can J Oncol 5:355-360
27. Michils G, Tejpar S, Thoelen R, van Cutsem E, Vermeesch JR, Fryns JP, Legius E, Matthijs G (2005) Large deletions of the APC gene in 15 % of mutation-negative patients with classical polyposis (FAP): a Belgian study. Hum Mutat 25:125-134
28. Morrow EM (2010) Genomic copy number variation in disorders of cognitive development. J Am Acad Child Adolesc Psychiatry 49:1091-1104
29. Müller A, Holzmann K, Kestler HA (2007) Visualization of genomic aberrations using Affymetrix SNP arrays. Bioinformatics 23:496-497
30. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Ogawa S (2005) A robust algorithm for copy number detection using highdensity oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65:6071-6079
31. Nørskov MS, Frikke-Schmidt R, Bojesen SE, Nordestgaard BG, Loft S, Tybjœrg-Hansen A (2011) Copy number variation in glutathione-S- transferase T1 and M1 predicts incidence and 5-year survival from prostate and bladder cancer, and incidence of corpus uteri cancer in the general population. Pharmacogenomics J 11:292-299
32. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC, Kirkness EF, Levy S, Feuk L, Scherer SW (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11:R52
33. Petersen GM, de Andrade M, Goggins M, Hruban RH, Bondy M, Korczak JF, Gallinger S, Lynch HT, Syngal S, Rabe KG, Seminara D, Klein AP (2006) Pancreatic cancer genetic epidemiology consortium. Cancer Epidemiol Biomarkers Prev 15:704-710
34. Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:512-520
35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
36. Sanders MA, Ampasala D, Basson MD (2009) DOCK5 and DOCK1 regulate Caco-2 intestinal epithelial cell spreading and migration on collagen IV. J Biol Chem 284:27-35
37. Schaschl H, Aitman TJ, Vyse TJ (2009) Copy number variation in the human genome and its implication in autoimmunity. Clin Exp Immunol 156:12-16
38. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C (T) method. Nat Protoc 3:1101-1108
39. Scrideli CA, Carlotti CG Jr, Okamoto OK, Andrade VS, Cortez MA, Motta FJ, Lucio-Eterovic AK, Neder L, Rosemberg S, Oba-Shinjo SM, Marie SK, Tone LG (2008) Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR. J Neurooncol 88:281-291
40. Shepherd R, Forbes SA, Beare D, Bamford S, Cole CG, Ward S, Bindal N, Gunasekaran P, Jia M, Kok CY, Leung K, Menzies A, Butler AP, Teague JW, Campbell PJ, Stratton MR, Futreal PA (2011) Data mining using the catalogue of somatic mutations in cancer BioMart. Database (Oxford) 2011: bar018 (print)
41. Shlien A, Tabori U, Marshall CR, Pienkowska M, Feuk L, Novokmet A, Nanda S, Druker H, Scherer SW, Malkin D (2008) Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome. Proc Natl Acad Sci USA 105:11264-11269
42. Stewart AF, Dandona S, Chen L, Assogba O, Belanger M, Ewart G, La Rose R, Doelle H, Williams K, Wells GA, McPherson R, Roberts R (2009) Kinesin family member 6 variant Trp719Arg does not associate with angiographically defined coronary artery disease in the Ottawa Heart Genomics Study. J Am Coll Cardiol 53:1471-1472
43. Taylor CF, Charlton RS, Burn J, Sheridan E, Taylor GR (2003) Genomic deletions in MSH2 or MLH1 are a frequent cause of hereditary non-polyposis colorectal cancer: identification of novel and recurrent deletions by MLPA. Hum Mutat 22:428-433
44. Tersmette AC, Petersen GM, Offerhaus GJ, Falatko FC, Brune KA, Goggins M, Rozenblum E, Wilentz RE, Yeo CJ, Cameron JL, Kern SE, Hruban RH (2001) Increased risk of incident pancreatic cancer among first-degree relatives of patients with familial pancreatic cancer. Clin Cancer Res 7:738-744
45. Tse KP, Su WH, Yang ML, Cheng HY, Tsang NM, Chang KP, Hao SP, Yao Shugart Y, Chang YS (2011) A gender-specific association of CNV at 6p21.3 with NPC susceptibility. Hum Mol Genet 20:2889-2896
46. Venkatachalam R, Verwiel ET, Kamping EJ, Hoenselaar E, Görgens H, Schackert HK, van Krieken JH, Ligtenberg MJ, Hoogerbrugge N, van Kessel AG, Kuiper RP (2011) Identification of candidate predisposing copy number variants in familial and early-onset colorectal cancer patients. Int J Cancer 129:1635-1642
47. Vincent A, Herman J, Schulick R, Hruban RH, Goggins M (2011) Pancreatic cancer. Lancet 378:607-620
48. Wang H, Linghu H, Wang J, Che YL, Xiang TX, Tang WX, Yao ZW (2010) The role of Crk/Dock180/Rac1 pathway in the malignant behavior of human ovarian cancer cell SKOV3. Tumour Biol 31:59-67
49. Wellcome Trust Case Control Consortium et al (2010) Genome-wide association study of CNVs in 16, 000 cases of eight common diseases and 3, 000 shared controls. Nature 464:713-720
50. Winchester L, Yau C, Ragoussis J (2009) Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 8:353-366
51. Yoshihara K, Tajima A, Adachi S, Quan J, Sekine M, Kase H, Yahata T, Inoue I, Tanaka K (2011) Germline copy number variations in BRCA1-associated ovarian cancer patients. Genes Chromosomes Cancer 50:167-177
52. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115:205-214