Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype

Human Molecular Genetics, 2016, Vol. 25, No. 12 2525–2538 doi: 10.1093/hmg/ddw116 Advance Access Publication Date: 22 April 2016 Original Article ORIGINAL ARTICLE Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype 1 Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy, 2Neonatology Unit, St. OrsolaMalpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy, 3Medical Genetics Unit and 4Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, BO, Italy *To whom the correspondence should be addressed at: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy. Tel: þ39 0512094117; Fax: þ39 0512094110; Email: Abstract A ‘Down Syndrome critical region’ (DSCR) sufficient to induce the most constant phenotypes of Down syndrome (DS) had been identified by studying partial (segmental) trisomy 21 (PT21) as an interval of 0.6–8.3 Mb within human chromosome 21 (Hsa21), although its existence was later questioned. We propose an innovative, systematic reanalysis of all described PT21 cases (from 1973 to 2015). In particular, we built an integrated, comparative map from 125 cases with or without DS fulfilling stringent cytogenetic and clinical criteria. The map allowed to define or exclude as candidates for DS fine Hsa21 sequence intervals, also integrating duplication copy number variants (CNVs) data. A highly restricted DSCR (HR-DSCR) of only 34 kb on distal 21q22.13 has been identified as the minimal region whose duplication is shared by all DS subjects and is absent in all non-DS subjects. Also being spared by any duplication CNV in healthy subjects, HR-DSCR is proposed as a candidate for the typical DS features, the intellectual disability and some facial phenotypes. HR-DSCR contains no known gene and has relevant homology only to the chimpanzee genome. Searching for HR-DSCR functional loci might become a priority for understanding the fundamental genotype-phenotype relationships in DS. Introduction The concept that the main symptoms and signs of Down syndrome (DS) may be caused by overexpression of one or a few genes located on a delimited, small region on human chromosome 21 (Hsa21) has had changing fortunes in the last decades. Since the fundamental discovery of Lejeune et al. (1), we know that Hsa21 is present in an extra copy in the cells of subjects † These authors contributed equally to this work. Received: February 2, 2016. Revised: April 12, 2016. Accepted: April 12, 2016 C The Author 2016. Published by Oxford University Press. V This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact 2525 Maria Chiara Pelleri1, Elena Cicchini1, Chiara Locatelli2, Lorenza Vitale1,†, Maria Caracausi1,†, Allison Piovesan1,†, Alessandro Rocca2, Giulia Poletti2, Marco Seri3, Pierluigi Strippoli1,* and Guido Cocchi4 2526 | Human Molecular Genetics, 2016, Vol. 25, No. 12 the human cytogenetic analysis in the early 1970s (19,20), it became possible to demonstrate that children with a phenotype indistinguishable from DS appeared to have only a specific portion of Hsa21 rather than a complete Hsa21 long arm (21q). Hsa21 short arm (21p) is considered genetically empty in practice, as shown by centric fusion (leading to robertsonian translocation) in which the loss of 21p is consistent with a DS phenotype indistinguishable from the one due to free trisomy 21 if the 21q dose is unbalanced (16,21) and with no clinical consequences if 21q dose is balanced (18,22,23). The main mechanisms leading to this so-called ‘partial’ or ‘segmental’ trisomy were described as discordant segregation of interstitially deleted chromosomes 21; translocations involving segments of 21q; tandem translocations with an incomplete long arm of replicated Hsa21 (24). On these bases, in 1974 Niebuhr was the first to put forward the hypothesis (25), by reviewing 14 previously described cases with tandem translocations of G-group chromosomes and reporting a new one, that ‘trisomy of a rather delimited segment on chromosome No. 21 is essential for the development of typical features in Down’s syndrome’, suggesting that ‘the very distal segment (21q22)’ (17.4 Mb) ‘may be pathogenetic in Down’s syndrome’, thus already excluding that 65% of Hsa21 (total length 46.7 Mb) may give a fundamental contribution to the very basic features of DS. In the subsequent 20 years, several single cases as well as case series of PT21 were reported. The development of fluorescence in situ hybridization (FISH) techniques (26) allowed a more detailed description of the duplicated 21q segments associated to DS culminating in the early 1990s in the suggestion that a delimited sequence interval on Hsa21 overlapping among different cases contributes significantly to the basic phenotype characteristic of trisomy 21. In particular, the data of Rahmani et al. (27) (two cases, D21S17-ETS2 interval, <3 Mb size), McCormick et al. (28) (16 cases, D21S55-COL6A1, 8.3 Mb) as well as Delabar et al. (29) (20 cases, D21S55-proximal to ERG, 0.6 Mb) converged toward a region within 21q22 and restricted up to 0.6 Mb, from 37.7 to 38.3 Mb on Hsa21. The first time that the term ‘Down Syndrome critical region’ (DSCR) was used appears to have been in Rahmani et al. (30); the terms ‘Minimal Chromosomal Region’ (MCR) (28), ‘Down Syndrome minimum critical region’ (DCR) (OMIM entry #190685) or ‘Down Syndrome minimal region’ (31) have also been used. Subsequently, in the naming of genes believed to be localized in the DSCR, the ‘C’ in the acronym was sometimes meant as ‘critical’ and sometimes ‘candidate’ (32). Currently, although the concept itself of ‘DSCR’ is questioned (see below), the term ‘critical’ has remained prevalent in the gene nomenclature and biomedical literature. This appears to be adequate because, if existing, the DSCR concept should indicate a region causing most critical, shared symptoms/signs of DS, rather than a region candidate for causing the (whole) phenotype of DS. The DSCR concept led to a flourishing of structural and functional studies of its content (33). Korenberg et al. (34) argued against a single DSCR, because in 3 of the 16 cases, they reported only proximal duplications of 21 were observed; Antonarakis (10) observed in this respect that more cases were necessary to clarify the contributions (...truncated)