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Elliott AM, Adam S, du Souich C, Lehman A, Nelson TN, van Karnebeek C, Alderman E, Armstrong L, Aubertin G, Blood K, Boelman C, Boerkoel C, Bretherick K, Brown L, Chijiwa C, Clarke L, Couse M, Creighton S, Watts-Dickens A, Gibson WT, Gill H, Tarailo-Graovac M, Hamilton S, Heran H, Horvath G, Huang L, Hulait GK, Koehn D, Lee HK, Lewis S, Lopez E, Louie K, Niederhoffer K, Matthews A, Meagher K, Peng JJ, Patel MS, Race S, Richmond P, Rupps R, Salvarinova R, Seath K, Selby K, Steinraths M, Stockler S, Tang K, Tyson C, van Allen M, Wasserman W, Mwenifumbo J, Friedman JM. Genome-wide Sequencing and the Clinical Diagnosis of Genetic Disease: The CAUSES Study. Human Genetics and Genomics Advances 2022; 3:100108. [PMID: 35599849 PMCID: PMC9117924 DOI: 10.1016/j.xhgg.2022.100108] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/16/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genome-wide sequencing (GWS) is a standard of care for diagnosis of suspected genetic disorders, but the proportion of patients found to have pathogenic or likely pathogenic variants ranges from less than 30% to more than 60% in reported studies. It has been suggested that the diagnostic rate can be improved by interpreting genomic variants in the context of each affected individual’s full clinical picture and by regular follow-up and reinterpretation of GWS laboratory results. Trio exome sequencing was performed in 415 families and trio genome sequencing in 85 families in the CAUSES study. The variants observed were interpreted by a multidisciplinary team including laboratory geneticists, bioinformaticians, clinical geneticists, genetic counselors, pediatric subspecialists, and the referring physician, and independently by a clinical laboratory using standard American College of Medical Genetics and Genomics (ACMG) criteria. Individuals were followed for an average of 5.1 years after testing, with clinical reassessment and reinterpretation of the GWS results as necessary. The multidisciplinary team established a diagnosis of genetic disease in 43.0% of the families at the time of initial GWS interpretation, and longitudinal follow-up and reinterpretation of GWS results produced new diagnoses in 17.2% of families whose initial GWS interpretation was uninformative or uncertain. Reinterpretation also resulted in rescinding a diagnosis in four families (1.9%). Of the families studied, 33.6% had ACMG pathogenic or likely pathogenic variants related to the clinical indication. Close collaboration among clinical geneticists, genetic counselors, laboratory geneticists, bioinformaticians, and individuals’ primary physicians, with ongoing follow-up, reanalysis, and reinterpretation over time, can improve the clinical value of GWS.
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Affiliation(s)
- Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Women's Health Research Institute, Vancouver, BC, Canada
| | - Shelin Adam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tanya N Nelson
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Emma Children's Hospital, Amsterdam, University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Emily Alderman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gudrun Aubertin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Katherine Blood
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Cyrus Boelman
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Cornelius Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Karla Bretherick
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Lindsay Brown
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Lorne Clarke
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Susan Creighton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Abby Watts-Dickens
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Harinder Gill
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Sara Hamilton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Harindar Heran
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gabriella Horvath
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Lijia Huang
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Gurdip K Hulait
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David Koehn
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Elena Lopez
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kristal Louie
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Karen Niederhoffer
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Allison Matthews
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Kirsten Meagher
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Junran J Peng
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Simone Race
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Phillip Richmond
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ramona Salvarinova
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Kimberly Seath
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathryn Selby
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Steinraths
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sylvia Stockler
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Kaoru Tang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Christine Tyson
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Margot van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Wyeth Wasserman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Pediatrics, Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Jill Mwenifumbo
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
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Szabados B, Rodriguez-Vida A, Duran I, Crabb S, van der Heijden M, Pous AF, Gravis G, Herranz UA, Protheroe A, Ravaud A, Maillet D, Mendez M, Suarez C, Linch M, Prendergast A, Tyson C, Mousa K, Castellano D, Powles T. 199O A phase II study investigating neoadjuvant atezolizumab in cisplatin-ineligible patients with muscle-invasive bladder cancer: Final analysis. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Fan KW, Shu MK, Eddib A, Tyson C. 2126 Perioperative Outcomes of Combined Gynecologic Oncology and Urogynecologic Surgeries. J Minim Invasive Gynecol 2019. [DOI: 10.1016/j.jmig.2019.09.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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4
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Shu MK, Fan KW, Tyson C, Eddib A. Postoperative Short-Term Outcomes of Robotic Sacrocolpoperineopexy Versus Robotic Sacrocolpopexy. J Minim Invasive Gynecol 2019. [DOI: 10.1016/j.jmig.2019.09.700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Pittet F, Tyson C, Herrington JA, Houdelier C, Lumineau S. Postnatal care generates phenotypic behavioural correlations in the Japanese quail. Behav Ecol Sociobiol 2019. [DOI: 10.1007/s00265-019-2735-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Yasin H, Gibson WT, Langlois S, Stowe RM, Tsang ES, Lee L, Poon J, Tran G, Tyson C, Wong CK, Marra MA, Friedman JM, Zahir FR. A distinct neurodevelopmental syndrome with intellectual disability, autism spectrum disorder, characteristic facies, and macrocephaly is caused by defects in CHD8. J Hum Genet 2019; 64:271-280. [PMID: 30670789 DOI: 10.1038/s10038-019-0561-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/13/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022]
Abstract
A decade ago, we described novel de novo submicroscopic deletions of chromosome 14q11.2 in three children with developmental delay, cognitive impairment, and similar dysmorphic features, including widely-spaced eyes, short nose with flat nasal bridge, long philtrum, prominent Cupid's bow of the upper lip, full lower lip, and auricular anomalies. We suggested that this constituted a new multiple congenital anomaly-intellectual disability syndrome due to defects in CHD8 and/or SUPT16H. The three patients in our original cohort were between 2 years and 3 years of age at the time. Here we present a fourth patient and clinical updates on our previous patients. To document the longitudinal course more fully, we integrate published reports of other patients and describe genotype-phenotype correlations among them. Children with the disorder present with developmental delay, intellectual disability, and/or autism spectrum disorder in addition to characteristic facies. Gastrointestinal and sleep problems are notable. The identification of multiple patients with the same genetic defect and characteristic clinical phenotype, confirms our suggestion that this is a syndromic disorder caused by haploinsufficiency or heterozygous loss of function of CHD8.
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Affiliation(s)
- Heba Yasin
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Departments of Psychiatry and Neurology, University of British Columbia, Vancouver, BC, Canada
| | - Erica S Tsang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Leora Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jenny Poon
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Grant Tran
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Christine Tyson
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Cytogenetics Laboratory, Royal Columbian Hospital, Coquitlam, BC, Canada
| | - Chi Kin Wong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Farah R Zahir
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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7
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Barber JCK, Sharp AJ, Hollox EJ, Tyson C. Copy number variation of the REXO1L1 gene cluster; euchromatic deletion variant or susceptibility factor? Eur J Hum Genet 2016; 25:8-9. [PMID: 27485411 DOI: 10.1038/ejhg.2016.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- John C K Barber
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, NY, USA
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Christine Tyson
- Department of Pathology, Cytogenetics Laboratory, Royal Columbian Hospital, New Westminster, British Columbia, Canada
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8
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Hitchcock E, Patankar JV, Tyson C, Hrynchak M, Hayden MR, Gibson WT. A novel microdeletion affecting the CETP gene raises HDL-associated cholesterol levels. Clin Genet 2015; 89:495-500. [PMID: 26126777 DOI: 10.1111/cge.12633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/27/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
We describe a novel, inherited 16q13 microdeletion that removes cholesteryl ester transfer protein (CETP) and several nearby genes. The proband was originally referred for severe childhood-onset obesity and moderate developmental delay, but his fasting lipid profile revealed relatively high levels of high density lipoprotein cholesterol (HDL-C) and relatively low levels of low density lipoprotein cholesterol (LDL-C) for age, despite his obesity. Testing of first-degree relatives identified two other microdeletion carriers. Functional assays in affected individuals showed decreased CETP mRNA expression and enzymatic activity. This microdeletion may or may not be pathogenic for obesity and developmental delay, but based on the lipid profile, the functional studies, and the phenotype of other patients with loss-of-function mutations of CETP, we believe this microdeletion to be antipathogenic for cardiovascular disease.
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Affiliation(s)
- E Hitchcock
- Child and Family Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - J V Patankar
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - C Tyson
- Cytogenetic Laboratory, Royal Columbian Hospital, New Westminster, Canada
| | - M Hrynchak
- Cytogenetic Laboratory, Royal Columbian Hospital, New Westminster, Canada
| | - M R Hayden
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - W T Gibson
- Child and Family Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Tyson C, McAndrew C, Tuma PL, Pegg I, Sarkar A. Automated nonparametric method for detection of step-like features in biological data sets. Cytometry A 2015; 87:393-404. [PMID: 25652364 DOI: 10.1002/cyto.a.22631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 12/19/2014] [Accepted: 12/28/2014] [Indexed: 11/06/2022]
Abstract
Experimental data from single-molecule DNA-protein experiments, such as experiments using optical traps or magnetic tweezers, typically contain steps, plateaus, or dwell regions that are obscured by thermal and other noise sources. We present a nonparametric method for detecting step-like features in noisy biological data sets. Our algorithm does not assume that the steps can be modeled as Heaviside functions or any particular parametric form. No assumptions about the noise source, such as whether the noise is Gaussian or colored, are made either. Instead, for detection of plateaus, the algorithm uses the novel method of analyzing a probability distribution function of the data values. The vast majority of previously published methods for step detection rely on statistical fitting of step functions with the flat segments linked by vertical segments. Our approach is intended for use on data which cannot be modelled as a series of step functions but applies to step functions as a special case. These type of data traces have, so far, been difficult to characterize effectively. We examine the performance of the algorithm through systematic simulation studies and illustrate the use of our algorithm to analyze single molecule DNA-protein micromanipulation experiments carried out by our laboratory. The simulation results and experimental validation suggest that our method is very robust, avoids overfitting, and functions effectively in the presence of noise sources characteristic of single molecule experiments.
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Affiliation(s)
- C Tyson
- Department of Biomedical Engineering, Catholic University of America, Washington, DC, 20064; Vitreous State Laboratory, Catholic University of America, Washington, DC, 20064
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Gerrie AS, Huang SJT, Bruyere H, Dalal C, Hrynchak M, Karsan A, Ramadan KM, Smith AC, Tyson C, Toze CL, Gillan TL. Population-based characterization of the genetic landscape of chronic lymphocytic leukemia patients referred for cytogenetic testing in British Columbia, Canada: the role of provincial laboratory standardization. Cancer Genet 2014; 207:316-25. [PMID: 25441686 DOI: 10.1016/j.cancergen.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 08/14/2014] [Accepted: 08/21/2014] [Indexed: 01/23/2023]
Abstract
Detection of recurrent chromosome abnormalities by fluorescence in situ hybridization (FISH) is an essential component of care in chronic lymphocytic leukemia (CLL) patients. In the province of British Columbia (BC), Canada, population 4.6 million, CLL patients receive uniform evaluation and therapy with FISH testing performed in three jurisdictions. The aims of this study were to (i) validate CLL-FISH testing among the BC cytogenetic laboratories to ensure standardization of results and (ii) characterize population-level CLL-FISH abnormalities by pooling provincial data. From 2004 to 2011, 585 consecutive patients underwent pretreatment CLL-FISH testing at laboratory A (50.1%), laboratory B (32.3%), or laboratory C (17.6%). For validation purposes, 26 CLL-FISH abnormalities were tested by each laboratory's protocol, with 91% result concordance. Discordant results involved percent abnormalities at or near cutoff values; therefore, a 10% universal cutoff was established when pooling results. Applying the universal cutoff to the provincial cohort, CLL-FISH abnormalities were detected in 74.9%: 54.9% 13q-, 18.8% +12, 8.5% 11q-, and 7.7% 17p-. In this large population-based cohort of patients referred for CLL-FISH testing, frequencies of abnormalities detected by FISH analysis were highly consistent with those reported in single-institution and clinical trial populations. Provinces or districts that work together to care for CLL patients can effectively pool data with appropriate laboratory validation to ensure standardization of results.
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Affiliation(s)
- Alina S Gerrie
- Leukemia/BMT Program of BC, Vancouver General Hospital and British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Steven J T Huang
- Leukemia/BMT Program of BC, Vancouver General Hospital and British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada; Pathology and Laboratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, Canada
| | - Helene Bruyere
- Pathology and Laboratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, Canada
| | - Chinmay Dalal
- Leukemia/BMT Program of BC, Vancouver General Hospital and British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Monica Hrynchak
- Cytogenetics Laboratory, Royal Columbian Hospital, New Westminster, Canada
| | - Aly Karsan
- Cancer Genetics Laboratory, Pathology and Laboratory Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Khaled M Ramadan
- Division of Hematology, St. Paul's Hospital, University of British Columbia, Vancouver, Canada
| | - Adam C Smith
- Cancer Genetics Laboratory, Pathology and Laboratory Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada; Instituto de Pesquisa Pelé Pequeno Princípe, Curitiba, Brazil
| | - Christine Tyson
- Cytogenetics Laboratory, Royal Columbian Hospital, New Westminster, Canada
| | - Cynthia L Toze
- Leukemia/BMT Program of BC, Vancouver General Hospital and British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Tanya L Gillan
- Pathology and Laboratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, Canada.
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Wang P, Carrion P, Qiao Y, Tyson C, Hrynchak M, Calli K, Lopez-Rangel E, Andrieux J, Delobel B, Duban-Bedu B, Thuresson AC, Annerén G, Liu X, Rajcan-Separovic E, Suzanne Lewis ME. Genotype-phenotype analysis of 18q12.1-q12.2 copy number variation in autism. Eur J Med Genet 2013; 56:420-5. [PMID: 23727450 DOI: 10.1016/j.ejmg.2013.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/14/2013] [Indexed: 01/18/2023]
Abstract
Autism Spectrum Disorders (ASD) are complex neurodevelopmental conditions characterized by delays in social interactions and communication as well as displays of restrictive/repetitive interests. DNA copy number variants have been identified as a genomic susceptibility factor in ASDs and imply significant genetic heterogeneity. We report a 7-year-old female with ADOS-G and ADI-R confirmed autistic disorder harbouring a de novo 4 Mb duplication (18q12.1). Our subject displays severely deficient expressive language, stereotypic and repetitive behaviours, mild intellectual disability (ID), focal epilepsy, short stature and absence of significant dysmorphic features. Search of the PubMed literature and DECIPHER database identified 4 additional cases involving 18q12.1 associated with autism and/or ID that overlap our case: one duplication, two deletions and one balanced translocation. Notably, autism and ID are seen with genomic gain or loss at 18q12.1, plus epilepsy and short stature in duplication cases, and hypotonia and tall stature in deletion cases. No consistent dysmorphic features were noted amongst the reviewed cases. We review prospective ASD/ID candidate genes integral to 18q12.1, including those coding for the desmocollin/desmoglein cluster, ring finger proteins 125 and 138, trafficking protein particle complex 8 and dystrobrevin-alpha. The collective clinical and molecular features common to microduplication 18q12.1 suggest that dosage-sensitive, position or contiguous gene effects may be associated in the etiopathogenesis of this autism-ID-epilepsy syndrome.
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Affiliation(s)
- Peter Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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12
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Qiao Y, Tyson C, Hrynchak M, Lopez-Rangel E, Hildebrand J, Martell S, Fawcett C, Kasmara L, Calli K, Harvard C, Liu X, Holden JJA, Lewis SME, Rajcan-Separovic E. Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability. Clin Genet 2012; 83:145-54. [PMID: 22369279 DOI: 10.1111/j.1399-0004.2012.01860.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Higher resolution whole-genome arrays facilitate the identification of smaller copy number variations (CNVs) and their integral genes contributing to autism and/or intellectual disability (ASD/ID). Our study describes the use of one of the highest resolution arrays, the Affymetrix(®) Cytogenetics 2.7M array, coupled with quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF) for detection and validation of small CNVs. We studied 82 subjects with ASD and ID in total (30 in the validation and 52 in the application cohort) and detected putatively pathogenic CNVs in 6/52 cases from the application cohort. This included a 130-kb maternal duplication spanning exons 64-79 of the DMD gene which was found in a 3-year-old boy manifesting autism and mild neuromotor delays. Other pathogenic CNVs involved 4p14, 12q24.31, 14q32.31, 15q13.2-13.3, and 17p13.3. We established the optimal experimental conditions which, when applied to select small CNVs for QMPSF confirmation, reduced the false positive rate from 60% to 25%. Our work suggests that selection of small CNVs based on the function of integral genes, followed by review of array experimental parameters resulting in highest confirmation rate using multiplex PCR, may enhance the usefulness of higher resolution platforms for ASD and ID gene discovery.
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Affiliation(s)
- Y Qiao
- BC Child and Family Research Institute, Vancouver, BC, Canada
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13
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Harvard C, Strong E, Mercier E, Colnaghi R, Alcantara D, Chow E, Martell S, Tyson C, Hrynchak M, McGillivray B, Hamilton S, Marles S, Mhanni A, Dawson AJ, Pavlidis P, Qiao Y, Holden JJ, Lewis SME, O'Driscoll M, Rajcan-Separovic E. Understanding the impact of 1q21.1 copy number variant. Orphanet J Rare Dis 2011; 6:54. [PMID: 21824431 PMCID: PMC3180300 DOI: 10.1186/1750-1172-6-54] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [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: 04/10/2011] [Accepted: 08/08/2011] [Indexed: 01/10/2023] Open
Abstract
Background 1q21.1 Copy Number Variant (CNV) is associated with a highly variable phenotype ranging from congenital anomalies, learning deficits/intellectual disability (ID), to a normal phenotype. Hence, the clinical significance of this CNV can be difficult to evaluate. Here we described the consequences of the 1q21.1 CNV on genome-wide gene expression and function of selected candidate genes within 1q21.1 using cell lines from clinically well described subjects. Methods and Results Eight subjects from 3 families were included in the study: six with a 1q21.1 deletion and two with a 1q21.1 duplication. High resolution Affymetrix 2.7M array was used to refine the 1q21.1 CNV breakpoints and exclude the presence of secondary CNVs of pathogenic relevance. Whole genome expression profiling, studied in lymphoblast cell lines (LBCs) from 5 subjects, showed enrichment of genes from 1q21.1 in the top 100 genes ranked based on correlation of expression with 1q21.1 copy number. The function of two top genes from 1q21.1, CHD1L/ALC1 and PRKAB2, was studied in detail in LBCs from a deletion and a duplication carrier. CHD1L/ALC1 is an enzyme with a role in chromatin modification and DNA damage response while PRKAB2 is a member of the AMP kinase complex, which senses and maintains systemic and cellular energy balance. The protein levels for CHD1L/ALC1 and PRKAB2 were changed in concordance with their copy number in both LBCs. A defect in chromatin remodeling was documented based on impaired decatenation (chromatid untangling) checkpoint (DCC) in both LBCs. This defect, reproduced by CHD1L/ALC1 siRNA, identifies a new role of CHD1L/ALC1 in DCC. Both LBCs also showed elevated levels of micronuclei following treatment with a Topoisomerase II inhibitor suggesting increased DNA breaks. AMP kinase function, specifically in the deletion containing LBCs, was attenuated. Conclusion Our studies are unique as they show for the first time that the 1q21.1 CNV not only causes changes in the expression of its key integral genes, associated with changes at the protein level, but also results in changes in their known function, in the case of AMPK, and newly identified function such as DCC activation in the case of CHD1L/ALC1. Our results support the use of patient lymphoblasts for dissecting the functional sequelae of genes integral to CNVs in carrier cell lines, ultimately enhancing understanding of biological processes which may contribute to the clinical phenotype.
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Affiliation(s)
- Chansonette Harvard
- Child and Family Research Institute, Molecular Cytogenetics and Array Laboratory, 950 West 28th Avenue, Vancouver, BC, Canada
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Rajcan-Separovic E, Diego-Alvarez D, Robinson WP, Tyson C, Qiao Y, Harvard C, Fawcett C, Kalousek D, Philipp T, Somerville MJ, Stephenson MD. Identification of copy number variants in miscarriages from couples with idiopathic recurrent pregnancy loss. Hum Reprod 2010; 25:2913-22. [PMID: 20847186 DOI: 10.1093/humrep/deq202] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Recurrent pregnancy loss (RPL), defined as two or more miscarriages, affects 3-5% of couples trying to establish a family. Despite extensive evaluation, no factor is identified in ∼40% of cases. In this study, we investigated the possibility that submicroscopic chromosomal changes, not detectable by conventional cytogenetic analysis, exist in miscarriages with normal karyotypes (46,XY or 46,XX) from couples with idiopathic RPL. METHODS Array comparative genomic hybridization (array-CGH) was used to assess for DNA copy number variants (CNVs) in 26 miscarriages with normal karyotypes. Parental array-CGH analysis was performed to determine if miscarriage CNVs were de novo or inherited. RESULTS There were 11 unique (previously not described) CNVs, all inherited, identified in 13 miscarriages from 8 couples. The maternal origin of two CNVs was of interest as they involved the imprinted genes TIMP2 and CTNNA3, which are only normally expressed from the maternal copy in the placenta. Two additional cohorts, consisting of 282 women with recurrent miscarriage (RM) and 61 fertile women, were screened for these two CNVs using a Quantitative Multiplex Fluorescent PCR of Short Fragments assay. One woman with RM, but none of the fertile women, carried the CTNNA3-associated CNV. CONCLUSIONS This preliminary study shows that array-CGH is useful for detecting CNVs in cases of RPL. Further investigations of CNVs, particularly those involving genes that are imprinted in placenta, in women with RPL could be worthwhile.
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Affiliation(s)
- E Rajcan-Separovic
- Department of Pathology and Lab Medicine, University of British Columbia, Vancouver, BC, Canada.
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Qiao Y, Harvard C, Tyson C, Liu X, Fawcett C, Pavlidis P, Holden JJA, Lewis MES, Rajcan-Separovic E. Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics. Hum Genet 2010; 128:179-94. [PMID: 20512354 DOI: 10.1007/s00439-010-0837-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 05/09/2010] [Indexed: 12/20/2022]
Abstract
Array CGH enables the detection of pathogenic copy number variants (CNVs) in 5-15% of individuals with intellectual disability (ID), making it a promising tool for uncovering ID candidate genes. However, most CNVs encompass multiple genes, making it difficult to identify key disease gene(s) underlying ID etiology. Using array CGH we identified 47 previously unreported unique CNVs in 45/255 probands. We prioritized ID candidate genes using five bioinformatic gene prioritization web tools. Gene priority lists were created by comparing integral genes from each CNV from our ID cohort with sets of training genes specific either to ID or randomly selected. Our findings suggest that different training sets alter gene prioritization only moderately; however, only the ID gene training set resulted in significant enrichment of genes with nervous system function (19%) in prioritized versus non-prioritized genes from the same de novo CNVs (7%, p < 0.05). This enrichment further increased to 31% when the five web tools were used in concert and included genes within mitogen-activated protein kinase (MAPK) and neuroactive ligand-receptor interaction pathways. Gene prioritization web tools enrich for genes with relevant function in ID and more readily facilitate the selection of ID candidate genes for functional studies, particularly for large CNVs.
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Affiliation(s)
- Y Qiao
- Department of Pathology (Cytogenetics), Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC, V5Z 4H4, Canada
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Rajcan-Separovic E, Qiao Y, Tyson C, Harvard C, Fawcett C, Kalousek D, Stephenson M, Philipp T. Genomic changes detected by array CGH in human embryos with developmental defects. Mol Hum Reprod 2009; 16:125-34. [PMID: 19778950 DOI: 10.1093/molehr/gap083] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Developmental abnormalities of human embryos can be visualized in utero using embryoscopy. Our previous embryoscopic and genetic evaluations detected developmental abnormalities in the majority of both euploid (74%) and aneuploid or polyploid (90%) miscarriages. Since we found the pattern of morphological changes to be similar in euploid and non-euploid embryos, we proposed that lethal submicroscopic changes, not detected by standard chromosome testing, may be responsible for miscarriage of euploid embryos. Whole genome oligo and bacterial artificial chromosome array comparative genome hybridization (CGH) was used to screen for submicroscopic chromosomal changes (DNA copy number variants or CNVs) in 17 euploid embryonic miscarriages, with a range of developmental abnormalities documented by embryoscopy. The CNV breakpoints were refined using a custom array (Agilent) with high resolution coverage of the CNVs. Six unique CNVs, previously not reported, were identified in 5 of the 17 embryos (29% of all cases or 50% of cases studied with higher resolution arrays). All six unique CNVs were <250 kb in size. On the basis of parental array CGH analysis, a de novo origin of a CNV was determined for one embryo (at 13q32.1) and suspected for another (at 10p15.3). Three CNVs, at Xq28, 1q25.3 and 7p14.3, were inherited and a CNV at 17p13.1 was of unknown origin. The genes contained within these unique CNVs will be discussed, with specific reference to rearrangements of syntaxin and tryptophan-aspartic acid (WD) repeat genes. Our report describes for the first time, de novo and inherited unique CNVs in euploid human embryos with specific developmental defects.
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Affiliation(s)
- E Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, BC, Canada, V5Z 4H4.
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Tyson C, Dawson A, Bal S, Tomiuk M, Anderson T, Tucker D, Riordan D, Chudoba I, Morash B, Mhanni A, Chudley A, McGillivray B, Parslow M, Rappold G, Roeth R, Fawcett C, Qiao Y, Harvard C, Rajcan-Separovic E. Molecular cytogenetic investigation of two patients with Y chromosome rearrangements and intellectual disability. Am J Med Genet A 2009; 149A:490-5. [DOI: 10.1002/ajmg.a.32535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Tyson C, Qiao Y, Harvard C, Liu X, Bernier FP, McGillivray B, Farrell SA, Arbour L, Chudley AE, Clarke L, Gibson W, Dyack S, McLeod R, Costa T, Vanallen MI, Yong SL, Graham GE, Macleod P, Patel MS, Hurlburt J, Holden JJ, Lewis SM, Rajcan-Separovic E. Submicroscopic deletions of 11q24-25 in individuals without Jacobsen syndrome: re-examination of the critical region by high-resolution array-CGH. Mol Cytogenet 2008; 1:23. [PMID: 19000322 PMCID: PMC2648978 DOI: 10.1186/1755-8166-1-23] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [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: 06/12/2008] [Accepted: 11/11/2008] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Jacobsen syndrome is a rare contiguous gene disorder that results from a terminal deletion of the long arm of chromosome 11. It is typically characterized by intellectual disability, a variety of physical anomalies and a distinctive facial appearance. The 11q deletion has traditionally been identified by routine chromosome analysis. Array-based comparative genomic hybridization (array-CGH) has offered new opportunities to identify and refine chromosomal abnormalities in regions known to be associated with clinical syndromes. RESULTS Using the 1 Mb BAC array (Spectral Genomics), we screened 70 chromosomally normal children with idiopathic intellectual disability (ID) and congenital abnormalities, and identified five cases with submicroscopic abnormalities believed to contribute to their phenotypes. Here, we provide detailed molecular cytogenetic descriptions and clinical presentation of two unrelated subjects with de novo submicroscopic deletions within chromosome bands 11q24-25. In subject 1 the chromosome rearrangement consisted of a 6.18 Mb deletion (from 128.25-134.43 Mb) and an adjacent 5.04 Mb duplication (from 123.15-128.19 Mb), while in subject 2, a 4.74 Mb interstitial deletion was found (from 124.29-129.03 Mb). Higher resolution array analysis (385 K Nimblegen) was used to refine all breakpoints. Deletions of the 11q24-25 region are known to be associated with Jacobsen syndrome (JBS: OMIM 147791). However, neither of the subjects had the typical features of JBS (trigonocephaly, platelet disorder, heart abnormalities). Both subjects had ID, dysmorphic features and additional phenotypic abnormalities: subject 1 had a kidney abnormality, bilateral preauricular pits, pectus excavatum, mild to moderate conductive hearing loss and behavioral concerns; subject 2 had macrocephaly, an abnormal MRI with delayed myelination, fifth finger shortening and squaring of all fingertips, and sensorineural hearing loss. CONCLUSION Two individuals with ID who did not have the typical clinical features of Jacobsen syndrome were found to have deletions within the JBS region at 11q24-25. Their rearrangements facilitate the refinement of the JBS critical region and suggest that a) deletion of at least 3 of the 4 platelet function critical genes (ETS-1, FLI-1 and NFRKB and JAM3) is necessary for thrombocytopenia; b) one of the critical regions for heart abnormalities (conotruncal heart defects) may lie within 129.03 - 130.6 Mb; c) deletions of KCNJ1 and ADAMTS15 may contribute to the renal anomalies in Jacobsen Syndrome; d) the critical region for MRI abnormalities involves a region from 124.6 - 129.03 Mb. Our results reiterate the benefits of array-CGH for description of new phenotype/genotype associations and refinement of previously established ones.
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Affiliation(s)
- Christine Tyson
- Department of Pathology and Laboratory Medicine and Child and Family Research Institute (CFRI), UBC, Vancouver, BC, Canada.
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Tyson C, Harvard C, Locker R, Friedman JM, Langlois S, Lewis MES, Van Allen M, Somerville M, Arbour L, Clarke L, McGilivray B, Yong SL, Siegel-Bartel J, Rajcan-Separovic E. Submicroscopic deletions and duplications in individuals with intellectual disability detected by array-CGH. Am J Med Genet A 2006; 139:173-85. [PMID: 16283669 DOI: 10.1002/ajmg.a.31015] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intellectual disability (ID) affects about 3% of the population (IQ < 70), and in about 40% of moderate (IQ 35-49) to severe ID (IQ < 34), and 70% of cases of mild ID (IQ 50-70), the etiology of the disease remains unknown. It has long been suspected that chromosomal gains and losses undetectable by routine cytogenetic analysis (i.e., less than 5-10 Mb in size) are implicated in ID of unknown etiology. Array CGH has recently been used to perform a genome-wide screen for submicroscopic gains and losses in individuals with a normal karyotype but with features suggestive of a chromosome abnormality. In two recent studies, the technique has demonstrated a approximately 15% detection rate for de novo copy number changes of individual clones or groups of clones. Here, we describe a study of 22 individuals with mild to moderate ID and nonsyndromic pattern of dysmorphic features suspicious of an underlying chromosome abnormality, using the 3 Mb and 1 Mb commercial arrays (Spectral Genomics). Deletions and duplications of 16 clones, previously described to show copy number variability in normal individuals [Iafrate et al., 2004; Lapierre et al., 2004; Schoumans et al., 2004; Vermeesch et al., 2005] were seen in 21/22 subjects and were considered polymorphisms. In addition, three subjects showed submicroscopic deletions and duplications not previously reported as normal variants. Two of these submicroscopic changes were of de novo origin (microdeletions at 7q36.3 and a microduplication at 11q12.3-13.1) and one was of unknown origin as parental testing of origin could not be performed (microduplication of Xp22.3). The clinical description of the three subjects with submicroscopic chromosomal changes at 7q36.3, 11q12.3-13.1, Xp22.3 is provided.
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Affiliation(s)
- C Tyson
- Department of Pathology, University of British Columbia, Vancouver, Canada
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20
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Tyson C, McGillivray B, Chijiwa C, Rajcan-Separovic E. Elucidation of a cryptic interstitial 7q31.3 deletion in a patient with a language disorder and mild mental retardation by array-CGH. ACTA ACUST UNITED AC 2004; 129A:254-60. [PMID: 15326624 DOI: 10.1002/ajmg.a.30245] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report on a 14-year-old boy who presented with bilateral cleft lip and palate, hearing loss, a language processing disorder, and mild mental retardation (MR). G-banded chromosome analysis of the patient and his family revealed he carried an apparently balanced de novo complex translocation involving chromosomes 5, 6, and 7. Chromosomal comparative genomic hybridization (CGH) was performed to investigate the possibility of any genomic imbalance as a result of the complex rearrangement. No abnormality was detected at any of the translocation breakpoint regions (5p13.2, 6p24, 7q21.1, and 7q21.3), nor was there any other imbalance which fell inside our significance level of 0.8-1.2. Array-CGH analysis was initiated to perform a higher resolution search for gains and losses, and revealed a deletion of two adjacent clones, CTB-133K23 and RP11-112P4, mapping to 7q31.3, which are 4.4 Mb apart. Fluorescence in situ hybridization (FISH) using these two clones confirmed the deletion. 7q31 has frequently been implicated in the search for genes involved in speech and language disorders. The specific 7q31.3 region deleted in our patient has significant overlap with some such areas of the genome. These findings are, therefore, of value in identifying genes involved in the speech and language phenotypes. This study has shown the importance of array-CGH in investigating patients who have clinical features suggestive of a chromosome abnormality, but with apparently balanced chromosome rearrangements. It has demonstrated that the array-CGH technique provides a much greater insight into submicroscopic chromosome imbalances than conventional cytogenetic techniques.
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Affiliation(s)
- Christine Tyson
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
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Hamner MB, Frueh BC, Ulmer HG, Huber MG, Twomey TJ, Tyson C, Arana GW. Psychotic features in chronic posttraumatic stress disorder and schizophrenia: comparative severity. J Nerv Ment Dis 2000; 188:217-21. [PMID: 10789998 DOI: 10.1097/00005053-200004000-00004] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Psychotic features are frequent in combat veterans with chronic posttraumatic stress disorder (PTSD), may correlate with severity of PTSD symptoms, and may reflect a distinct subtype of the disorder. These psychotic features include auditory and visual hallucinations and delusional thinking that is usually paranoid in nature. Psychotic features may be under-recognized in chronic PTSD because patients are reluctant to report these symptoms and because they may not have overt changes in affect or bizarre delusions characteristic of other psychoses, e.g., schizophrenia. To further assess these phenomena, we compared clinical ratings on the Positive and Negative Syndrome Scale (PANSS) and other assessments, including the Clinical Global Impression Scale and the Structured Clinical Interview with Psychotic Screen, in veterans meeting DSM-IV criteria for chronic PTSD with well-defined comorbid psychotic features (N = 40) or chronic schizophrenia (N = 40). The patients with schizophrenia had modestly higher composite PANSS scores and positive symptom scores although average scores in both groups were moderate to severe in intensity. Negative symptom and general psychopathology subscale scores were comparable in both groups. Regarding specific positive symptoms, hallucinations were comparable between groups in severity; however, schizophrenia patients had slightly more intense delusions and conceptual disorganization. These data further validate the occurrence of positive as well as negative symptoms of psychosis in chronic PTSD in a range of severity that may approach that of patients with schizophrenia. Although meeting DSM-IV criteria for two different major psychiatric disorders, these two patient populations were remarkably similar with respect to not only positive but also negative symptoms.
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Affiliation(s)
- M B Hamner
- Ralph H. Johnson VA Medical Center, Department of Psychiatry, Medical University of South Carolina, Charleston 29401, USA
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22
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Thomas S, Tyson C. Multimedia: a new look at HIM classroom instruction. J AHIMA 1998; 69:67-9. [PMID: 10180613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- S Thomas
- Houston Community College System, TX, USA
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Reigh G, McMahon H, Ishizaki M, Ohara T, Shimane K, Esumi Y, Green C, Tyson C, Ninomiya S. Cytochrome P450 species involved in the metabolism of quinoline. Carcinogenesis 1996; 17:1989-96. [PMID: 8824525 DOI: 10.1093/carcin/17.9.1989] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Quinoline is a hepatocarcinogen in rats and mice and a well-known mutagen in bacteria after incubation with rat liver microsomes. The specific cytochrome P450 enzymes involved in quinoline metabolism in human and rat liver microsomes were determined using cDNA-expressed cytochrome P450s, correlations with specific cytochrome P450-linked monooxygenase activities in human liver microsomes and inhibition by specific inhibitors and antibodies. CYP2A6 is the principal cytochrome P450 involved in the formation of quinoline-1-oxide in human liver microsomes (correlation coefficient r = 0.95), but is formed in only minute quantities in rat liver microsomes. CYP2E1 is the principal cytochrome P450 involved in the formation of 3-hydroxyquinoline (r = 0.93) in human liver microsomes and is involved in the formation in rat liver microsomes. A high correlation coefficient (r = 0.91) between CYP2A6 activity and quinoline-5,6-diol formation in human liver microsomes was observed, but this most likely reflects the involvement of CYP2A6 in the formation of quinoline-5,6-epoxide, from which the quinoline-5,6-diol is formed, as conversion of quinoline-5,6-epoxide to quinoline-5,6-diol on incubation of the epoxide with CYP2A6 could not be demonstrated. A cDNA-expressed human microsomal epoxide hydrolase, however, efficiently converted the epoxide to the diol and the microsomal epoxide inhibitor cyclohexene oxide inhibited quinoline-5,6-diol formation in rat liver microsomes. A preliminary kinetic analysis of quinoline metabolism in human liver microsomes was carried out and Eadie-Hofstee plots indicate that the formation of quinoline-5,6-diol is monophasic, while that of quinoline-1-oxide and 3-hydroxyquinoline is biphasic.
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Affiliation(s)
- G Reigh
- Daiichi Pure Chemicals Co. Ltd., Tokai, Ibaraki, Japan
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Skett P, Tyson C, Guillouzo A, Maier P. Report on the international workshop on the use of human in vitro liver preparations to study drug metabolism in drug development. Held at Utrecht, The Netherlands, 6-8 September 1994. Biochem Pharmacol 1995; 50:280-5. [PMID: 7632175 DOI: 10.1016/0006-2952(95)90011-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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