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Whole-Exome Sequencing Is a Powerful Approach for Establishing View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Groningen University of Groningen Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly Rump, Patrick; Jazayeri, Omid; van Dijk-Bos, Krista; Johansson, Leonnart F.; van Essen, Anthonie J; Verheij, Johanna B G M; Veenstra-Knol, Hermine E; Redeker, Egbert J W; Mannens, Marcel M A M; Swertz, Morris A Published in: BMC Medical Genomics DOI: 10.1186/s12920-016-0167-8 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2016 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Rump, P., Jazayeri, O., van Dijk-Bos, K., Johansson, L. F., van Essen, A. J., Verheij, J. B. G. M., ... Sikkema-Raddatz, B. (2016). Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly. BMC Medical Genomics, 9(1), [7]. https://doi.org/10.1186/s12920-016-0167-8 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 12-11-2019 Rump et al. BMC Medical Genomics (2016) 9:7 DOI 10.1186/s12920-016-0167-8 RESEARCHARTICLE Open Access Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly Patrick Rump1, Omid Jazayeri1, Krista K. van Dijk-Bos1, Lennart F. Johansson1,3, Anthonie J. van Essen1, Johanna B. G. M. Verheij1, Hermine E. Veenstra-Knol1, Egbert J. W. Redeker2, Marcel M. A. M. Mannens2, Morris A. Swertz3, Behrooz Z. Alizadeh4, Conny M. A. van Ravenswaaij-Arts1, Richard J. Sinke1 and Birgit Sikkema-Raddatz1* Abstract Background: Clinical and genetic heterogeneity in monogenetic disorders represents a major diagnostic challenge. Although the presence of particular clinical features may aid in identifying a specific cause in some cases, the majority of patients remain undiagnosed. Here, we investigated the utility of whole-exome sequencing as a diagnostic approach for establishing a molecular diagnosis in a highly heterogeneous group of patients with varied intellectual disability and microcephaly. Methods: Whole-exome sequencing was performed in 38 patients, including three sib-pairs, in addition to or in parallel with genetic analyses that were performed during the diagnostic work-up of the study participants. Results: In ten out of these 35 families (29 %), we found mutations in genes already known to be related to a disorder in which microcephaly is a main feature. Two unrelated patients had mutations in the ASPM gene. In seven other patients we found mutations in RAB3GAP1, RNASEH2B, KIF11, ERCC8, CASK, DYRK1A and BRCA2. In one of the sib-pairs, mutations were found in the RTTN gene. Mutations were present in seven out of our ten families with an established etiological diagnosis with recessive inheritance. Conclusions: We demonstrate that whole-exome sequencing is a powerful tool for the diagnostic evaluation of patients with highly heterogeneous neurodevelopmental disorders such as intellectual disability with microcephaly. Our results confirm that autosomal recessive disorders are highly prevalent among patients with microcephaly. Keywords: Autosomal recessive inheritance, ASPM, BRCA2, CASK, DYRK1A, ERCC8, KIF11, Microcephaly, RAB3GAP1 RNASEH2B, RTTN, Whole-exome sequencing Background develop later after birth. It can occur as a more or less Microcephaly, a disproportionally small head size defined isolated finding or as one of the features of a more as occipitofrontal circumference at or below −3 standard complex syndrome. To date, according to the London deviations (SD), is an important neurological sign usually Medical Database [2], more than 800 syndromes with associated with developmental delays and intellectual microcephaly have been described, reflecting an enormous disability [1]. Microcephaly can be congenital or may number of possible diagnoses. Microcephaly may stem from a wide variety of genetic or non-genetic conditions * Correspondence: [email protected] and is considered to be a consequence of abnormal brain Patrick Rump and Omid Jazayeri are shared first authors. development. Non-genetic causes include foetal alcohol 1 Department of Genetics, University of Groningen, University Medical Centre exposure, perinatal infections, asphyxia or haemorrhage. Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands Full list of author information is available at the end of the article Microcephaly can also occur in patients with inborn errors © 2016 Rump et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Rump et al. BMC Medical Genomics (2016) 9:7 Page 2 of 9 of metabolism, but this explains only a small proportion of The clinical characteristics of all 38 patients are summa- the total cases [3]. In the majority of patients a genetic rized in Table 1. The average age of the patients was cause is suspected [4]. Chromosomal abnormalities may 10 years (range 0 to 57 years). The majority (87 %) were account for 15–20 % of patients [5]. In a retrospective children, with only five patients over 18 years of age. study of 680 children with microcephaly [6], a specific Severe microcephaly was defined as an occipital frontal genetic cause was detected in 15.3 % of them, with numer- head circumference of at least 3 SDs below the age-related ical chromosome aberrations accounting for 6.8 % and mean according to Dutch national reference curves. The microdeletions/duplications and monogenetic disorders mean occipital frontal head circumference Z-score for our accounting for the other 8.5 %. Over the last few years the patients was −4.5 SD (range −3to−8 SD). Consanguinity number of genes related to microcephaly has been rising, was reported for the parents of six patients (patients# 16, primarily as a result of the increased use of whole-exome 23, 27, 28, 29, 35), including one of the three sib-pairs. sequencing (for an overview see [7]). This clinical and Phenotype information was retrieved from medical genetic heterogeneity represents a major diagnostic chal- records and provided by the referring physicians. lenge. Although the presence of additional clinical findings All patients had undergone genetic testing during may aid in identifying a specific cause in some cases, the their routine diagnostic work-up. In addition to whole- majority of patients with microcephaly remain undiag- exomesequencing,thework-upmayhaveincluded nosed. Yet an early and specific diagnosis is important standard chromosome analysis, metabolic screening, or because it can provide relevant information about DNA sequencing of individual or multiple genes. On aver- disease prognosis, appropriate medical or supportive age, 2.8 DNA tests (range 0 to 9 tests) were performed per care, reproductive consequences for parents and other family (Additional file 1: Table S1). The most frequently family members, and prenatal diagnostic options. It may tested gene was ASPM. This gene was analysed in seven also preclude unnecessary further, and possibly invasive, (20 %) of the families. diagnostic tests and evaluations. The diagnostic work-up of microcephaly is extensive and Microarray analysis includes brain imaging, metabolic and ophthalmologic eval- SNP array analysis was performed in all patients prior uations, skin or muscle biopsies, karyotyping or microarray to inclusion using the IlluminaHumanCytoSNP-12 v2.1 analysis, and mutation analyses of microcephaly genes. DNA Analysis BeadChip following the manufacturer’s However, the use of targeted approaches, such as candidate instructions (Illumina, San Diego, CA, USA). Normalized gene testing by Sanger sequencing, is rather limited and intensity and allelic ratios were analysed using GenomeS- their diagnostic yield is generally low. In contrast, because tudio Data Analysis Software and the cnvPartition v3.1.6 whole-exome sequencing does not require a priori know- algorithm to assess copy number variation. No causal ledge of the gene or genes responsible for the disorder copy number variants were found (data not shown). under investigation [8], it has been proven to be a very Homozygosity was
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