Mapping genomic deletions down to the base: A quantitative copy number scanning approach used to characterise and clone the breakpoints of a recurrent 7p14.2p15.3 deletion

Human Genetics

Volumn 115, Issue 6, 2004, Pages 459-467

  Dunø, Morten ^a   Hove, Hanne ^a   Kirchhoff, Maria ^a   Devriendt, Koenraad ^b   Schwartz, Marianne ^a  

^a Rigshospitalet   (Denmark)

^b UNIVERSITY HOSPITALS LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; HISTONE DEACETYLASE; HOX PROTEIN;

ARTICLE; CASE REPORT; CHILD; CHROMOSOME 7P; CHROMOSOME BREAKAGE; CHROMOSOME INVERSION; CLINICAL FEATURE; FEMALE; GENE DELETION; GENE DISRUPTION; GENE LOCUS; GENE MAPPING; GENE NUMBER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC PREDISPOSITION; HAND FOOT SYNDROME; HEARING IMPAIRMENT; HUMAN; MALE; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

CHILD, PRESCHOOL; CHROMOSOMES, HUMAN, PAIR 7; CLONING, MOLECULAR; CYTOGENETICS; DNA; FACIES; FEMALE; GENE DELETION; GENOME, HUMAN; HISTONE DEACETYLASES; HUMANS; KARYOTYPING; MALE; MENTAL RETARDATION; MICROSATELLITE REPEATS; MODELS, GENETIC; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; RECEPTORS, ESTROGEN; REPRESSOR PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SYNDROME;

EID: 9544220660     PISSN: 03406717     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00439-004-1174-y     Document Type: Article

References (39)

1. Armour JA, Sismani C, Patsalis PC, Cross G (2000) Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res 28:605-609 10.1093/nar/28.2.605, 1:CAS:528:DC%2BD3cXhtVSktbo%3D, 10606661
2. Armour JA, Barton DE, Cockburn DJ, Taylor GR (2002) The detection of large deletions or duplications in genomic DNA. Hum Mutat 20:325-337 10.1002/humu.10133, 1:CAS:528:DC%2BD38XptV2nurY%3D, 12402329
3. Bischoff AM, Luijendijk MW, Huygen PL, van Duijnhoven G, De Leenheer EM, Oudesluijs GG, Van Laer L, Cremers FP, Cremers CW, Kremer H (2004) A novel mutation identified in the DFNA5 gene in a Dutch family: A clinical and genetic evaluation. Audiol Neurootol 9:34-46 10.1159/000074185, 1:CAS:528:DC%2BD3sXpvVeksL0%3D, 14676472
4. Cai T, Yu P, Tagle DA, Xia J (1999) Duplication of 7p21.2→pter due to maternal 7p;21q translocation: Implications for critical segment assignment in the 7p duplication syndrome. Am J Med Genet 86:305-311 10.1002/(SICI)1096-8628(19991008)86:4<305::AID-AJMG1>3.3.CO;2-2, 1:STN:280:DyaK1MvisFSntg%3D%3D, 10494083
5. Chotai KA, Brueton LA, van Herwerden L, Garrett C, Hinkel GK, Schinzel A, Mueller RF, Speleman F, Winter RM (1994) Six cases of 7p deletion: clinical, cytogenetic, and molecular studies. Am J Med Genet 51:270-276 1:STN:280:ByuA2MvitlI%3D, 7521123
6. Cox H, Stewart H, Hall L, Donnai D (2002) Phenotypic spectrum of interstitial 7p duplication in mosaic and non-mosaic forms. Am J Med Genet 109:306-310 10.1002/ajmg.10368, 11992485
7. David D, Cardoso J, Marques BB, Marques R, Silva ED, Santos H, Boavida MG (2003) Molecular characterization of a familial translocation implicates disruption of HDAC9 and possible position effect on TGFbeta2 in the pathogenesis of Peters' anomaly. Genomics 81:489-503 10.1016/S0888-7543(03)00046-6, 1:CAS:528:DC%2BD3sXivVCrtLg%3D, 12706107
8. Devriendt K, Jaeken J, Matthijs G, Van Esch H, Debeer P, Gewillig M, Fryns JP (1999) Haploinsufficiency of the HOXA gene cluster, in a patient with hand-foot-genital syndrome, velopharyngeal insufficiency, and persistent patent ductus Botalli. Am J Hum Genet 65:249-251 10.1086/302452, 1:STN:280:DyaK1M3psVKjtg%3D%3D, 10364539
9. Frisen L, Lagerstedt K, Tapper-Persson M, Kockum I, Nordenskjold A (2003) A novel duplication in the HOXA13 gene in a family with atypical hand-foot-genital syndrome. J Med Genet 40:e49 10.1136/jmg.40.4.e49, 1:STN:280:DC%2BD3s7lvF2lug%3D%3D, 12676922
10. Ginzinger DG (2002) Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Exp Hematol 30:503-512 10.1016/S0301-472X(02)00806-8, 1:CAS:528:DC%2BD38XksFOksb8%3D, 12063017
11. Goodman FR (2002) Limb malformations and the human HOX genes. Am J Med Genet 112:256-265 10.1002/ajmg.10776, 12357469
12. Higuchi R, Fockler C, Dollinger G, Watson R (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (N Y) 11:1026-1030 1:STN:280:ByyA2sfntVQ%3D
13. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, et al (2003) The DNA sequence of human chromosome 7. Nature 424:157-164 10.1038/nature01782, 1:CAS:528:DC%2BD3sXlt1Cktb4%3D, 12853948
14. Johnson D, Horsley SW, Moloney DM, Oldridge M, Twigg SR, Walsh S, Barrow M, Njolstad PR, Kunz J, Ashworth GJ, Wall SA, Kearney L, Wilkie AO (1998) A comprehensive screen for TWIST mutations in patients with craniosynostosis identifies a new microdeletion syndrome of chromosome band 7p21.1. Am J Hum Genet 63:1282-1293 10.1086/302122, 1:CAS:528:DyaK1cXnvVGht78%3D, 9792856
15. Kirchhoff M, Gerdes T, Rose H, Maahr J, Ottesen AM, Lundsteen C (1998) Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 31:163-173 10.1002/(SICI)1097-0320(19980301)31:3<163::AID-CYTO3>3.3.CO;2-1, 1:CAS:528:DyaK1cXit1Kit78%3D, 9515715
16. Kirchhoff M, Rose H, Maahr J, Gerdes T, Bugge M, Tommerup N, Tumer Z, Lespinasse J, Jensen PK, Wirth J, Lundsteen C (2000) High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes. Eur J Hum Genet 8:661-668 10.1038/sj.ejhg.5200512, 1:CAS:528:DC%2BD3cXntFOmtb8%3D, 10980571
17. Kirchhoff M, Rose H, Lundsteen C (2001) High resolution comparative genomic hybridisation in clinical cytogenetics. J Med Genet 38:740-744 10.1136/jmg.38.11.740, 1:CAS:528:DC%2BD3MXptVKqsL0%3D, 11694545
18. Kirchhoff M, Pedersen S, Kjeldsen E, Rose H, Dunø M, Kølvraa S, Lundsteen C (2004) A prospective study comparing HR-CGH and subtelomeric FISH for investigation of mentally retarded and dysmorphic individuals and an update of a study using only HR-CGH. Am J Med Genet 127A:111-117 10.1002/ajmg.a.20678, 15108196
19. Knoll JH, Rogan PK (2003) Sequence-based, in situ detection of chromosomal abnormalities at high resolution. Am J Med Genet 121A:245-257 10.1002/ajmg.a.20123, 12923866
20. Kozma C, Haddad BR, Meck JM (2000) Trisomy 7p resulting from 7p15;9p24 translocation: Report of a new case and review of associated medical complications. Am J Med Genet 91:286-290 10.1002/(SICI)1096-8628(20000410)91:4<286::AID-AJMG9>3.0.CO;2-2, 1:STN:280:DC%2BD3c3ivFCjug%3D%3D, 10766985
21. Megarbane A, Le Lorc HM, Elghezal H, Joly G, Gosset P, Souraty N, Samaras L, Prieur M, Vekemans M, Turleau C, Romana SP (2001) Pure partial 7p trisomy including the TWIST , HOXA , and GLI3 genes. J Med Genet 38:178-182 10.1136/jmg.38.3.178, 1:STN:280:DC%2BD3M3msFGgsw%3D%3D, 11303510
22. Mortlock DP, Innis JW (1997) Mutation of HOXA13 in hand-foot-genital syndrome. Nat Genet 15:179-180 1:CAS:528:DyaK2sXhtVOltLo%3D, 9020844
23. Nimmakayalu MA, Gotter AL, Shaikh TH, Emanuel BS (2003) A novel sequence-based approach to localize translocation breakpoints identifies the molecular basis of a t(4;22). Hum Mol Genet 12:2817-2825 10.1093/hmg/ddg301, 1:CAS:528:DC%2BD3sXos1Wgtr4%3D, 12952865
24. Nystrom-Lahti M, Kristo P, Nicolaides NC, Chang SY, Aaltonen LA, Moisio AL, Jarvinen HJ, Mecklin JP, Kinzler KW, Vogelstein B et al (1995) Founding mutations and Alu-mediated recombination in hereditary colon cancer. Nat Med 1:1203-1206 1:CAS:528:DyaK2MXptFahsLs%3D, 7584997
25. Petrij-Bosch A, Peelen T, van Vliet M, van Eijk R, Olmer R, Drusedau M, Hogervorst FB, Hageman S, Arts PJ, Ligtenberg MJ, Meijers-Heijboer H, Klijn JG, Vasen HF, Cornelisse CJ, van 't Veer LJ, Bakker E, van Ommen GJ, Devilee P (1997) BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nat Genet 17:341-345
26. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45 1:STN:280:DC%2BD38nis12jtw%3D%3D, 11328886
27. Prediger EA (2001) Quantitating mRNAs with relative and competitive RT-PCR. Methods Mol Biol 160:49-63 10.1385/1-59259-233-3:049, 1:CAS:528:DC%2BD3MXhtlajs70%3D, 11265305
28. Reish O, Berry SA, Dewald G, King RA (1996) Duplication of 7p: Further delineation of the phenotype and restriction of the critical region to the distal part of the short arm. Am J Med Genet 61:21-25 10.1002/(SICI)1096-8628(19960102)61:1<21::AID-AJMG4>3.3.CO;2-2, 1:STN:280:BymA2c7pvVQ%3D, 8741912
29. Rowland JS, Barton DE, Taylor GR (2001) A comparison of methods for gene dosage analysis in HMSN type 1. J Med Genet 38:90-95 10.1136/jmg.38.2.90, 1:CAS:528:DC%2BD3MXhsFWmur8%3D, 11158172
30. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57 10.1093/nar/gnf056, 12060695
31. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Res 13:103-107 10.1101/gr.809403, 1:CAS:528:DC%2BD3sXnvFGlsg%3D%3D, 12529312
32. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23:1087-1088 1:CAS:528:DyaK2MXlsVSrs70%3D, 7731798
33. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN (2003) Human gene mutation database (HGMD): 2003 update. Hum Mutat 21:577-581 10.1002/humu.10212, 1:CAS:528:DC%2BD3sXkvVyhtrk%3D, 12754702
34. Tharapel SA, Kadandale JS (2002) Primed in situ labeling (PRINS) for evaluation of gene deletions in cancer. Am J Med Genet 107:123-126 10.1002/ajmg.10105, 11807886
35. Utsch B, Becker K, Brock D, Lentze MJ, Bidlingmaier F, Ludwig M (2002) A novel stable polyalanine [poly(A)] expansion in the HOXA13 gene associated with hand-foot-genital syndrome: Proper function of poly(A)-harbouring transcription factors depends on a critical repeat length? Hum Genet 110:488-494 10.1007/s00439-002-0712-8, 1:CAS:528:DC%2BD38Xkt1WmsLY%3D, 12073020
36. Van Laer L, Huizing EH, Verstreken M, van Zuijlen D, Wauters JG, Bossuyt PJ, Van de Heyning P, McGuirt WT, Smith RJ, Willems PJ, Legan PK, Richardson GP, Van Camp G (1998) Nonsyndromic hearing impairment is associated with a mutation in DFNA5 . Nat Genet 20:194-197 10.1038/2503, 9771715
37. Yan H, Papadopoulos N, Marra G, Perrera C, Jiricny J, Boland CR, Lynch HT, Chadwick RB, de la Chapelle A, Berg K, Eshleman JR, Yuan W, Markowitz S, Laken SJ, Lengauer C, Kinzler KW, Vogelstein B (2000) Conversion of diploidy to haploidy. Nature 403:723-724 10.1038/35002251, 1:CAS:528:DC%2BD3cXhsVSqt7c%3D, 10693791
38. Yu C, Meng X, Zhang S, Zhao G, Hu L, Kong X (2003) A 3-nucleotide deletion in the polypyrimidine tract of intron 7 of the DFNA5 gene causes nonsyndromic hearing impairment in a Chinese family. Genomics 82:575-579 10.1016/S0888-7543(03)00175-7, 1:CAS:528:DC%2BD3sXotVSjsr8%3D, 14559215
39. Zhou X, Marks PA, Rifkind RA, Richon VM (2001) Cloning and characterization of a histone deacetylase, HDAC9 . Proc Natl Acad Sci USA 98:10572*10577 10.1073/pnas.191375098, 1:CAS:528:DC%2BD3MXntVGnur0%3D, 11535832