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Milicic L, Vacher M, Porter T, Doré V, Burnham SC, Bourgeat P, Shishegar R, Doecke J, Armstrong NJ, Tankard R, Maruff P, Masters CL, Rowe CC, Villemagne VL, Laws SM. Comprehensive analysis of epigenetic clocks reveals associations between disproportionate biological ageing and hippocampal volume. GeroScience 2022; 44:1807-1823. [PMID: 35445885 PMCID: PMC9213584 DOI: 10.1007/s11357-022-00558-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
The concept of age acceleration, the difference between biological age and chronological age, is of growing interest, particularly with respect to age-related disorders, such as Alzheimer's Disease (AD). Whilst studies have reported associations with AD risk and related phenotypes, there remains a lack of consensus on these associations. Here we aimed to comprehensively investigate the relationship between five recognised measures of age acceleration, based on DNA methylation patterns (DNAm age), and cross-sectional and longitudinal cognition and AD-related neuroimaging phenotypes (volumetric MRI and Amyloid-β PET) in the Australian Imaging, Biomarkers and Lifestyle (AIBL) and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Significant associations were observed between age acceleration using the Hannum epigenetic clock and cross-sectional hippocampal volume in AIBL and replicated in ADNI. In AIBL, several other findings were observed cross-sectionally, including a significant association between hippocampal volume and the Hannum and Phenoage epigenetic clocks. Further, significant associations were also observed between hippocampal volume and the Zhang and Phenoage epigenetic clocks within Amyloid-β positive individuals. However, these were not validated within the ADNI cohort. No associations between age acceleration and other Alzheimer's disease-related phenotypes, including measures of cognition or brain Amyloid-β burden, were observed, and there was no association with longitudinal change in any phenotype. This study presents a link between age acceleration, as determined using DNA methylation, and hippocampal volume that was statistically significant across two highly characterised cohorts. The results presented in this study contribute to a growing literature that supports the role of epigenetic modifications in ageing and AD-related phenotypes.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- CSIRO Health and Biosecurity, Australian E-Health Research Centre, Floreat, Western Australia, 6014, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Vincent Doré
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
| | - Samantha C Burnham
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
| | - Pierrick Bourgeat
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Rosita Shishegar
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | - James Doecke
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Bentley, Western Australia, Australia
| | - Rick Tankard
- School of Mathematics and Statistics, Murdoch University, Perth, Western Australia, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
- Cogstate Ltd, Melbourne, VIC, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christopher C Rowe
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Victor L Villemagne
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia.
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia.
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia.
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Cameron-Christie SR, Wilde J, Gray A, Tankard R, Bahlo M, Markie D, Evans HM, Robertson SP. Genetic investigation into an increased susceptibility to biliary atresia in an extended New Zealand Māori family. BMC Med Genomics 2018; 11:121. [PMID: 30563518 PMCID: PMC6299523 DOI: 10.1186/s12920-018-0440-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
Background Biliary atresia (BA), a fibrosing disorder of the developing biliary tract leading to liver failure in infancy, has an elevated incidence in indigenous New Zealand (NZ) Māori. We investigated a high rate of BA in a group of children (n = 12) belonging to a single Māori iwi (or ‘tribe’, related through a remote ancestor). Methods Population and geographical data was used to estimate the rate of BA in Māori sub-groups, and a pedigree linking most of the affected children was constructed from oral and documented history. Array genotyping was used to examine hypotheses about the inheritance of a possible genetic risk factor, and the history of the affected population, and Exome Sequencing to search for candidate genes. Results Most of these affected children (n = 7) link to a self-reported pedigree and carry a 50-fold increase in BA risk over unrelated Māori (χ2 = 296P < 0.001, 95% CI 23–111). Genetic analysis using FEstim and SNP array genotypes revealed no evidence for elevated consanguinity between parents of affected children (FEstim: F (2,21) = 0.469, P > 0.63). Genome-wide quantitation of intervals of contiguous, homozygous-by-state markers reached a similar conclusion (F (2,399) = 1.99, P = 0.138). Principal component analysis and investigation with STRUCTURE found no evidence of increased allele frequency of either a recessive variant, or additive, low-risk variants due to reproductive isolation. To identify candidate causal factors, Exome Sequencing datasets were scrutinised for shared rare coding variants across 8 affected individuals. No rare, non-synonymous, phylogenetically conserved variants were common to 6 or more affected children. Conclusion The substantially elevated risk for development of BA in this subgroup could be mediated by genetic factors, but the iwi exhibits no properties indicative of recent or remote reproductive isolation. Resolution of any risk loci may rely on extensive genomic sequencing studies in this iwi or investigation of other mechnaisms such as copy number variation. Electronic supplementary material The online version of this article (10.1186/s12920-018-0440-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophia R Cameron-Christie
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Justin Wilde
- Department of Paediatrics, Tauranga Hospital, Tauranga, New Zealand
| | - Andrew Gray
- Department of Preventive and Social Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Rick Tankard
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David Markie
- Department of Pathology, University of Otago, Dunedin, 9054, New Zealand
| | - Helen M Evans
- Paediatric Gastroenterology and Hepatology, Starship Children's Health, 2 Park Road, Grafton, Auckland, 1023, New Zealand
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand.
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Marsh APL, Heron D, Edwards TJ, Quartier A, Galea C, Nava C, Rastetter A, Moutard ML, Anderson V, Bitoun P, Bunt J, Faudet A, Garel C, Gillies G, Gobius I, Guegan J, Heide S, Keren B, Lesne F, Lukic V, Mandelstam SA, McGillivray G, McIlroy A, Méneret A, Mignot C, Morcom LR, Odent S, Paolino A, Pope K, Riant F, Robinson GA, Spencer-Smith M, Srour M, Stephenson SEM, Tankard R, Trouillard O, Welniarz Q, Wood A, Brice A, Rouleau G, Attié-Bitach T, Delatycki MB, Mandel JL, Amor DJ, Roze E, Piton A, Bahlo M, Billette de Villemeur T, Sherr EH, Leventer RJ, Richards LJ, Lockhart PJ, Depienne C. Mutations in DCC cause isolated agenesis of the corpus callosum with incomplete penetrance. Nat Genet 2017; 49:511-514. [PMID: 28250454 DOI: 10.1038/ng.3794] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/25/2017] [Indexed: 12/15/2022]
Abstract
Brain malformations involving the corpus callosum are common in children with developmental disabilities. We identified DCC mutations in four families and five sporadic individuals with isolated agenesis of the corpus callosum (ACC) without intellectual disability. DCC mutations result in variable dominant phenotypes with decreased penetrance, including mirror movements and ACC associated with a favorable developmental prognosis. Possible phenotypic modifiers include the type and location of mutation and the sex of the individual.
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Affiliation(s)
- Ashley P L Marsh
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France.,Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France
| | - Timothy J Edwards
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia.,School of Medicine, University of Queensland, Herston, Brisbane, Australia
| | - Angélique Quartier
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France
| | - Charles Galea
- Drug Delivery, Disposition and Dynamics (D4), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Agnès Rastetter
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Marie-Laure Moutard
- AP-HP, Hôpital Trousseau, Service de Neuropédiatrie, Paris, France.,UPMC, GRC ConCer-LD, Sorbonne Université, Paris, France.,Centre de Référence `Neurogénétique', Paris, France
| | - Vicki Anderson
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Pierre Bitoun
- Génétique Médicale, CHU Paris Nord, Hôpital Jean Verdier, Bondy, France
| | - Jens Bunt
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Anne Faudet
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Catherine Garel
- AP-HP GHUEP, Hôpital Armand Trousseau, Service de Radiologie, Paris, France
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Ilan Gobius
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | | | - Solveig Heide
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Fabien Lesne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Vesna Lukic
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Simone A Mandelstam
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Department of Radiology, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Alissandra McIlroy
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Aurélie Méneret
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Neurologie, Paris, France
| | - Cyril Mignot
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France.,Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France
| | - Laura R Morcom
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence CLAD-Ouest, CHU Rennes, Rennes, France.,UMR 6290 CNRS, IGDR Institut de Génétique et Développement de Rennes, Université de Rennes 1, Rennes, France
| | - Annalisa Paolino
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Florence Riant
- AP-HP, Groupe Hospitalier Saint-Louis -La Riboisière -Fernand Vidal, Laboratoire de Génétique, Paris, France
| | - Gail A Robinson
- Neuropsychology Research Unit, School of Psychology, University of Queensland, Brisbane, Australia
| | - Megan Spencer-Smith
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Clayton, Victoria, Australia
| | - Myriam Srour
- Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University Health Center, Montreal, Quebec, Canada
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Rick Tankard
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Oriane Trouillard
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Quentin Welniarz
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,Institut de Biologie Paris Seine, Neuroscience Paris Seine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Amanda Wood
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Alexis Brice
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Guy Rouleau
- Department of Neurology and Neurosurgery, McGill University Health Center, Montreal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Tania Attié-Bitach
- INSERM U1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris-Descartes University, Sorbonne Paris Cité and Imagine Institute, Paris, France.,AP-HP, Hôpital Necker-Enfants Malades, Département de Génétique, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Jean-Louis Mandel
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - David J Amor
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Emmanuel Roze
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Neurologie, Paris, France
| | - Amélie Piton
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Thierry Billette de Villemeur
- Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France.,AP-HP, Hôpital Trousseau, Service de Neuropédiatrie, Paris, France.,UPMC, GRC ConCer-LD, Sorbonne Université, Paris, France.,INSERM U1141, Paris, France
| | - Elliott H Sherr
- Department of Neurology, UCSF Benioff Children's Hospital, San Francisco, California, USA
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Neuroscience Research Group, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,Department of Neurology, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Linda J Richards
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia.,University of Queensland, School of Biomedical Sciences, St. Lucia, Brisbane, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Christel Depienne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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4
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Amor DJ, Marsh APL, Storey E, Tankard R, Gillies G, Delatycki MB, Pope K, Bromhead C, Leventer RJ, Bahlo M, Lockhart PJ. Heterozygous mutations in HSD17B4 cause juvenile peroxisomal D-bifunctional protein deficiency. Neurol Genet 2016; 2:e114. [PMID: 27790638 PMCID: PMC5070413 DOI: 10.1212/nxg.0000000000000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/06/2016] [Indexed: 11/15/2022]
Abstract
Objective: To determine the genetic cause of slowly progressive cerebellar ataxia, sensorineural deafness, and hypergonadotropic hypogonadism in 5 patients from 3 different families. Methods: The patients comprised 2 sib pairs and 1 sporadic patient. Clinical assessment included history, physical examination, and brain MRI. Linkage analysis was performed separately on the 2 sets of sib pairs using single nucleotide polymorphism microarrays, followed by analysis of the intersection of the regions. Exome sequencing was performed on 1 affected patient with variant filtering and prioritization undertaken using these intersected regions. Results: Using a combination of sequencing technologies, we identified compound heterozygous mutations in HSD17B4 in all 5 affected patients. In all 3 families, peroxisomal D-bifunctional protein (DBP) deficiency was caused by compound heterozygosity for 1 nonsense/deletion mutation and 1 missense mutation. Conclusions: We describe 5 patients with juvenile DBP deficiency from 3 different families, bringing the total number of reported patients to 14, from 8 families. This report broadens and consolidates the phenotype associated with juvenile DBP deficiency.
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Affiliation(s)
- David J Amor
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Ashley P L Marsh
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Elsdon Storey
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Rick Tankard
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Greta Gillies
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Kate Pope
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Catherine Bromhead
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Richard J Leventer
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Melanie Bahlo
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Murdoch Childrens Research Institute (D.J.A., A.P.L.M., G.G., M.B.D., K.P., R.J.L., P.J.L.), Royal Children's Hospital (D.J.A., M.B.D., R.J.L.), Parkville; Department of Paediatrics (D.J.A., A.P.L.M., M.B.D., C.B., R.J.L., P.J.L.), Department of Medical Biology (R.T., M.B.), The University of Melbourne; Department of Medicine (Neuroscience) (E.S.), Central Clinical School, Monash University; and Population Health and Immunity Division (R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia
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5
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Marsh APL, Lukic V, Pope K, Bromhead C, Tankard R, Ryan MM, Yiu EM, Sim JCH, Delatycki MB, Amor DJ, McGillivray G, Sherr EH, Bahlo M, Leventer RJ, Lockhart PJ. Complete callosal agenesis, pontocerebellar hypoplasia, and axonal neuropathy due to AMPD2 loss. Neurol Genet 2015; 1:e16. [PMID: 27066553 PMCID: PMC4807911 DOI: 10.1212/nxg.0000000000000014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 06/09/2015] [Indexed: 11/23/2022]
Abstract
Objective: To determine the molecular basis of a severe neurologic disorder in a large consanguineous family with complete agenesis of the corpus callosum (ACC), pontocerebellar hypoplasia (PCH), and peripheral axonal neuropathy. Methods: Assessment included clinical evaluation, neuroimaging, and nerve conduction studies (NCSs). Linkage analysis used genotypes from 7 family members, and the exome of 3 affected siblings was sequenced. Molecular analyses used Sanger sequencing to perform segregation studies and cohort analysis and Western blot of patient-derived cells. Results: Affected family members presented with postnatal microcephaly and profound developmental delay, with early death in 3. Neuroimaging, including a fetal MRI at 30 weeks, showed complete ACC and PCH. Clinical evaluation showed areflexia, and NCSs revealed a severe axonal neuropathy in the 2 individuals available for electrophysiologic study. A novel homozygous stopgain mutation in adenosine monophosphate deaminase 2 (AMPD2) was identified within the linkage region on chromosome 1. Molecular analyses confirmed that the mutation segregated with disease and resulted in the loss of AMPD2. Subsequent screening of a cohort of 42 unrelated individuals with related imaging phenotypes did not reveal additional AMPD2 mutations. Conclusions: We describe a family with a novel stopgain mutation in AMPD2. We expand the phenotype recently described as PCH type 9 to include progressive postnatal microcephaly, complete ACC, and peripheral axonal neuropathy. Screening of additional individuals with related imaging phenotypes failed to identify mutations in AMPD2, suggesting that AMPD2 mutations are not a common cause of combined callosal and pontocerebellar defects.
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Affiliation(s)
- Ashley P L Marsh
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Vesna Lukic
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Catherine Bromhead
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Rick Tankard
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Monique M Ryan
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Joe C H Sim
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - David J Amor
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - George McGillivray
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Elliott H Sherr
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Melanie Bahlo
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Richard J Leventer
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research (A.P.L.M., K.P., E.M.Y., J.C.H.S., M.B.D., P.J.L.), Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Bioinformatics Division (V.L., C.B., R.T., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Neurology (M.M.R., E.M.Y., R.J.L.) and Department of Paediatrics (A.P.L.M., M.M.R., E.M.Y., M.B.D., D.J.A., R.J.L., P.J.L.), The University of Melbourne, Royal Children's Hospital, Parkville, Australia; Victorian Clinical Genetics Services (D.J.A., G.M.) and Neuroscience Research (M.M.R., R.J.L.), Murdoch Childrens Research Institute, Parkville, Australia; Department of Neurology (E.H.S.), UCSF Benioff Children's Hospital, San Francisco, CA; Clinical Genetics (M.B.D.), Austin Health, Heidelberg, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (R.T., M.B.), The University of Melbourne, Parkville, Australia
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6
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Hildebrand MS, Tankard R, Gazina EV, Damiano JA, Lawrence KM, Dahl HHM, Regan BM, Shearer AE, Smith RJH, Marini C, Guerrini R, Labate A, Gambardella A, Tinuper P, Lichetta L, Baldassari S, Bisulli F, Pippucci T, Scheffer IE, Reid CA, Petrou S, Bahlo M, Berkovic SF. PRIMA1 mutation: a new cause of nocturnal frontal lobe epilepsy. Ann Clin Transl Neurol 2015; 2:821-30. [PMID: 26339676 PMCID: PMC4554443 DOI: 10.1002/acn3.224] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/21/2015] [Accepted: 05/29/2015] [Indexed: 12/17/2022] Open
Abstract
Objective Nocturnal frontal lobe epilepsy (NFLE) can be sporadic or autosomal dominant; some families have nicotinic acetylcholine receptor subunit mutations. We report a novel autosomal recessive phenotype in a single family and identify the causative gene. Methods Whole exome sequencing data was used to map the family, thereby narrowing exome search space, and then to identify the mutation. Results Linkage analysis using exome sequence data from two affected and two unaffected subjects showed homozygous linkage peaks on chromosomes 7, 8, 13, and 14 with maximum LOD scores between 1.5 and 1.93. Exome variant filtering under these peaks revealed that the affected siblings were homozygous for a novel splice site mutation (c.93+2T>C) in the PRIMA1 gene on chromosome 14. No additional PRIMA1 mutations were found in 300 other NFLE cases. The c.93+2T>C mutation was shown to lead to skipping of the first coding exon of the PRIMA1 mRNA using a minigene system. Interpretation PRIMA1 is a transmembrane protein that anchors acetylcholinesterase (AChE), an enzyme hydrolyzing acetycholine, to membrane rafts of neurons. PRiMA knockout mice have reduction of AChE and accumulation of acetylcholine at the synapse; our minigene analysis suggests that the c.93+2T>C mutation leads to knockout of PRIMA1. Mutations with gain of function effects in acetylcholine receptor subunits cause autosomal dominant NFLE. Thus, enhanced cholinergic responses are the likely cause of the severe NFLE and intellectual disability segregating in this family, representing the first recessive case to be reported and the first PRIMA1 mutation implicated in disease.
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Affiliation(s)
- Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
| | - Rick Tankard
- Bioinformatics Division, The Walter and Eliza Hall Institute Melbourne, Victoria, Australia
| | - Elena V Gazina
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne Melbourne, Victoria, Australia
| | - John A Damiano
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
| | - Kate M Lawrence
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
| | - Hans-Henrik M Dahl
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
| | - Brigid M Regan
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
| | - Aiden Eliot Shearer
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics Iowa City, Iowa
| | - Richard J H Smith
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics Iowa City, Iowa
| | - Carla Marini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital-University of Florence Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital-University of Florence Florence, Italy
| | - Angelo Labate
- Institute of Neurology, University Magna Græcia Catanzaro, Italy ; Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR) Germaneto, CZ, Italy
| | - Antonio Gambardella
- Institute of Neurology, University Magna Græcia Catanzaro, Italy ; Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR) Germaneto, CZ, Italy
| | - Paolo Tinuper
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi and Department of Medical and Surgical Sciences, University of Bologna Bologna, Italy
| | - Laura Lichetta
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi and Department of Medical and Surgical Sciences, University of Bologna Bologna, Italy
| | - Sara Baldassari
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi and Department of Medical and Surgical Sciences, University of Bologna Bologna, Italy
| | - Francesca Bisulli
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi and Department of Medical and Surgical Sciences, University of Bologna Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi and Department of Medical and Surgical Sciences, University of Bologna Bologna, Italy
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia ; Department of Paediatrics, Royal Children's Hospital, University of Melbourne Melbourne, Victoria, Australia
| | - Christopher A Reid
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne Melbourne, Victoria, Australia
| | - Steven Petrou
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbogurne Melbourne, Victoria, Australia
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7
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Bahlo M, Tankard R, Lukic V, Oliver KL, Smith KR. Using familial information for variant filtering in high-throughput sequencing studies. Hum Genet 2014; 133:1331-41. [PMID: 25129038 PMCID: PMC4185103 DOI: 10.1007/s00439-014-1479-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/07/2014] [Indexed: 12/30/2022]
Abstract
High-throughput sequencing studies (HTS) have been highly successful in identifying the genetic causes of human disease, particularly those following Mendelian inheritance. Many HTS studies to date have been performed without utilizing available family relationships between samples. Here, we discuss the many merits and occasional pitfalls of using identity by descent information in conjunction with HTS studies. These methods are not only applicable to family studies but are also useful in cohorts of apparently unrelated, ‘sporadic’ cases and small families underpowered for linkage and allow inference of relationships between individuals. Incorporating familial/pedigree information not only provides powerful filtering options for the extensive variant lists that are usually produced by HTS but also allows valuable quality control checks, insights into the genetic model and the genotypic status of individuals of interest. In particular, these methods are valuable for challenging discovery scenarios in HTS analysis, such as in the study of populations poorly represented in variant databases typically used for filtering, and in the case of poor-quality HTS data.
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Affiliation(s)
- Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia,
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8
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Azmanov DN, Chamova T, Tankard R, Gelev V, Bynevelt M, Florez L, Tzoneva D, Zlatareva D, Guergueltcheva V, Bahlo M, Tournev I, Kalaydjieva L. Challenges of diagnostic exome sequencing in an inbred founder population. Mol Genet Genomic Med 2013; 1:71-6. [PMID: 24498604 PMCID: PMC3865571 DOI: 10.1002/mgg3.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 11/17/2022] Open
Abstract
Exome sequencing was used as a diagnostic tool in a Roma/Gypsy family with three subjects (one deceased) affected by lissencephaly with cerebellar hypoplasia (LCH), a clinically and genetically heterogeneous diagnostic category. Data analysis identified high levels of unreported inbreeding, with multiple rare/novel “deleterious” variants occurring in the homozygous state in the affected individuals. Step-wise filtering was facilitated by the inclusion of parental samples in the analysis and the availability of ethnically matched control exome data. We identified a novel mutation, p.Asp487Tyr, in the VLDLR gene involved in the Reelin developmental pathway and associated with a rare form of LCH, the Dysequilibrium Syndrome. p.Asp487Tyr is the third reported missense mutation in this gene and the first example of a change affecting directly the functionally crucial β-propeller domain. An unexpected additional finding was a second unique mutation (p.Asn494His) with high scores of predicted pathogenicity in KCNV2, a gene implicated in a rare eye disorder, retinal cone dystrophy type 3B. This result raised diagnostic and counseling challenges that could be resolved through mutation screening of a large panel of healthy population controls. The strategy and findings of this study may inform the search for new disease mutations in the largest European genetic isolate.
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Affiliation(s)
- Dimitar N Azmanov
- Laboratory for Molecular Genetics, Centre for Medical Research/Western Australian Institute for Medical Research, The University of Western Australia Perth, WA, Australia
| | | | - Rick Tankard
- Bioinformatics Division, The Walter and Eliza Hall Institute Melbourne, VIC, Australia
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy, Sofia University Sofia, Bulgaria
| | - Michael Bynevelt
- Department of Surgery, School of Medicine, The University of Western Australia Perth, WA, Australia ; Neurological Intervention and Imaging Service (WA), Sir Charles Gairdner Hospital Perth, WA, Australia
| | - Laura Florez
- Laboratory for Molecular Genetics, Centre for Medical Research/Western Australian Institute for Medical Research, The University of Western Australia Perth, WA, Australia
| | - Dochka Tzoneva
- Department of Anesthesiology and Intensive Care, University Hospital "Alexandrovska" Sofia, Bulgaria
| | - Dora Zlatareva
- Department of Diagnostic Imaging, University Hospital "Alexandrovska" Sofia, Bulgaria
| | | | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute Melbourne, VIC, Australia ; Department of Mathematics and Statistics, The University of Melbourne Melbourne, VIC, Australia
| | - Ivailo Tournev
- Department of Neurology, Medical University Sofia, Bulgaria ; Department of Cognitive Science and Psychology, New Bulgarian University Sofia, Bulgaria
| | - Luba Kalaydjieva
- Laboratory for Molecular Genetics, Centre for Medical Research/Western Australian Institute for Medical Research, The University of Western Australia Perth, WA, Australia
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