Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders (virtual)

Balanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome and contribute substantial risk for developmental disorders (DDs). However, the rarity and lack of systematic screening for BCRs in the population has precluded unbiased analyses of the genomic features and mechanisms associated with risk for DDs versus normal developmental outcomes. Here, we sequenced and analyzed 1,420 BCR breakpoints across 710 individuals, including 406 DD cases and the first large-scale collection of 304 control BCR carriers. We found that BCRs were not more likely to disrupt genes in DD cases than controls, but were seven-fold more likely to disrupt genes associated with dominant DDs (21.3% of cases vs. 3.4% of controls; P = 1.60×10−12). Moreover, BCRs that did not disrupt a known DD gene were significantly enriched for breakpoints that altered topologically associated domains (TADs) containing dominant DD genes in cases compared to controls (odds ratio [OR] = 1.43, P = 0.036). We discovered six TADs enriched for noncoding BCRs (false discovery rate < 0.1) that contained known DD genes ( MEF2C, FOXG1, SOX9, BCL11A, BCL11B , and SATB2 ) and represent candidate pathogenic long-range positional effect (LRPE) loci. These six TADs were collectively disrupted in 7.4% of the DD cohort. Phased Hi-C analyses of five cases with noncoding BCR breakpoints localized to one of these putative LRPEs, the 5q14.3 TAD encompassing MEF2C , confirmed extensive disruption to local 3D chromatin structures and reduced frequency of contact between the MEF2C promoter and annotated enhancers. We further identified six genomic features enriched in TADs preferentially disrupted by noncoding BCRs in DD cases versus controls and used these features to build a model to predict TADs at risk for LRPEs across the genome. These results emphasize the potential impact of noncoding structural variants to cause LRPEs in unsolved DD cases, as well as the complex interaction of features associated with predicting three-dimensional chromatin structures intolerant to disruption. ### Competing Interest Statement M.E.T. receives research funding and/or reagents from Levo Therapeutics, Microsoft Inc, and Illumina Inc. E.L.A. receives in-kind support from IBM and Illumina Inc. M.M.M. and A.C.S.F. are employees of Illumina Inc. A.S.F. is employed by HERAX. All other authors declare no competing interests. ### Funding Statement This work was supported by grants from the The Danish National Research Foundation (WJC048 to N.T.), the Lundbeck Foundation (2007-1172; 2009-3999; 2010-6206; 2013-14290 to N.T.), the Danish Council for Independent Research (4183-00482B to N.T.), the National Institutes of Health (GM061354 to M.E.T, C.C.M, J.F.G., and E.L.; HD081256 to M.E.T.; MH115957 to M.E.T.; HD099547 to M.E.T.; HD091797 to M.E.T.; UM1HG009375 to E.L.A; RM1HG011016-01A1 to E.L.A.; HD090780 to S.L.P.S.; R00DE026824 to H.B.; GM007748 and DC012466 to B.B.C.; T32HG002295 to R.L.C.), the Simons Foundation for Autism Research (#573206 to M.E.T.), the National Science Foundation (NSF PHY-2019745 to E.L.A.; GRFP #2017240332 to R.L.C), Massachusetts General Hospital (Fund for Medical Discovery Fundamental Research Fellowship Award to C.L.), the Canadian Institutes of Health Research (Postdoctoral Fellowship to C.L.), the Welch Foundation (Q-1866 to E.L.A.), a McNair Medical Institute Scholar Award (to E.L.A.), a US-Israel Binational Science Foundation Award (2019276 to E.L.A.), the Behavioral Plasticity Research Institute (NSF DBI-2021795 to E.L.A.), the Investigator Grant Award Program (IGAP) BC Childrens Hospital Research Institute (to S.L.), the Czech Ministries of Health and Education (NU22-07-00165 and LM2018132 to Z.S.), the Estonian Research Council grant (PRG471 to K.O.), the Genome BC Grant (GR007838 to S.L.), the New Zealand eScience Infrastructure (to C.A.S.), the The IHC Foundation, Rutherford Discovery Fellowship administered by the Royal Society of New Zealand (to J.C.J.), the Sao Paulo Research Foundation (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo to A.C.S.F. and A.M.V.M.), the Council of Scientific & Industrial Research (to L.R.K.), the Fundamental Research Grant Scheme of the Malaysian Ministry of Higher Education (No. FRGS/1/2019/SKK08/UKM/02/9 to S.C.T.), the Polish National Centre of Science (No 2020/37/B/NZ5/00549 to M.K.), the funding support provided by Caroline Jones-Carrick and Collin Carrick (to H.G.K.), and the startup funding of the Qatar Biomedical Research Institute at Hamad Bin Khalifa University (to H.G.K.). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All studies were approved by respective institutional review boards (IRB). Informed consent was obtained from all subjects or their legal representative for participation in the study when the IRB so required. The Mass General Brigham Human Research Committee (MGBHRC) Institutional Review Board (IRB) gave ethical approval for this work: Study Protocol 2013P000323, Genomic Studies of Human Neurodevelopment (September 07, 2018). Protocols undergo annual continuing review by MGBHRC IRB. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All reported breakpoints and case phenotypes have been made available in Supplementary Tables 1 and 2.