Genome-wide analysis of Ollier disease: Is it all in the genes?

Orphanet Journal of Rare Diseases

Volumn 6, Issue 1, 2011, Pages

  Pansuriya, Twinkal C ^a   Oosting, Jan ^a   Krenács, Tibor ^b   Taminiau, Antonie H M ^a   Verdegaal, Suzan H M ^a   Sangiorgi, Luca ^c   Sciot, Raf ^d   Hogendoorn, Pancras C W ^a   Szuhai, Karoly ^a   Bovée, Judith V M G ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b SEMMELWEIS UNIVERSITY   (Hungary)

^c RIZZOLI ORTHOPAEDIC INSTITUTE   (Italy)

^d UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; AGED; ARTICLE; CHILD; CHONDROSARCOMA; CHROMOSOME 3P; CHROMOSOME 5Q; CHROMOSOME 6Q; CHROMOSOME 9P; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DISEASE COURSE; DOWN REGULATION; ENCHONDROMATOSIS; EPIGENETICS; FEMALE; GENE DELETION; GENE EXPRESSION; GENOME ANALYSIS; HETEROZYGOSITY LOSS; HUMAN; HUMAN TISSUE; MALE; MALIGNANT TRANSFORMATION; POINT MUTATION; PRESCHOOL CHILD; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE MICROARRAY; UPREGULATION; GENETIC ASSOCIATION; GENETICS; IMMUNOHISTOCHEMISTRY; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

CHONDROSARCOMA; ENCHONDROMATOSIS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IMMUNOHISTOCHEMISTRY; LOSS OF HETEROZYGOSITY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 78651368719     PISSN: None     EISSN: 17501172     Source Type: Journal    
DOI: 10.1186/1750-1172-6-2     Document Type: Article

References (40)

1. Chondromas: enchondroma, periosteal chondroma, and enchondromatosis. DR Lucas JA Bridge, World Health Organization classification of tumours. Pathology and genetics of tumours of soft tissue and bone Lyon: IARC Press, Fletcher CDM, Unni KK, Mertens F, 2002 237 240
2. Enchondromatosis: insights on the different subtypes. T Pansuriya HM Kroon JVMG Bovée, Int J Clin Exp Pathol 2010 3 557 569 20661403
3. Enchondromatosis: Ollier disease and Maffucci syndrome. F Mertens KK Unni, World Health Organization Classification of Tumours. Pathology and genetics of tumours of soft tissue and bone Lyon: IARC Press, Fletcher CDM, Unni KK, Mertens F, 2002 356 357
4. Cartilage tumours and bone development: molecular pathology and possible therapeutic targets. JVMG Bovée PCW Hogendoorn JS Wunder BA Alman, Nat Rev Cancer 2010 10 481 488 20535132
5. Osteochondroma. J Khurana F Abdul-Karim JVMG Bovée, World Health Organization classification of tumours. Pathology and genetics of tumours of soft tissue and bone Lyon (France): IARC Press, Fletcher CDM, Unni KK, Mertens F, 2002 234 236
6. A mutant PTH/PTHrP type I receptor in enchondromatosis. S Hopyan N Gokgoz R Poon RC Gensure C Yu WG Cole RS Bell H Juppner IL Andrulis JS Wunder, et al. Nat Genet 2002 30 306 310 10.1038/ng844 11850620
7. PTHR1 mutations associated with Ollier disease result in receptor loss of function. A Couvineau V Wouters G Bertrand C Rouyer B Gerard LM Boon B Grandchamp M Vikkula C Silve, Hum Mol Genet 2008 17 2766 2775 10.1093/hmg/ddn176 18559376
8. Enchondromatosis (Ollier disease, Maffucci syndrome) is not caused by the PTHR1 mutation p.R150C. LB Rozeman L Sangiorgi IH Bruijn P Mainil-Varlet F Bertoni AM Cleton-Jansen PCW Hogendoorn JVMG Bovée, Hum Mutat 2004 24 466 473 10.1002/humu.20095 15523647
9. Ollier disease. C Silve H Juppner, Orphanet J Rare Dis 2006 1 37 10.1186/1750-1172-1-37 16995932
10. McCune-Albright syndrome. MM Cohen Jr GP Siegal, World Health Organization Classification of Tumours. Pathology & Genetics. Tumours of Soft Tissue and Bone Lyon: IARC Press, Fletcher CDM, Unni KK, Mertens F, 2002 357 359
11. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. K Lindblad-Toh DM Tanenbaum MJ Daly E Winchester WO Lui A Villapakkam SE Stanton C Larsson TJ Hudson BE Johnson, et al. Nat Biotechnol 2000 18 1001 1005 10.1038/79269 10973224
12. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. X Zhao C Li JG Paez K Chin PA Janne TH Chen L Girard J Minna D Christiani C Leo, et al. Cancer Res 2004 64 3060 3071 10.1158/0008-5472.CAN-03-3308 15126342
13. Prognostic factors in chondrosarcoma of bone. A clinicopathologic analysis with emphasis on histologic grading. HL Evans AG Ayala MM Romsdahl, Cancer 1977 40 818 831 10.1002/1097-0142(197708)40:2<818::AID- CNCR2820400234>3.0.CO;2-B 890662
14. EXT-mutation analysis and loss of heterozygosity in sporadic and hereditary osteochondromas and secondary chondrosarcomas. JVMG Bovée AM Cleton-Jansen W Wuyts G Caethoven AHM Taminiau E Bakker HW Van CJ Cornelisse PCW Hogendoorn, Am J Hum Genet 1999 65 689 698 10441575
15. A simple salting out procedure for extracting DNA from human nucleated cells. SA Miller HF Polesky, Nucleic Acids Res 1988 16 1215 10.1093/nar/16.3. 1215 3344216
16. High quality RNA isolation from tumours with low cellularity and high extracellular matrix component for cDNA microarrays: application to chondrosarcoma. HJ Baelde AM Cleton-Jansen H van Beerendonk M Namba JVMG Bovée PCW Hogendoorn, J Clin Pathol 2001 54 778 782 11577126
17. Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. S Lin B Carvalho DJ Cutler DE Arking A Chakravarti RA Irizarry, Genome Biol 2008 9 63 10.1186/gb-2008-9-4-r63 18387188
18. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. H Bengtsson P Wirapati TP Speed, Bioinformatics 2009 25 2149 2156 10.1093/bioinformatics/btp371 19535535
19. Genome-wide allelic state analysis on flow-sorted tumor fractions provides an accurate measure of chromosomal aberrations. WE Corver A Middeldorp NT Ter Haar ES Jordanova PM van ER van CJ Cornelisse GJ Fleuren H Morreau J Oosting, et al. Cancer Res 2008 68 10333 10340 10.1158/0008-5472.CAN-08-2665 19074902
20. Frequent occurrence of uniparental disomy in colorectal cancer. CL Andersen C Wiuf M Kruhoffer M Korsgaard S Laurberg TF Orntoft, Carcinogenesis 2007 28 38 48 10.1093/carcin/bgl086 16774939
21. A homozygous deletion of a normal variation locus in a patient with hearing loss from non-consanguineous parents. J Knijnenburg SA Oberstein K Frei T Lucas AC Gijsbers CA Ruivenkamp HJ Tanke K Szuhai, J Med Genet 2009 46 412 417 10.1136/jmg.2008.063685 19246478
22. Model-based variance-stabilizing transformation for Illumina microarray data. SM Lin P Du W Huber WA Kibbe, Nucleic Acids Res 2008 36 11 10.1093/nar/gkm1075 18178591
23. beadarray: R classes and methods for Illumina bead-based data. MJ Dunning ML Smith ME Ritchie S Tavare, Bioinformatics 2007 23 2183 2184 10.1093/bioinformatics/btm311 17586828
24. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. GK Smyth, Stat Appl Genet Mol Biol 2004 3 Article3 16646809
25. Reduction of VEGF-A and CTGF expression in diabetic nephropathy is associated with podocyte loss. HJ Baelde M Eikmans DW Lappin PP Doran D Hohenadel PT Brinkkoetter FJ Van der Woude R Waldherr TJ Rabelink HE De, et al. Kidney Int 2007 71 637 645 10.1038/sj.ki.5002101 17264876
26. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. J Vandesompele K De Preter F Pattyn B Poppe N Van Roy A De Paepe F Speleman, Genome Biol 2002 3 esearch0034.1 0034.11 10.1186/gb-2002-3-7-research0034
27. Up-regulation of PTHrP and Bcl-2 expression characterizes the progression of osteochondroma towards peripheral chondrosarcoma and is a late event in central chondrosarcoma. JVMG Bovée LJCM Van den Broek AM Cleton-Jansen PCW Hogendoorn, Lab Invest 2000 80 1925 1933 11140704
28. Integrated detection and population-genetic analysis of SNPs and copy number variation. SA McCarroll FG Kuruvilla JM Korn S Cawley J Nemesh A Wysoker MH Shapero PI de Bakker JB Maller A Kirby, et al. Nat Genet 2008 40 1166 1174 10.1038/ng.238 18776908
29. Copy-number variation and association studies of human disease. SA McCarroll DM Altshuler, Nat Genet 2007 39 37 S42 10.1038/ng2080 17597780
30. Array-comparative genomic hybridization of central chondrosarcoma - Identification of ribosomal protein S6 and cyclin-dependent kinase 4 as candidate target genes for genomic aberrations. LB Rozeman K Szuhai YM Schrage C Rosenberg HJ Tanke AHM Taminiau AM Cleton-Jansen JVMG Bovée PCW Hogendoorn, Cancer 2006 107 380 388 10.1002/cncr.22001 16779802
31. Signatures of mutation and selection in the cancer genome. GR Bignell CD Greenman H Davies AP Butler S Edkins JM Andrews G Buck L Chen D Beare C Latimer, et al. Nature 2010 463 893 898 10.1038/nature08768 20164919
32. Ivan M Roitt, Essential Immunology Blackwell Scientific Publications 1988
33. Lack of association between polymorphism of the human cyclic GMP-dependent protein kinase gene and obesity. SO Zakharkin AT Belay JR Fernandez LV De JL Kennedy MB Sokolowski DB Allison, Int J Obes (Lond) 2005 29 872 874 10.1038/sj.ijo.0802973 15917860
34. EB-1, a tyrosine kinase signal transduction gene, is transcriptionally activated in the t(1;19) subset of pre-B ALL, which express oncoprotein E2a-Pbx1. X Fu S McGrath M Pasillas S Nakazawa MP Kamps, Oncogene 1999 18 4920 4929 10.1038/sj.onc.1202874 10490826
35. Induction of pluripotent stem cells from fibroblast cultures. K Takahashi K Okita M Nakagawa S Yamanaka, Nat Protoc 2007 2 3081 3089 10.1038/nprot.2007. 418 18079707
36. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. NL Sobreira ET Cirulli D Avramopoulos E Wohler GL Oswald EL Stevens D Ge KV Shianna JP Smith JM Maia, et al. PLoS Genet 2010 6 1000991 10.1371/journal.pgen.1000991 20577567
37. Deletion 1p in a low-grade chondrosarcoma in a patient with Ollier disease. YY Ozisik AM Meloni SS Spanier CH Bush KL Kingsley AA Sandberg, Cancer Genet Cytogenet 1998 105 128 133 10.1016/S0165-4608(98)00027-2 9723029
38. Malignant progression in multiple enchondromatosis (Ollier's disease): an autopsy-based molecular genetic study. JVMG Bovée JF van Roggen AM Cleton-Jansen AH Taminiau HJ Van der Woude PCW Hogendoorn, Hum Pathol 2000 31 1299 1303 11070122
39. Emerging pathways in the development of chondrosarcoma of bone and implications for targeted treatment. JVMG Bovée AM Cleton-Jansen AHM Taminiau PCW Hogendoorn, Lancet Oncology 2005 6 599 607 16054571
40. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. CG Mullighan CB Miller I Radtke LA Phillips J Dalton J Ma D White TP Hughes MM Le Beau CH Pui, et al. Nature 2008 453 110 114 10.1038/nature06866 18408710