Publications by authors named "Slavé Petrovski"

78 Publications

Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis.

Commun Biol 2021 Mar 23;4(1):392. Epub 2021 Mar 23.

Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.

Idiopathic pulmonary fibrosis (IPF) is a fatal disorder characterised by progressive, destructive lung scarring. Despite substantial progress, the genetic determinants of this disease remain incompletely defined. Using whole genome and whole exome sequencing data from 752 individuals with sporadic IPF and 119,055 UK Biobank controls, we performed a variant-level exome-wide association study (ExWAS) and gene-level collapsing analyses. Our variant-level analysis revealed a novel association between a rare missense variant in SPDL1 and IPF (NM_017785.5:g.169588475 G > A p.Arg20Gln; p = 2.4 × 10, odds ratio = 2.87, 95% confidence interval: 2.03-4.07). This signal was independently replicated in the FinnGen cohort, which contains 1028 cases and 196,986 controls (combined p = 2.2 × 10), firmly associating this variant as an IPF risk allele. SPDL1 encodes Spindly, a protein involved in mitotic checkpoint signalling during cell division that has not been previously described in fibrosis. To the best of our knowledge, these results highlight a novel mechanism underlying IPF, providing the potential for new therapeutic discoveries in a disease of great unmet need.
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http://dx.doi.org/10.1038/s42003-021-01910-yDOI Listing
March 2021

Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning.

Nat Commun 2021 03 8;12(1):1504. Epub 2021 Mar 8.

Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.

Elucidating functionality in non-coding regions is a key challenge in human genomics. It has been shown that intolerance to variation of coding and proximal non-coding sequence is a strong predictor of human disease relevance. Here, we integrate intolerance to variation, functional genomic annotations and primary genomic sequence to build JARVIS: a comprehensive deep learning model to prioritize non-coding regions, outperforming other human lineage-specific scores. Despite being agnostic to evolutionary conservation, JARVIS performs comparably or outperforms conservation-based scores in classifying pathogenic single-nucleotide and structural variants. In constructing JARVIS, we introduce the genome-wide residual variation intolerance score (gwRVIS), applying a sliding-window approach to whole genome sequencing data from 62,784 individuals. gwRVIS distinguishes Mendelian disease genes from more tolerant CCDS regions and highlights ultra-conserved non-coding elements as the most intolerant regions in the human genome. Both JARVIS and gwRVIS capture previously inaccessible human-lineage constraint information and will enhance our understanding of the non-coding genome.
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http://dx.doi.org/10.1038/s41467-021-21790-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7940646PMC
March 2021

Spontaneous Coronary Artery Dissection: Insights on Rare Genetic Variation From Genome Sequencing.

Circ Genom Precis Med 2020 12 30;13(6):e003030. Epub 2020 Oct 30.

Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, United Kingdom (A.A.B., T.R.W., S.E.H., D.P., A.A.-H., A.W., D.K., N.J.S., D.A.).

Background: Spontaneous coronary artery dissection (SCAD) occurs when an epicardial coronary artery is narrowed or occluded by an intramural hematoma. SCAD mainly affects women and is associated with pregnancy and systemic arteriopathies, particularly fibromuscular dysplasia. Variants in several genes, such as those causing connective tissue disorders, have been implicated; however, the genetic architecture is poorly understood. Here, we aim to better understand the diagnostic yield of rare variant genetic testing among a cohort of SCAD survivors and to identify genes or gene sets that have a significant enrichment of rare variants.

Methods: We sequenced a cohort of 384 SCAD survivors from the United Kingdom, alongside 13 722 UK Biobank controls and a validation cohort of 92 SCAD survivors. We performed a research diagnostic screen for pathogenic variants and exome-wide and gene-set rare variant collapsing analyses.

Results: The majority of patients within both cohorts are female, 29% of the study cohort and 14% validation cohort have a remote arteriopathy. Four cases across the 2 cohorts had a diagnosed connective tissue disorder. We identified pathogenic or likely pathogenic variants in 7 genes (, , , , , , and ) in 14/384 cases in the study cohort and in 1/92 cases in the validation cohort. In our rare variant collapsing analysis, was the highest-ranked gene, and several functionally plausible genes were enriched for rare variants, although no gene achieved study-wide statistical significance. Gene-set enrichment analysis suggested a role for additional genes involved in renal function.

Conclusions: By studying the largest sequenced cohort of SCAD survivors, we demonstrate that, based on current knowledge, only a small proportion have a pathogenic variant that could explain their disease. Our findings strengthen the overlap between SCAD and renal and connective tissue disorders, and we highlight several new genes for future validation.
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http://dx.doi.org/10.1161/CIRCGEN.120.003030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748045PMC
December 2020

Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.

Am J Hum Genet 2020 05;106(5):659-678

Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 1 Francis Crick Avenue, CB2 0RE Cambridge, UK. Electronic address:

Access to large-scale genomics datasets has increased the utility of hypothesis-free genome-wide analyses. However, gene signals are often insufficiently powered to reach experiment-wide significance, triggering a process of laborious triaging of genomic-association-study results. We introduce mantis-ml, a multi-dimensional, multi-step machine-learning framework that allows objective assessment of the biological relevance of genes to disease studies. Mantis-ml is an automated machine-learning framework that follows a multi-model approach of stochastic semi-supervised learning to rank disease-associated genes through iterative learning sessions on random balanced datasets across the protein-coding exome. When applied to a range of human diseases, including chronic kidney disease (CKD), epilepsy, and amyotrophic lateral sclerosis (ALS), mantis-ml achieved an average area under curve (AUC) prediction performance of 0.81-0.89. Critically, to prove its value as a tool that can be used to interpret exome-wide association studies, we overlapped mantis-ml predictions with data from published cohort-level association studies. We found a statistically significant enrichment of high mantis-ml predictions among the highest-ranked genes from hypothesis-free cohort-level statistics, indicating a substantial improvement over the performance of current state-of-the-art methods and pointing to the capture of true prioritization signals for disease-associated genes. Finally, we introduce a generic mantis-ml score (GMS) trained with over 1,200 features as a generic-disease-likelihood estimator, outperforming published gene-level scores. In addition to our tool, we provide a gene prioritization atlas that includes mantis-ml's predictions across ten disease areas and empowers researchers to interactively navigate through the gene-triaging framework. Mantis-ml is an intuitive tool that supports the objective triaging of large-scale genomic discovery studies and enhances our understanding of complex genotype-phenotype associations.
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http://dx.doi.org/10.1016/j.ajhg.2020.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212270PMC
May 2020

Antiepileptic Drug Teratogenicity and De Novo Genetic Variation Load.

Ann Neurol 2020 06 15;87(6):897-906. Epub 2020 Apr 15.

Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.

Objective: The mechanisms by which antiepileptic drugs (AEDs) cause birth defects (BDs) are unknown. Data suggest that AED-induced BDs may result from a genome-wide increase of de novo variants in the embryo, a mechanism that we investigated.

Methods: Whole exome sequencing data from child-parent trios were interrogated for de novo single-nucleotide variants/indels (dnSNVs/indels) and de novo copy number variants (dnCNVs). Generalized linear models were applied to assess de novo variant burdens in children exposed prenatally to AEDs (AED-exposed children) versus children without BDs not exposed prenatally to AEDs (AED-unexposed unaffected children), and AED-exposed children with BDs versus those without BDs, adjusting for confounders. Fisher exact test was used to compare categorical data.

Results: Sixty-seven child-parent trios were included: 10 with AED-exposed children with BDs, 46 with AED-exposed unaffected children, and 11 with AED-unexposed unaffected children. The dnSNV/indel burden did not differ between AED-exposed children and AED-unexposed unaffected children (median dnSNV/indel number/child [range] = 3 [0-7] vs 3 [1-5], p = 0.50). Among AED-exposed children, there were no significant differences between those with BDs and those unaffected. Likely deleterious dnSNVs/indels were detected in 9 of 67 (13%) children, none of whom had BDs. The proportion of cases harboring likely deleterious dnSNVs/indels did not differ significantly between AED-unexposed and AED-exposed children. The dnCNV burden was not associated with AED exposure or birth outcome.

Interpretation: Our study indicates that prenatal AED exposure does not increase the burden of de novo variants, and that this mechanism is not a major contributor to AED-induced BDs. These results can be incorporated in routine patient counseling. ANN NEUROL 2020;87:897-906.
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http://dx.doi.org/10.1002/ana.25724DOI Listing
June 2020

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in .

NPJ Genom Med 2019 2;4:31. Epub 2019 Dec 2.

2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK.

The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for a lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 putative transcript models. Our annotations increase the transcriptional 'footprint' of these genes by over 674 kb. Using as a case study, due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome or a similar phenotype with a panel of exon sequences representing eight established genes and identified two de novo variants that now - through improved gene annotation - are ascribed to residing among our exons. These two (from 122 screened people, 1.6%) molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously classified intronic Dravet syndrome-associated variant that now lies within a deeply conserved exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders.
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http://dx.doi.org/10.1038/s41525-019-0106-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889285PMC
December 2019

Rare-variant collapsing analyses for complex traits: guidelines and applications.

Nat Rev Genet 2019 12 11;20(12):747-759. Epub 2019 Oct 11.

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

The first phase of genome-wide association studies (GWAS) assessed the role of common variation in human disease. Advances optimizing and economizing high-throughput sequencing have enabled a second phase of association studies that assess the contribution of rare variation to complex disease in all protein-coding genes. Unlike the early microarray-based studies, sequencing-based studies catalogue the full range of genetic variation, including the evolutionarily youngest forms. Although the experience with common variants helped establish relevant standards for genome-wide studies, the analysis of rare variation introduces several challenges that require novel analysis approaches.
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http://dx.doi.org/10.1038/s41576-019-0177-4DOI Listing
December 2019

Epilepsy genetics: clinical impacts and biological insights.

Lancet Neurol 2020 01 4;19(1):93-100. Epub 2019 Sep 4.

Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia. Electronic address:

Genomics now has an increasingly important role in neurology clinics. Regarding the epilepsies, innovations centred around technology, analytics, and collaboration have led to remarkable progress in gene discovery and have revealed the diverse array of genetic mechanisms and neurobiological pathways that contribute to these disorders. The new genomic era can present a challenge to clinicians, who now find themselves asked to interpret and apply genetic data to their daily management of patients with epilepsy. Navigation of this new era will require genetic literacy and familiarity with research advances in epilepsy genetics. Genetic epilepsy diagnoses now directly affect clinical care, and their importance will only increase as new targeted treatments continue to emerge. At the same time, new genetic insights challenge us to move from a deterministic view of genetic changes to a more nuanced appreciation of genetic risk within complex neurobiological systems that give rise to epilepsy.
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http://dx.doi.org/10.1016/S1474-4422(19)30269-8DOI Listing
January 2020

De novo GRIN variants in NMDA receptor M2 channel pore-forming loop are associated with neurological diseases.

Hum Mutat 2019 12 10;40(12):2393-2413. Epub 2019 Sep 10.

Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia.

N-methyl-D-aspartate receptors (NMDARs) mediate slow excitatory postsynaptic transmission in the central nervous system, thereby exerting a critical role in neuronal development and brain function. Rare genetic variants in the GRIN genes encoding NMDAR subunits segregated with neurological disorders. Here, we summarize the clinical presentations for 18 patients harboring 12 de novo missense variants in GRIN1, GRIN2A, and GRIN2B that alter residues in the M2 re-entrant loop, a region that lines the pore and is intolerant to missense variation. These de novo variants were identified in children with a set of neurological and neuropsychiatric conditions. Evaluation of the receptor cell surface expression, pharmacological properties, and biophysical characteristics show that these variants can have modest changes in agonist potency, proton inhibition, and surface expression. However, voltage-dependent magnesium inhibition is significantly reduced in all variants. The NMDARs hosting a single copy of a mutant subunit showed a dominant reduction in magnesium inhibition for some variants. These variant NMDARs also show reduced calcium permeability and single-channel conductance, as well as altered open probability. The data suggest that M2 missense variants increase NMDAR charge transfer in addition to varied and complex influences on NMDAR functional properties, which may underlie the patients' phenotypes.
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http://dx.doi.org/10.1002/humu.23895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874887PMC
December 2019

De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies.

Am J Hum Genet 2019 09 8;105(3):640-657. Epub 2019 Aug 8.

Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's National Health Service Foundation Trust, Birmingham, B15 2TG, UK. Electronic address:

The identification of genetic variants implicated in human developmental disorders has been revolutionized by second-generation sequencing combined with international pooling of cases. Here, we describe seven individuals who have diverse yet overlapping developmental anomalies, and who all have de novo missense FBXW11 variants identified by whole exome or whole genome sequencing and not reported in the gnomAD database. Their phenotypes include striking neurodevelopmental, digital, jaw, and eye anomalies, and in one individual, features resembling Noonan syndrome, a condition caused by dysregulated RAS signaling. FBXW11 encodes an F-box protein, part of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex, involved in ubiquitination and proteasomal degradation and thus fundamental to many protein regulatory processes. FBXW11 targets include β-catenin and GLI transcription factors, key mediators of Wnt and Hh signaling, respectively, critical to digital, neurological, and eye development. Structural analyses indicate affected residues cluster at the surface of the loops of the substrate-binding domain of FBXW11, and the variants are predicted to destabilize the protein and/or its interactions. In situ hybridization studies on human and zebrafish embryonic tissues demonstrate FBXW11 is expressed in the developing eye, brain, mandibular processes, and limb buds or pectoral fins. Knockdown of the zebrafish FBXW11 orthologs fbxw11a and fbxw11b resulted in embryos with smaller, misshapen, and underdeveloped eyes and abnormal jaw and pectoral fin development. Our findings support the role of FBXW11 in multiple developmental processes, including those involving the brain, eye, digits, and jaw.
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http://dx.doi.org/10.1016/j.ajhg.2019.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731360PMC
September 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

MTR-Viewer: identifying regions within genes under purifying selection.

Nucleic Acids Res 2019 07;47(W1):W121-W126

Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC 3052, Australia.

Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifying selection. Here, we present the MTR-Viewer, a web-server enabling easy visualization at the gene or variant level of the Missense Tolerance Ratio (MTR), a measure of regional intolerance to missense variation calculated using variation from 240 000 exome and genome sequences. The MTR-Viewer enables exploration of MTR calculations, using different sliding windows, for over 18 000 human protein-coding genes and 85 000 alternative transcripts. Users can also view MTR scores calculated for specific ethnicities, to enable easy exploration of regions that may be under different selective pressure. The spatial distribution of population and known disease variants is also displayed on the protein's domain structure. Intolerant regions were found to be highly enriched for ClinVar pathogenic and COSMIC somatic missense variants (Mann-Whitney U test P < 2.2 × 10-16). As the MTR is not biased by known domains and protein features, it can highlight functionally important regions within genes overlooked or inaccessible by traditional methods. MTR-Viewer is freely available via a user friendly web-server at http://biosig.unimelb.edu.au/mtr-viewer/.
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http://dx.doi.org/10.1093/nar/gkz457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602522PMC
July 2019

Exome-Based Rare-Variant Analyses in CKD.

J Am Soc Nephrol 2019 06 13;30(6):1109-1122. Epub 2019 May 13.

Division of Nephrology, Department of Medicine, Columbia University, New York, New York;

Background: Studies have identified many common genetic associations that influence renal function and all-cause CKD, but these explain only a small fraction of variance in these traits. The contribution of rare variants has not been systematically examined.

Methods: We performed exome sequencing of 3150 individuals, who collectively encompassed diverse CKD subtypes, and 9563 controls. To detect causal genes and evaluate the contribution of rare variants we used collapsing analysis, in which we compared the proportion of cases and controls carrying rare variants per gene.

Results: The analyses captured five established monogenic causes of CKD: variants in , , and achieved study-wide significance, and we observed suggestive case enrichment for and . Beyond known disease-associated genes, collapsing analyses incorporating regional variant intolerance identified suggestive dominant signals in and several other candidate genes. Biallelic mutations in cause carnitine palmitoyltransferase II deficiency, sometimes associated with rhabdomyolysis and acute renal injury. Genetic modifier analysis among cases with risk genotypes identified a suggestive signal in , implicated in Xia-Gibbs syndrome, which involves intellectual disability and other features. On the basis of the observed distribution of rare variants, we estimate that a two- to three-fold larger cohort would provide 80% power to implicate new genes for all-cause CKD.

Conclusions: This study demonstrates that rare-variant collapsing analyses can validate known genes and identify candidate genes and modifiers for kidney disease. In so doing, these findings provide a motivation for larger-scale investigation of rare-variant risk contributions across major clinical CKD categories.
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http://dx.doi.org/10.1681/ASN.2018090909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551770PMC
June 2019

Lung Transplant Outcomes in Patients With Pulmonary Fibrosis With Telomere-Related Gene Variants.

Chest 2019 09 9;156(3):477-485. Epub 2019 Apr 9.

Duke University Medical Center, Durham, NC.

Background: Pulmonary fibrosis (PF) is the most common disease indication for lung transplantation. Our recent work implicated an excess of rare genetic variants in the telomere-related genes TERT, RTEL1, and PARN in PF disease risk. The impact of such variants on posttransplant outcomes is uncertain. The objective of this study was to determine if patients with these PF-associated variants have altered rates of posttransplant acute rejection (AR), chronic lung allograft dysfunction (CLAD), and survival.

Methods: The study cohort consisted of 262 PF lung transplant recipients previously genetically characterized by whole exome sequencing. Thirty-one patients (11.8%) had variants in TERT, RTEL1, or PARN, whereas 231 (88.2%) did not. Multivariate Cox proportional hazards models adjusted for relevant clinical variables were used to assess the outcomes of death and CLAD. The AR burden was quantified and compared over the first posttransplant year.

Results: Patients with PF with disease-associated variants in TERT, RTEL1, or PARN had a significantly higher risk of death (adjusted hazard ratio [HR], 1.82; 95% CI, 1.07-3.08; P = .03) and CLAD (adjusted HR, 2.88; 95% CI, 1.42-5.87; P = .004) than patients without these variants. There was no difference in AR burden or rates of grade 3 primary graft dysfunction between the two groups.

Conclusions: Rare variants in the telomere-related genes TERT, RTEL1, or PARN are associated with poor posttransplant outcomes among PF lung transplant recipients. Further research is needed to understand the biological mechanisms by which telomere-related variants increase the risk for death and CLAD.
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http://dx.doi.org/10.1016/j.chest.2019.03.030DOI Listing
September 2019

A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS.

Genome Res 2019 05 2;29(5):809-818. Epub 2019 Apr 2.

Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, 10032, USA.

Large-scale sequencing efforts in amyotrophic lateral sclerosis (ALS) have implicated novel genes using gene-based collapsing methods. However, pathogenic mutations may be concentrated in specific genic regions. To address this, we developed two collapsing strategies: One focuses rare variation collapsing on homology-based protein domains as the unit for collapsing, and the other is a gene-level approach that, unlike standard methods, leverages existing evidence of purifying selection against missense variation on said domains. The application of these two collapsing methods to 3093 ALS cases and 8186 controls of European ancestry, and also 3239 cases and 11,808 controls of diversified populations, pinpoints risk regions of ALS genes, including , , , and While not clearly implicating novel ALS genes, the new analyses not only pinpoint risk regions in known genes but also highlight candidate genes as well.
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http://dx.doi.org/10.1101/gr.243592.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499321PMC
May 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

Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study.

Lancet 2019 02 31;393(10173):758-767. Epub 2019 Jan 31.

Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA. Electronic address:

Background: Identification of chromosomal aneuploidies and copy number variants that are associated with fetal structural anomalies has substantial value. Although whole-exome sequencing (WES) has been applied to case series of a few selected prenatal cases, its value in routine clinical settings has not been prospectively assessed in a large unselected cohort of fetuses with structural anomalies. We therefore aimed to determine the incremental diagnostic yield (ie, the added value) of WES following uninformative results of standard investigations with karyotype testing and chromosomal microarray in an unselected cohort of sequential pregnancies showing fetal structural anomalies.

Methods: In this prospective cohort study, the parents of fetuses who were found to have a structural anomaly in a prenatal ultrasound were screened for possible participation in the study. These participants were predominantly identified in or were referred to the Columbia University Carmen and John Thain Center for Prenatal Pediatrics (New York, NY, USA). Fetuses with confirmed aneuploidy or a causal pathogenic copy number variant were excluded from WES analyses. By use of WES of the fetuses and parents (parent-fetus trios), we identified genetic variants that indicated an underlying cause (diagnostic genetic variants) and genetic variants that met the criteria of bioinformatic signatures that had previously been described to be significantly enriched among diagnostic genetic variants.

Findings: Between April 24, 2015, and April 19, 2017, 517 sequentially identified pregnant women found to have fetuses with a structural anomaly were screened for their eligibility for inclusion in our study. 71 (14%) couples declined testing, 87 (17%) trios were missing at least one DNA sample (from either parent or the fetus), 69 (13%) trios had a clinically relevant abnormal karyotype or chromosomal microarray finding, 51 (10%) couples did not consent to WES or withdrew consent, and five (1%) samples were not of good enough quality for analysis. DNA samples from 234 (45%) eligible trios were therefore used for analysis of the primary outcome. By use of trio sequence data, we identified diagnostic genetic variants in 24 (10%) families. Mutations with bioinformatic signatures that were indicative of pathogenicity but with insufficient evidence to be considered diagnostic were also evaluated; 46 (20%) of the 234 fetuses assessed were found to have such signatures.

Interpretation: Our analysis of WES data in a prospective cohort of unselected fetuses with structural anomalies shows the value added by WES following the use of routine genetic tests. Our findings suggest that, in cases of fetal anomalies in which assessment with karyotype testing and chromosomal microarray fail to determine the underlying cause of a structural anomaly, WES can add clinically relevant information that could assist current management of a pregnancy. The unique challenges of WES-based prenatal diagnostics require analysis by a multidisciplinary team of perinatal practitioners and laboratory specialists.

Funding: Institute for Genomic Medicine (Columbia University Irving Medical Center).
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http://dx.doi.org/10.1016/S0140-6736(18)32042-7DOI Listing
February 2019

Development of a rapid functional assay that predicts GLUT1 disease severity.

Neurol Genet 2018 Dec 6;4(6):e297. Epub 2018 Dec 6.

Florey Institute of Neuroscience and Mental Health (S.M.Z., S.A.M., S.M., E.V.G., A.M.P., G.D.J., I.E.S., C.A.R., S. Petrou.); Department of Medicine (RMH) University of Melbourne (S.M.Z., S. Petrovski, M.S.H., J.D., S. Petrou); Department of Medicine (Austin Health) (M.S.H., J.D., S.F.B., I.E.S.), University of Melbourne, Heidelberg; Department of Neurology and Epileptology (H.L., Y.G.W.), Hertie Institute for Clinical Brain Research, University of Tübingen; School of Biosciences (A.M.P.), University of Melbourne, Parkville, Australia; APHP (S.A.), Hôpital Robert Debré, Service de Neurologie Pédiatrique; Univ Paris Diderot (S.A.), Sorbonne Paris Cité, INSERM UMR1141, Paris, France; and Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville, Australia.

Objective: To examine the genotype to phenotype connection in glucose transporter type 1 (GLUT1) deficiency and whether a simple functional assay can predict disease outcome from genetic sequence alone.

Methods: GLUT1 deficiency, due to mutations in , causes a wide range of epilepsies. One possible mechanism for this is variable impact of mutations on GLUT1 function. To test this, we measured glucose transport by GLUT1 variants identified in population controls and patients with mild to severe epilepsies. Controls were reference sequence from the NCBI and 4 population missense variants chosen from public reference control databases. Nine variants associated with epilepsies or movement disorders, with normal intellect in all individuals, formed the mild group. The severe group included 5 missense variants associated with classical GLUT1 encephalopathy. GLUT1 variants were expressed in oocytes, and glucose uptake was measured to determine kinetics (V) and affinity (K).

Results: Disease severity inversely correlated with rate of glucose transport between control (V = 28 ± 5), mild (V = 16 ± 3), and severe (V = 3 ± 1) groups, respectively. Affinities of glucose binding in control (K = 55 ± 18) and mild (K = 43 ± 10) groups were not significantly different, whereas affinity was indeterminate in the severe group because of low transport rates. Simplified analysis of glucose transport at high concentration (100 mM) was equally effective at separating the groups.

Conclusions: Disease severity can be partly explained by the extent of GLUT1 dysfunction. This simple oocyte assay complements genetic and clinical assessments. In prenatal diagnosis, this simple oocyte glucose uptake assay could be useful because standard clinical assessments are not available.
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http://dx.doi.org/10.1212/NXG.0000000000000297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290489PMC
December 2018

Diagnostic Utility of Exome Sequencing for Kidney Disease.

N Engl J Med 2019 01 26;380(2):142-151. Epub 2018 Dec 26.

From the Departments of Medicine (E.E.G., M.M., H.M.-R., Y.L., J.Z., J.N., P.K., W.Y.L., A.M., S. Piva, B.H.K., D.C., R.R., D.B., M.D., H.S., X.M., K.M., O.B., J.R., P.C., G.B.A., A.S.B., W.A., D.J.C., R.J.C., G.K.D., M.K.R., S.M., S.S.-C., K.K., A.G.G.) and Pediatrics (N.S.U.), Division of Nephrology, the Departments of Pathology (V.S.A.), Biomedical Informatics (D.A.F., C.W.), and Urology (S.A.), the Institute for Genomic Medicine (S.K., B.C., Z.R., J.B., C.D.M., C.M.M., N.D., D.B.G., A.G.G.) and the Department of Genetics and Development (D.B.G.), Hammer Health Sciences, and the Department of Epidemiology, Mailman School of Public Health (S.M.), Columbia University, New York; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, Innovative Medicines and Early Development (IMED) Biotech Unit, Cambridge, United Kingdom (S.C.-C., S. Petrovski, C.H., J.F., R.M., A.P.); and the Department of Medical Science, Renal Unit, Uppsala University Hospital, Uppsala, Sweden (B.C.F.).

Background: Exome sequencing is emerging as a first-line diagnostic method in some clinical disciplines, but its usefulness has yet to be examined for most constitutional disorders in adults, including chronic kidney disease, which affects more than 1 in 10 persons globally.

Methods: We conducted exome sequencing and diagnostic analysis in two cohorts totaling 3315 patients with chronic kidney disease. We assessed the diagnostic yield and, among the patients for whom detailed clinical data were available, the clinical implications of diagnostic and other medically relevant findings.

Results: In all, 3037 patients (91.6%) were over 21 years of age, and 1179 (35.6%) were of self-identified non-European ancestry. We detected diagnostic variants in 307 of the 3315 patients (9.3%), encompassing 66 different monogenic disorders. Of the disorders detected, 39 (59%) were found in only a single patient. Diagnostic variants were detected across all clinically defined categories, including congenital or cystic renal disease (127 of 531 patients [23.9%]) and nephropathy of unknown origin (48 of 281 patients [17.1%]). Of the 2187 patients assessed, 34 (1.6%) had genetic findings for medically actionable disorders that, although unrelated to their nephropathy, would also lead to subspecialty referral and inform renal management.

Conclusions: Exome sequencing in a combined cohort of more than 3000 patients with chronic kidney disease yielded a genetic diagnosis in just under 10% of cases. (Funded by the National Institutes of Health and others.).
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http://dx.doi.org/10.1056/NEJMoa1806891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510541PMC
January 2019

Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay.

Am J Hum Genet 2019 01 20;104(1):164-178. Epub 2018 Dec 20.

Department of Pediatrics, CHU Sainte-Justine Research Center and University of Montreal, Montreal, QC H3T 1C5, Canada. Electronic address:

SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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http://dx.doi.org/10.1016/j.ajhg.2018.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323608PMC
January 2019

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.

PLoS Comput Biol 2018 10 1;14(10):e1006506. Epub 2018 Oct 1.

Cambridge Computational Biology Institute, University of Cambridge, Cambridge, United Kingdom.

Here we present an open-source R package 'meaRtools' that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models of neurological disorders and to evaluate pharmaceutical compounds. meaRtools provides core algorithms for MEA spike train analysis, feature extraction, statistical analysis and plotting of multiple MEA recordings with multiple genotypes and treatments. meaRtools functionality covers novel solutions for spike train analysis, including algorithms to assess electrode cross-correlation using the spike train tiling coefficient (STTC), mutual information, synchronized bursts and entropy within cultured wells. Also integrated is a solution to account for bursts variability originating from mixed-cell neuronal cultures. The package provides a statistical platform built specifically for MEA data that can combine multiple MEA recordings and compare extracted features between different genetic models or treatments. We demonstrate the utilization of meaRtools to successfully identify epilepsy-like phenotypes in neuronal networks from Celf4 knockout mice. The package is freely available under the GPL license (GPL> = 3) and is updated frequently on the CRAN web-server repository. The package, along with full documentation can be downloaded from: https://cran.r-project.org/web/packages/meaRtools/.
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http://dx.doi.org/10.1371/journal.pcbi.1006506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181426PMC
October 2018

Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature.

Am J Med Genet A 2018 11 8;176(11):2259-2275. Epub 2018 Sep 8.

Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center (CUMC), New York, New York.

De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition, cutaneous mastocytosis, reported once before in a patient with a GNB1 variant, was observed in three additional patients, providing further evidence for an association to GNB1. We will review clinical and molecular data of these new cases and all previously reported cases to further define the phenotype and establish possible genotype-phenotype correlations.
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http://dx.doi.org/10.1002/ajmg.a.40472DOI Listing
November 2018

Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer's disease.

Ann Clin Transl Neurol 2018 Jul 24;5(7):832-842. Epub 2018 May 24.

The Taub Institute for Research on Alzheimer's Disease and the Aging Brain College of Physicians and Surgeons Columbia University The New York Presbyterian Hospital New York New York.

Objective: The genetic bases of Alzheimer's disease remain uncertain. An international effort to fully articulate genetic risks and protective factors is underway with the hope of identifying potential therapeutic targets and preventive strategies. The goal here was to identify and characterize the frequency and impact of rare and ultra-rare variants in Alzheimer's disease, using whole-exome sequencing in 20,197 individuals.

Methods: We used a gene-based collapsing analysis of loss-of-function ultra-rare variants in a case-control study design with data from the Washington Heights-Inwood Columbia Aging Project, the Alzheimer's Disease Sequencing Project and unrelated individuals from the Institute of Genomic Medicine at Columbia University.

Results: We identified 19 cases carrying extremely rare loss-of-function variants among a collection of 6,965 cases and a single loss-of-function variant among 13,252 controls ( = 2.17 × 10; OR: 36.2 [95% CI: 5.8-1493.0]). Age-at-onset was 7 years earlier for patients with qualifying variant compared with noncarriers. No other gene attained a study-wide level of statistical significance, but multiple top-ranked genes, including , and were among candidates for follow-up studies.

Interpretation: This study implicates ultra-rare, loss-of-function variants in as a significant genetic risk factor for Alzheimer's disease and provides a comprehensive dataset comparing the burden of rare variation in nearly all human genes in Alzheimer's disease cases and controls. This is the first investigation to establish a genome-wide statistically significant association between multiple extremely rare loss-of-function variants in and Alzheimer's disease in a large whole-exome study of unrelated cases and controls.
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http://dx.doi.org/10.1002/acn3.582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043775PMC
July 2018

A comprehensive approach to identifying repurposed drugs to treat SCN8A epilepsy.

Epilepsia 2018 04 25;59(4):802-813. Epub 2018 Mar 25.

Pairnomix, Plymouth, MN, USA.

Objective: Many previous studies of drug repurposing have relied on literature review followed by evaluation of a limited number of candidate compounds. Here, we demonstrate the feasibility of a more comprehensive approach using high-throughput screening to identify inhibitors of a gain-of-function mutation in the SCN8A gene associated with severe pediatric epilepsy.

Methods: We developed cellular models expressing wild-type or an R1872Q mutation in the Na 1.6 sodium channel encoded by SCN8A. Voltage clamp experiments in HEK-293 cells expressing the SCN8A R1872Q mutation demonstrated a leftward shift in sodium channel activation as well as delayed inactivation; both changes are consistent with a gain-of-function mutation. We next developed a fluorescence-based, sodium flux assay and used it to assess an extensive library of approved drugs, including a panel of antiepileptic drugs, for inhibitory activity in the mutated cell line. Lead candidates were evaluated in follow-on studies to generate concentration-response curves for inhibiting sodium influx. Select compounds of clinical interest were evaluated by electrophysiology to further characterize drug effects on wild-type and mutant sodium channel functions.

Results: The screen identified 90 drugs that significantly inhibited sodium influx in the R1872Q cell line. Four drugs of potential clinical interest-amitriptyline, carvedilol, nilvadipine, and carbamazepine-were further investigated and demonstrated concentration-dependent inhibition of sodium channel currents.

Significance: A comprehensive drug repurposing screen identified potential new candidates for the treatment of epilepsy caused by the R1872Q mutation in the SCN8A gene.
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http://dx.doi.org/10.1111/epi.14037DOI Listing
April 2018

eHealth as a Facilitator of Precision Medicine in Epilepsy.

Biomed Hub 2017 Nov-Dec;2(Suppl 1):137-145. Epub 2017 Nov 21.

Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.

Epilepsy is a chronic neurological condition that affects approximately 50 million people worldwide. Current treatments are inadequate and around a third of patients continue to experience uncontrolled seizures. The genetic architecture of many of the epilepsies makes them amenable to next-generation sequencing technologies, enabling a molecular diagnosis in an increasing proportion of patients. As a result, rare but remarkable examples of precision therapeutics in epilepsy are emerging. Coordinated research efforts are required to increase the diagnostic yield of sequencing and translate diagnosis to improved prognosis. This review explores the potential of eHealth technologies in facilitating and accelerating precision therapeutics in epilepsy. We describe the state of the art in precision diagnostics and therapeutics in epilepsy and identify opportunities for eHealth to accelerate the realisation of precision therapeutics via patient registries, research-enabled electronic health records, and connected health solutions.
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http://dx.doi.org/10.1159/000481793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945901PMC
November 2017

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.

Authors:
Sébastien Küry Geeske M van Woerden Thomas Besnard Martina Proietti Onori Xénia Latypova Meghan C Towne Megan T Cho Trine E Prescott Melissa A Ploeg Stephan Sanders Holly A F Stessman Aurora Pujol Ben Distel Laurie A Robak Jonathan A Bernstein Anne-Sophie Denommé-Pichon Gaëtan Lesca Elizabeth A Sellars Jonathan Berg Wilfrid Carré Øyvind Løvold Busk Bregje W M van Bon Jeff L Waugh Matthew Deardorff George E Hoganson Katherine B Bosanko Diana S Johnson Tabib Dabir Øystein Lunde Holla Ajoy Sarkar Kristian Tveten Julitta de Bellescize Geir J Braathen Paulien A Terhal Dorothy K Grange Arie van Haeringen Christina Lam Ghayda Mirzaa Jennifer Burton Elizabeth J Bhoj Jessica Douglas Avni B Santani Addie I Nesbitt Katherine L Helbig Marisa V Andrews Amber Begtrup Sha Tang Koen L I van Gassen Jane Juusola Kimberly Foss Gregory M Enns Ute Moog Katrin Hinderhofer Nagarajan Paramasivam Sharyn Lincoln Brandon H Kusako Pierre Lindenbaum Eric Charpentier Catherine B Nowak Elouan Cherot Thomas Simonet Claudia A L Ruivenkamp Sihoun Hahn Catherine A Brownstein Fan Xia Sébastien Schmitt Wallid Deb Dominique Bonneau Mathilde Nizon Delphine Quinquis Jamel Chelly Gabrielle Rudolf Damien Sanlaville Philippe Parent Brigitte Gilbert-Dussardier Annick Toutain Vernon R Sutton Jenny Thies Lisenka E L M Peart-Vissers Pierre Boisseau Marie Vincent Andreas M Grabrucker Christèle Dubourg Wen-Hann Tan Nienke E Verbeek Martin Granzow Gijs W E Santen Jay Shendure Bertrand Isidor Laurent Pasquier Richard Redon Yaping Yang Matthew W State Tjitske Kleefstra Benjamin Cogné Slavé Petrovski Kyle Retterer Evan E Eichler Jill A Rosenfeld Pankaj B Agrawal Stéphane Bézieau Sylvie Odent Ype Elgersma Sandra Mercier

Am J Hum Genet 2017 Nov;101(5):768-788

CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes Cedex 1, France.

Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway.
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http://dx.doi.org/10.1016/j.ajhg.2017.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673671PMC
November 2017

Gain-of-function HCN2 variants in genetic epilepsy.

Hum Mutat 2018 02 13;39(2):202-209. Epub 2017 Nov 13.

Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia.

Genetic generalized epilepsy (GGE) is a common epilepsy syndrome that encompasses seizure disorders characterized by spike-and-wave discharges (SWDs). Pacemaker hyperpolarization-activated cyclic nucleotide-gated channels (HCN) are considered integral to SWD genesis, making them an ideal gene candidate for GGE. We identified HCN2 missense variants from a large cohort of 585 GGE patients, recruited by the Epilepsy Phenome-Genome Project (EPGP), and performed functional analysis using two-electrode voltage clamp recordings from Xenopus oocytes. The p.S632W variant was identified in a patient with idiopathic photosensitive occipital epilepsy and segregated in the family. This variant was also independently identified in an unrelated patient with childhood absence seizures from a European cohort of 238 familial GGE cases. The p.V246M variant was identified in a patient with photo-sensitive GGE and his father diagnosed with juvenile myoclonic epilepsy. Functional studies revealed that both p.S632W and p.V246M had an identical functional impact including a depolarizing shift in the voltage dependence of activation that is consistent with a gain-of-function. In contrast, no biophysical changes resulted from the introduction of common population variants, p.E280K and p.A705T, and the p.R756C variant from EPGP that did not segregate with disease. Our data suggest that HCN2 variants can confer susceptibility to GGE via a gain-of-function mechanism.
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http://dx.doi.org/10.1002/humu.23357DOI Listing
February 2018

Loss-of-function variants in NFIA provide further support that NFIA is a critical gene in 1p32-p31 deletion syndrome: A four patient series.

Am J Med Genet A 2017 Dec 22;173(12):3158-3164. Epub 2017 Sep 22.

Department of Pediatrics, Division of Clinical Genetics, Columbia University Medical Center (CUMC), New York, New York.

The association between 1p32-p31 contiguous gene deletions and a distinct phenotype that includes anomalies of the corpus callosum, ventriculomegaly, developmental delay, seizures, and dysmorphic features has been long recognized and described. Recently, the observation of overlapping phenotypes in patients with chromosome translocations that disrupt NFIA (Nuclear factor I/A), a gene within this deleted region, and NFIA intragenic deletions has led to the hypothesis that NFIA is a critical gene within this region. The wide application and increasing accessibility of whole exome sequencing (WES) has helped identify new cases to support this hypothesis. Here, we describe four patients with loss-of-function variants in the NFIA gene identified through WES. The clinical presentation of these patients significantly overlaps with the phenotype described in previously reported cases of 1p32-p31 deletion syndrome, NFIA gene disruptions and intragenic NFIA deletions. Our cohort includes a mother and daughter as well as an unrelated individual who share the same nonsense variant (c.205C>T, p.Arg69Ter; NM_001145512.1). We also report a patient with a frameshift NFIA variant (c.159_160dupCC, p.Gln54ProfsTer49). We have compared published cases of 1p32-p31 microdeletion syndrome, translocations resulting in NFIA gene disruption, intragenic deletions, and loss-of-function mutations (including our four patients) to reveal that abnormalities of the corpus callosum, ventriculomegaly/hydrocephalus, macrocephaly, Chiari I malformation, dysmorphic features, developmental delay, hypotonia, and urinary tract defects are common findings. The consistent overlap in clinical presentation provides further evidence of the critical role of NFIA haploinsufficiency in the development of the 1p32-p31 microdeletion syndrome phenotype.
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http://dx.doi.org/10.1002/ajmg.a.38460DOI Listing
December 2017

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation.

Genome Res 2017 10 1;27(10):1715-1729. Epub 2017 Sep 1.

Department of Medicine, The University of Melbourne, Austin Health and Royal Melbourne Hospital, Melbourne, Victoria 3010, Australia.

Gene panel and exome sequencing have revealed a high rate of molecular diagnoses among diseases where the genetic architecture has proven suitable for sequencing approaches, with a large number of distinct and highly penetrant causal variants identified among a growing list of disease genes. The challenge is, given the DNA sequence of a new patient, to distinguish disease-causing from benign variants. Large samples of human standing variation data highlight regional variation in the tolerance to missense variation within the protein-coding sequence of genes. This information is not well captured by existing bioinformatic tools, but is effective in improving variant interpretation. To address this limitation in existing tools, we introduce the missense tolerance ratio (MTR), which summarizes available human standing variation data within genes to encapsulate population level genetic variation. We find that patient-ascertained pathogenic variants preferentially cluster in low MTR regions ( < 0.005) of well-informed genes. By evaluating 20 publicly available predictive tools across genes linked to epilepsy, we also highlight the importance of understanding the empirical null distribution of existing prediction tools, as these vary across genes. Subsequently integrating the MTR with the empirically selected bioinformatic tools in a gene-specific approach demonstrates a clear improvement in the ability to predict pathogenic missense variants from background missense variation in disease genes. Among an independent test sample of case and control missense variants, case variants (0.83 median score) consistently achieve higher pathogenicity prediction probabilities than control variants (0.02 median score; Mann-Whitney test, < 1 × 10). We focus on the application to epilepsy genes; however, the framework is applicable to disease genes beyond epilepsy.
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http://dx.doi.org/10.1101/gr.226589.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630035PMC
October 2017