The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies Jan O. Korbela,b,c,1, Tal Tirosh-Wagnerd,1, Alexander Eckehart Urbane,f,1, Xiao-Ning Chend, Maya Kasowskie, Li Daid, Fabian Grubertf, Chandra Erdmang, Michael C. Gaod, Ken Langeh,i, Eric M. Sobelh, Gillian M. Barlowd, Arthur S. Aylsworthj,k, Nancy J. Carpenterl, Robin Dawn Clarkm, Monika Y. Cohenn, Eric Dorano, Tzipora Falik-Zaccaip, Susan O. Lewinq, Ira T. Lotto, Barbara C. McGillivrayr, John B. Moeschlers, Mark J. Pettenatit, Siegfried M. Pueschelu, Kathleen W. Raoj,k,v, Lisa G. Shafferw, Mordechai Shohatx, Alexander J. Van Ripery, Dorothy Warburtonz,aa, Sherman Weissmanf, Mark B. Gersteina, Michael Snydera,e,2, and Julie R. Korenbergd,h,bb,2 Departments of aMolecular Biophysics and Biochemistry, eMolecular, Cellular, and Developmental Biology, and fGenetics, Yale University School of Medicine, New Haven, CT 06520; bEuropean Molecular Biology Laboratory, 69117 Heidelberg, Germany; cEuropean Molecular Biology Laboratory (EMBL) Outstation Hinxton, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; dMedical Genetics Institute, Cedars–Sinai Medical Center, Los Angeles, CA 90048; gDepartment of Statistics, Yale University, New Haven, CT 06520; Departments of hHuman Genetics, and iBiomathematics, University of California, Los Angeles, CA 90095; Departments of jPediatrics and kGenetics, University of North Carolina, Chapel Hill, NC 27599; lCenter for Genetic Testing, Tulsa, OK 74136; mDivision of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA 92354; nDepartment of Genetics, Kinderzentrum Munich, 81377 Munich, Germany; oDepartment of Pediatrics and Neurology, Irvine Medical Center, University of California, Orange, CA 92868; pInstitute of Human Genetics, Western Galilee Hospital, Nahariya 22100, Israel; qSection of Clinical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84132; rDepartment of Medical Genetics, Women’s Health Centre, University of British Columbia, Vancouver, BC, Canada V6H 3V5; sSection of Clinical Genetics, Department of Pediatrics, Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756; tDepartment of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157; uChild Development Center, Rhode Island Hospital, Providence RI 02902; vDepartment of Pathology, University of North Carolina, Chapel Hill, NC 27514; wSignature Genomic Laboratories, Spokane, WA 99207; xRecanati Institute for Medical Genetics, Rabin Medical Center, Tel Aviv University, Petah Tikva, 49100 Israel; yGenetics Department, Kaiser Permanente Medical Offices, Sacramento, CA 95815; zDepartment of Genetics and Development, Columbia University, New York, NY 10032; aaChildren’s Hospital of New York, New York, NY 10032; and bbDepartment of Pediatrics, Center for Integrated Neurosciences and Human Behavior, The Brain Institute, University of Utah, Salt Lake City, UT 84108 Edited by Joseph R. Ecker, The Salk Institute for Biological Studies, La Jolla, CA, and approved May 29, 2009 (received for review December 30, 2008) Down syndrome (DS), or trisomy 21, is a common disorder associated gene–disease links have often been based on indirect evidence from with several complex clinical phenotypes. Although several hypoth- cellular or animal models (6, 7). Moreover, current hypotheses eses have been put forward, it is unclear as to whether particular gene argue for the existence of a critical region, the DS consensus region loci on chromosome 21 (HSA21) are sufficient to cause DS and its (DSCR), responsible for most severe DS features (6, 8, 9), or associated features. Here we present a high-resolution genetic map presume the causative role of a small set of genes including DSCR1 of DS phenotypes based on an analysis of 30 subjects carrying rare and DYRK1A,orAPP, for these phenotypes (6, 7). segmental trisomies of various regions of HSA21. By using state-of- By using state-of-the-art genomics together with a large panel of the-art genomics technologies we mapped segmental trisomies at partially trisomic individuals, we present the highest resolution DS exon-level resolution and identified discrete regions of 1.8–16.3 Mb phenotype map to date and identify distinct genomic regions that likely to be involved in the development of 8 DS phenotypes, 4 of likely contribute to the manifestation of 8 DS features. Four of these which are congenital malformations, including acute megakaryocytic phenotypes have never been associated with a particular region of leukemia, transient myeloproliferative disorder, Hirschsprung dis- HSA21. The map also enables us to rule out the necessary GENETICS ease, duodenal stenosis, imperforate anus, severe mental retardation, contribution of other HSA21 regions, thus providing strong evi- DS-Alzheimer Disease, and DS-specific congenital heart disease dence against the existence of a single DSCR, and a lack of support (DSCHD). Our DS-phenotypic maps located DSCHD to a <2-Mb inter- for the necessary synergistic roles of DSCR1 and DYRK1A,orAPP, val. Furthermore, the map enabled us to present evidence against the as predominant contributors to many DS phenotypes. necessary involvement of other loci as well as specific hypotheses that have been put forward in relation to the etiology of DS—i.e., the Results and Discussion presence of a single DS consensus region and the sufficiency of DSCR1 To construct a high-resolution map of DS we assembled a panel and DYRK1A,orAPP, in causing several severe DS phenotypes. Our of 30 individuals with rare, segmental trisomies 21 whose clinical study demonstrates the value of combining advanced genomics with features are summarized in Table 1. Nine patients are described cohorts of rare patients for studying DS, a prototype for the role of for the first time, 16 were reassessed with respect to phenotype, copy-number variation in complex disease. ͉ ͉ ͉ copy number variants genomic structural variation human genome Author contributions: J.O.K., T.T.-W., A.E.U., S.W., M. Snyder, and J.R.K. designed research; congenital heart disease ͉ leukemia J.O.K., T.T.-W., A.E.U., X.-N.C., M.K., L.D., F.G., M.C.G., K.L., E.M.S., G.M.B., A.S.A., N.J.C., R.D.C., M.Y.C., E.D., T.F.-Z., S.O.L., I.T.L., B.C.M., J.B.M., M.J.P., S.M.P., K.W.R., L.G.S., M. Shohat, A.J.V.R., D.W., M.B.G., M. Snyder, and J.R.K. performed research; C.E., K.L., and or over two decades trisomy 21 has represented a prototype E.M.S. contributed new reagents/analytic tools; J.O.K., T.T.-W., A.E.U., M. Snyder, and J.R.K. Fdisorder for the study of human aneuploidy and copy-number analyzed data; and J.O.K., T.T.-W., A.E.U., M. Snyder, and J.R.K. wrote the paper. variation (1, 2), but the genes responsible for most Down syndrome The authors declare no conflict of interest. (DS) phenotypes are still unknown. The analysis of several over- This article is a PNAS Direct Submission. lapping segmental trisomies 21 has led to the suggestion that dosage Freely available online through the PNAS open access option. alteration through duplication of an extended region on chromo- 1J.O.K, T.T.-W., and A.E.U. contributed equally to this work. some 21 (HSA21) is associated with DS features (2–5, 42). How- 2To whom correspondence may be addressed. E-mail: [email protected] or ever, humans with segmental trisomy 21 are rare, and thus human- [email protected]. based DS-phenotypic maps have been of low resolution, far beyond This article contains supporting information online at www.pnas.org/cgi/content/full/ the level of few or single genes, or even exons. Consequently, 0813248106/DCSupplemental. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0813248106 PNAS ͉ July 21, 2009 ͉ vol. 106 ͉ no. 29 ͉ 12031–12036 Downloaded by guest on September 30, 2021 Table 1. Major clinical features of patients Feature JL JG GY IS MI WB JS KG GP KJ BS HOU WS MJF WA DS SOS SW MB ZSC JJS STO SOL JSB NA NO BA SM HAD PM DSCHD – – – – – – PDA† – – – AVSD*† ASD* – – AVSD§ – ϩ TOF*†‡ – TOF*†‡ MI† VSD* VSD*†‡ – ASD – AVSD PS† AVSD VSD*†‡ AMKL – – – – – – – – – – – ϩ –– ––– – – – – – – – –– –– –– TMD – – – – – – – – – – – – ϩ ––––––––ϩ –––––––– HSCR – – – – – – – – – – – – – – – – ϩ* ϩ* ϩ*– – – – – –– – DST – – – – – – ϩ*––– – ––– ––– –– – –– – ––– – IA –––––––––– – ––– ––– –––– ϩ*– – –– –– –– MR Ͻ30 P 59 Nor M M M M-P 85 70 52 ϩ 47 P M M 69 P M 42 P P 52 Numbers represent full scale IQ test. ϩ, phenotype present; –, phenotype not present; AVSD, atrioventricular septal defect; PDA, patent ductus arteriosus; ASD, atrial septal defect; TOF, tetralogy of Fallot; MI, mitral insufficiency; VSD, ventricular septal defect; PS, pulmonic stenosis; blank, no information available; P, profound MR; M, moderate MR. *Surgically repaired. †Determined by echocardiogram. ‡Determined by cardiac catheterization. §Determined by autopsy. molecular cytogenetics, and breakpoints, and 5 were previously phenotype) and expressivity (variation of the phenotype, such as published (2, 10). We note that the ability to parse DS genes to types of congenital heart disease) as is seen in full trisomy 21. phenotypes is determined by 3 factors: (i) phenotypic resolution, Specifically, we mapped HSA21 chromosomal rearrangements determined by the high-risk ratio of a given feature for DS versus across patients by successively and systematically applying several normal and by the number of affected individuals; (ii) molecular technologies