High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor (original) (raw)
References
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE (2002) Recent segmental duplications in the human genome. Science 297:1003–1007 ArticlePubMedCAS Google Scholar
Barbouti A, Stankiewicz P, Nusbaum C, Cuomo C, Cook A, Hoglund M, Johansson B, Hagemeijer A, Park SS, Mitelman F, Lupski JR, Fioretos T (2004) The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 74:1–10 ArticlePubMedCAS Google Scholar
Biegel JA (1999) Cytogenetics and molecular genetics of childhood brain tumors. Neuro-oncology 1:139–151 ArticlePubMedCAS Google Scholar
Biegel JA (2006) Molecular genetics of atypical teratoid/rhabdoid tumor. Neurosurg Focus 20:E11 PubMed Google Scholar
Biegel JA, Rorke LB, Packer RJ, Emanuel BS (1990) Monosomy 22 in rhabdoid or atypical tumors of the brain. J Neurosurg 73:710–714 ArticlePubMedCAS Google Scholar
Biegel JA, Zhou JY, Rorke LB, Stenstrom C, Wainwright LM, Fogelgren B (1999) Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. Cancer Res 59:74–79 PubMedCAS Google Scholar
Biegel JA, Tan L, Zhang F, Wainwright L, Russo P, Rorke LB (2002) Alterations of the hSNF5/INI1 gene in central nervous system atypical teratoid/rhabdoid tumors and renal and extrarenal rhabdoid tumors. Clin Cancer Res 8:3461–3467 PubMedCAS Google Scholar
Biggar SR, Crabtree GR (1999) Continuous and widespread roles for the Swi–Snf complex in transcription. EMBO J 18:2254–2264 ArticlePubMedCAS Google Scholar
Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14:287–295 ArticlePubMedCAS Google Scholar
Bourdeaut F, Freneaux P, Thuille B, Lellouch-Tubiana A, Nicolas A, Couturier J, Pierron G, Sainte-Rose C, Bergeron C, Bouvier R, Rialland X, Laurence V, Michon J, Sastre-Garau X, Delattre O (2007) hSNF5/INI1-deficient tumours and rhabdoid tumours are convergent but not fully overlapping entities. J Pathol 211:323–330 ArticlePubMedCAS Google Scholar
Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38:75–81 ArticlePubMedCAS Google Scholar
Cox C, Bignell G, Greenman C, Stabenau A, Warren W, Stephens P, Davies H, Watt S, Teague J, Edkins S, Birney E, Easton DF, Wooster R, Futreal PA, Stratton MR (2005) A survey of homozygous deletions in human cancer genomes. Proc Natl Acad Sci 102:4542–4547 ArticlePubMedCAS Google Scholar
Edelmann L, Pandita RK, Morrow BE (1999) Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet 64:1076–1086 ArticlePubMedCAS Google Scholar
Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJ, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Zahir F, Eydoux P, Marra MA (2006) Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet 79:500–513 ArticlePubMedCAS Google Scholar
Gibcus JH, Kok K, Menkema L, Hermsen MA, Mastik M, Kluin PM, van der Wal JE, Schuuring E (2007) High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications. Hum Genet 121:187–201 ArticlePubMedCAS Google Scholar
Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38:82–85 ArticlePubMedCAS Google Scholar
Janne PA, Li C, Zhao X, Girard L, Chen TH, Minna J, Christiani DC, Johnson BE, Meyerson M (2004) High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 23:2716–2726 ArticlePubMedCAS Google Scholar
Janson K, Nedzi LA, David O, Schorin M, Walsh JW, Bhattacharjee M, Pridjian G, Tan L, Judkins AR, Biegel JA (2005) Predisposition to atypical teratoid/rhabdoid tumor due to an inherited INI1 mutation. Pediatr Blood Cancer 47:279–284 Article Google Scholar
Kusafuka T, Miao J, Yoneda A, Kuroda S, Fukuzawa M (2004) Novel germ-line deletion of SNF5/INI1/SMARCB1 gene in neonate presenting with congenital malignant rhabdoid tumor of kidney and brain primitive neuroectodermal tumor. Genes Chromosomes Cancer 40:133–139 ArticlePubMedCAS Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921 ArticlePubMedCAS Google Scholar
Langdon JA, Lamont JM, Scott DK, Dyer S, Prebble E, Bown N, Grundy RG, Ellison DW, Clifford SC (2006) Combined genome-wide allelotyping and copy number analysis identify frequent genetic losses without copy number reduction in medulloblastoma. Genes Chromosomes Cancer 45:47–60 ArticlePubMedCAS Google Scholar
Maris JM, Hii G, Gelfand CA, Varde S, White PS, Rappaport E, Surrey S, Fortina P (2005) Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform. Genome Res 15:1168–1176 ArticlePubMedCAS Google Scholar
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM (2006) Common deletion polymorphisms in the human genome. Nat Genet 38:86–92 ArticlePubMedCAS Google Scholar
McDonald-McGinn DM, Reilly A, Wallgren-Pettersson C, Hoyme HE, Yang SP, Adam MP, Zackai EH, Sullivan KE (2006) Malignancy in chromosome 22q11.2 deletion syndrome (DiGeorge syndrome/velocardiofacial syndrome). Am J Med Genet A 140:906–909 PubMed Google Scholar
McTaggart KE, Budarf ML, Driscoll DA, Emanuel BS, Ferreira P, McDermid HE (1998) Cat eye syndrome chromosome breakpoint clustering: identification of two intervals also associated with 22q11 deletion syndrome breakpoints. Cytogenet Cell Genet 81:222–228 ArticlePubMedCAS Google Scholar
Mendrzyk F, Korshunov A, Toedt G, Schwarz F, Korn B, Joos S, Hochhaus A, Schoch C, Lichter P, Radlwimmer B (2006) Isochromosome breakpoints on 17p in medulloblastoma are flanked by different classes of DNA sequence repeats. Genes Chromosomes Cancer 45:401–410 ArticlePubMedCAS Google Scholar
Ming JE, Geiger E, James AC, Ciprero KL, Nimmakayalu M, Zhang Y, Huang A, Vaddi M, Rappaport E, Zackai EH, Shaikh TH (2006) Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum Mutat 27:467–473 ArticlePubMedCAS Google Scholar
Muchardt C, Yaniv M (1999) The mammalian SWI/SNF complex and the control of cell growth. Sem Cell Dev Biol 10:189–195 ArticleCAS Google Scholar
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 high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65:6071–6079 ArticlePubMedCAS Google Scholar
Raisanen J, Biegel JA, Hatanpaa KJ, Judkins A, White CL, Perry A (2005) Chromosome 22q deletions in atypical teratoid/rhabdoid tumors in adults. Brain Pathol 15:23–28 ArticlePubMedCAS Google Scholar
Rauch A, Pfeiffer RA, Leipold G, Singer H, Tigges M, Hofbeck M (1999) A novel 22q11.2 microdeletion in DiGeorge syndrome. Am J Hum Genet 64:659–666 ArticlePubMedCAS Google Scholar
Saitta SC, McGrath JM, Mensch H, Shaikh TH, Zackai EH, Emanuel BS (1999) A 22q11.2 deletion that excludes UFD1L and CDC45L in a patient with conotruncal and craniofacial defects. Am J Hum Genet 65:562–566 ArticlePubMedCAS Google Scholar
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M (2004) Large-scale copy number polymorphism in the human genome. Science 305:525–528 ArticlePubMedCAS Google Scholar
Sevenet N, Sheridan E, Amram D, Schneider P, Handgretinger R, Delattre O (1999) Constitutional mutations of the hSNF5/INI1 gene predispose to a variety of cancers. Am J Hum Genet 65:1342–1348 ArticlePubMedCAS Google Scholar
Shaikh TH, Kurahashi H, Saitta SC, O’Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS (2000) Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis. Hum Mol Genet 9:489–501 ArticlePubMedCAS Google Scholar
Shaikh TH, O’Connor RJ, Pierpont ME, McGrath J, Hacker AM, Nimmakayalu M, Geiger E, Emanuel BS, Saitta SC (2007) Low copy repeats mediate distal chromosome 22q11.2 deletions: sequence analysis predicts breakpoint mechanisms. Genome Res 17:482–491 ArticlePubMedCAS Google Scholar
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE (2005) Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77:78–88 ArticlePubMedCAS Google Scholar
Shaw CJ, Lupski JR (2004) Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet 13(Spec No 1):R57–R64 ArticlePubMedCAS Google Scholar
Taylor MD, Gokgoz N, Andrulis IL, Mainprize TG, Drake JM, Rutka JT (2000) Familial posterior fossa brain tumors of infancy secondary to germline mutation of the hSNF5 gene. Am J Hum Genet 66:1403–1406 ArticlePubMedCAS Google Scholar
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE (2005) Fine-scale structural variation of the human genome. Nat Genet 37:727–732 ArticlePubMedCAS Google Scholar
Versteege I, Sevenet N, Lange J, Rousseau-Merck MF, Ambros P, Handgretinger R, Aurias A, Delattre O (1998) Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394:203–206 ArticlePubMedCAS Google Scholar
Wieser R, Fritz B, Ullmann R, Muller I, Galhuber M, Storlazzi CT, Ramaswamy A, Christiansen H, Shimizu N, Rehder H (2005) Novel rearrangement of chromosome band 22q11.2 causing 22q11 microdeletion syndrome-like phenotype and rhabdoid tumor of the kidney. Hum Mutat 26:78–83 ArticlePubMedCAS Google Scholar
Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64:3060–3071 ArticlePubMedCAS Google Scholar