Enhancer Chip: Detecting Human Copy Number Variations in Regulatory Elements

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Savarese, Marco ^a,b   Piluso, Giulio ^a   Orteschi, Daniela ^c   Di Fruscio, Giuseppina ^a   Dionisi, Manuela ^a   Blanco, Francesca del Vecchio ^a   Torella, Annalaura ^a   Giugliano, Teresa ^a   Iacomino, Michele ^a   Zollino, Marcella ^c   Neri, Giovanni ^c   Nigro, Vincenzo ^a,b  

^a SECOND UNIVERSITY OF NAPLES   (Italy)

^b TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^c FONDAZIONE POLICLINICO UNIVERSITARIO A GEMELLI IRCCS   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CENTROMERE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA MICROARRAY; ENHANCER REGION; FEMALE; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENOME ANALYSIS; HUMAN; MALE; PATHOGENICITY; PROCESS DESIGN; TELOMERE; VALIDATION PROCESS;

COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; FEMALE; HUMANS; MALE; REAL-TIME POLYMERASE CHAIN REACTION; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

EID: 84871434557     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052264     Document Type: Article

References (29)

1. Klopocki E, Mundlos S, (2011) Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev Genomics Hum Genet 12: 53-72.
2. Narlikar L, Ovcharenko I, (2009) Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic 8: 215-230.
3. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
4. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
5. Visel A, Minovitsky S, Dubchak I, Pennacchio LA, (2007) VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res 35: D88-92.
6. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321-1325.
7. Kleinjan DA, van Heyningen V, (2005) Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 76: 8-32.
8. Kioussis D, Vanin E, deLange T, Flavell RA, Grosveld FG, (1983) Beta-globin gene inactivation by DNA translocation in gamma beta-thalassaemia. Nature 306: 662-666.
9. Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, et al. (2003) A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12: 1725-1735.
10. Grice EA, Rochelle ES, Green ED, Chakravarti A, McCallion AS, (2005) Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer. Hum Mol Genet 14: 3837-3845.
11. Visel A, Rubin EM, Pennacchio LA, (2009) Genomic views of distant-acting enhancers. Nature 461: 199-205.
12. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, et al. (2011) Large-scale discovery of enhancers from human heart tissue. Nat Genet 44: 89-93.
13. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, et al. (2010) Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86: 749-764.
14. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
15. Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, et al. (2009) DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet 84: 524-533.
16. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
17. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
18. Taylor J, Schenck I, Blankenberg D, Nekrutenko A (2007) Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics Chapter 10: Unit 10 15.
19. Yatsenko SA, Shaw CA, Ou Z, Pursley AN, Patel A, et al. (2009) Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA. J Mol Diagn 11: 226-237.
20. Itsara A, Cooper GM, Baker C, Girirajan S, Li J, et al. (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 84: 148-161.
21. Marcinkowska M, Szymanski M, Krzyzosiak WJ, Kozlowski P, (2011) Copy number variation of microRNA genes in the human genome. BMC Genomics 12: 183.
22. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, et al. (2007) Deletion of ultraconserved elements yields viable mice. PLoS Biol 5: e234.
23. Crolla JA, van Heyningen V, (2002) Frequent chromosome aberrations revealed by molecular cytogenetic studies in patients with aniridia. Am J Hum Genet 71: 1138-1149.
24. Lehmann OJ, Sowden JC, Carlsson P, Jordan T, Bhattacharya SS, (2003) Fox's in development and disease. Trends Genet 19: 339-344.
25. Pfeifer D, Kist R, Dewar K, Devon K, Lander ES, et al. (1999) Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: evidence for an extended control region. Am J Hum Genet 65: 111-124.
26. Belloni E, Muenke M, Roessler E, Traverso G, Siegel-Bartelt J, et al. (1996) Identification of Sonic hedgehog as a candidate gene responsible for holoprosencephaly. Nat Genet 14: 353-356.
27. Wong LJ, Dimmock D, Geraghty MT, Quan R, Lichter-Konecki U, et al. (2008) Utility of oligonucleotide array-based comparative genomic hybridization for detection of target gene deletions. Clin Chem 54: 1141-1148.
28. Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, et al. (2010) Detection of clinically relevant exonic copy-number changes by array CGH. Hum Mutat 31: 1326-1342.
29. Piluso G, Dionisi M, Del Vecchio Blanco F, Torella A, Aurino S, et al. (2011) Motor chip: a comparative genomic hybridization microarray for copy-number mutations in 245 neuromuscular disorders. Clin Chem 57: 1584-1596.