Publications by authors named "Anna Lehman"

69 Publications

Utilization of telehealth in paediatric genome-wide sequencing: Health services implementation issues in the CAUSES Study.

J Telemed Telecare 2021 Jan 20:1357633X20982737. Epub 2021 Jan 20.

Department of Medical Genetics, University of British Columbia, Canada.

Introduction: Genome-wide sequencing (exome or whole genome) is transforming the care and management of paediatric patients with a rare disease because of its diagnostic capabilities. Genome-wide sequencing is most effective when both parents and the child are sequenced as a trio. Genetic counselling is recommended for all families considering genome-wide sequencing. Although telehealth is well established in genetic counselling for hereditary cancer and prenatal genetics, its use with genome-wide sequencing has not been well studied. The CAUSES Clinic at BC Children's and Women's Hospitals was a translational paediatric trio-based genome-wide sequencing initiative. Pre-test genetic counselling via telehealth (at a clinical site near the family's residence) was offered to families who had been previously evaluated by a clinical geneticist. We report on the first 300 families seen in the CAUSES clinic and compare health services implementation issues of families seen via telehealth versus on-site.

Methods: Demographics, cost to families (travel and time), time to first appointment, complete trio sample accrual and diagnostic rates were studied.

Results: Of the 300 patients, 58 (19%) were seen via telehealth and 242 (81%) were seen on-site for pre-test counselling. The mean time to completion of accrual of trio samples in the telehealth group was 56.3 (standard deviation ±87.3) days versus 18.9 (standard deviation ±62.4) days in the onsite group ( < 2.2 × 10). The mean per-family estimated actual or potential travel/time cost savings were greater in the telehealth group (Can$987; standard deviation = Can$1151) than for those seen on-site (Can$305; standard deviation = Can$589) ( = 0.0004).

Conclusions: Telehealth allowed for access to genome-wide sequencing for families in remote communities and for them to avoid significant travel and time costs; however, there was a significant delay to accrual of the complete trio samples in the telehealth group, impacting on time of result reporting and delaying diagnoses for families for whom genome-wide sequencing was diagnostic.
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http://dx.doi.org/10.1177/1357633X20982737DOI Listing
January 2021

mutations identified in autism spectrum disorder using forward genetics.

Elife 2020 12 22;9. Epub 2020 Dec 22.

Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States.

Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified as a candidate ASD gene. To validate our discovery, we generated a knockout mouse model () and confirmed that inactivating disrupts vocalization. In addition, mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.
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http://dx.doi.org/10.7554/eLife.56883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755391PMC
December 2020

Histone H3.3 beyond cancer: Germline mutations in cause a previously unidentified neurodegenerative disorder in 46 patients.

Authors:
Laura Bryant Dong Li Samuel G Cox Dylan Marchione Evan F Joiner Khadija Wilson Kevin Janssen Pearl Lee Michael E March Divya Nair Elliott Sherr Brieana Fregeau Klaas J Wierenga Alexandrea Wadley Grazia M S Mancini Nina Powell-Hamilton Jiddeke van de Kamp Theresa Grebe John Dean Alison Ross Heather P Crawford Zoe Powis Megan T Cho Marcia C Willing Linda Manwaring Rachel Schot Caroline Nava Alexandra Afenjar Davor Lessel Matias Wagner Thomas Klopstock Juliane Winkelmann Claudia B Catarino Kyle Retterer Jane L Schuette Jeffrey W Innis Amy Pizzino Sabine Lüttgen Jonas Denecke Tim M Strom Kristin G Monaghan Zuo-Fei Yuan Holly Dubbs Renee Bend Jennifer A Lee Michael J Lyons Julia Hoefele Roman Günthner Heiko Reutter Boris Keren Kelly Radtke Omar Sherbini Cameron Mrokse Katherine L Helbig Sylvie Odent Benjamin Cogne Sandra Mercier Stephane Bezieau Thomas Besnard Sebastien Kury Richard Redon Karit Reinson Monica H Wojcik Katrin Õunap Pilvi Ilves A Micheil Innes Kristin D Kernohan Gregory Costain M Stephen Meyn David Chitayat Elaine Zackai Anna Lehman Hilary Kitson Martin G Martin Julian A Martinez-Agosto Stan F Nelson Christina G S Palmer Jeanette C Papp Neil H Parker Janet S Sinsheimer Eric Vilain Jijun Wan Amanda J Yoon Allison Zheng Elise Brimble Giovanni Battista Ferrero Francesca Clementina Radio Diana Carli Sabina Barresi Alfredo Brusco Marco Tartaglia Jennifer Muncy Thomas Luis Umana Marjan M Weiss Garrett Gotway K E Stuurman Michelle L Thompson Kirsty McWalter Constance T R M Stumpel Servi J C Stevens Alexander P A Stegmann Kristian Tveten Arve Vøllo Trine Prescott Christina Fagerberg Lone Walentin Laulund Martin J Larsen Melissa Byler Robert Roger Lebel Anna C Hurst Joy Dean Samantha A Schrier Vergano Jennifer Norman Saadet Mercimek-Andrews Juanita Neira Margot I Van Allen Nicola Longo Elizabeth Sellars Raymond J Louie Sara S Cathey Elly Brokamp Delphine Heron Molly Snyder Adeline Vanderver Celeste Simon Xavier de la Cruz Natália Padilla J Gage Crump Wendy Chung Benjamin Garcia Hakon H Hakonarson Elizabeth J Bhoj

Sci Adv 2020 Dec 2;6(49). Epub 2020 Dec 2.

Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A () or with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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http://dx.doi.org/10.1126/sciadv.abc9207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821880PMC
December 2020

JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome.

Genet Med 2021 Feb 20;23(2):374-383. Epub 2020 Oct 20.

Department of Pediatrics, University of Montreal, Montreal, QC, Canada.

Purpose: JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype.

Methods: Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2.

Results: We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2.

Conclusion: We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.
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http://dx.doi.org/10.1038/s41436-020-00992-zDOI Listing
February 2021

Integration of genetic counsellors in genomic testing triage: Outcomes of a Genomic Consultation Service in British Columbia, Canada.

Eur J Med Genet 2020 Aug 13:104024. Epub 2020 Aug 13.

Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.

Purpose: Clinical diagnostic genome-wide (exome or genome) sequencing (GWS) in British Columbia requires funding approval by a provincial agency on a case-by-case basis. The CAUSES Clinic was a pediatric translational trio-based GWS study at BC Children's and Women's Hospitals. Referrals to the CAUSES Clinic were made through a Genomic Consultation Service (GCS), a multidisciplinary team led by genetic counsellors that provided advice regarding genomic testing for physicians considering GWS for their patients. Here we review the outcomes of the GCS, focusing on patients not recommended for the CAUSES Study.

Methods: Demographic, clinical, and testing data were abstracted from patient charts. Logistic regression analysis was used to explore associations between demographic and clinical variables and two outcomes: the type of recommendation and referring physicians' decisions to follow the recommendation.

Results: Of 972 GCS referrals, 248 patients were not referred to the CAUSES Study. GWS (vs. a targeted test; e.g. multi-gene panel) was more likely to be recommended to physicians of patients with ID than physicians of patients without ID (OR = 2.98; 95% CI = 1.46 to 6.27; n = 149). In total, 40% of physicians who were recommended to pursue clinical genomic testing submitted an application for funding approval; 71% of applications were approved for funding. Among approved tests, 50% resulted in a diagnosis, including 33% of targeted tests and 82% of GWS tests (χ (1) = 5.0, p = 0.026).

Conclusion: The GCS provided an effective model in which physicians can interface with genetic specialists, including genetic counsellors, to facilitate appropriate genomic test selection.
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http://dx.doi.org/10.1016/j.ejmg.2020.104024DOI Listing
August 2020

High rate of hypertension in patients with m.3243A>G MELAS mutations and POLG variants.

Mitochondrion 2020 07 2;53:194-202. Epub 2020 Jun 2.

Biomedical Physiology & Kinesiology, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada. Electronic address:

Animal studies suggest that decreased vascular mitochondrial DNA copy number can promote hypertension. We conducted a chart review of blood pressure and hemodynamics in patients with either mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS, n = 36) or individuals with variants in the mitochondrial DNA polymerase gamma (POLG, n = 26). The latter included both pathogenic variants and variants of unknown significance (VUS). Hypertension rates (MELAS 50%, POLG 50%) were elevated relative to Canadian norms in 20-39 (MELAS) and 40-59 (MELAS and POLG) years of age groups. Peripheral resistance was high in the hypertensive versus normotensive patients, potentially indicative of microvascular disease. Despite antihypertensive treatment, systolic blood pressure remained elevated in the POLG versus MELAS group. The risk of hypertension was not associated with MELAS heteroplasmy. Hypertension rates were not different between individuals with known pathogenic POLG variants and those with VUS, including common variants. Hypertension (HT) also did not differ between patients with POLG variants with (n = 17) and without chronic progressive external opthalmoplegia (n = 9) (CPEO). HT was associated with variants in all three functional domains of POLG. These findings suggest that both pathogenic variants and several VUS in the POLG gene may promote human hypertension and extend our past reports that increased risk of HT is associated with MELAS.
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http://dx.doi.org/10.1016/j.mito.2020.05.011DOI Listing
July 2020

GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome.

Clin Genet 2020 08 25;98(2):126-137. Epub 2020 May 25.

Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.

Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
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http://dx.doi.org/10.1111/cge.13769DOI Listing
August 2020

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7.

Authors:
Laura Castilla-Vallmanya Kaja K Selmer Clémantine Dimartino Raquel Rabionet Bernardo Blanco-Sánchez Sandra Yang Margot R F Reijnders Antonie J van Essen Myriam Oufadem Magnus D Vigeland Barbro Stadheim Gunnar Houge Helen Cox Helen Kingston Jill Clayton-Smith Jeffrey W Innis Maria Iascone Anna Cereda Sara Gabbiadini Wendy K Chung Victoria Sanders Joel Charrow Emily Bryant John Millichap Antonio Vitobello Christel Thauvin Frederic Tran Mau-Them Laurence Faivre Gaetan Lesca Audrey Labalme Christelle Rougeot Nicolas Chatron Damien Sanlaville Katherine M Christensen Amelia Kirby Raymond Lewandowski Rachel Gannaway Maha Aly Anna Lehman Lorne Clarke Luitgard Graul-Neumann Christiane Zweier Davor Lessel Bernarda Lozic Ingvild Aukrust Ryan Peretz Robert Stratton Thomas Smol Anne Dieux-Coëslier Joanna Meira Elizabeth Wohler Nara Sobreira Erin M Beaver Jennifer Heeley Lauren C Briere Frances A High David A Sweetser Melissa A Walker Catherine E Keegan Parul Jayakar Marwan Shinawi Wilhelmina S Kerstjens-Frederikse Dawn L Earl Victoria M Siu Emma Reesor Tony Yao Robert A Hegele Olena M Vaske Shannon Rego Kevin A Shapiro Brian Wong Michael J Gambello Marie McDonald Danielle Karlowicz Roberto Colombo Alessandro Serretti Lynn Pais Anne O'Donnell-Luria Alison Wray Simon Sadedin Belinda Chong Tiong Y Tan John Christodoulou Susan M White Anne Slavotinek Deborah Barbouth Dayna Morel Swols Mélanie Parisot Christine Bole-Feysot Patrick Nitschké Véronique Pingault Arnold Munnich Megan T Cho Valérie Cormier-Daire Susanna Balcells Stanislas Lyonnet Daniel Grinberg Jeanne Amiel Roser Urreizti Christopher T Gordon

Genet Med 2020 Jul 7;22(7):1215-1226. Epub 2020 May 7.

Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.

Purpose: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.

Methods: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.

Results: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.

Conclusion: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.
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http://dx.doi.org/10.1038/s41436-020-0792-7DOI Listing
July 2020

The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms.

Am J Hum Genet 2020 02;106(2):143-152

Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address:

Advances in genomics have transformed our ability to identify the genetic causes of rare diseases (RDs), yet we have a limited understanding of the mechanistic roles of most genes in health and disease. When a novel RD gene is first discovered, there is minimal insight into its biological function, the pathogenic mechanisms of disease-causing variants, and how therapy might be approached. To address this gap, the Canadian Rare Diseases Models and Mechanisms (RDMM) Network was established to connect clinicians discovering new disease genes with Canadian scientists able to study equivalent genes and pathways in model organisms (MOs). The Network is built around a registry of more than 500 Canadian MO scientists, representing expertise for over 7,500 human genes. RDMM uses a committee process to identify and evaluate clinician-MO scientist collaborations and approve 25,000 Canadian dollars in catalyst funding. To date, we have made 85 clinician-MO scientist connections and funded 105 projects. These collaborations help confirm variant pathogenicity and unravel the molecular mechanisms of RD, and also test novel therapies and lead to long-term collaborations. To expand the impact and reach of this model, we made the RDMM Registry open-source, portable, and customizable, and we freely share our committee structures and processes. We are currently working with emerging networks in Europe, Australia, and Japan to link international RDMM networks and registries and enable matches across borders. We will continue to create meaningful collaborations, generate knowledge, and advance RD research locally and globally for the benefit of patients and families living with RD.
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http://dx.doi.org/10.1016/j.ajhg.2020.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010971PMC
February 2020

De novo TBR1 variants cause a neurocognitive phenotype with ID and autistic traits: report of 25 new individuals and review of the literature.

Eur J Hum Genet 2020 06 31;28(6):770-782. Epub 2020 Jan 31.

Centre de Génétique et Centre de Référence Maladies Rares (Anomalies du Développement de l'Interrégion Est), Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France.

TBR1, a T-box transcription factor expressed in the cerebral cortex, regulates the expression of several candidate genes for autism spectrum disorders (ASD). Although TBR1 has been reported as a high-confidence risk gene for ASD and intellectual disability (ID) in functional and clinical reports since 2011, TBR1 has only recently been recorded as a human disease gene in the OMIM database. Currently, the neurodevelopmental disorders and structural brain anomalies associated with TBR1 variants are not well characterized. Through international data sharing, we collected data from 25 unreported individuals and compared them with data from the literature. We evaluated structural brain anomalies in seven individuals by analysis of MRI images, and compared these with anomalies observed in TBR1 mutant mice. The phenotype included ID in all individuals, associated to autistic traits in 76% of them. No recognizable facial phenotype could be identified. MRI analysis revealed a reduction of the anterior commissure and suggested new features including dysplastic hippocampus and subtle neocortical dysgenesis. This report supports the role of TBR1 in ID associated with autistic traits and suggests new structural brain malformations in humans. We hope this work will help geneticists to interpret TBR1 variants and diagnose ASD probands.
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http://dx.doi.org/10.1038/s41431-020-0571-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253452PMC
June 2020

Renpenning syndrome in a female.

Am J Med Genet A 2020 03 16;182(3):498-503. Epub 2019 Dec 16.

Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.

Renpenning syndrome (OMIM: 309500) is a rare X-linked disorder that causes intellectual disability, microcephaly, short stature, a variety of eye anomalies, and characteristic craniofacial features. This condition results from pathogenic variation of PQBP1, a polyglutamine-binding protein involved in transcription and pre-mRNA splicing. Renpenning syndrome has only been reported in affected males. Carrier females do not usually have clinical features, and in reported families with Renpenning syndrome, most female carriers exhibit favorable skewing of X-chromosome inactivation. We describe a female with syndromic features typical of Renpenning syndrome. She was identified by exome sequencing to have a de novo heterozygous c.459_462delAGAG mutation in PQBP1 (Xp11.23), affecting the AG hexamer in exon 4, which is the most common causative mutation in this syndrome. Streaky hypopigmentation of the skin was observed, supporting a hypothesized presence of an actively expressed, PQBP1 mutation-bearing X-chromosome in some cells. X-inactivation studies on peripheral blood cells demonstrated complete skewing in both the proband and her mother with preferential inactivation of the maternal X chromosome in the child. We demonstrated expression of the PQBP1 mutant transcript in leukocytes of the affected girl. Therefore, it is highly likely that the PQBP1 mutation arose from the paternal X chromosome.
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http://dx.doi.org/10.1002/ajmg.a.61451DOI Listing
March 2020

Strabismus in Children With Intellectual Disability: Part of a Broader Motor Control Phenotype?

Pediatr Neurol 2019 11 11;100:87-91. Epub 2019 Apr 11.

Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada. Electronic address:

Purpose: Intellectual disability (ID) results from a heterogeneous group of disorders and affects 1% to 2% of children. ID frequently occurs in association with other clinical features such as seizures or malformations. We suspected that strabismus might also be unusually frequent in this population and that it might be associated with ID groups affecting motor control.

Methods: We reviewed phenotypic descriptors, extracted from medical records, for a heterogeneous series of 222 probands with ID who had been enrolled in a study of clinical application of exome sequencing. We estimated the frequency of strabismus and other common clinical features and explored statistical associations between them. Data from Population Data British Columbia and Online Mendelian Inheritance in Man were also examined for confirmation of our observations.

Results: Strabismus had a higher prevalence among probands with ID than in the general population (odds ratio = 5.46). Moreover, probands with both ID and strabismus were more likely to have problems affecting motor control than those with ID and no strabismus (odds ratio = 2.84). Hypotonia was one of the most common motor control subgroups affecting the ID probands, and a frequent co-occurrence of strabismus and hypotonia was also observed (odds ratio = 2.51) and supported by related gene literature review. There was no evidence for associations between strabismus and other frequent clinical features.

Conclusion: Strabismus is a frequent feature in individuals with ID. The frequent co-occurrence of strabismus and motor control phenotypes, in particular hypotonia, suggests that a common cerebellar mechanism or pathway may underlie these phenotypes.
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http://dx.doi.org/10.1016/j.pediatrneurol.2019.04.002DOI Listing
November 2019

De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia.

Am J Hum Genet 2019 08 25;105(2):283-301. Epub 2019 Jul 25.

Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands. Electronic address:

The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.
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http://dx.doi.org/10.1016/j.ajhg.2019.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699192PMC
August 2019

Novel Exonic Deletions in TTC7A in a Newborn with Multiple Intestinal Atresia and Combined Immunodeficiency.

J Clin Immunol 2019 08 24;39(6):616-619. Epub 2019 Jul 24.

Department of Pathology and Laboratory Medicine, British Columbia Children's and Women's Hospital, The University of British Columbia, 4480 Oak St, Vancouver, BC, V6H3N1, Canada.

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http://dx.doi.org/10.1007/s10875-019-00669-6DOI Listing
August 2019

RAPIDOMICS: rapid genome-wide sequencing in a neonatal intensive care unit-successes and challenges.

Eur J Pediatr 2019 Aug 7;178(8):1207-1218. Epub 2019 Jun 7.

Division of Neonatology, Department of Paediatrics, University of British Columbia, Vancouver, Canada.

Genetic disorders are one of the leading causes of infant mortality and are frequent in neonatal intensive care units (NICUs). Rapid genome-wide sequencing (GWS; whole genome or exome sequencing (ES)), due to its diagnostic capabilities and immediate impacts on medical management, is becoming an appealing testing option in the NICU setting. RAPIDOMICS was a trio-based rapid ES pilot study of 25 babies with suspected genetic disorders in the BC Women's Hospital NICU. ES and bioinformatic analysis were performed after careful patient ascertainment. Trio analysis was performed using an in-house pipeline reporting variants in known disease-causing genes. Variants interpreted by the research team as definitely or possibly causal of the infant's phenotype were Sanger validated in a clinical laboratory. The average time to preliminary diagnosis was 7.2 days. Sanger validation was pursued in 15 patients for 13 autosomal dominant and 2 autosomal recessive disorders, with an overall diagnostic rate (partial or complete) of 60%.Conclusion: In total, 72% of patients enrolled had a genomic diagnosis achieved through ES, multi-gene panel testing or chromosomal microarray analysis. Among these, there was an 83% rate of significant and immediate impact on medical decision-making directly related to new knowledge of the diagnosis. Health service implementation challenges and successes are discussed. What is Known: • Rapid genome-wide sequencing in the neonatal intensive care setting has a greater diagnostic hit rate and impact on medical management than conventional genetic testing. However, the impact of consultation with genetics and patient ascertainment requires further investigation. What is New: • This study demonstrates the importance of genetic consultation and careful patient selection prior to pursuing exome sequencing (ES). • In total, 15/25 (60%) patients achieved a diagnosis through ES and 18/25 (72%) through ES, multi-gene panel testing or chromosomal microarray analysis with 83% of those having immediate effects on medical management.
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http://dx.doi.org/10.1007/s00431-019-03399-4DOI Listing
August 2019

New developmental syndromes: Understanding the family experience.

J Genet Couns 2019 04 2;28(2):202-212. Epub 2019 Apr 2.

Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.

Increased application of next generation sequencing has led to the discovery of a multitude of new neurodevelopmental syndromes, contributing to an increased diagnostic rate for exome sequencing from 25% originally to 40% currently. Owing to the recent recognition of these syndromes, as well as the types of large-scale studies (with limited phenotype information) often making these discoveries, these disorders may be poorly characterized clinically. As a result there is very limited information and disorder-specific support available to patients and families. We used a qualitative approach to explore how families experience a diagnosis of a new syndrome. We conducted semi-structured telephone interviews with parents and adult siblings of children who received a diagnosis of a new syndrome after whole exome sequencing (WES) performed through a translational research study. The interviews were recorded, transcribed verbatim, and transcripts were analyzed using grounded theory methods. Analysis of the 12 interviews revealed that a lack of information about the child's condition continues to play a large role in these families' experiences even after diagnosis. Almost all (92%) participants expressed ongoing uncertainty about their child's health and future. Most (83%) participants were interested in identifying other families with the same syndrome, which was related to both social support and seeking of information. Interestingly, 33% of participants worried about the child's risk for cancer due to their syndrome. Our results highlight some of the needs of families of children with new syndromes, and emphasize important issues care providers should address in pre- and post-test genetic counseling for WES and whole genome sequencing.
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http://dx.doi.org/10.1002/jgc4.1121DOI Listing
April 2019

Genomic deletions upstream of lamin B1 lead to atypical autosomal dominant leukodystrophy.

Neurol Genet 2019 Feb 24;5(1):e305. Epub 2019 Jan 24.

Department of Human Genetics (B.N., Q.S.P.), Graduate School of Public Health, University of Pittsburgh; Department of Medical Sciences (E.G., A.B.), University of Torino, Italy; Department of Radiology (R.R.), Uppsala University, Sweden; Department of Medical Genetics (A.L.), British Columbia Children's Hospital, Vancouver, Canada; Department of Genome Sciences (M. Spielmann), University of Washington, Seattle; Department of Pediatrics (M.K.K., R.A., M.K.), McGovern Medical School, University of Texas, Houston; Departments of Clinical Genomics and Neurology (R.G.), Mayo Clinic, Rochester, MN; Department of Pathology (M.A.), King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Imaging (M. Sharma), Western University, London, Canada; Departments of Pathology and Clinical Neurological Sciences (R.H.), Western University and London Health Sciences Centre, Canada; Office of the Clinical Director (W.A.G., C.T.), NHGRI; and NIH Undiagnosed Diseases Program (W.A.G., C.T.), Office of the Director, NIH, Bethesda, MD.

Objective: Clinical, radiologic, and molecular analysis of patients with genomic deletions upstream of the gene.

Methods: Detailed neurologic, MRI examinations, custom array comparative genomic hybridization (aCGH) analysis, and expression analysis were performed in patients at different clinical centers. All procedures were approved by institutional review boards of the respective institutions.

Results: Five patients from 3 independent families presented at ages ranging from 32 to 52 years with neurologic symptoms that included progressive hypophonia, upper and lower limb weakness and spasticity, and cerebellar dysfunction and MRIs characterized by widespread white matter alterations. Patients had unique nonrecurrent deletions upstream of the , varying in size from 250 kb to 670 kb. Deletion junctions were embedded in repetitive elements. Expression analysis revealed increased expression in patient cells.

Conclusions: Our findings confirmed the association between upstream deletions and leukodystrophy previously reported in a single family, expanding the phenotypic and molecular description of this condition. Although clinical and radiologic features overlapped with those of autosomal dominant leukodystrophy because of duplications, patients with deletions upstream of had an earlier age at symptom onset, lacked early dysautonomia, and appeared to have lesser involvement of the cerebellum and sparing of the spinal cord diameter on MRI. aCGH analysis defined a smaller minimal critical region required for disease causation and revealed that deletions occur at repetitive DNA genomic elements. Search for structural variants (duplications and upstream deletions) should be an integral part of the investigation of patients with autosomal dominant adult-onset leukodystrophy.
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http://dx.doi.org/10.1212/NXG.0000000000000305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384018PMC
February 2019

Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability.

Authors:
Benjamin Cogné Sophie Ehresmann Eliane Beauregard-Lacroix Justine Rousseau Thomas Besnard Thomas Garcia Slavé Petrovski Shiri Avni Kirsty McWalter Patrick R Blackburn Stephan J Sanders Kévin Uguen Jacqueline Harris Julie S Cohen Moira Blyth Anna Lehman Jonathan Berg Mindy H Li Usha Kini Shelagh Joss Charlotte von der Lippe Christopher T Gordon Jennifer B Humberson Laurie Robak Daryl A Scott Vernon R Sutton Cara M Skraban Jennifer J Johnston Annapurna Poduri Magnus Nordenskjöld Vandana Shashi Erica H Gerkes Ernie M H F Bongers Christian Gilissen Yuri A Zarate Malin Kvarnung Kevin P Lally Peggy A Kulch Brina Daniels Andres Hernandez-Garcia Nicholas Stong Julie McGaughran Kyle Retterer Kristian Tveten Jennifer Sullivan Madeleine R Geisheker Asbjorg Stray-Pedersen Jennifer M Tarpinian Eric W Klee Julie C Sapp Jacob Zyskind Øystein L Holla Emma Bedoukian Francesca Filippini Anne Guimier Arnaud Picard Øyvind L Busk Jaya Punetha Rolph Pfundt Anna Lindstrand Ann Nordgren Fayth Kalb Megha Desai Ashley Harmon Ebanks Shalini N Jhangiani Tammie Dewan Zeynep H Coban Akdemir Aida Telegrafi Elaine H Zackai Amber Begtrup Xiaofei Song Annick Toutain Ingrid M Wentzensen Sylvie Odent Dominique Bonneau Xénia Latypova Wallid Deb Sylvia Redon Frédéric Bilan Marine Legendre Caitlin Troyer Kerri Whitlock Oana Caluseriu Marine I Murphree Pavel N Pichurin Katherine Agre Ralitza Gavrilova Tuula Rinne Meredith Park Catherine Shain Erin L Heinzen Rui Xiao Jeanne Amiel Stanislas Lyonnet Bertrand Isidor Leslie G Biesecker Dan Lowenstein Jennifer E Posey Anne-Sophie Denommé-Pichon Claude Férec Xiang-Jiao Yang Jill A Rosenfeld Brigitte Gilbert-Dussardier Séverine Audebert-Bellanger Richard Redon Holly A F Stessman Christoffer Nellaker Yaping Yang James R Lupski David B Goldstein Evan E Eichler Francois Bolduc Stéphane Bézieau Sébastien Küry Philippe M Campeau

Am J Hum Genet 2019 03 28;104(3):530-541. Epub 2019 Feb 28.

Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T1J4, Canada. Electronic address:

Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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http://dx.doi.org/10.1016/j.ajhg.2019.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407527PMC
March 2019

Sialic acid catabolism by N-acetylneuraminate pyruvate lyase is essential for muscle function.

JCI Insight 2018 12 20;3(24). Epub 2018 Dec 20.

Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, Netherlands.

Sialic acids are important components of glycoproteins and glycolipids essential for cellular communication, infection, and metastasis. The importance of sialic acid biosynthesis in human physiology is well illustrated by the severe metabolic disorders in this pathway. However, the biological role of sialic acid catabolism in humans remains unclear. Here, we present evidence that sialic acid catabolism is important for heart and skeletal muscle function and development in humans and zebrafish. In two siblings, presenting with sialuria, exercise intolerance/muscle wasting, and cardiac symptoms in the brother, compound heterozygous mutations [chr1:182775324C>T (c.187C>T; p.Arg63Cys) and chr1:182772897A>G (c.133A>G; p.Asn45Asp)] were found in the N-acetylneuraminate pyruvate lyase gene (NPL). In vitro, NPL activity and sialic acid catabolism were affected, with a cell-type-specific reduction of N-acetyl mannosamine (ManNAc). A knockdown of NPL in zebrafish resulted in severe skeletal myopathy and cardiac edema, mimicking the human phenotype. The phenotype was rescued by expression of wild-type human NPL but not by the p.Arg63Cys or p.Asn45Asp mutants. Importantly, the myopathy phenotype in zebrafish embryos was rescued by treatment with the catabolic products of NPL: N-acetyl glucosamine (GlcNAc) and ManNAc; the latter also rescuing the cardiac phenotype. In conclusion, we provide the first report to our knowledge of a human defect in sialic acid catabolism, which implicates an important role of the sialic acid catabolic pathway in mammalian muscle physiology, and suggests opportunities for monosaccharide replacement therapy in human patients.
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http://dx.doi.org/10.1172/jci.insight.122373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338320PMC
December 2018

NBEA: Developmental disease gene with early generalized epilepsy phenotypes.

Ann Neurol 2018 11 25;84(5):788-795. Epub 2018 Oct 25.

Columbia University Medical Center, Institute for Genomic Medicine, New York, NY.

NBEA is a candidate gene for autism, and de novo variants have been reported in neurodevelopmental disease (NDD) cohorts. However, NBEA has not been rigorously evaluated as a disease gene, and associated phenotypes have not been delineated. We identified 24 de novo NBEA variants in patients with NDD, establishing NBEA as an NDD gene. Most patients had epilepsy with onset in the first few years of life, often characterized by generalized seizure types, including myoclonic and atonic seizures. Our data show a broader phenotypic spectrum than previously described, including a myoclonic-astatic epilepsy-like phenotype in a subset of patients. Ann Neurol 2018;84:796-803.
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http://dx.doi.org/10.1002/ana.25350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249120PMC
November 2018

Familial impairment of vocal cord mobility in childhood with clubfoot.

Clin Dysmorphol 2018 Oct;27(4):116-121

British Columbia Children's Hospital Research Institute.

We report on a family with three siblings, male and female, affected by congenital bilateral limitation of vocal cord abduction, with the additional finding of clubfeet in two. The paternal family history suggests an autosomal dominant inheritance. The siblings and father also have mild craniofacial features, which may be an expression of variability or may be unrelated. The association between congenital vocal cord paralysis and clubfeet has been reported with additional major features or in the context of Charcot-Marie-Tooth disease. However, the two in isolation have only been reported in one other family previously. Genomic analyses of the family, including chromosomal microarray and exome sequencing, showed neither a likely pathogenic variant in a known disease gene nor a compelling candidate gene variant. We propose that the association of these two findings constitutes a novel recognizable phenotype, for which a genetic cause remains undetermined.
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http://dx.doi.org/10.1097/MCD.0000000000000227DOI Listing
October 2018

The Genomic Consultation Service: A clinical service designed to improve patient selection for genome-wide sequencing in British Columbia.

Mol Genet Genomic Med 2018 May 30. Epub 2018 May 30.

Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.

Background: Access to clinical diagnostic genome-wide sequencing (GWS; exome or whole genome sequencing) is limited in British Columbia. The establishment of a translational research initiative (CAUSES) to provide diagnostic genome-wide sequencing for 500 children necessitated the development of a genomic consultation service, a clinical service established to provide consultation for physicians considering GWS for their pediatric patients throughout British Columbia. The Genomic Consultation Service provides patient-specific genomic advice that may include: GWS, multi-gene panel, single gene test, referral to medical genetics for clinical evaluation, or no genetic testing. Here, we describe and evaluate this service.

Methods: We analyzed referral patterns, patient demographics, clinical indications, and genomic advice provided during the first year of this service. Comparison of outcomes from the first 6 months versus the last 6 months was performed.

Results: A total of 407 referrals (238 males and 169 females [p = .0006]) were processed in the first year. Only children were eligible for referral and average patient age was 8 years. Medical genetics was the most frequent referring discipline, followed by biochemical disease and pediatric neurology, respectively. Most patients (68%) had syndromic intellectual disability. There was a significant difference in the frequency of referrals not appropriate for GWS in the first versus the second 6 months of the service (75/220 vs. 42/187; p = .01) suggesting increasing awareness of testing criteria by referring physicians.

Conclusion: This triage service is utilized throughout the province and appears to be an important factor in the high diagnostic rate (>40%) achieved in our GWS program.
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http://dx.doi.org/10.1002/mgg3.410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081221PMC
May 2018

De novo mutations in the SET nuclear proto-oncogene, encoding a component of the inhibitor of histone acetyltransferases (INHAT) complex in patients with nonsyndromic intellectual disability.

Hum Mutat 2018 07 10;39(7):1014-1023. Epub 2018 May 10.

Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands.

The role of disturbed chromatin remodeling in the pathogenesis of intellectual disability (ID) is well established and illustrated by de novo mutations found in a plethora of genes encoding for proteins of the epigenetic regulatory machinery. We describe mutations in the "SET nuclear proto-oncogene" (SET), encoding a component of the "inhibitor of histone acetyltransferases" (INHAT) complex, involved in transcriptional silencing. Using whole exome sequencing, four patients were identified with de novo mutations in the SET gene. Additionally, an affected mother and child were detected who carried a frameshift variant in SET. Four patients were found in literature. The de novo mutations in patients affected all four known SET mRNA transcripts. LoF mutations in SET are exceedingly rare in the normal population and, if present, affect only one transcript. The pivotal role of SET in neurogenesis is evident from in vitro and animal models. SET interacts with numerous proteins involved in histone modification, including proteins encoded by known autosomal dominant ID genes, that is, EP300, CREBBP, SETBP1, KMT2A, RAC1, and CTCF. Our study identifies SET as a new component of epigenetic regulatory modules underlying human cognitive disorders, and as a first member of the Nucleosome Assembly Protein (NAP) family implicated in ID.
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http://dx.doi.org/10.1002/humu.23541DOI Listing
July 2018

p.Met233Val in a Complex Neurodegenerative Movement and Neuropsychiatric Disorder.

J Mov Disord 2018 Jan 11;11(1):45-48. Epub 2018 Jan 11.

Pacific Parkinson's Research Centre and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.

Mutations in presenilin 1 () are the most common cause of autosomal dominant Alzheimer's disease. Here, we report a Canadian-Vietnamese family carrying a p.Met233Val mutation with an exceptionally early and severe presentation that includes a wide range of atypical symptoms, including prominent ataxia, Parkinsonism, spasticity, dystonia, action tremor, myoclonus, bulbar symptoms, seizures, hallucinations and behavioral changes. Whole-exome sequencing (WES) was performed on the affected proband after many assessments over several years proved diagnostically inconclusive. The results were analyzed using the AnnEx "Annotated Exomes" browser (http://annex.can.ubc.ca), a web-based platform that facilitates WES variant annotation and interpretation. High-throughput sequencing can be especially informative for complex neurological disorders, and WES warrants consideration as a first-line clinical test. Data analyses facilitated by web-based bioinformatics tools have great potential for novel insight, although confirmatory, diagnostically accredited Sanger sequencing is recommended prior to reporting.
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http://dx.doi.org/10.14802/jmd.17066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790629PMC
January 2018

The cost and diagnostic yield of exome sequencing for children with suspected genetic disorders: a benchmarking study.

Genet Med 2018 09 4;20(9):1013-1021. Epub 2018 Jan 4.

Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.

Purpose: This study aimed to generate benchmark estimates for the cost, diagnostic yield, and cost per positive diagnosis of diagnostic exome sequencing (ES) in heterogeneous pediatric patient populations and to illustrate how the design of an ES service can influence its cost and yield.

Methods: A literature review and Monte Carlo simulations were used to generate benchmark estimates for singleton and trio ES. A cost model for the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, which is testing a proposed delivery model for diagnostic ES in British Columbia, is used to illustrate the potential effects of changing the service design.

Results: The benchmark diagnostic yield was 34.3% (95% confidence interval (CI): 23.2-46.5) for trio ES and 26.5% (95% CI: 12.9-42.9) for singleton ES. The benchmark cost of delivery was C$6,437 (95% CI: $5,305-$7,704) in 2016 Canadian dollars (US$4,859; 4,391€) for trio ES and C$2,576 (95% CI: $1,993-$3,270) (US$1,944; 1,757€) for singleton ES. Scenario models for CAUSES suggest that alternative service designs could reduce costs but might lead to a higher cost per diagnosis due to lower yields.

Conclusion: Broad conclusions about the cost-effectiveness of ES should be drawn with caution when relying on studies that use cost or yield assumptions that lie at the extremes of the benchmark ranges.
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http://dx.doi.org/10.1038/gim.2017.226DOI Listing
September 2018

Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders.

Am J Hum Genet 2018 01 21;102(1):175-187. Epub 2017 Dec 21.

Manchester Centre for Genomic Medicine, Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK. Electronic address:

Histone lysine methyltransferases (KMTs) and demethylases (KDMs) underpin gene regulation. Here we demonstrate that variants causing haploinsufficiency of KMTs and KDMs are frequently encountered in individuals with developmental disorders. Using a combination of human variation databases and existing animal models, we determine 22 KMTs and KDMs as additional candidates for dominantly inherited developmental disorders. We show that KMTs and KDMs that are associated with, or are candidates for, dominant developmental disorders tend to have a higher level of transcription, longer canonical transcripts, more interactors, and a higher number and more types of post-translational modifications than other KMT and KDMs. We provide evidence to firmly associate KMT2C, ASH1L, and KMT5B haploinsufficiency with dominant developmental disorders. Whereas KMT2C or ASH1L haploinsufficiency results in a predominantly neurodevelopmental phenotype with occasional physical anomalies, KMT5B mutations cause an overgrowth syndrome with intellectual disability. We further expand the phenotypic spectrum of KMT2B-related disorders and show that some individuals can have severe developmental delay without dystonia at least until mid-childhood. Additionally, we describe a recessive histone lysine-methylation defect caused by homozygous or compound heterozygous KDM5B variants and resulting in a recognizable syndrome with developmental delay, facial dysmorphism, and camptodactyly. Collectively, these results emphasize the significance of histone lysine methylation in normal human development and the importance of this process in human developmental disorders. Our results demonstrate that systematic clinically oriented pathway-based analysis of genomic data can accelerate the discovery of rare genetic disorders.
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http://dx.doi.org/10.1016/j.ajhg.2017.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778085PMC
January 2018

Correlation of novel PAX6 gene abnormalities in aniridia and clinical presentation.

Can J Ophthalmol 2017 Dec 6;52(6):570-577. Epub 2017 Jul 6.

Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, B.C. Electronic address:

Objective: To describe the clinical presentation and genotype of subjects with aniridia with a particular focus on foveal hypoplasia.

Design: Prospective cohort study.

Participants: Thirty-three Canadian participants with aniridia and of various ethnic backgrounds residing in British Columbia.

Methods: Full ophthalmic examinations and posterior segment spectral domain-optical coherence tomography (SD-OCT) imaging were performed. Foveal hypoplasia was graded independently by 2 staff ophthalmologists. PAX6 sequencing was performed and chromosomal 11p anomalies investigated. Candidate gene and single-nucleotide polymorphism sequencing in genes functionally related to PAX6 were also studied.

Results: Best corrected visual acuities in the cohort ranged from 0.0 logMAR to no light perception. Total absence of iris tissue was seen in the majority (42 of 66 eyes). In those in whom SD-OCT was possible, foveal hypoplasia was seen in the majority (45 of 56 eyes, 80%). Molecular genetic defects involving PAX6 were identified in 30 participants (91%), including 4 novel PAX6 mutations (Gly18Val; Ser65ProfsX14; Met337ArgfsX18; Ser321CysfsX34) and 4 novel chromosome 11p deletions inclusive of PAX6 or a known PAX6 regulatory region.

Conclusions: The number of PAX6 mutations associated with aniridia continues to increase. Variable foveal architecture despite nearly identical anterior segment disease in 4 participants with an Ex9 ELP4-Ex4 DCDC1 deletion suggested that molecular cues causing variation in disease in the posterior segment differ from those at play in the anterior segment. Results in 3 patients without identifiable PAX6 mutations and a review of the literature suggest that such cases be described as phenocopies rather than actual cases of the syndrome of aniridia.
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http://dx.doi.org/10.1016/j.jcjo.2017.04.006DOI Listing
December 2017

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

Authors:
Fadi F Hamdan Candace T Myers Patrick Cossette Philippe Lemay Dan Spiegelman Alexandre Dionne Laporte Christina Nassif Ousmane Diallo Jean Monlong Maxime Cadieux-Dion Sylvia Dobrzeniecka Caroline Meloche Kyle Retterer Megan T Cho Jill A Rosenfeld Weimin Bi Christine Massicotte Marguerite Miguet Ledia Brunga Brigid M Regan Kelly Mo Cory Tam Amy Schneider Georgie Hollingsworth David R FitzPatrick Alan Donaldson Natalie Canham Edward Blair Bronwyn Kerr Andrew E Fry Rhys H Thomas Joss Shelagh Jane A Hurst Helen Brittain Moira Blyth Robert Roger Lebel Erica H Gerkes Laura Davis-Keppen Quinn Stein Wendy K Chung Sara J Dorison Paul J Benke Emily Fassi Nicole Corsten-Janssen Erik-Jan Kamsteeg Frederic T Mau-Them Ange-Line Bruel Alain Verloes Katrin Õunap Monica H Wojcik Dara V F Albert Sunita Venkateswaran Tyson Ware Dean Jones Yu-Chi Liu Shekeeb S Mohammad Peyman Bizargity Carlos A Bacino Vincenzo Leuzzi Simone Martinelli Bruno Dallapiccola Marco Tartaglia Lubov Blumkin Klaas J Wierenga Gabriela Purcarin James J O'Byrne Sylvia Stockler Anna Lehman Boris Keren Marie-Christine Nougues Cyril Mignot Stéphane Auvin Caroline Nava Susan M Hiatt Martina Bebin Yunru Shao Fernando Scaglia Seema R Lalani Richard E Frye Imad T Jarjour Stéphanie Jacques Renee-Myriam Boucher Emilie Riou Myriam Srour Lionel Carmant Anne Lortie Philippe Major Paola Diadori François Dubeau Guy D'Anjou Guillaume Bourque Samuel F Berkovic Lynette G Sadleir Philippe M Campeau Zoha Kibar Ronald G Lafrenière Simon L Girard Saadet Mercimek-Mahmutoglu Cyrus Boelman Guy A Rouleau Ingrid E Scheffer Heather C Mefford Danielle M Andrade Elsa Rossignol Berge A Minassian Jacques L Michaud

Am J Hum Genet 2017 Nov;101(5):664-685

Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada; Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada; Department of Pediatrics, Université de Montréal, Montreal, QC H3T1C5, Canada. Electronic address:

Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.
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http://dx.doi.org/10.1016/j.ajhg.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673604PMC
November 2017

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.

Brain 2017 Oct;140(10):2610-2622

Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.

Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype-phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors.
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http://dx.doi.org/10.1093/brain/awx203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080423PMC
October 2017

FOXP1 haploinsufficiency: Phenotypes beyond behavior and intellectual disability?

Am J Med Genet A 2017 Dec 8;173(12):3172-3181. Epub 2017 Sep 8.

Department of Pediatrics, University of South Dakota and Sanford Health, Sioux Falls, South Dakota.

The forkhead box (FOX) transcription factors have roles in development, carcinogenesis, metabolism, and immunity. In humans FOXP1 mutations have been associated with language and speech defects, intellectual disability, autism spectrum disorder, facial dysmorphisms, and congenital anomalies of the kidney and urinary tract. In mice, Foxp1 plays critical roles in development of the spinal motor neurons, lymphocytes, cardiomyocytes, foregut, and skeleton. We hypothesized therefore that mutations of FOXP1 affect additional tissues in some humans. Supporting this hypothesis, we describe two individuals with novel variants of FOXP1 (NM_032682.5:c.975-2A>C and NM_032682.5:c.1574G>A) and additional features. One had a lung disease resembling neuroendocrine cell hyperplasia of infancy (NEHI), and the second had a skeletal disorder with undertubulation of the long bones and relapsing-remitting fevers associated with flushing and edema. Although attribution of these traits to mutation of FOXP1 requires ascertainment of additional patients, we hypothesize that the variable expression of these additional features might arise by means of stochastic developmental variation.
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http://dx.doi.org/10.1002/ajmg.a.38462DOI Listing
December 2017