Publications 2013

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, Fitzpatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Vooren SV, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, Leeuw ND, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN.
Eur J Hum Genet. 2013 Nov 6. doi: 10.1038/ejhg.2013.249. [Epub ahead of print]


A de novo non-sense mutation in ZBTB18 in a patient with features of the 1q43q44 microdeletion syndrome. de Munnik SA, García-Miñaúr S, Hoischen A, van Bon BW, Boycott KM, Schoots J, Hoefsloot LH, Knoers NV, Bongers EM, Brunner HG.
Eur J Hum Genet. 2013 Nov 6. doi: 10.1038/ejhg.2013.249. [Epub ahead of print]


Survival rates for goblet cell carcinoma of the appendix. Vissers LE, Ten Broek RP, Bosch AM.
Neuroendocrinology. 2013;98(2):170. doi: 10.1159/000355005. Epub 2013 Sep 20. No abstract available.


Improved exome prioritization of disease genes through cross species phenotype comparison. Robinson P, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall C, Lewis SE, Washington N, Bauer S, Seelow DS, Krawitz P, Gilissen C, Haendel M, Smedley D.
Genome Res. 2013 Oct 25. [Epub ahead of print]


Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing. Schuurs-Hoeijmakers JH, Vulto-van Silfhout AT, Vissers LE, van de Vondervoort II, van Bon BW, de Ligt J, Gilissen C, Hehir-Kwa JY, Neveling K, Del Rosario M, Hira G, Reitano S, Vitello A, Failla P, Greco D, Fichera M, Galesi O, Kleefstra T, Greally MT, Ockeloen CW, Willemsen MH, Bongers EM, Janssen IM, Pfundt R, Veltman JA, Romano C, Willemsen MA, van Bokhoven H, Brunner HG, de Vries BB, de Brouwer AP.
J Med Genet. 2013 Dec;50(12):802-11. doi: 10.1136/jmedgenet-2013-101644. Epub 2013 Oct 11.


A Post-Hoc Comparison of the Utility of Sanger Sequencing and Exome Sequencing for the Diagnosis of Heterogeneous Diseases. Neveling K, Feenstra I, Gilissen C, Hoefsloot LH, Kamsteeg EJ, Mensenkamp AR, Rodenburg RJ, Yntema HG, Spruijt L, Vermeer S, Rinne T, van Gassen KL, Bodmer D, Lugtenberg D, de Reuver R, Buijsman W, Derks RC, Wieskamp N, van den Heuvel B, Ligtenberg MJ, Kremer H, Koolen DA, van de Warrenburg BP, Cremers FP, Marcelis CL, Smeitink JA, Wortmann SB, van Zelst-Stams WA, Veltman JA, Brunner HG, Scheffer H, Nelen MR.
Hum Mutat. 2013 Sep 30. doi: 10.1002/humu.22450. [Epub ahead of print]


Mutations in the Mevalonate Kinase (MVK) Gene Cause Nonsyndromic Retinitis Pigmentosa. Siemiatkowska AM, Ingeborgh van den Born L, Martin van Hagen P, Stoffels M, Neveling K, Henkes A, Kipping-Geertsema M, Hoefsloot LH, Hoyng CB, Simon A, den Hollander AI, Cremers FP, Collin RW.
Ophthalmology. 2013 Sep 28. doi:pii: S0161-6420(13)00692-1. 10.1016/j.ophtha.2013.07.052. [Epub ahead of print]


Coffin-Siris Syndrome and the BAF Complex: Genotype-Phenotype Study in 63 Patients. Santen GW, Aten E, Vulto-van Silfhout AT, Pottinger C, van Bon BW, van Minderhout IJ, Snowdowne R, van der Lans CA, Boogaard M, Linssen MM, Vijfhuizen L, van der Wielen MJ, Vollebregt MJ; Coffin-Siris consortium, Breuning MH, Kriek M, van Haeringen A, den Dunnen JT, Hoischen A, Clayton-Smith J, de Vries BB, Hennekam RC, van Belzen MJ, Almureikhi M, Baban A, Barbosa M, Ben-Omran T, Berry K, Bigoni S, Boute O, Brueton L, van der Burgt I, Canham N, Chandler KE, Chrzanowska K, Collins AL, de Toni T, Dean J, den Hollander NS, Flore LA, Fryer A, Gardham A, Graham JM Jr, Harrison V, Horn D, Jongmans MC, Josifova D, Kant SG, Kapoor S, Kingston H, Kini U, Kleefstra T, Krajewska-Walasek M, Kramer N, Maas SM, Maciel P, Mancini GM, Maystadt I, McKee S, Milunsky JM, Nampoothiri S, Newbury-Ecob R, Nikkel SM, Parker MJ, Pérez-Jurado LA, Robertson SP, Rooryck C, Shears D, Silengo M, Singh A, Smigiel R, Soares G, Splitt M, Stewart H, Sweeney E, Tassabehji M, Tuysuz B, van Eerde AM, Vincent-Delorme C, Wilson LC, Yesil G.
Hum Mutat. 2013 Nov;34(11):1519-28. doi: 10.1002/humu.22394. Epub 2013 Aug 30.


Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic). Claustres M, Kožich V, Dequeker E, Fowler B, Hehir-Kwa JY, Miller K, Oosterwijk C, Peterlin B, van Ravenswaaij-Arts C, Zimmermann U, Zuffardi O, Hastings RJ, Barton DE.
Eur J Hum Genet. 2013 Aug 14. doi: 10.1038/ejhg.2013.125. [Epub ahead of print]


Reliable noninvasive prenatal testing by massively parallel sequencing of circulating cell-free DNA from maternal plasma processed up to 24h after venipuncture. Buysse K, Beulen L, Gomes I, Gilissen C, Keesmaat C, Janssen IM, Derks-Willemen JJ, de Ligt J, Feenstra I, Bekker MN, van Vugt JM, Geurts van Kessel A, Vissers LE, Faas BH.
Clin Biochem. 2013 Aug 8. doi:pii: S0009-9120(13)00353-6. 10.1016/j.clinbiochem.2013.07.020. [Epub ahead of print]


Coffin-Siris syndrome and the BAF-complex: genotype-phenotype study in 63 patients Santen GW, Aten E, Vulto-van Silfhout AT, Pottinger C, van Bon BW, van Minderhout IJ, Snowdowne R, van der Lans CA, Boogaard M, Linssen MM, Vijfhuizen L, van der Wielen MJ, Vollebregt MJ; the Coffin-Siris consortium, Breuning MH, Kriek M, van Haeringen A, den Dunnen JT, Hoischen A, Clayton-Smith J, de Vries BB, Hennekam RC, van Belzen MJ.
Hum Mutat. 2013 Aug 8. doi: 10.1002/humu.22394. [Epub ahead of print]


A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy. de Brouwer AP, Nabuurs SB, Verhaart IE, Oudakker AR, Hordijk R, Yntema HG, Hordijk-Hos JM, Voesenek K, de Vries BB, van Essen T, Chen W, Hu H, Chelly J, den Dunnen JT, Kalscheuer VM, Aartsma-Rus AM, Hamel BC, van Bokhoven H, Kleefstra T
Eur J Hum Genet. 2013 Jul 31. doi: 10.1038/ejhg.2013.169. [Epub ahead of print]


Pathogenic or Not? Assessing the Clinical Relevance of Copy Number Variants. Hehir-Kwa JY, Pfundt R, Veltman JA, de Leeuw N.
Clin Genet. 2013 Jul 29. doi: 10.1111/cge.12242. [Epub ahead of print]


Exome sequencing identifies putative drivers of progression of transient myeloproliferative disorder to AMKL in infants with Down syndrome. Nikolaev SI, Santoni F, Vannier A, Falconnet E, Giarin E, Basso G, Hoischen A, Veltman JA, Groet J, Nizetic D, Antonarakis SE
Blood. 2013 Jul 25;122(4):554-61. doi: 10.1182/blood-2013-03-491936. Epub 2013 Jun 3


Detection of clinically relevant copy number variants with whole exome sequencing. de Ligt J, Boone PM, Pfundt R, Vissers LE, Richmond T, Geoghegan J, O'Moore K, de Leeuw N, Shaw C, Brunner HG, Lupski JR, Veltman JA, Hehir-Kwa JY.
Hum Mutat. 2013 Jul 24. doi: 10.1002/humu.22387. [Epub ahead of print]


An update on ECARUCA, the European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations. Vulto-van Silfhout AT, van Ravenswaaij CM, Hehir-Kwa JY, Verwiel ET, Dirks R, van Vooren S, Schinzel A, de Vries BB, de Leeuw N.
Eur J Med Genet. 2013 Jul 12. pii: S1769-7212(13)00139-0. doi: 10.1016/j.ejmg.2013.06.010. [Epub ahead of print]


Novel PI3K? Mutation in a 44-Year-Old Man with Chronic Infections and Chronic Pelvic Pain Bojarski EF, Strauss AC, Fagin AP, Plantinga TS, Hoischen A, Veltman J, Allsop SA, Granadillo VJ, William A, Netea MG, Dimitrakoff J.
PLoS One. 2013 Jul 8;8(7):e68118. doi: 10.1371/journal.pone.0068118. Print 2013.


Mutations in GDP-Mannose Pyrophosphorylase B Cause Congenital and Limb-Girdle Muscular Dystrophies Associated with Hypoglycosylation of a-Dystroglycan Carss KJ, Stevens E, Foley AR, Cirak S, Riemersma M, Torelli S, Hoischen A, Willer T, van Scherpenzeel M, Moore SA, Messina S, Bertini E, Bönnemann CG, Abdenur JE, Grosmann CM, Kesari A, Punetha J, Quinlivan R, Waddell LB, Young HK, Wraige E, Yau S, Brodd L, Feng L, Sewry C, Macarthur DG, North KN, Hoffman E, Stemple DL, Hurles ME, van Bokhoven H, Campbell KP, Lefeber DJ; UK10K Consortium, Lin YY, Muntoni F.
Am J Hum Genet. 2013 Jun 11. pii: S0002-9297(13)00222-X. doi: 10.1016/j.ajhg.2013.05.009. [Epub ahead of print]


Mutations in RAB28, Encoding a Farnesylated Small GTPase, Are Associated with Autosomal-Recessive Cone-Rod Dystrophy. Roosing S, Rohrschneider K, Beryozkin A, Sharon D, Weisschuh N, Staller J, Kohl S, Zelinger L, Peters TA, Neveling K, Strom TM; European Retinal Disease Consortium, van den Born LI, Hoyng CB, Klaver CC, Roepman R, Wissinger B, Banin E, Cremers FP, den Hollander AI.
Am J Hum Genet. 2013 Jun 4. pii: S0002-9297(13)00218-8. doi: 10.1016/j.ajhg.2013.05.005. [Epub ahead of print]


Exome sequencing identifies putative drivers of progression of transient myeloproliferative disorder to AMKL in infants with Down Syndrome. Nikolaev SI, Santoni F, Vannier A, Falconnet E, Giarin E, Basso G, Hoischen A, Veltman JA, Groet J, Nizetic D, Antonarakis SE.
Blood. 2013 Jun 3. [Epub ahead of print](2013)


The Genome of the Netherlands: design, and project goals. Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui A, Ye K, Guryev V, Vermaat M, van Dijk F, Francioli LC, Jan Hottenga J, Laros JF, Li Q, Li Y, Cao H, Chen R, Du Y, Li N, Cao S, van Setten J, Menelaou A, Pulit SL, Hehir-Kwa JY, Beekman M, Elbers CC, Byelas H, de Craen AJ, Deelen P, Dijkstra M, T den Dunnen J, de Knijff P, Houwing-Duistermaat J, Koval V, Estrada K, Hofman A, Kanterakis A, Enckevort DV, Mai H, Kattenberg M, van Leeuwen EM, Neerincx PB, Oostra B, Rivadeneira F, Suchiman EH, Uitterlinden AG, Willemsen G, Wolffenbuttel BH, Wang J, de Bakker PI, van Ommen GJ, van Duijn CM.
Eur J Hum Genet. 2013 May 29. doi: 10.1038/ejhg.2013.118. [Epub ahead of print]


A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy. Jonckheere AI, Renkema GH, Bras M, van den Heuvel LP, Hoischen A, Gilissen C, Nabuurs SB, Huynen MA, de Vries MC, Smeitink JA, Rodenburg RJ
Brain. 2013 May;136(Pt 5):1544-54. doi: 10.1093/brain/awt086. Epub 2013 Apr 18.


Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans. Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ.
Nat Commun. 2013;4:1342. doi: 10.1038/ncomms2343.


Mutations in ANTXR1 Cause GAPO Syndrome. Viktor Stránecký,1,9 Alexander Hoischen,2,9 Hana Hartmannová,1,9 Maha S. Zaki,3 Amit Chaudhary,4 Enrique Zudaire,4 Lenka Nosková,1 Veronika Barešová,1 Anna Pristoupilová,1 Katerina Hodañ ová,1Jana Sovová,1 Helena Hulková,1 Lenka Piherová,1 Jayne Y. Hehir-Kwa,2 Deepthi de Silva,5 Manouri P. Senanayake,6 Sameh Farrag,7 Jirí Zeman,7 Pavel Martásek,7 Alice Baxová,8 Hanan H. Afifi,3 Brad St. Croix,4 Han G. Brunner,2 Samia Temtamy,3 and Stanislav Kmoch1,*
Mutations in ANTXR1 Cause GAPO Syndrome, The American Journal of Human Genetics(2013), http://dx.doi.org/10.1016/j.ajhg.2013.03.023

A novel marine nitrite-oxidizing Nitrospira species from Dutch coastal North Sea water. Haaijer SC, Ji K, van Niftrik L, Hoischen A, Speth D, Jetten MS, Damsté JS, Op den Camp HJ.
Front Microbiol. 2013;4:60. doi: 10.3389/fmicb.2013.00060. Epub 2013 Mar 18.


Towards embryonic-like scaffolds for skin tissue engineering: identification of effector molecules and construction of scaffolds. Uijtdewilligen PJ, Versteeg EM, Gilissen C, van Reijmersdal SV, Schoppmeyer R, Wismans RG, Daamen WF, van Kuppevelt TH.
J Tissue Eng Regen Med. 2013 Mar 7. doi: 10.1002/term.1725. [Epub ahead of print]


Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis. Coste B, Houge G, Murray MF, Stitziel N, Bandell M, Giovanni MA, Philippakis A, Hoischen A, Riemer G, Steen U, Steen VM, Mathur J, Cox J, Lebo M, Rehm H, Weiss ST, Wood JN, Maas RL, Sunyaev SR, Patapoutian A.
Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4667-72. doi: 10.1073/pnas.1221400110. Epub 2013 Mar 4.


Exome sequencing identifies DYNC2H1 mutations as a common cause of asphyxiating thoracic dystrophy (Jeune syndrome) without major polydactyly, renal or retinal involvement. Schmidts M, Arts HH, Bongers EM, Yap Z, Oud MM, Antony D, Duijkers L, Emes RD, Stalker J, Yntema JB, Plagnol V, Hoischen A, Gilissen C, Forsythe E, Lausch E, Veltman JA, Roeleveld N, Superti-Furga A, Kutkowska-Kazmierczak A, Kamsteeg EJ, Elçioglu N, van Maarle MC, Graul-Neumann LM, Devriendt K, Smithson SF, Wellesley D, Verbeek NE, Hennekam RC, Kayserili H, Scambler PJ, Beales PL; UK10K, Knoers NV, Roepman R, Mitchison HM.
J Med Genet. 2013 Mar 14. [Epub ahead of print]


Point mutations as a source of de novo genetic disease. de Ligt J, Veltman JA, Vissers LE
Curr Opin Genet Dev. 2013 Feb 28. pii: S0959-437X(13)00017-8. doi: 10.1016/j.gde.2013.01.007. [Epub ahead of print]


Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C; Genome of the Netherlands Consortium, de Bakker PI, Sunyaev SR.
PLoS Genet. 2013;9(2):e1003301. doi: 10.1371/journal.pgen.1003301. Epub 2013 Feb 28.


MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study. Makrythanasis P, van Bon BW, Steehouwer M, Rodríguez-Santiago B, Simpson M, Dias P, Anderlid BM, Arts P, Bhat M, Augello B, Biamino E, Bongers EM, Del Campo M, Cordeiro I, Cueto-González AM, Cuscó I, Deshpande C, Frysira E, Louise Izatt, Flores R, Galán E, Gener B, Gilissen C, Granneman SM, Hoyer J, Yntema HG, Kets CM, Koolen DA, Marcelis CL, Medeira A, Micale L, Mohammed S, de Munnik SA, Nordgren A, Reardon SP, Revencu N, Roscioli T, Ruiterkamp-Versteeg M, Santos HG, Schoumans J, Schuurs-Hoeijmakers JH, Silengo MC, Toledo L, Vendrell T, van der Burgt I, van Lier B, Zweier C, Reymond A, Trembath RC, Perez-Jurado L, Dupont J, de Vries BB, Brunner HG, Veltman JA, Merla G, Antonarakis SE, Hoischen A.
Clin Genet. 2013 Jan 16. doi: 10.1111/cge.12081. [Epub ahead of print]


Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans. Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ.
Nat Commun. 2013;4:1342. doi: 10.1038/ncomms2343.