REPORT Cryptic and Complex Chromosomal Aberrations in Early-Onset Neuropsychiatric Disorders Harrison Brand, 1,2,9 Vamsee Pillalamarri, 1,9 Ryan L. Collins, 1 Stacey Eggert, 1,2,3 Colm O’Dushlaine, 4 Ellen B. Braaten, 5 Matthew R. Stone, 1 Kimberly Chambert, 4 Nathan D. Doty, 5 Carrie Hanscom, 1 Jill A. Rosenfeld, 6,10 Hillary Ditmars, 1 Jessica Blais, 1 Ryan Mills, 7 Charles Lee, 8 James F. Gusella, 1,2,3,4 Steven McCarroll, 3,4 Jordan W. Smoller, 1,4,5 Michael E. Talkowski, 1,2,4,5, * and Alysa E. Doyle 1,4,5, * Structural variation (SV) is a significant component of the genetic etiology of both neurodevelopmental and psychiatric disorders; how- ever, routine guidelines for clinical genetic screening have been established only in the former category. Genome-wide chromosomal microarray (CMA) can detect genomic imbalances such as copy-number variants (CNVs), but balanced chromosomal abnormalities (BCAs) still require karyotyping for clinical detection. Moreover, submicroscopic BCAs and subarray threshold CNVs are intractable, or cryptic, to both CMA and karyotyping. Here, we performed whole-genome sequencing using large-insert jumping libraries to delin- eate both cytogenetically visible and cryptic SVs in a single test among 30 clinically referred youth representing a range of severe neuro- psychiatric conditions. We detected 96 SVs per person on average that passed filtering criteria above our highest-confidence resolution (6,305 bp) and an additional 111 SVs per genome below this resolution. These SVs rearranged 3.8 Mb of genomic sequence and resulted in 42 putative loss-of-function (LoF) or gain-of-function mutations per person. We estimate that 80% of the LoF variants were cryptic to clinical CMA. We found myriad complex and cryptic rearrangements, including a ‘‘paired’’ duplication (360 kb, 169 kb) that flanks a 5.25 Mb inversion that appears in 7 additional cases from clinical CNV data among 47,562 individuals. Following convergent genomic profiling of these independent clinical CNV data, we interpreted three SVs to be of potential clinical significance. These data indicate that sequence-based delineation of the full SV mutational spectrum warrants exploration in youth referred for neuropsychiatric evalu- ation and clinical diagnostic SV screening more broadly. Structural variation (SV) is a major component of the ge- netic etiology of neurodevelopmental disorders. In recent years, enrichment of large, de novo copy-number variants (CNVs) and balanced chromosomal abnormalities (BCAs) has been reported and replicated in youth with autism spectrum disorder (ASD [MIM 209850]), developmental delay (DD), and intellectual disability (ID). 1–5 At present, genetic testing is frequently included in diagnostic evalua- tion of such youth, with chromosomal microarray (CMA) serving as the recommended first-tier genetic screen since 2010 based on a consensus statement in this journal. 6–8 For ASD, the use of CMA reflects the recognition that, in addition to the subset of cases with clinical features that can indicate a known genetic syndrome (e.g., Fragile X [MIM 300624]), nonsyndromic cases may benefit from genome-wide CNV evaluation. 9 Nonetheless, despite rec- ommendations that extend across the full autism spec- trum, genetic testing is not pursued for all individuals. 10 A significantly increased burden of large CNVs has also been observed in psychiatric disorders, including attention deficit hyperactivity disorder (ADHD [MIM 143465]), Tourette syndrome (MIM 137580), schizophrenia (MIM 181500), and early-onset psychosis and bipolar disorder (MIM 125480). 11–15 Notably, psychiatric and neurodeve- lopmental conditions often co-occur, 16 and findings for both rare SVs and common polymorphic risk variants suggest an overlapping etiology. 17,18 There is no current consensus on CMA or even general genetic testing for psychiatric disorders, although its potential benefit in this population has been discussed. 19,20 Array-based technologies such as CMA can capture relative dosage imbalances that are a consequence of aneuploidy, CNV, and unbalanced translocation. In devel- opmental disorders, the implementation of CMA as a first-tier genome-wide screen has significantly improved diagnostic yield over conventional karyotyping or gene- based mutation screening. One study of 6,539 consecutive referrals to Signature Genomics identified at least one clin- ically significant CNV in 17.6%–22.5% of cases, depending on the resolution of the array test performed (whole- genome BAC versus oligonucleotide). 21 In referrals for whom no causal genetic lesion is detected, however, addi- tional SV testing is rarely pursued for mutations that are cryptic to CMA (defined herein as below the resolution 1 Psychiatric and Neurodevelopmental Genetics Unit, Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; 2 Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; 3 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; 4 Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; 5 Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; 6 Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA; 7 Departments of Computational Medicine & Bioinformatics and Human Genetics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA; 8 The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA 9 These authors contributed equally to this work 10 Present address: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA *Correspondence: talkowski@chgr.mgh.harvard.edu (M.E.T.), doylea@helix.mgh.harvard.edu (A.E.D.) http://dx.doi.org/10.1016/j.ajhg.2014.09.005. Ó2014 by The American Society of Human Genetics. All rights reserved. 454 The American Journal of Human Genetics 95, 454–461, October 2, 2014