European Journal of Human Genetics (2019) 27:909–918 https://doi.org/10.1038/s41431-019-0335-3 ARTICLE Multiple genomic copy number variants associated with periventricular nodular heterotopia indicate extreme genetic heterogeneity 1 1 1 1 1 1 Elena Cellini ● Annalisa Vetro ● Valerio Conti ● Carla Marini ● Viola Doccini ● Claudia Clementella ● 1 2 2 3,4 Elena Parrini ● Sabrina Giglio ● Matteo Della Monica ● Marco Fichera ● 4 1,5 Sebastiano Antonino Musumeci ● Renzo Guerrini Received: 13 March 2018 / Accepted: 18 December 2018 / Published online: 25 January 2019 © European Society of Human Genetics 2019 Abstract Periventricular nodular heterotopia (PNH) is a brain malformation in which nodules of neurons are ectopically retained along the lateral ventricles. Genetic causes include FLNA abnormalities (classical X-linked PNH), rare variants in ARFGEF2, DCHS1, ERMARD, FAT4, INTS8, MAP1B, MCPH1, and NEDD4L, as well as several chromosomal abnormalities. We performed array-CGH in 106 patients with different malformations of cortical development (MCD) and looked for common 1234567890();,: 1234567890();,: pathways possibly involved in PNH. Forty-two patients, including two parent/proband couples, exhibited PNH associated or not with other brain abnormalities, 44 had polymicrogyria and 20 had rarer MCDs. We found an enrichment of either large rearrangements or cryptic copy number variants (CNVs) in PNH (15/42, 35.7%) vs polymicrogyria (4/44, 9.1%) (i.e., 5.6 times increased risk for PNH of carrying a pathogenic CNV). CNVs in seven genomic regions (2p11.2q12.1, 4p15, 14q11.2q12, 16p13.3, 19q13.33, 20q13.33, 22q11) represented novel, potentially causative, associations with PNH. Through in silico analysis of genes included in imbalances whose breakpoints were clearly detailed, we detected in 9/12 unrelated patients in our series and in 15/24 previously published patients, a significant (P < 0.05) overrepresentation of genes involved in vesicle-mediated transport. Rare genomic imbalances, either small CNVs or large rearrangements, are cumulatively a frequent cause of PNH. Dysregulation of specific cellular mechanisms might play a key pathogenic role in PNH but it remains to be determined whether this is exerted through single genes or the cumulative dosage effect of more genes. Array-CGH should be considered as a first-line diagnostic test in PNH, especially if sporadic and non-classical. Introduction These authors contributed equally to this work: Elena Cellini, Annalisa Vetro Periventricular nodular heterotopia (PNH) is a mal- formation of cortical development (MCD) in which Supplementary information The online version of this article (https:// doi.org/10.1038/s41431-019-0335-3) contains supplementary nodules of heterotopic gray matter fail to migrate into the material, which is available to authorized users. developing cortex and accumulate along the walls of the lateral ventricles. PNH is usually detected using brain * Renzo Guerrini magnetic resonance imaging (MRI) in patients with epi- [email protected] lepsy, intellectual disability, or both, and is highly het- 1 Pediatric Neurology, Neurogenetics and Neurobiology Unit and erogeneous in severity and distribution, occurring as Laboratories, Meyer Children’s Hospital, University of Florence, either an isolated abnormality or part of more complex Florence, Italy developmental brain disorders. In the so-called “classical 2 Medical Genetics Unit, Meyer Children’s Hospital, University of form”, bilateral clusters of confluent nodules extend along Florence, Florence, Italy the walls of the lateral ventricles [1]. Less typical forms 3 Department of Biomedical and Biotechnological Sciences, include less prominent bilateral or unilateral nodules of Medical Genetics, University of Catania, Catania, Italy different size, variably positioned along the lateral ven- 4 Oasi Research Institute - IRCCS, Troina, EN, Italy tricles [2]. Genetic etiology of PNH is also heterogeneous, 5 IRCCS Stella Maris, Pisa, Italy with single-nucleotide variants (SNVs) or deletions of the 910 E. Cellini et al. FLNA gene being the most frequent cause of the classical patients with other MCDs (specified in Supplementary X-linked form (Mendelian Inheritance in Man (MIM): Table 2). #300049) [1, 3]. Rare variants in other genes account for a In all patients in group 1, we ruled out SNVs and dele- few reports (Supplementary Table 1A). In particular, tions/duplications of the FLNA gene using Sanger sequen- biallelic variants in ARFGEF2 [4], INTS8 [5], MCPH1 cing and Multiplex Ligation-dependent Probe [6], FAT4,andDCHS1 [7] cause recessive forms of PNH, Amplification, as previously described [1]. In all the 106 with or without syndromic features, while heterozygous patients we performed array-CGH analysis using the 180K variants in NEDD4L [8]andERMARD (C6orf70)[9, 10] Agilent platform (Agilent Technologies, Santa Clara, CA, have been associated to syndromic dominant forms of USA) according to the manufacturer’s instructions and PNH. Heterozygous SNVs in MAP1B have recently been reporting the genomic coordinates according to the reported in sporadic and familial epilepsy-associated PNH NCBI37/hg19 assembly. To confirm the deletions/duplica- [11]. Overall, 24 distinct genomic rearrangements have tions identified by array-CGH, we used quantitative SYBR been described in 66 patients with PNH, exhibiting either Green I-based real-time PCR on a LightCycler Real-Time syndromic or non-syndromic phenotypes (Table 1b, PCR (Roche Diagnostics, Basel, Switzerland). Primers and Supplementary Table 1B). conditions are available upon request. We present clinical and genetic data on 15 patients We classified CNVs as pathogenic or benign considering with PNH carrying pathogenic genomic imbalances, their frequency in the general population (http://dgv.tcag.ca/ including two parent/proband couples. Eight such dgv/app/home) and their inheritance status. In patients 2, 3, patients had been included in previous publications from and 5 and their parents, we performed karyotype and our team [9, 12–14], while seven (five sporadic and two fluorescence in situ hybridization on peripheral blood familial) had not been described before (Table 1a, b). We lymphocytes by standard procedures to confirm or better report seven genomic regions (2p11.2q12.1, 4p15, characterize the copy number changes highlighted by array- 14q11.2q12, 16p13.3, 19q13.33, 20q13.33, 22q11) which CGH and investigate parental carrier status for balanced represent novel, potentially causative, associations with chromosome translocations. We evaluated the genomic PNH. context of each CNV using the University of California, This series points to an increased prevalence of both Santa Cruz (UCSC) Genome Browser (https://genome-euro. large rearrangements and cryptic copy number variants ucsc.edu/). Relevant data were submitted to DECIPHER (CNVs) in PNH (15/42, 35.7%) with respect to poly- (DatabasE of Chromosomal Imbalance and Phenotype in microgyria (4/44, 9.1%). In spite of clinical and genetic Humans using Ensembl Resources; https://decipher.sanger. heterogeneity of PNH, it appears that genes coding for ac.uk/index). vesicle trafficking proteins are overrepresented in CNVs associated with this malformation. Statistical analysis To test the hypothesis that patients with PNH might be more Subjects and methods likely to harbor pathogenic genomic imbalances with respect to those with the other most frequent MCD, we Patient ascertainment and genetic investigations calculated and compared the frequency of such imbalances between group 1 (PNH) and group 2 (PMG). We could not We obtained written informed consent for genetic investi- identify pathogenic imbalances in group 3. We calculated gations and publication of the results for all patients parti- the odds ratio (OR) using the EpiInfo software v6 cipating in the study. The Ethics Committee of the Tuscany (http://www.cdc.gov/EpiInfo/) and considered a P value Region, Italy, approved this study within the framework of < 0.05 as statistically significant. the EU project “DESIRE” (FP7, grant agreement 602531). To explore whether pathogenic imbalances carried by We reviewed clinical and MRI data of 106 individuals patients with PNH were enriched for specific classes of with MCD who were studied with array-comparative genes, we used the statistical overrepresentation test tool genomic hybridization (array-CGH) and grouped them in available at the PANTHER (Protein ANnotation THrough three categories according to the MCD subtype (Supple- Evolutionary Relationships) database website (http://www. mentary Table 2). pantherdb.org/)[15]. We performed the overrepresentation Group 1, including 42 patients with PNH, isolated or test in PNH-associated CNVs in our database (15 patients, associated with other malformations, including poly- Table 1a, b) and repeated the analysis for those CNVs microgyria, corpus callosum abnormalities, enlarged or whose genomic boundaries were previously published in dysmorphic lateral ventricles; group 2, including 44 patients detail by other groups (24 patients, Supplementary with polymicrogyria (PMG) only; group 3, including 20 Table 1B). Multiple genomic copy number variants associated with periventricular nodular heterotopia... 911 Table 1a Unpublished patients with PNH and pathogenic genomic imbalances identified in this study Patient Age; PNH type Additional MRI Epilepsy: age onset; Cognition Clinical features Genomic coordinates (hg19); size of the Inheritance DECIPHER gender abnormalities seizure types; outcome CNV ID #1; Fig.