Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls

Human Mutation

Volumn 30, Issue 9, 2009, Pages

  Makrythanasis, Periklis ^a   Kapranov, Philipp ^b,j   Bartoloni, Lucia ^a   Reymond, Alexandre ^c   Deutsch, Samuel ^a   Guigó, Roderic ^d,e   Denoeud, France ^d   Drenkow, Jorg ^b   Rossier, Colette ^a   Ariani, Francesca ^f   Capra, Valeria ^g   Excoffier, Laurent ^h   Renieri, Alessandra ^f   Gingeras, Thomas R ^b,i   Antonarakis, Stylianos E ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b Thermo Fisher Scientific   (United States)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

^d INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^e CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^f UNIVERSITY OF SIENA   (Italy)

^g G GASLINI INSTITUTE   (Italy)

^h UNIVERSITY OF BERN   (Switzerland)

ⁱ Cold Spring Harbor Laboratory ^*  (United States)

^j Helicos BioSciences   (United States)

more..

Author keywords

MECP2; Positive selection; RACEfrags; Rare variants; Rett syndrome; SNP

Indexed keywords

DNA; METHYL CPG BINDING PROTEIN 2;

ARTICLE; CDKL5 GENE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; ETHNIC GROUP; EXON; FEMALE; FORCE; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; MECP2 GENE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RACEFRAGS GENE; RETT SYNDROME; SAMPLE;

DNA MUTATIONAL ANALYSIS; EXONS; FEMALE; GENETIC VARIATION; HUMANS; MALE; METHYL-CPG-BINDING PROTEIN 2; PROTEIN-SERINE-THREONINE KINASES; RETT SYNDROME;

EID: 69549107705     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.21073     Document Type: Article

References (35)

1. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. 1999. Rett syndrome is caused by mutations in Xlinked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23(2):185-188 (Pubitemid 29455390)
2. Antonarakis SE, Beckmann JS. 2006. Mendelian disorders deserve more attention. Nat Rev Genet 7(4):277-282
3. Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA. 2005. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 14(1):59-69.
4. Bienvenu T, Philippe C, De Roux N, Raynaud M, Bonnefond JP, Pasquier L, Lesca G, Mancini J, Jonveaux P, Moncla A and others. 2006. The incidence of Rett syndrome in France. Pediatr Neurol 34(5):372-375
5. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE and others. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799-816.
6. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N and others. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22(3):231-238
7. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. 2005. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15(11):1553-1565
8. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G and others. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308(5725):1149-1154
9. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J and others. 2007. Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17(6):746-759
10. Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR and others. 2008. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods.
11. Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, Neubauer J, Tandon A, Schirmer C, McDonald GJ and others. 2007. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 39(5):638-644
12. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, Weder A, Cooper R, Lipshutz R, Chakravarti A. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22(3):239-247 (Pubitemid 29297249)
13. Hutter S, Vilella AJ, Rozas J. 2006. Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinformatics 7:409. (Pubitemid 44468826)
14. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6):996-1006.
15. Kiemeney LA, Thorlacius S, Sulem P, Geller F, Aben KK, Stacey SN, Gudmundsson J, Jakobsdottir M, Bergthorsson JT, Sigurdsson A and others. 2008. Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat Genet.
16. Kriaucionis S, Bird A. 2004. The major form of MeCP2 has a novel N-terminus generated by alternative splicing. Nucleic Acids Res 32(5):1818-1823 (Pubitemid 38832727)
17. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G and others. 2007. The diploid genome sequence of an individual human. PLoS Biol 5(10):e254.
18. Livingston RJ, von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ, Gowrisankar S, Aronow BJ, Weiss RB, Nickerson DA. 2004. Pattern of sequence variation across 213 environmental response genes. Genome Res 14(10A):1821-1831 (Pubitemid 39386496)
19. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M and others. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 17(6):760-774
20. Mari F, Azimonti S, Bertani I, Bolognese F, Colombo E, Caselli R, Scala E, Longo I, Grosso S, Pescucci C and others. 2005. CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the early-onset seizure variant of Rett syndrome. Hum Mol Genet 14(14):1935-1946.
21. Mencarelli MA, Kleefstra T, Katzaki E, Papa FT, Cohen M, Pfundt R, Ariani F, Meloni I, Mari F, Renieri A. 2009. 14q12 Microdeletion syndrome and congenital variant of Rett syndrome. Eur J Med Genet.
22. Mnatzakanian GN, Lohi H, Munteanu I, Alfred SE, Yamada T, MacLeod PJ, Jones JR, Scherer SW, Schanen NC, Friez MJ and others. 2004. A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome. Nat Genet 36(4):339-341
23. Percy AK, Lane JB. 2004. Rett syndrome: clinical and molecular update. Curr Opin Pediatr 16(6):670-677
24. Renieri A, Mari F, Mencarelli MA, Scala E, Ariani F, Longo I, Meloni I, Cevenini G, Pini G, Hayek G and others. 2009. Diagnostic criteria for the Zappella variant of Rett syndrome (the preserved speech variant). Brain Dev 31(3):208-216
25. Sampieri K, Meloni I, Scala E, Ariani F, Caselli R, Pescucci C, Longo I, Artuso R, Bruttini M, Mencarelli MA and others. 2007. Italian Rett database and biobank. Hum Mutat 28(4):329-335
26. Scala E, Ariani F, Mari F, Caselli R, Pescucci C, Longo I, Meloni I, Giachino D, Bruttini M, Hayek G and others. 2005. CDKL5/STK9 is mutated in Rett syndrome variant with infantile spasms. J Med Genet 42(2):103-107
27. Segawa M, Nomura Y. 2005. Rett syndrome. Curr Opin Neurol 18(2):97-104.
28. Tao J, Van Esch H, Hagedorn-Greiwe M, Hoffmann K, Moser B, Raynaud M, Sperner J, Fryns JP, Schwinger E, Gecz J and others. 2004. Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5/STK9) gene are associated with severe neurodevelopmental retardation. Am J Hum Genet 75(6):1149-1154
29. Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J. 2005. VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21(11):2791-2793 (Pubitemid 40852332)
30. Wan M, Lee SS, Zhang X, Houwink-Manville I, Song HR, Amir RE, Budden S, Naidu S, Pereira JL, Lo IF and others. 1999. Rett syndrome and beyond: recurrent spontaneous and familial MECP2 mutations at CpG hotspots. Am J Hum Genet 65(6):1520-1529
31. Weaving LS, Christodoulou J, Williamson SL, Friend KL, McKenzie OL, Archer H, Evans J, Clarke A, Pelka GJ, Tam PP and others. 2004. Mutations of CDKL5 cause a severe neurodevelopmental disorder with infantile spasms and mental retardation. Am J Hum Genet 75(6):1079-1093
32. Weaving LS, Ellaway CJ, Gecz J, Christodoulou J. 2005. Rett syndrome: clinical review and genetic update. J Med Genet 42(1):1-7. (Pubitemid 40187114)
33. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT and others. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872-876
34. Yeager M, Xiao N, Hayes RB, Bouffard P, Desany B, Burdett L, Orr N, Matthews C, Qi L, Crenshaw A and others. 2008. Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum Genet 124(2):161-170
35. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, Prendergast J, Olschwang S, Chiang T, Crowdy E and others. 2007. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 39(8):989-994