Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs

Human Mutation

Volumn 30, Issue 1, 2009, Pages 107-114

  Vreeswijk, Maaike P G ^a   Kraan, Jaennelle N ^a   Van Der Klift, Heleen M ^a   Vink, Geraldine R ^a   Cornelisse, Cees J ^a   Wijnen, Juul T ^a   Bakker, Egbert ^a   Van Asperen, Christi J ^a   Devilee, Peter ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

BRCA1; BRCA2; Clinical significance; Intronic variants; RNA analysis; Splice site prediction; Unclassified variants

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; DNA; RNA;

ARTICLE; CONTROLLED STUDY; GENE LOCATION; GENE MUTATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; IN VITRO STUDY; INTRON; PRIORITY JOURNAL; RNA SPLICING;

ADULT; BASE SEQUENCE; BRCA1 PROTEIN; BRCA2 PROTEIN; BREAST NEOPLASMS; FEMALE; GENETIC VARIATION; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; RNA SPLICE SITES; RNA SPLICING; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 58349088957     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20811     Document Type: Article

References (42)

1. Anonymous. 1996. Statement of the American Society of Clinical Oncology: genetic testing for cancer susceptibility, Adopted on February 20, 1996. J Clin Oncol 14:1730-1736.
2. Bonatti F, Pepe C, Tancredi M, Lombardi G, Aretini P, Sensi E, Falaschi E, Cipollini G, Bevilacqua G, Caligo MA. 2006. RNA-based analysis of BRCA1 and BRCA2 gene alterations. Cancer Genet Cytogenet 170:93-101.
3. Brose MS, Volpe P, Paul K, Stopfer JE, Colligon TA, Calzone KA, Weber BL. 2004. Characterization of two novel BRCA1 germ-line mutations involving splice donor sites. Genet Test 8:133-138.
4. Campos B, Diez O, Domenech M, Baena M, Balmana J, Sanz J, Ramirez A, Alonso C, Baiget M. 2003. RNA analysis of eight BRCA1 and BRCA2 unclassified variants identified in breast/ovarian cancer families from Spain. Hum Mutat 22:337.
5. Cartegni L, Chew SL, Krainer AR. 2002. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3:285-298.
6. Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. 2003. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res 31:3568-3571.
7. Chen X, Truong TT, Weaver J, Bove BA, Cattie K, Armstrong BA, Daly MB, Godwin AK. 2006. Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Hum Mutat 27:427-435.
8. Chenevix-Trench G, Healey S, Lakhani S, Waring P, Cummings M, Brinkworth R, Deffenbaugh AM, Burbidge LA, Pruss D, Judkins T, Scholl T, Bekessy A, Marsh A, Lovelock P, Wong M, Tesoriero A, Renard H, Southey M, Hopper JL, Yannoukakos K, Brown M, Easton D, Tavtigian SV, Goldgar D, Spurdle AB. 2006. Genetic and histopathologic evaluation of BRCA1 and BRCA2 DNA sequence variants of unknown clinical significance. Cancer Res 66:2019-2027.
9. Claes K, Poppe B, Machackova E, Coene I, Foretova L, De Paepe A, Messiaen L. 2003. Differentiating pathogenic mutations from polymorphic alterations in the splice sites of BRCA1 and BRCA2. Genes Chromosomes Cancer 37:314-320.
10. den Dunnen JT, Antonarakis SE. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15:7-12.
11. Diez O, Gutierrez-Enriquez S, Cajal T, Alonso C, Balmana J, Llort G. 2007. Caution should be used when interpreting alterations affecting the exon 3 of the BRCA2 gene in breast/ovarian cancer families. J Clin Oncol 25:5035-5036.
12. Fairbrother WG, Yeh RF, Sharp PA, Burge CB. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297:1007-1013.
13. Fetzer S, Tworek HA, Piver MS, DiCioccio RA. 1999. Classification of IVS1-10T-> C as a polymorphism of BRCA1. Cancer Genet Cytogenet 113:58-64.
14. Goldgar DE, Easton DF, Deffenbaugh AM, Monteiro ANA, Tavtigian SV, Couch FJ. 2004. Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am J Hum Genet 75:535-544.
15. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S. 1996. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 24:3439-3452.
16. Hofmann W, Horn D, Huttner C, Classen E, Scherneck S. 2003. The BRCA2 variant 8204G > A is a splicing mutation and results in an in frame deletion of the gene. J Med Genet 40:23e.
17. Hogervorst F, Cornelis R, Bout M, Van Vliet M, Oosterwijk J, Olmer R, Bakker B, Klijn J, Vasen H, Meijers-Heijboer H, Menko F, Cornelisse C, den Dunnen J, Devilee P, Van Ommen G-J. 1995. Rapid detection of BRCA1 mutations by the protein truncation test. Nature Genet 10:208-212.
18. Keaton JC, Nielsen DR, Hendrickson BC, Pyne MT, Scheuer L, Ward BE, Brothman AR, Scholl T. 2003. A biochemical analysis demonstrates that the BRCA1 intronic variant IVS10-2A-> C is a mutation. J Hum Genet 48:399-403.
19. Laskie OK, DiCioccio RA, McGuire V, Whittemore AS. 2001. A BRCA1 variant, IVS23+1G-> A, causes abnormal RNA splicing by deleting exon 23. Cancer Genet Cytogenet 127:188-190.
20. Machado PM, Brandao RD, Cavaco BM, Eugenio J, Bento S, Nave M, Rodrigues P, Fernandes A, Vaz F. 2007. Screening for a BRCA2 rearrangement in high-risk breast/ovarian cancer families: evidence for a founder effect and analysis of the associated phenotypes. J Clin Oncol 25:2027-2034.
21. Miki Y, Swensen J, Shattuck-Eidens D, Futreal P, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett L, Ding W, Bell R, Rosenthal J, Hussey C, Tran T, McClure M, Frye C, Hattier T, Phelps R, Haugen-Strano A, Katcher H, Yakumo K, Gholami Z, Shaffer D, Stone S, Bayer S, Wray C, Bogden R, Dayananth P, Ward J, Tonin P, Narod S, Bristow P, Norris F, Meera Khan P, Morrison P, Rosteck P, Lai M, Barrett J, Lewis C, Neuhausen S, Cannon-Albright L, Goldgar R, Kamb A, Wiseman R, Skolnick M. 1994. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266:66-71.
22. Milner J, Fuks F, Hughesdavies L, Kouzarides T. 2000. The BRCA2 activation domain associates with and is phosphorylated by a cellular protein kinase. Oncogene 19:4441-4445.
23. Milner J, Ponder B, Hughes Davies L, Seltmann M, Kouzarides T. 1997. Transcriptional activation functions in BRCA2. Nature 386:772-773.
24. Nalla VK, Rogan PK. 2005. Automated splicing mutation analysis by information theory. Hum Mutat 25:334-342.
25. Nordling M, Karlsson P, Wahlstrom J, Engwall Y, Wallgren A, Martinsson T. 1998. A large deletion disrupts the exon 3 transcription activation domain of the BRCA2 gene in a breast/ovarian cancer family. Cancer Res 58:1372-1375.
26. Petrij-Bosch A, Peelen T, Van Vliet M, Van Eijk R, Olmer R, Drüsedau M, Hogervorst FBL, Hageman S, Arts PJW, Ligtenberg MJL, Meijers-Heijboer H, Klijn JGM, Vasen HFA, Cornelisse CJ, Van't Veer LJ, Bakker E, Van Ommen G-JB, Devilee P. 1997. BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nat Genet 17:341-345.
27. Petrucelli N, Lazebnik N, Huelsman KM, Lazebnik RS. 2002. Clinical interpretation and recommendations for patients with a variant of uncertain significance in BRCA1 or BRCA2: a survey of genetic counseling practice. Genet Test 6:107-113.
28. Pettigrew C, Wayte N, Lovelock PK, Tavtigian SV, Chenevix-Trench G, Spurdle AB, Brown MA. 2005. Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms. Breast Cancer Res 7:R929-R939.
29. Pettigrew CA, Wayte N, Wronski A, Lovelock PK, Spurdle AB, Brown MA. Colocalisation of predicted exonic splicing enhancers in BRCA2 with reported sequence variants. Breast Cancer Res Treat (in press).
30. Pyne MT, Brothman AR, Ward B, Pruss D, Hendrickson BC, Scholl T. 2000. The BRCA2 genetic variant IVS7+2T-> G is a mutation. J Hum Genet 45:351-357.
31. Reese MG, Eeckman FH, Kulp D, Haussler D. 1997. Improved splice site detection in Genie. J Comput Biol 4:311-323.
32. Santarosa M, Dolcetti R, Magri MD, Crivellari D, Tibiletti MG, Gallo A, Tumolo S, Dellapuppa L, Furlan D, Boiocchi M, Viel A. 1999. BRCA1 and BRCA2 genes: role in hereditary breast and ovarian cancer in Italy. Int J Cancer 83:5-9.
33. Scholl T, Pyne MT, Russo D, Ward BE. 1999a. BRCA1 IVS16+6T> C is a deleterious mutation that creates an aberrant transcript by activating a cryptic splice donor site. Am J Med Genet 85:113-116.
34. Scholl T, Pyne MT, Ward B, Pruss D. 1999b. Biochemical and genetic characterization shows that the BRCA1 IVS20 insertion is a polymorphism. J Med Genet 36:571-572.
35. Shapiro MB, Senapathy P. 1987. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res 15:7155-7174.
36. Tesoriero AA, Wong EM, Jenkins MA, Hopper JL, Brown MA, Chenevix-Trench G, Spurdle AB, Southey MC. 2005. Molecular characterization and cancer risk associated with BRCA1 and BRCA2 splice site variants identified in multiple-case breast cancer families. Hum Mutat 26:495.
37. Van der Hout AH, Van den Ouweland AMW, van der Luijt RB, Gille HJP, Bodmer D, Bruggenwirth H, Mulder IM, van der Vlies P, Elfferich P, Huisman MT, ten Berge AM, Kromosoeto J, Jansen RPM, van Zon PHA, Vriesman T, Arts N, Lange MBD, Oosterwijk JC, Meijers-Heijboer H, Ausems MGEM, Hoogerbrugge N, Verhoef S, Halley DJJ, Vos YJ, Hogervorst F, Ligtenberg M, Hofstra RMW. 2006. A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2: application in a Dutch cancer clinic setting. Hum Mutat 27:654-666.
38. Vink GR, Van Asperen CJ, Devilee P, Breuning MH, Bakker E. 2005. Unclassified variants in disease-causing genes: nonuniformity of genetic testing and counselling, a proposal for guidelines. Eur J Hum Genet 13:525-527.
39. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. 2004. Systematic identification and analysis of exonic splicing silencers. Cell 119:831-845.
40. Wimmer K, Eckart M, Rehder H, Fonatsch C. 2000. Illegitimate splicing of the NF1 gene in healthy individuals mimics mutation-induced splicing alterations in NF1 patients. Hum Genet 106:311-313.
41. Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C, Micklem G, Barfoot R, Hamoudi R, Patel S, Rice C, Biggs P, Hashim Y, Smith A, Connor F, Arason A, Gudmundsson J, Ficenec D, Kelsell D, Ford D, Tonin P, Bishop DT, Spurr NK, Ponder BAJ, Eeles R, Peto J, Devilee P, Cornelisse CJ, Lynch H, Narod S, Lenoir G, Egilsson V, Barkardottir RB, Easton DF, Bentley DR, Futreal PA, Ashworth A, Stratton MR. 1995. Identification of the breast cancer susceptibility gene BRCA2. Nature 378:789-792.
42. Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11:377-394.