Outfoxed by RBFOX1-A caution about ascertainment bias

American Journal of Medical Genetics, Part A

Volumn 164, Issue 6, 2014, Pages 1411-1418

  Kamien, Benjamin ^a,b   Lionel, Anath C ^c,d   Bain, Nicole ^e   Scherer, Stephen W ^c,d   Hunter, Matthew ^a,b,f  

^a Hunter Genetics   (Australia)

^b UNIVERSITY OF NEWCASTLE   (Australia)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e JOHN HUNTER HOSPITAL   (Australia)

^f Hunter Genetics   (Australia)

Author keywords

A2BP1; Ascertainment bias; Autism spectrum disorder; DNA copy number variation; FOX1; Genetic susceptibility; RBFOX1

Indexed keywords

RNA BINDING PROTEIN; RBFOX1 PROTEIN, HUMAN;

ANXIETY DISORDER; ARTICLE; ATTENTION DEFICIT DISORDER; AUTISM; CASE REPORT; CHILD; CLINICAL FEATURE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; DEVELOPMENTAL DISORDER; FAMILY HISTORY; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC SUSCEPTIBILITY; HUMAN; INTRON; MALE; OPPOSITIONAL DEFIANT DISORDER; PEDIGREE ANALYSIS; PRESCHOOL CHILD; PRIORITY JOURNAL; RBFOX1 GENE; SCHOOL CHILD; SPEECH DELAY; STATISTICAL BIAS; GENETIC PREDISPOSITION; GENETICS;

CHILD; CHILD DEVELOPMENT DISORDERS, PERVASIVE; CHILD, PRESCHOOL; DEVELOPMENTAL DISABILITIES; DNA COPY NUMBER VARIATIONS; FEMALE; GENE DELETION; GENE DUPLICATION; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; RNA-BINDING PROTEINS;

EID: 84899905682     PISSN: 15524825     EISSN: 15524833     Source Type: Journal    
DOI: 10.1002/ajmg.a.36458     Document Type: Article

References (21)

1. Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467:52-58.
2. Bierut LJ, Agrawal A, Bucholz KK, Doheny KF, Laurie C, Pugh E, Fisher S, Fox L, Howells W, Bertelsen S, Hinrichs AL, Almasy L, Breslau N, Culverhouse RC, Dick DM, Edenberg HJ, Foroud T, Grucza RA, Hatsukami D, Hesselbrock V, Johnson EO, Kramer J, Krueger RF, Kuperman S, Lynskey M, Mann K, Neuman RJ, Nöthen MM, Nurnberger JI Jr, Porjesz B, Ridinger M, Saccone NL, Saccone SF, Schuckit MA, Tischfield JA, Wang JC, Rietschel M, Goate AM. Rice JP, Gene Environment Association Studies Consortium. 2010. A genome-wide association study of alcohol dependence. Proc Natl Acad Sci USA 107:5082-5087.
3. Bhalla K, Phillips HA, Crawford J, McKenzie OL, Mulley JC, Eyre H, Gardner AE, Kremmidiotis G, Callen DF. 2004. The de novo chromosome 16 translocations of two patients with abnormal phenotypes [mental retardation and epilepsy] disrupt the A2BP1 gene. J Hum Genet 49:308-311.
4. Cottrell CE, Bir N, Varga E, Alvarez CE, Bouyain S, Zernzach R, Thrush DL, Evans J, Trimarchi M, Butter EM, Cunningham D, Gastier-Foster JM, McBride KL, Herman GE. 2011. Contactin 4 as an autism susceptibility locus. Autism Res 4:189-199.
5. Coviello AD, Haring R, Wellons M, Vaidya D, Lehtimäki T, Keildson S, Lunetta KL, He C, Fornage M, Lagou V, Mangino M, Onland-Moret NC, Chen B, Eriksson J, Garcia M, Liu YM, Koster A, Lohman K, Lyytikäinen LP, Petersen AK, Prescott J, Stolk L, Vandenput L, Wood AR, Zhuang WV, Ruokonen A, Hartikainen AL, Pouta A, Bandinelli S, Biffar R, Brabant G, Cox DG, Chen Y, Cummings S, Ferrucci L, Gunter MJ, Hankinson SE, Martikainen H, Hofman A, Homuth G, Illig T, Jansson JO, Johnson AD, Karasik D, Karlsson M, Kettunen J, Kiel DP, Kraft P, Liu J, Ljunggren Ö, Lorentzon M, Maggio M, Markus MR, Mellström D, Miljkovic I, Mirel D, Nelson S, Morin Papunen L, Peeters PH, Prokopenko I, Raffel L, Reincke M, Reiner AP, Rexrode K, Rivadeneira F, Schwartz SM, Siscovick D, Soranzo N, Stöckl D, Tworoger S, Uitterlinden AG, van Gils CH, Vasan RS, Wichmann HE, Zhai G, Bhasin S, Bidlingmaier M, Chanock SJ, De Vivo I, Harris TB, Hunter DJ, Kähönen M, Liu S, Ouyang P, Spector TD, van der Schouw YT, Viikari J, Wallaschofski H, McCarthy MI, Frayling TM, Murray A, Franks S, Järvelin MR, de Jong FH, Raitakari O, Teumer A, Ohlsson C, Murabito JM, Perry JR. 2012. A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. PLoS Genet 8:e1002805.
6. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P. 2010. Genome-wide association study of CNVs in 16, 000 cases of eight common diseases and 3, 000 shared controls. Nature 464:713-720.
7. Davis LK, Maltman N, Mosconi MW, Macmillan C, Schmitt L, Moore K, Francis SM, Jacob S, Sweeney JA, Cook EH. 2012. Rare inherited A2BP1 deletion in a proband with autism and developmental hemiparesis. Am J Med Genet A 158A:1654-1661.
8. Elia J, Gai X, Xie HM, Perin JC, Geiger E, Glessner JT, D'arcy M, deBerardinis R, Frackelton E, Kim C, Lantieri F, Muganga BM, Wang L, Takeda T, Rappaport EF, Grant SF, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, White PS. 2010. Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry 15:637-646.
9. Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. 2009. DECIPHER: Database of chromosomal imbalance and phenotype in humans using ensembl resources. Am J Hum Genet 84:524-533.
10. Heil KM, Schaaf CP. 2013. The genetics of autism spectrum disorders: A guide for clinicians. Curr Psychiatry Rep 15:334.
11. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951.
12. Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, Schreiber S. 2006. PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet 9:55-61.
13. Lal D, Trucks H, Møller RS, Hjalgrim H, Koeleman BP, de Kovel CG, Visscher F, Weber YG, Lerche H, Becker F, Schankin CJ, Neubauer BA, Surges R, Kunz WS, Zimprich F, Franke A, Illig T, Ried JS, Leu C, Nürnberg P. Sander T, EMINet Consortium, EPICURE Consortium. 2013. Rare exonic deletions of the RBFOX1 gene increase risk of idiopathic generalized epilepsy. Epilepsia 54:265-271.
14. Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, Wilkes K, Alvarez-Retuerto A, Whichello A, Powell CM, Rao K, Cook E, Geschwind DH. 2007. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am J Med Genet B Neuropsychiatr Genet 144B:869-876.
15. Mikhail FM, Lose EJ, Robin NH, Descartes MD, Rutledge KD, Rutledge SL, Korf BR, Carroll AJ. 2011. Clinically relevant single gene or intragenic deletions encompassing critical neurodevelopmental genes in patients with developmental delay, mental retardation, and/or autism spectrum disorders. Am J Med Genet A 155A:2386-2396.
16. Palmer E, Ketteridge C, Parr JR, Baird G, Le Couteur A. 2011. Autism spectrum disorder diagnostic assessments: improvements since publication of the National Autism Plan for Children. Arch Dis Child 96:473-475.
17. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI Jr, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C. 2010. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466:368-372.
18. Silversides CK, Lionel AC, Costain G, Merico D, Migita O, Liu B, Yuen T, Rickaby J, Thiruvahindrapuram B, Marshall CR, Scherer SW, Bassett AS. 2012. Rare copy number variations in adults with tetralogy of Fallot implicate novel risk gene pathways. PLoS Genet 8:e1002843.
19. Stewart AF, Dandona S, Chen L, Assogba O, Belanger M, Weart C, LaRose R, Doelle H, Williams K, Wells GA, McPherson R, Roberts R. 2009. Kinesin family member 6 variant TRp719Arg does not associate with angiographically defined coronary artery disease in the Ottawa Heart Genomics Study. J Am Coll Cardiol 53:1471-1472.
20. Zhao WW. 2013. Intragenic deletion of RBFOX1 associated with neurodevelopmental/neuropsychiatric disorders and possibly other clinical presentations. Mol Cytogenet 6:26.
21. Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S. 2007. Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet 122:345-353.