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Deignan JL, Gregg AR, Grody WW, Guo MH, Kearney H, Monaghan KG, Raraigh KS, Taylor J, Zepeda-Mendoza CJ, Ziats C. Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100867. [PMID: 37310422 DOI: 10.1016/j.gim.2023.100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/14/2023] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Anthony R Gregg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
| | - Wayne W Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Michael H Guo
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hutton Kearney
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | | | - Karen S Raraigh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jennifer Taylor
- American College of Medical Genetics and Genomics, Bethesda, MD
| | | | - Catherine Ziats
- Division of Genetics, Department of Pediatrics, Dell Medical School, University of Texas, Austin, TX
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2
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Deignan JL, De Castro M, Horner VL, Johnston T, Macaya D, Maleszewski JJ, Reddi HV, Tayeh MK. Points to consider in the practice of postmortem genetic testing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100017. [PMID: 36799919 DOI: 10.1016/j.gim.2023.100017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/18/2023] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA Health, Los Angeles, CA
| | - Mauricio De Castro
- DHA Genetics Reference Laboratory, Air Force Medical Genetics Center, Keesler Air Force Base, Biloxi, MS; Division of Medical Genetics, Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS
| | - Vanessa L Horner
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI; Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, WI
| | | | | | | | - Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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3
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David KL, Deignan JL. Moving toward more consistency in variant classification and clinical action. Genet Med 2023; 25:12-15. [PMID: 36399133 DOI: 10.1016/j.gim.2022.09.014] [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] [Received: 07/11/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Karen L David
- Department of Medicine, NewYork-Presbyterian Brooklyn Methodist Hospital, Brooklyn, NY.
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA
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4
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Chao EC, Astbury C, Deignan JL, Pronold M, Reddi HV, Weitzel JN. Incidental detection of acquired variants in germline genetic and genomic testing: a points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1179-1184. [PMID: 33864022 DOI: 10.1038/s41436-021-01138-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/04/2023] Open
Affiliation(s)
- Elizabeth C Chao
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA.,Ambry Genetics, Aliso Viejo, CA, USA
| | - Caroline Astbury
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Honey V Reddi
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
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5
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Fliedner A, Kirchner P, Wiesener A, van de Beek I, Waisfisz Q, van Haelst M, Scott DA, Lalani SR, Rosenfeld JA, Azamian MS, Xia F, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Noh GJ, Lippa N, Alkelai A, Aggarwal V, Agre KE, Gavrilova R, Mirzaa GM, Straussberg R, Cohen R, Horist B, Krishnamurthy V, McWalter K, Juusola J, Davis-Keppen L, Ohden L, van Slegtenhorst M, de Man SA, Ekici AB, Gregor A, van de Laar I, Zweier C, Nelson SF, Grody WW, Lee H, Deignan JL, Kang SH, Arboleda VA, Senaratne TN, Dorrani N, Dutra-Clarke MS, Kianmahd J, Hinkamp FL, Neustadt AM, Martinez-Agosto JA, Fogel BL, Quintero-Rivera F. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Am J Hum Genet 2020; 107:544-554. [PMID: 32730804 DOI: 10.1016/j.ajhg.2020.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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6
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Schmidt JL, Pizzino A, Nicholl J, Foley A, Wang Y, Rosenfeld JA, Mighion L, Bean L, da Silva C, Cho MT, Truty R, Garcia J, Speare V, Blanco K, Powis Z, Hobson GM, Kirwin S, Krock B, Lee H, Deignan JL, Westemeyer MA, Subaran RL, Thiffault I, Tsai EA, Fang T, Helman G, Vanderver A. Estimating the relative frequency of leukodystrophies and recommendations for carrier screening in the era of next-generation sequencing. Am J Med Genet A 2020; 182:1906-1912. [PMID: 32573057 DOI: 10.1002/ajmg.a.61641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/25/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 11/09/2022]
Abstract
Leukodystrophies are a heterogeneous group of heritable disorders characterized by abnormal brain white matter signal on magnetic resonance imaging (MRI) and primary involvement of the cellular components of myelin. Previous estimates suggest the incidence of leukodystrophies as a whole to be 1 in 7,000 individuals, however the frequency of specific diagnoses relative to others has not been described. Next generation sequencing approaches offer the opportunity to redefine our understanding of the relative frequency of different leukodystrophies. We assessed the relative frequency of all 30 leukodystrophies (associated with 55 genes) in more than 49,000 exomes. We identified a relatively high frequency of disorders previously thought of as very rare, including Aicardi Goutières Syndrome, TUBB4A-related leukodystrophy, Peroxisomal biogenesis disorders, POLR3-related Leukodystrophy, Vanishing White Matter, and Pelizaeus-Merzbacher Disease. Despite the relative frequency of these conditions, carrier-screening laboratories regularly test only 20 of the 55 leukodystrophy-related genes, and do not test at all, or test only one or a few, genes for some of the higher frequency disorders. Relative frequency of leukodystrophies previously considered very rare suggests these disorders may benefit from expanded carrier screening.
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Affiliation(s)
- Johanna L Schmidt
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amy Pizzino
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Allison Foley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yue Wang
- Department of Molecular & Human Genetics, Baylor College of Medicine, and Baylor Genetics Laboratories, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, and Baylor Genetics Laboratories, Houston, Texas, USA
| | | | | | | | | | | | | | | | | | - Zoe Powis
- Ambry Genetics, Aliso Viejo, California, USA
| | - Grace M Hobson
- Nemours/Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Susan Kirwin
- Nemours/Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | | | | | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | | | | | - Guy Helman
- Murdoch Children' Research Institute, The Royal Children's Hospital, Parkville, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Adeline Vanderver
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Deignan JL, Astbury C, Cutting GR, Del Gaudio D, Gregg AR, Grody WW, Monaghan KG, Richards S. CFTR variant testing: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1288-1295. [PMID: 32404922 DOI: 10.1038/s41436-020-0822-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 04/22/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 11/09/2022] Open
Abstract
Pathogenic variants in the CFTR gene are causative of classic cystic fibrosis (CF) as well as some nonclassic CF phenotypes. In 2001, CF became the first target of pan-ethnic universal carrier screening by molecular methods. The American College of Medical Genetics and Genomics (ACMG) recommended a core panel of 23 disease-causing variants as the minimal set to be included in pan-ethnic carrier screening of individuals with no family history of the disease, and these variants were usually assessed using targeted methods. The original recommendation also left open the option for laboratories to offer expanded CFTR variant panels; however, at the time, expanded CFTR variant panels were met with some controversy on the basis of the available technologies and the limited phenotypic knowledge of rare variants. Both of those aspects have now evolved, prompting this update of the ACMG technical standards for CFTR variant testing.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caroline Astbury
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Del Gaudio
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Baylor University Medical Center, Dallas, TX, USA
| | - Wayne W Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Sue Richards
- Department of Molecular and Medical Genetics, Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR, USA
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8
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Deignan JL, Chao E, Gannon JL, Greely HT, Hagman KDF, Mao R, Topper S. Points to consider when assessing relationships (or suspecting misattributed relationships) during family-based clinical genomic testing: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1285-1287. [PMID: 32404921 DOI: 10.1038/s41436-020-0821-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Jennifer L Gannon
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Henry T Greely
- Center for Law and the Biosciences, Stanford Law School, Stanford, CA, USA
| | | | - Rong Mao
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
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9
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Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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10
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Eno CC, Barton SK, Dorrani N, Cederbaum SD, Deignan JL, Grody WW. Confidential genetic testing and electronic health records: A survey of current practices among Huntington disease testing centers. Mol Genet Genomic Med 2019; 8:e1026. [PMID: 31701651 PMCID: PMC6978271 DOI: 10.1002/mgg3.1026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/17/2019] [Accepted: 09/25/2019] [Indexed: 01/03/2023] Open
Abstract
Background Clinical care teams providing presymptomatic genetic testing often employ advanced confidentiality practices for documentation and result storage. However, patient requests for increased confidentiality may be in conflict with the legal obligations of medical providers to document patient care activities in the electronic health record (EHR). Huntington disease presents a representative case study for investigating the ways centers currently balance the requirements of EHRs with the privacy demands of patients seeking presymptomatic genetic testing. Methods We surveyed 23 HD centers (53% response rate) regarding their use of the EHR for presymptomatic HD testing. Results Our survey revealed that clinical care teams and laboratories have each developed their own practices, which are cumbersome and often include EHR avoidance. We found that a majority of HD care teams record appointments in the EHR (91%), often using vague notes. Approximately half of the care teams (52%) keep presymptomatic results of out of the EHR. Conclusion As genetic knowledge grows, linking more genes to late‐onset conditions, institutions will benefit from having professional recommendations to guide development of policies for EHR documentation of presymptomatic genetic results. Policies must be sensitive to the ethical differences and patient demands for presymptomatic genetic testing compared to those undergoing confirmatory genetic testing.
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11
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Harrison SM, Dolinksy JS, Chen W, Collins CD, Das S, Deignan JL, Garber KB, Garcia J, Jarinova O, Knight Johnson AE, Koskenvuo JW, Lee H, Mao R, Mar-Heyming R, McFaddin AS, Moyer K, Nagan N, Rentas S, Santani AB, Seppälä EH, Shirts BH, Tidwell T, Topper S, Vincent LM, Vinette K, Rehm HL. Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach. Hum Mutat 2019; 39:1641-1649. [PMID: 30311378 DOI: 10.1002/humu.23643] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 05/02/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 11/09/2022]
Abstract
ClinVar provides open access to variant classifications shared from many clinical laboratories. Although most classifications are consistent across laboratories, classification differences exist. To facilitate resolution of classification differences on a large scale, clinical laboratories were encouraged to reassess outlier classifications of variants with medically significant differences (MSDs). Outliers were identified by first comparing ClinVar submissions from 41 clinical laboratories to detect variants with MSDs between the laboratories (650 variants). Next, MSDs were filtered for variants with ≥3 classifications (244 variants), of which 87.6% (213 variants) had a majority consensus in ClinVar, thus allowing for identification of outlier classifications in need of reassessment. Laboratories with outlier classifications were sent a custom report and encouraged to reassess variants. Results were returned for 204 (96%) variants, of which 62.3% (127) were resolved. Of those 127, 64.6% (82) were resolved due to reassessment prompted by this study and 35.4% (45) resolved by a previously completed reassessment. This study demonstrates a scalable approach to classification resolution and capitalizes on the value of data sharing within ClinVar. These activities will help the community move toward more consistent variant classifications, which will improve the care of patients with, or at risk for, genetic disorders.
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Affiliation(s)
- Steven M Harrison
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Wenjie Chen
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
| | - Christin D Collins
- EGL Genetics, Tucker, Georgia.,Global Laboratory Services, PerkinElmer Genomics, Branford, Connecticut
| | - Soma Das
- Department of Human Genetics, The University of Chicago, Chicago, Illinois
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | | | - John Garcia
- Invitae Corporation, San Francisco, California
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | | | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - Andrew S McFaddin
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Narasimhan Nagan
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
| | - Stefan Rentas
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Avni B Santani
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Scott Topper
- Invitae Corporation, San Francisco, California.,Color Genomics, South San Francisco, California
| | | | - Kathy Vinette
- Molecular Diagnostics Laboratory, A. I. duPont Hospital for Children, Wilmington, Delaware
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston
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12
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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Deignan JL, Chung WK, Kearney HM, Monaghan KG, Rehder CW, Chao EC. Points to consider in the reevaluation and reanalysis of genomic test results: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2019; 21:1267-1270. [PMID: 31015575 DOI: 10.1038/s41436-019-0478-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Wendy K Chung
- Departments of Medicine and Pediatrics, Columbia University, New York, NY, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Catherine W Rehder
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth C Chao
- Department of Pediatrics, University of California Irvine, Irvine, CA, USA
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14
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David KL, Best RG, Brenman LM, Bush L, Deignan JL, Flannery D, Hoffman JD, Holm I, Miller DT, O'Leary J, Pyeritz RE. Patient re-contact after revision of genomic test results: points to consider-a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2018; 21:769-771. [PMID: 30578420 DOI: 10.1038/s41436-018-0391-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karen L David
- Division of Genetics, Department of Medicine, NewYork-Presbyterian Brooklyn Methodist Hospital, Brooklyn, NY, USA.
| | - Robert G Best
- University of South Carolina School of Medicine Greenville and Greenville Health System, Greenville, SC, USA
| | - Leslie Manace Brenman
- Regional Precision Tracking and Genetics Department, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lynn Bush
- Pediatric Clinical Genetics, Columbia University Medical Center, New York, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David Flannery
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jodi D Hoffman
- Division of Genetics, Department of Pediatrics, Boston Medical Center, Boston, MA, USA
| | - Ingrid Holm
- Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Reed E Pyeritz
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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15
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Hiemenz MC, Ostrow DG, Busse TM, Buckley J, Maglinte DT, Bootwalla M, Done J, Ji J, Raca G, Ryutov A, Xu X, Zhen CJ, Conroy JM, Hazard FK, Deignan JL, Rogers BB, Treece AL, Parham DM, Gai X, Judkins AR, Triche TJ, Biegel JA. OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies. J Mol Diagn 2018; 20:765-776. [PMID: 30138724 DOI: 10.1016/j.jmoldx.2018.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/22/2018] [Accepted: 06/11/2018] [Indexed: 02/08/2023] Open
Abstract
The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.
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Affiliation(s)
- Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California.
| | - Dejerianne G Ostrow
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Tracy M Busse
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan Buckley
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Dennis T Maglinte
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moiz Bootwalla
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - James Done
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Alex Ryutov
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Xinjie Xu
- Cytogenetics and Genomic Microarray, ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Chao Jie Zhen
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Jeffrey M Conroy
- OmniSeq Inc., Buffalo, New York; Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Florette K Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Beverly B Rogers
- Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Amanda L Treece
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Denver, Colorado
| | - David M Parham
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Xiaowu Gai
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
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16
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Mullegama SV, Klein SD, Nguyen DC, Kim A, Signer R, Fox M, Dorrani N, Hendershot A, Mardach R, Suddath R, Dipple K, Vilain E, Wong DA, Deignan JL, D. Cederbaum S, Grody WW, Martinez-Agosto JA. Is it time to retire fragile X testing as a first-tier test for developmental delay, intellectual disability, and autism spectrum disorder? Genet Med 2017; 19:S1098-3600(21)04769-9. [DOI: 10.1038/gim.2017.146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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17
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O'Daniel JM, McLaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, Bowling KM, Chao EC, Chung WK, Conlin LK, Cooper GM, Das S, Deignan JL, Dorschner MO, Evans JP, Ghazani AA, Goddard KA, Gornick M, Farwell Hagman KD, Hambuch T, Hegde M, Hindorff LA, Holm IA, Jarvik GP, Knight Johnson A, Mighion L, Morra M, Plon SE, Punj S, Richards CS, Santani A, Shirts BH, Spinner NB, Tang S, Weck KE, Wolf SM, Yang Y, Rehm HL. A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories. Genet Med 2016; 19:575-582. [PMID: 27811861 PMCID: PMC5415437 DOI: 10.1038/gim.2016.152] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 05/22/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022] Open
Abstract
PURPOSE While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation and reporting of clinically significant variants. This study aimed to examine workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization. METHODS Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing, to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free text responses, later clarified with phone interviews. RESULTS Twenty-one laboratories participated. Practices highly concordant across all groups included: consent documentation, multi-person case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation, and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing or patient access to data. CONCLUSION This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas development of best practice guidelines may be helpful.
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Affiliation(s)
- Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather M McLaughlin
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Bick
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California, USA.,Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, California, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York, USA.,Department of Medicine, Columbia University, New York, New York, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Michael O Dorschner
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Arezou A Ghazani
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Katrina A Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Michele Gornick
- Department of Internal Medicine, Center for Bioethics Social Science and Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Madhuri Hegde
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gail P Jarvik
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Amy Knight Johnson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Lindsey Mighion
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | | | - Sharon E Plon
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sumit Punj
- Department of Molecular and Medical Genetics, Oregon Health &Science University, Portland, Oregon, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health &Science University, Portland, Oregon, USA
| | - Avni Santani
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, California, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Susan M Wolf
- Consortium on Law and Values in Health, Environment &the Life Sciences, Law School, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine and Baylor Miraca Genetics Laboratories, Houston, Texas, USA
| | - Heidi L Rehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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18
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Bie AS, Fernandez-Guerra P, Birkler RID, Nisemblat S, Pelnena D, Lu X, Deignan JL, Lee H, Dorrani N, Corydon TJ, Palmfeldt J, Bivina L, Azem A, Herman K, Bross P. Effects of a Mutation in the HSPE1 Gene Encoding the Mitochondrial Co-chaperonin HSP10 and Its Potential Association with a Neurological and Developmental Disorder. Front Mol Biosci 2016; 3:65. [PMID: 27774450 PMCID: PMC5053987 DOI: 10.3389/fmolb.2016.00065] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
We here report molecular investigations of a missense mutation in the HSPE1 gene encoding the HSP10 subunit of the HSP60/ HSP10 chaperonin complex that assists protein folding in the mitochondrial matrix. The mutation was identified in an infant who came to clinical attention due to infantile spasms at 3 months of age. Clinical exome sequencing revealed heterozygosity for a HSPE1 NM_002157.2:c.217C>T de novo mutation causing replacement of leucine with phenylalanine at position 73 of the HSP10 protein. This variation has never been observed in public exome sequencing databases or the literature. To evaluate whether the mutation may be disease-associated we investigated its effects by in vitro and ex vivo studies. Our in vitro studies indicated that the purified mutant protein was functional, yet its thermal stability, spontaneous refolding propensity, and resistance to proteolytic treatment were profoundly impaired. Mass spectrometric analysis of patient fibroblasts revealed barely detectable levels of HSP10-p.Leu73Phe protein resulting in an almost 2-fold decrease of the ratio of HSP10 to HSP60 subunits. Amounts of the mitochondrial superoxide dismutase SOD2, a protein whose folding is known to strongly depend on the HSP60/HSP10 complex, were decreased to approximately 20% in patient fibroblasts in spite of unchanged SOD2 transcript levels. As a likely consequence, mitochondrial superoxide levels were increased about 2-fold. Although, we cannot exclude other causative or contributing factors, our experimental data support the notion that the HSP10-p.Leu73Phe mutation could be the cause or a strong contributing factor for the disorder in the described patient.
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Affiliation(s)
- Anne S Bie
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Paula Fernandez-Guerra
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Rune I D Birkler
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Shahar Nisemblat
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Dita Pelnena
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Xinping Lu
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles Los Angeles, CA, USA
| | - Naghmeh Dorrani
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los AngelesLos Angeles, CA, USA; Department of Pediatrics, David Geffen School of Medicine at University of California, Los AngelesLos Angeles, CA, USA
| | | | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Liga Bivina
- Division of Genomic Medicine, Department of Pediatrics, UC Davis Health System Sacramento, CA, USA
| | - Abdussalam Azem
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Kristin Herman
- Division of Genomic Medicine, Department of Pediatrics, UC Davis Health System Sacramento, CA, USA
| | - Peter Bross
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
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19
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Baudhuin LM, Funke BH, Bean LH, Deignan JL, Hofherr S, Miller DT, Nagan N, Santani A, Saunders C. Classifying Germline Sequence Variants in the Era of Next-Generation Sequencing. Clin Chem 2016; 62:799-806. [PMID: 26861553 DOI: 10.1373/clinchem.2015.247874] [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] [Received: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Linnea M Baudhuin
- Associate Professor of Laboratory Medicine and Pathology, Co-director, Personalized Genomics Laboratory and Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN;
| | - Birgit H Funke
- Associate Director, Laboratory for Molecular Medicine at Partners HealthCare/Personalized Medicine, Cambridge, MA, Associate Professor of Pathology, Harvard Medical School/Massachusetts General Hospital, Boston, MA
| | - Lora H Bean
- Senior Director, Molecular Laboratory, Emory Genetics Laboratory, Decatur, GA
| | - Joshua L Deignan
- Associate Director, UCLA Molecular Diagnostics Laboratories, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sean Hofherr
- Director, Molecular Diagnostics and Biochemical Genetics, Division of Laboratory Medicine, Children's National Medical Center, Washington, DC
| | - David T Miller
- Medical Director, Claritas Genomics, Cambridge, MA, Medical Geneticist, Division of Genetics and Genomics, Boston Children's Hospital, Associate Professor of Pediatrics, Harvard Medical School, Boston, MA
| | - Narasimhan Nagan
- Director, Integrated Genetics, Laboratory Corporation of America® Holdings, Westborough, MA
| | - Avni Santani
- Director, Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, Assistant Professor of Clinical Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Carol Saunders
- Director, Molecular Genetics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO
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20
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Abstract
This unit describes a recommended approach to identifying causal genetic variants in an individual suspected of having cystic fibrosis. An introduction to the genetics and clinical presentation of cystic fibrosis is initially presented, followed by a description of the two main strategies used in the molecular diagnosis of cystic fibrosis: (1) an initial targeted variant panel used to detect only the most common cystic fibrosis-causing variants in the CFTR gene, and (2) sequencing of the entire coding region of the CFTR gene to detect additional rare causal CFTR variants. Finally, the unit concludes with a discussion regarding the analytic and clinical validity of these approaches.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Divisions of Medical Genetics and Molecular Diagnostics, Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
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21
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Babkina N, Deignan JL, Lee H, Vilain E, Sankar R, Giurgea I, Mowat D, Graham JM. Early Infantile Epileptic Encephalopathy with a de novo variant in ZEB2 identified by exome sequencing. Eur J Med Genet 2015; 59:70-4. [PMID: 26721324 DOI: 10.1016/j.ejmg.2015.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 11/08/2015] [Accepted: 12/19/2015] [Indexed: 12/12/2022]
Abstract
Early Infantile Epileptic Encephalopathy (EIEE) presents shortly after birth with frequent, severe seizures, a burst-suppression EEG pattern, and progressive disturbance of cerebral function. We present a case of EIEE associated with a de novo missense variant in ZEB2. Heterozygous truncating mutations or deletions in ZEB2 are known to cause Mowat-Wilson syndrome (MWS), which is characterized by seizures with onset in the second year of life, distinctive dysmorphic facial features and malformations that were absent in this patient. This unique case expands the range of phenotypes associated with variants in ZEB2 and indicates that this gene should be included in the molecular investigation of EIEE cases.
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Affiliation(s)
- Natalia Babkina
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Raman Sankar
- Department of Neurology, Pediatrics and Children's Discovery and Innovation Institute at Mattel Children's Hospital, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Irina Giurgea
- Service de Biochimie Génétique, INSERM U955 Equipe 11, Hôpital Henri Mondor, 94000 Créteil, France
| | - David Mowat
- Department of Medical Genetics, Sydney Children's Hospital, School of Women's and Children's Health, University of New South Wales, Australia
| | - John M Graham
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
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22
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Kansal R, Li X, Shen J, Samuel D, Laningham F, Lee H, Panigrahi GB, Shuen A, Kantarci S, Dorrani N, Reiss J, Shintaku P, Deignan JL, Strom SP, Pearson CE, Vilain E, Grody WW. An infant withMLH3variants,FOXG1-duplication and multiple, benign cranial and spinal tumors: A clinical exome sequencing study. Genes Chromosomes Cancer 2015; 55:131-42. [DOI: 10.1002/gcc.22319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 12/27/2022] Open
Affiliation(s)
- Rina Kansal
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Xinmin Li
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Joseph Shen
- Medical Genetics and Metabolism; Valley Children's Hospital; Madera CA 93636
| | - David Samuel
- Hematology/Oncology, Valley Children's Hospital; Madera CA 93636
| | - Fred Laningham
- Department of Radiology; Valley Children's Hospital; Madera CA 93636
| | - Hane Lee
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Gagan B. Panigrahi
- Program of Genetics & Genome Biology; The Hospital for Sick Children, Peter Gilgan Center for Research and Learning; Toronto Ontario MSG 0A4 Canada
| | - Andrew Shuen
- Program of Genetics & Genome Biology; The Hospital for Sick Children, Peter Gilgan Center for Research and Learning; Toronto Ontario MSG 0A4 Canada
- Program of Molecular Genetics, University of Toronto; Toronto, Ontario M5S 1A1 Canada
| | - Sibel Kantarci
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Naghmeh Dorrani
- Pediatrics, University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Jean Reiss
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Peter Shintaku
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Joshua L. Deignan
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Samuel P. Strom
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Christopher E. Pearson
- Program of Genetics & Genome Biology; The Hospital for Sick Children, Peter Gilgan Center for Research and Learning; Toronto Ontario MSG 0A4 Canada
- Program of Molecular Genetics, University of Toronto; Toronto, Ontario M5S 1A1 Canada
| | - Eric Vilain
- Pediatrics, University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
- Human Genetics, University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
| | - Wayne W. Grody
- Pathology and Laboratory Medicine; University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
- Pediatrics, University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
- Human Genetics, University of California at Los Angeles, David Geffen School of Medicine; Los Angeles CA 90095
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23
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Ji J, Lee H, Argiropoulos B, Dorrani N, Mann J, Martinez-Agosto JA, Gomez-Ospina N, Gallant N, Bernstein JA, Hudgins L, Slattery L, Isidor B, Le Caignec C, David A, Obersztyn E, Wiśniowiecka-Kowalnik B, Fox M, Deignan JL, Vilain E, Hendricks E, Horton Harr M, Noon SE, Jackson JR, Wilkens A, Mirzaa G, Salamon N, Abramson J, Zackai EH, Krantz I, Innes AM, Nelson SF, Grody WW, Quintero-Rivera F. DYRK1A haploinsufficiency causes a new recognizable syndrome with microcephaly, intellectual disability, speech impairment, and distinct facies. Eur J Hum Genet 2015; 23:1473-81. [PMID: 25944381 PMCID: PMC4613469 DOI: 10.1038/ejhg.2015.71] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 01/24/2023] Open
Abstract
Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A (DYRK1A ) is a highly conserved gene located in the Down syndrome critical region. It has an important role in early development and regulation of neuronal proliferation. Microdeletions of chromosome 21q22.12q22.3 that include DYRK1A (21q22.13) are rare and only a few pathogenic single-nucleotide variants (SNVs) in the DYRK1A gene have been described, so as of yet, the landscape of DYRK1A disruptions and their associated phenotype has not been fully explored. We have identified 14 individuals with de novo heterozygous variants of DYRK1A; five with microdeletions, three with small insertions or deletions (INDELs) and six with deleterious SNVs. The analysis of our cohort and comparison with published cases reveals that phenotypes are consistent among individuals with the 21q22.12q22.3 microdeletion and those with translocation, SNVs, or INDELs within DYRK1A. All individuals shared congenital microcephaly at birth, intellectual disability, developmental delay, severe speech impairment, short stature, and distinct facial features. The severity of the microcephaly varied from -2 SD to -5 SD. Seizures, structural brain abnormalities, eye defects, ataxia/broad-based gait, intrauterine growth restriction, minor skeletal abnormalities, and feeding difficulties were present in two-thirds of all affected individuals. Our study demonstrates that haploinsufficiency of DYRK1A results in a new recognizable syndrome, which should be considered in individuals with Angelman syndrome-like features and distinct facial features. Our report represents the largest cohort of individuals with DYRK1A disruptions to date, and is the first attempt to define consistent genotype-phenotype correlations among subjects with 21q22.13 microdeletions and DYRK1A SNVs or small INDELs.
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Affiliation(s)
- Jianling Ji
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
| | - Bob Argiropoulos
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, AB, Canada
| | - Naghmeh Dorrani
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Natalie Gallant
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louanne Hudgins
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Leah Slattery
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, and Inserm UMR957, Faculté de Médecine, Nantes, France
| | - Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, and Inserm UMR957, Faculté de Médecine, Nantes, France
| | - Albert David
- CHU Nantes, Service de Génétique Médicale, and Inserm UMR957, Faculté de Médecine, Nantes, France
| | | | | | - Michelle Fox
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
| | - Eric Vilain
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | | | - Margaret Horton Harr
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Noon
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessi R Jackson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alisha Wilkens
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ghayda Mirzaa
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Noriko Salamon
- Department of Radiology, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, CA, USA
- The Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences–Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, AB, Canada
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, CA, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, CA, USA
- UCLA Clinical Genomics Center, Los Angeles, CA, USA
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24
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Abstract
Exome sequencing has recently been elevated to the standard of care for genetic diagnostic testing, particularly for genetically diverse and clinically heterogeneous disorders. This review provides a clinically oriented discussion of the next-generation sequencing technology that makes exome sequencing possible and how such technology is applied to the diagnosis of Mendelian disease, including clinically significant de novo variation, interpretation of variants of uncertain clinical significance, the future potential for genetic assessments of disease risk, and the substantial benefits in diagnostic efficiency. Important caveats are also discussed, including the implications of incidental or secondary findings detected during exome sequencing and the relationship of exome sequencing to other methods of clinical genomic testing, such as chromosomal microarray and genome sequencing. Overall, the widespread adoption and use of exome sequencing in routine clinical practice is expected to improve diagnosis rates and reduce test costs, while leading to improvements in patient outcomes and a renewed emphasis on disease management.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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25
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Cherukuri DP, Deignan JL, Das K, Grody WW, Herschman H. Instability of a dinucleotide repeat in the 3'-untranslated region (UTR) of the microsomal prostaglandin E synthase-1 (mPGES-1) gene in microsatellite instability-high (MSI-H) colorectal carcinoma. Mol Oncol 2015; 9:1252-8. [PMID: 25817443 DOI: 10.1016/j.molonc.2015.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 12/02/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/22/2022] Open
Abstract
DNA mismatch-repair gene mutations, with consequent loss of functional protein expression, result in microsatellite instability (MSI). Microsatellite sequences are found in coding regions and in regulatory regions of genes (i.e., 5'-UTRs and 3'-UTRs). In addition to being a surrogate marker of defective mismatch repair, deletion or insertion microsatellite sequences can dysregulate gene expression in MSI-H (microsatellite instability-high) tumors. The microsomal prostaglandin E synthase-1 (mPGES-1) gene product, mPGES-1, participates in prostaglandin E2 (PGE2) production. Moreover, mPGES-1 is often overexpressed in human colorectal tumors, and is thought to contribute to progression of these tumors. Here we identified a dinucleotide repeat, (GT)24, in the mPGES-1 gene 3' untranslated region (3'-UTR), and analyzed its mutation frequencies in MSI-H and microsatellite stable (MSS) tumors. The (GT)24 repeat exhibited instability in all MSI-H tumors examined (14), but not in any of the MSS tumors (13). In most cases, (GT)24 repeat instability resulted in insertion of additional GT units. We also determined mPGES-1 mRNA levels in MSI-H and MSS colorectal cancer cell lines. Three of four previously designated "MSI-H" cell lines showed higher mPGES-1 mRNA levels compared to MSS cell lines; correlations between elevated mPGES-1 mRNA levels and microsatellite (GT)24 repeat characteristics are present for all six cell lines. Our results demonstrate that mPGES-1 is a target gene of defective mismatch repair in human colorectal cancer, with functional consequence.
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Affiliation(s)
- Durga Prasad Cherukuri
- Department of Pharmacology and UCLA Intercampus Medical Genetics Training Program, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Joshua L Deignan
- Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kingshuk Das
- Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Wayne W Grody
- Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Harvey Herschman
- Department of Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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26
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Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning MA, Kwan A, Hudgins L, Barthelemy F, Miceli MC, Quintero-Rivera F, Kantarci S, Strom SP, Deignan JL, Grody WW, Vilain E, Nelson SF. De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay. Am J Hum Genet 2015; 96:498-506. [PMID: 25728775 DOI: 10.1016/j.ajhg.2015.01.017] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/20/2015] [Indexed: 12/19/2022] Open
Abstract
Chromatin remodeling through histone acetyltransferase (HAT) and histone deactylase (HDAC) enzymes affects fundamental cellular processes including the cell-cycle, cell differentiation, metabolism, and apoptosis. Nonsense mutations in genes that are involved in histone acetylation and deacetylation result in multiple congenital anomalies with most individuals displaying significant developmental delay, microcephaly and dysmorphism. Here, we report a syndrome caused by de novo heterozygous nonsense mutations in KAT6A (a.k.a., MOZ, MYST3) identified by clinical exome sequencing (CES) in four independent families. The same de novo nonsense mutation (c.3385C>T [p.Arg1129∗]) was observed in three individuals, and the fourth individual had a nearby de novo nonsense mutation (c.3070C>T [p.Arg1024∗]). Neither of these variants was present in 1,815 in-house exomes or in public databases. Common features among all four probands include primary microcephaly, global developmental delay including profound speech delay, and craniofacial dysmorphism, as well as more varied features such as feeding difficulties, cardiac defects, and ocular anomalies. We further demonstrate that KAT6A mutations result in dysregulation of H3K9 and H3K18 acetylation and altered P53 signaling. Through histone and non-histone acetylation, KAT6A affects multiple cellular processes and illustrates the complex role of acetylation in regulating development and disease.
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Affiliation(s)
- Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA
| | - Neda Zadeh
- Division of Medical Genetics, CHOC Children's Hospital of Orange County, CA 92868, USA; Genetics Center, Orange, CA 92868, USA
| | - Mary Willis
- Department of Pediatrics, Naval Medical Center, San Diego, 92134, USA
| | - Colleen Forsyth Macmurdo
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melanie A Manning
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrea Kwan
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louanne Hudgins
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florian Barthelemy
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - M Carrie Miceli
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Taylor S, Bennett KM, Deignan JL, Hendrix EC, Orton SM, Verma S, Schutzbank TE. Molecular pathology curriculum for medical laboratory scientists: A report of the association for molecular pathology training and education committee. J Mol Diagn 2015; 16:288-96. [PMID: 24745724 DOI: 10.1016/j.jmoldx.2014.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 01/31/2014] [Accepted: 02/12/2014] [Indexed: 11/29/2022] Open
Abstract
Molecular diagnostics is a rapidly growing specialty in the clinical laboratory assessment of pathology. Educational programs in medical laboratory science and specialized programs in molecular diagnostics must address the training of clinical scientists in molecular diagnostics, but the educational curriculum for this field is not well defined. Moreover, our understanding of underlying genetic contributions to specific diseases and the technologies used in molecular diagnostics laboratories change rapidly, challenging providers of training programs in molecular diagnostics to keep their curriculum current and relevant. In this article, we provide curriculum recommendations to molecular diagnostics training providers at both the baccalaureate and master's level of education. We base our recommendations on several factors. First, we considered National Accrediting Agency for Clinical Laboratory Sciences guidelines for accreditation of molecular diagnostics programs, because educational programs in clinical laboratory science should obtain its accreditation. Second, the guidelines of several of the best known certifying agencies for clinical laboratory scientists were incorporated into our recommendations. Finally, we relied on feedback from current employers of molecular diagnostics scientists, regarding the skills and knowledge that they believe are essential for clinical scientists who will be performing molecular testing in their laboratories. We have compiled these data into recommendations for a molecular diagnostics curriculum at both the baccalaureate and master's level of education.
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Affiliation(s)
- Sara Taylor
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Department of Medical Laboratory Science, Tarleton State University, Fort Worth, Texas.
| | - Katie M Bennett
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Department of Laboratory Sciences and Primary Care, Molecular Pathology and Clinical Laboratory Science, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Joshua L Deignan
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Ericka C Hendrix
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Department of Laboratory Sciences and Primary Care, Molecular Pathology and Clinical Laboratory Science, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Susan M Orton
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Diagnostics Division, Metabolon, Inc., Research Triangle Park, North Carolina
| | - Shalini Verma
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Division of Molecular Genetic Pathology and Hematopathology, Clarient, Inc., Aliso Viejo, California
| | - Ted E Schutzbank
- Medical Laboratory Scientist Curriculum Task Force of the Association for Molecular Pathology (AMP) Training and Education Committee, Bethesda, Maryland; Laboratory Services, St John's Hospital and Medical Center, Grosse Point Woods, Michigan
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Fogel BL, Lee H, Deignan JL, Strom SP, Kantarci S, Wang X, Quintero-Rivera F, Vilain E, Grody WW, Perlman S, Geschwind DH, Nelson SF. Exome sequencing in the clinical diagnosis of sporadic or familial cerebellar ataxia. JAMA Neurol 2015; 71:1237-46. [PMID: 25133958 DOI: 10.1001/jamaneurol.2014.1944] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
IMPORTANCE Cerebellar ataxias are a diverse collection of neurologic disorders with causes ranging from common acquired etiologies to rare genetic conditions. Numerous genetic disorders have been associated with chronic progressive ataxia and this consequently presents a diagnostic challenge for the clinician regarding how to approach and prioritize genetic testing in patients with such clinically heterogeneous phenotypes. Additionally, while the value of genetic testing in early-onset and/or familial cases seems clear, many patients with ataxia present sporadically with adult onset of symptoms and the contribution of genetic variation to the phenotype of these patients has not yet been established. OBJECTIVE To investigate the contribution of genetic disease in a population of patients with predominantly adult- and sporadic-onset cerebellar ataxia. DESIGN, SETTING, AND PARTICIPANTS We examined a consecutive series of 76 patients presenting to a tertiary referral center for evaluation of chronic progressive cerebellar ataxia. MAIN OUTCOMES AND MEASURES Next-generation exome sequencing coupled with comprehensive bioinformatic analysis, phenotypic analysis, and clinical correlation. RESULTS We identified clinically relevant genetic information in more than 60% of patients studied (n = 46), including diagnostic pathogenic gene variants in 21% (n = 16), a notable yield given the diverse genetics and clinical heterogeneity of the cerebellar ataxias. CONCLUSIONS AND RELEVANCE This study demonstrated that clinical exome sequencing in patients with adult-onset and sporadic presentations of ataxia is a high-yield test, providing a definitive diagnosis in more than one-fifth of patients and suggesting a potential diagnosis in more than one-third to guide additional phenotyping and diagnostic evaluation. Therefore, clinical exome sequencing is an appropriate consideration in the routine genetic evaluation of all patients presenting with chronic progressive cerebellar ataxia.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles
| | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles
| | - Xizhe Wang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles
| | - Eric Vilain
- UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles4Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles5Department of Pediatrics, David Geffen School of
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles4Department of Human Genetics
| | - Susan Perlman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles4Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles
| | - Stanley F Nelson
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles2Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles3UCLA Clin
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Kapp JR, Diss T, Spicer J, Gandy M, Schrijver I, Jennings LJ, Li MM, Tsongalis GJ, de Castro DG, Bridge JA, Wallace A, Deignan JL, Hing S, Butler R, Verghese E, Latham GJ, Hamoudi RA. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. J Clin Pathol 2014; 68:111-8. [PMID: 25430497 PMCID: PMC4316935 DOI: 10.1136/jclinpath-2014-202644] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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] [Indexed: 12/31/2022]
Abstract
Aims Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. Methods 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. Results Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p<0.0001), and yield variation from engineered samples was not significant (p=0.3782). Two laboratories failed DNA extraction from samples that may be attributed to operator error. DNA extraction protocols themselves were not found to contribute significant variation. 10/13 labs reported yields averaging 235.8 ng (95% CI 90.7 to 380.9) from cell-negative samples, which was attributed to issues with spectrophotometry. DNA measurements using Qubit Fluorometry demonstrated a median fivefold overestimation of DNA quantity by Nanodrop Spectrophotometry. DNA integrity and PCR inhibition were factors not found to contribute significant variation. Conclusions In this study, we provide evidence demonstrating that variation in pre-PCR steps is prevalent and may detrimentally affect the patient's ability to receive critical therapy. We provide recommendations for preanalytical workflow optimisation that may reduce errors in down-stream sequencing and for next-generation sequencing library generation.
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Affiliation(s)
- Joshua R Kapp
- Division of Surgery and Interventional Sciences, University College London, London, UK
| | - Tim Diss
- University College London Advanced Diagnostics, University College London, London, UK
| | - James Spicer
- Division of Research Oncology, Guy's and St. Thomas' Hospital NHS Trust, London, UK
| | - Michael Gandy
- University College London Advanced Diagnostics, University College London, London, UK
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, USA
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Marilyn M Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | | | | | - Julia A Bridge
- Department of Pathology, University of Nebraska Medical Center, Omaha, USA
| | - Andrew Wallace
- Regional Genetics Laboratory, Central Manchester University Hospital NHS Trust, Manchester, UK
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, USA
| | - Sandra Hing
- Paediatric Malignancy Department, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Rachel Butler
- All Wales Genetics Laboratory, Cardiff and Vale NHS Trust, Cardiff, UK
| | - Eldo Verghese
- Pathology and Tumour biology, University of Leeds, Leeds, UK
| | | | - Rifat A Hamoudi
- Division of Surgery and Interventional Sciences, University College London, London, UK
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Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CGS, Dipple KM, Grody WW, Vilain E, Nelson SF. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 2014; 312:1880-7. [PMID: 25326637 PMCID: PMC4278636 DOI: 10.1001/jama.2014.14604] [Citation(s) in RCA: 704] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
IMPORTANCE Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders. OBJECTIVE To report on initial clinical indications for CES referrals and molecular diagnostic rates for different indications and for different test types. DESIGN, SETTING, AND PARTICIPANTS Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available. MAIN OUTCOMES AND MEASURES Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES. RESULTS Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 [95% CI, 1.6-33.1]) of trio-CES was due to the identification of de novo and compound heterozygous variants. CONCLUSIONS AND RELEVANCE In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Naghmeh Dorrani
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Kingshuk Das
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Traci Toy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Bret Harry
- Institute for Digital Research and Education, University of California, Los Angeles
| | - Michael Yourshaw
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Michelle Fox
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Brent L Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles
| | - Julian A Martinez-Agosto
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
| | - Derek A Wong
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Vivian Y Chang
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Perry B Shieh
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles7Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Katrina M Dipple
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen
| | - Eric Vilain
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Ge
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Strom SP, Lozano R, Lee H, Dorrani N, Mann J, O'Lague PF, Mans N, Deignan JL, Vilain E, Nelson SF, Grody WW, Quintero-Rivera F. De Novo variants in the KMT2A (MLL) gene causing atypical Wiedemann-Steiner syndrome in two unrelated individuals identified by clinical exome sequencing. BMC Med Genet 2014; 15:49. [PMID: 24886118 PMCID: PMC4072606 DOI: 10.1186/1471-2350-15-49] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/10/2014] [Indexed: 01/23/2023]
Abstract
Background Wiedemann-Steiner Syndrome (WSS) is characterized by short stature, a variety of dysmorphic facial and skeletal features, characteristic hypertrichosis cubiti (excessive hair on the elbows), mild-to-moderate developmental delay and intellectual disability. [MIM#: 605130]. Here we report two unrelated children for whom clinical exome sequencing of parent-proband trios was performed at UCLA, resulting in a molecular diagnosis of WSS and atypical clinical presentation. Case presentation For patient 1, clinical features at 9 years of age included developmental delay, craniofacial abnormalities, and multiple minor anomalies. Patient 2 presented at 1 year of age with developmental delay, microphthalmia, partial 3–4 left hand syndactyly, and craniofacial abnormalities. A de novo missense c.4342T>C variant and a de novo splice site c.4086+G>A variant were identified in the KMT2A gene in patients 1 and 2, respectively. Conclusions Based on the clinical and molecular findings, both patients appear to have novel presentations of WSS. As the hallmark hypertrichosis cubiti was not initially appreciated in either case, this syndrome was not suspected during the clinical evaluation. This report expands the phenotypic spectrum of the clinical phenotypes and KMT2A variants associated with WSS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Fabiola Quintero-Rivera
- Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, Deignan JL. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet Med 2014; 16:510-5. [PMID: 24406459 PMCID: PMC4079763 DOI: 10.1038/gim.2013.183] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 07/10/2013] [Accepted: 10/18/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose Sanger sequencing is currently considered the gold standard methodology for clinical molecular diagnostic testing. However, next generation sequencing (NGS) has already emerged as a much more efficient means to identify genetic variants within gene panels, the exome, or the genome. We sought to assess the accuracy of NGS variant identification in our clinical genomics laboratory with the goal of establishing a quality score threshold for confirmatory Sanger-based testing. Methods Confirmation data for reported results from 144 sequential clinical exome sequencing cases (94 unique variants) and an additional set of 16 variants from comparable research samples were analyzed. Results 103 of 110 total SNVs analyzed had a quality score ≥Q500, 103 (100%) of which were confirmed by Sanger sequencing. Of the remaining 7 variants with quality scores <Q500, 6 were confirmed by Sanger sequencing (85%). Conclusions For single nucleotide variants, we predict we will be able to reduce our Sanger confirmation workload going forward by 70–80%. This serves as a proof of principle that as long as sufficient validation and quality control measures are implemented, the volume of Sanger confirmation can be reduced, alleviating a significant amount of the labor and cost burden on clinical laboratories wishing to utilize NGS technology. However, Sanger confirmation of low quality single nucleotide variants and all indels (insertions or deletions less than 10 bp) remains necessary at this time in our laboratory.
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Affiliation(s)
- Samuel P Strom
- 1] Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA [2] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kingshuk Das
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Eric Vilain
- 1] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA [2] Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Stanley F Nelson
- 1] Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA [2] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Wayne W Grody
- 1] Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA [2] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA [3] Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
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Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15:733-47. [PMID: 23887774 PMCID: PMC4098820 DOI: 10.1038/gim.2013.92] [Citation(s) in RCA: 619] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 05/30/2013] [Indexed: 01/01/2023] Open
Abstract
Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are being made. It is now feasible to analyze an individual's near-complete exome or genome to assist in the diagnosis of a wide array of clinical scenarios. Next-generation sequencing technologies are also facilitating further advances in therapeutic decision making and disease prediction for at-risk patients. However, with rapid advances come additional challenges involving the clinical validation and use of these constantly evolving technologies and platforms in clinical laboratories. To assist clinical laboratories with the validation of next-generation sequencing methods and platforms, the ongoing monitoring of next-generation sequencing testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics has developed the following professional standards and guidelines.
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Affiliation(s)
- Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.
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Palmer CGS, Boudreault P, Baldwin EE, Fox M, Deignan JL, Kobayashi Y, Sininger Y, Grody W, Sinsheimer JS. Deaf genetic testing and psychological well-being in deaf adults. J Genet Couns 2013; 22:492-507. [PMID: 23430402 DOI: 10.1007/s10897-013-9573-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
Limited data suggest that enhanced self-knowledge from genetic information related to non-medical traits can have a positive impact on psychological well-being. Deaf individuals undertake genetic testing for deaf genes to increase self-knowledge. Because deafness is considered a non-medical trait by many individuals, we hypothesized that deaf individuals receiving a genetic explanation for why they are deaf will experience increased psychological well-being. We report results from a prospective, longitudinal study to determine the impact of genetic testing (GJB2, Cx26; GJB6, Cx30) on perceived personal control (PPC), anxiety, and depression in deaf adults (N = 209) assessed following pre-test genetic counseling as well as 1-month and 6-months following test result disclosure. Participants were classified as Cx positive (n = 82) or Cx negative/inconclusive (n = 127). There was significant evidence for Cx group differences in PPC and anxiety over time (PPC: Cx group*time interaction p = 0.0007; anxiety: Cx group*time interaction p = 0.002), where PPC scores were significantly higher, and anxiety scores were significantly lower for the Cx positive group relative to the negative/inconclusive group following test result disclosure. Compared to pre-test, PPC scores increased at 1-month (p = 0.07) and anxiety scores decreased at 6-months (p = 0.03) for the Cx positive group. In contrast, PPC scores decreased (p = 0.009, p < 0.0001) and anxiety scores increased (p = 0.09, p = 0.02) for the Cx negative/inconclusive group at 1- and 6-months post test result disclosure. Genetic testing for deaf genes affects the psychological well-being of deaf individuals. Increasing deaf adults' access to genetic testing may potentially enhance self-knowledge and increase psychological well-being for those who receive a genetic explanation, which could offer downstream health benefits.
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Affiliation(s)
- Christina G S Palmer
- Department of Psychiatry & Biobehavioral Sciences, University of California-Los Angeles, CA, USA.
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Ong FS, Vakil H, Xue Y, Kuo JZ, Shah KH, Lee RB, Bernstein KE, Rimoin DL, Getzug T, Das K, Deignan JL, Rotter JI, Grody WW. The M694V mutation in Armenian-Americans: a 10-year retrospective study of MEFV mutation testing for familial Mediterranean fever at UCLA. Clin Genet 2012; 84:55-9. [PMID: 23038988 DOI: 10.1111/cge.12029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/25/2012] [Accepted: 09/25/2012] [Indexed: 11/28/2022]
Abstract
Familial Mediterranean fever (FMF), inherited in an autosomal recessive manner, is a systemic auto-inflammatory disorder characterized by recurrent attacks of fever with peritonitis, pleuritis, synovitis and erysipeloid rash. The marenostrin-encoding fever (MEFV) gene, located on chromosome 16p13.3, is the only gene in which mutations are currently known to cause FMF. To correlate specific genotypes with adverse phenotypes of affected populations residing in the Western United States, a retrospective case series review was conducted of all MEFV gene mutation testing completed at UCLA Clinical Molecular Diagnostic Laboratory between February 2002 and February 2012, followed by clinical chart review of all subjects who either have a single or double mutation. All 12 common mutations in the MEFV gene were analyzed and the M694V variant was found to be associated with an adverse FMF clinical outcome in the Armenian-American population, manifested by earlier onset of disease, increased severity of disease, and renal amyloidosis.
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Affiliation(s)
- F S Ong
- Department of Biomedical Sciences; Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90095, USA
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Gallant NM, Leydiker K, Tang H, Feuchtbaum L, Lorey F, Puckett R, Deignan JL, Neidich J, Dorrani N, Chang E, Barshop BA, Cederbaum SD, Abdenur JE, Wang RY. Biochemical, molecular, and clinical characteristics of children with short chain acyl-CoA dehydrogenase deficiency detected by newborn screening in California. Mol Genet Metab 2012; 106:55-61. [PMID: 22424739 DOI: 10.1016/j.ymgme.2012.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [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] [Received: 11/30/2011] [Revised: 02/05/2012] [Accepted: 02/05/2012] [Indexed: 11/27/2022]
Abstract
BACKGROUND Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is an autosomal recessive inborn error of mitochondrial fatty acid oxidation with highly variable biochemical, genetic, and clinical characteristics. SCADD has been associated with accumulation of butyryl-CoA byproducts, including butyrylcarnitine (C4), butyrylglycine, ethylmalonic acid (EMA), and methylsuccinic acid (MS) in body fluid and tissues. Differences in genotype frequencies have been shown between patients diagnosed clinically versus those diagnosed by newborn screening. Moreover, while patients diagnosed clinically have a variable clinical presentation including developmental delay, ketotic hypoglycemia, epilepsy and behavioral disorders, studies suggest patients diagnosed by newborn screening are largely asymptomatic. Scant information is published about the biochemical, genetic and clinical outcome of SCADD patients diagnosed by newborn screening. METHODS We collected California newborn screening, follow-up biochemical levels, and ACADS mutation data from September, 2005 through April, 2010. We retrospectively reviewed available data on SCADD cases diagnosed by newborn screening for clinical outcomes. RESULTS During the study period, 2,632,058 newborns were screened and 76 confirmed SCADD cases were identified. No correlations between initial C4 value and follow-up biochemical markers (C4, EMA or MS levels) were found in the 76 cases studied. We found significant correlation between urine EMA versus MS, and correlation between follow-up C4 versus urine EMA. Of 22 cases where ACADS gene sequencing was performed: 7 had two or more deleterious mutations; 8 were compound heterozygotes for a deleterious mutation and common variant; 7 were homozygous for the common variant c.625G>A; and 1 was heterozygous for c.625G>A. Significant increases in mean urine EMA and MS levels were noted in patients with two or more deleterious mutations versus mutation heterozygotes or common polymorphism homozygotes. Clinical outcome data was available in 31 patients with follow-up extending from 0.5 to 60 months. None developed epilepsy or behavioral disorders, and three patients had isolated speech delay. Hypoglycemia occurred in two patients, both in the neonatal period. The first patient had concomitant meconium aspiration; the other presented with central apnea, poor feeding, and hypotonia. The latter, a c.625G>A homozygote, has had persistent elevations in both short- and medium-chain acylcarnitines; diagnostic workup in this case is extensive and ongoing. CONCLUSIONS This study examines the largest series to date of SCADD patients identified by newborn screening. Our results suggest that confirmatory tests may be useful to differentiate patients with common variants from those with deleterious mutations. This study also provides evidence to suggest that, even when associated with deleterious mutations, SCADD diagnosed by newborn screening presents largely as a benign condition.
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Affiliation(s)
- Natalie M Gallant
- Department of Pediatrics, University of California at Los Angeles, Los Angeles, CA, USA
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Ong FS, Deignan JL, Kuo JZ, Bernstein KE, Rotter JI, Grody WW, Das K. Clinical utility of pharmacogenetic biomarkers in cardiovascular therapeutics: a challenge for clinical implementation. Pharmacogenomics 2012; 13:465-75. [PMID: 22380001 PMCID: PMC3306231 DOI: 10.2217/pgs.12.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the past decade, significant strides have been made in the area of cardiovascular pharmacogenomic research, with the discovery of associations between certain genotypes and drug-response phenotypes. While the motivations for personalized and predictive medicine are promising for patient care and support a model of health system efficiency, the implementation of pharmacogenomics for cardiovascular therapeutics on a population scale faces substantial challenges. The greatest obstacle to clinical implementation of cardiovascular pharmacogenetics may be the lack of both reproducibility and agreement about the validity and utility of the findings. In this review, we present the scientific evidence in the literature for diagnostic variants for the US FDA-labeled cardiovascular therapies, namely CYP2C19 and clopidogrel, CYP2C9/VKORC1 and warfarin, and CYP2D6/ADRB1 and β-blockers. We also discuss the effect of HMGCR/LDLR in decreasing the effectiveness of low-density lipoprotein cholesterol with statin therapy, the SLCO1B1 genotype and simvastatin myotoxicity, and ADRB1/ADD1 for antihypertensive response.
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Affiliation(s)
- Frank S Ong
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Deignan JL, Grody WW. Ordering genetic tests and interpreting the results. Adv Otorhinolaryngol 2011; 70:18-24. [PMID: 21358180 DOI: 10.1159/000322466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
As the number of clinical genetic laboratories becomes more abundant, it will become increasingly challenging for clinicians in the medical and surgical specialties to navigate the vast menus of testing available and decide upon the most appropriate approach for molecular diagnosis of a particular disorder. There are many associated ethical and psychosocial issues involved with ordering clinical genetic tests of which practitioners need to remain aware, including predictive testing of minors, implications of the test result for other family members, theoretical risks of insurance or employment discrimination, and how to appropriately counsel families once test results have been finalized and reported. Finally, as the field of genetic testing changes so rapidly, it will be of great help for otolaryngologists to familiarize themselves and remain up to date with the general terminology and interpretive criteria that go into clinical molecular genetic laboratory reports, in order to make it useful and understandable to clinicians and patients.
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Quintero-Rivera F, Deignan JL, Peredo J, Grody WW, Crandall B, Sims M, Cederbaum SD. An exon 1 deletion in OTC identified using chromosomal microarray analysis in a mother and her two affected deceased newborns: implications for the prenatal diagnosis of ornithine transcarbamylase deficiency. Mol Genet Metab 2010; 101:413-6. [PMID: 20817516 DOI: 10.1016/j.ymgme.2010.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [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] [Received: 06/15/2010] [Revised: 08/06/2010] [Accepted: 08/07/2010] [Indexed: 11/24/2022]
Abstract
We describe the outcome of two consecutive pregnancies with a clinical presentation of ornithine transcarbamylase (OTC) deficiency (OTCD) without a molecular diagnosis. A 119kb deletion on Xp11.4 including the OTC gene was detected in the mother. The same deletion was identified in the blood spots from deceased male newborns. In patients with a clinical and biochemical presentation of OTCD and negative OTC sequencing, whole genome or targeted chromosomal microarray analysis (CMA) with coverage of the OTC and neighboring genes should be performed as a reflex test.
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Affiliation(s)
- Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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Yang X, Peterson L, Thieringer R, Deignan JL, Wang X, Zhu J, Wang S, Zhong H, Stepaniants S, Beaulaurier J, Wang IM, Rosa R, Cumiskey AM, Luo JMJ, Luo Q, Shah K, Xiao J, Nickle D, Plump A, Schadt EE, Lusis AJ, Lum PY. Identification and validation of genes affecting aortic lesions in mice. J Clin Invest 2010; 120:2414-22. [PMID: 20577049 DOI: 10.1172/jci42742] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 05/12/2010] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis represents the most significant risk factor for coronary artery disease (CAD), the leading cause of death in developed countries. To better understand the pathogenesis of atherosclerosis, we applied a likeli-hood-based model selection method to infer gene-disease causality relationships for the aortic lesion trait in a segregating mouse population demonstrating a spectrum of susceptibility to developing atherosclerotic lesions. We identified 292 genes that tested causal for aortic lesions from liver and adipose tissues of these mice, and we experimentally validated one of these candidate causal genes, complement component 3a receptor 1 (C3ar1), using a knockout mouse model. We also found that genes identified by this method overlapped with genes progressively regulated in the aortic arches of 2 mouse models of atherosclerosis during atherosclerotic lesion development. By comparing our gene set with findings from public human genome-wide association studies (GWAS) of CAD and related traits, we found that 5 genes identified by our study overlapped with published studies in humans in which they were identified as risk factors for multiple atherosclerosis-related pathologies, including myocardial infarction, serum uric acid levels, mean platelet volume, aortic root size, and heart failure. Candidate causal genes were also found to be enriched with CAD risk polymorphisms identified by the Wellcome Trust Case Control Consortium (WTCCC). Our findings therefore validate the ability of causality testing procedures to provide insights into the mechanisms underlying atherosclerosis development.
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Affiliation(s)
- Xia Yang
- Department of Molecular Profiling, Rosetta Inpharmactics LLC, a wholly owned subsidiary of Merck & Co. Inc., Seattle, Washington, USA
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Deignan JL, De Deyn PP, Cederbaum SD, Fuchshuber A, Roth B, Gsell W, Marescau B. Guanidino compound levels in blood, cerebrospinal fluid, and post-mortem brain material of patients with argininemia. Mol Genet Metab 2010; 100 Suppl 1:S31-6. [PMID: 20176499 DOI: 10.1016/j.ymgme.2010.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [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] [Received: 01/10/2010] [Revised: 01/13/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
Abstract
The paucity of hyperammonemic crises together with spasticity, only seen in human arginase I deficient patients and not in patients with other urea cycle disorders, forces a search for candidates other than ammonia to associate with the pathophysiology and symptomatology. Therefore, we determined arginine together with some catabolites of arginine in blood and cerebrospinal fluid of these patients as well as in extremely rare post-mortem brain material of two patients with argininemia. The levels of alpha-keto-delta-guanidinovaleric acid, argininic acid and alpha-N-acetylarginine correlate with the arginine levels in blood and cerebrospinal fluid of patients with imposed or spontaneous protein restriction. The levels in blood are higher than the upper limit of normal in all studied patients. In addition to the highly increased levels of these same compounds in blood of a child with argininemia, the increase of guanidinoacetic acid, 24h before death, is remarkable. However, the manifest increases of these studied catabolites of arginine are not seen in post-mortem brain material of the same pediatric patient. Otherwise a clear increase of guanidinoacetic acid in post-mortem brain material of an adult patient was shown. A similar, comparable increase of homoarginine in both studied post-mortem brain materials is observed. Therefore the study of the pathobiochemistry of arginine in argininemia must be completed in the future by the determination of the end catabolites of the nitric oxide and agmatine biosynthesis pathways in the knockouts as well as in the patients to evaluate their role, together with the here studied catabolites, as candidates for association with pathophysiology and symptomatology.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
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Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, Torosyan G, Majid S, Falkard B, Kleinhanz RR, Karlsson J, Castellani LW, Mumick S, Wang K, Xie T, Coon M, Zhang C, Estrada-Smith D, Farber CR, Wang SS, van Nas A, Ghazalpour A, Zhang B, Macneil DJ, Lamb JR, Dipple KM, Reitman ML, Mehrabian M, Lum PY, Schadt EE, Lusis AJ, Drake TA. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet 2009; 41:415-23. [PMID: 19270708 PMCID: PMC2837947 DOI: 10.1038/ng.325] [Citation(s) in RCA: 227] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 01/13/2009] [Indexed: 02/06/2023]
Abstract
A major task in dissecting the genetics of complex traits is to identify causal genes for disease phenotypes. We previously developed a method to infer causal relationships among genes through the integration of DNA variation, gene transcription, and phenotypic information. Here we validated our method through the characterization of transgenic and knockout mouse models of candidate genes that were predicted to be causal for abdominal obesity. Perturbation of eight out of the nine genes, with Gas7, Me1 and Gpx3 being novel, resulted in significant changes in obesity related traits. Liver expression signatures revealed alterations in common metabolic pathways and networks contributing to abdominal obesity and overlapped with a macrophage-enriched metabolic network module that is highly associated with metabolic traits in mice and humans. Integration of gene expression in the design and analysis of traditional F2 intercross studies allows high confidence prediction of causal genes and identification of involved pathways and networks.
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Affiliation(s)
- Xia Yang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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Deignan JL, Marescau B, Livesay JC, Iyer RK, De Deyn PP, Cederbaum SD, Grody WW. Increased plasma and tissue guanidino compounds in a mouse model of hyperargininemia. Mol Genet Metab 2008; 93:172-8. [PMID: 17997338 DOI: 10.1016/j.ymgme.2007.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
Abstract
In humans, arginase I (AI)-deficiency results in hyperargininemia, a metabolic disorder with symptoms of progressive neurological and intellectual impairment, spasticity, persistent growth retardation, and episodic hyperammonemia. A deficiency of arginase II (AII) has never been detected and the clinical disorder, if any, associated with its deficiency has not been defined. Since the spasticity and paucity of hyperammonemic crises seen in human AI-deficient patients are not features of the other urea cycle disorders, the likelihood of ammonia as the main neuropathogenic agent becomes extremely low, and the modest elevations of arginine seen in the brains of our mouse model of hyperargininemia make it an unlikely candidate as well. Specific guanidino compounds, direct or indirect metabolites of arginine, are elevated in the blood of patients with uremia. Other guanidino compounds are also increased in plasma and cerebrospinal fluid of hyperargininemic patients making them plausible as neurotoxins in these disorders. We analyzed several guanidino compounds in our arginase single and double knockout animals and found that alpha-keto-delta-guanidinovaleric acid, alpha-N-acetylarginine, and argininic acid were increased in the brain tissue from the AI knockout and double knockout animals. Several compounds were also increased in the plasma, liver, and kidneys. This is the first time that several of the guanidino compounds have been shown to be elevated in the brain tissue of an arginase-deficient mammal, and it further supports their possible role as the neuropathogenic agents responsible for the complications seen in arginase deficiency.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
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Deignan JL, Cederbaum SD, Grody WW. Contrasting features of urea cycle disorders in human patients and knockout mouse models. Mol Genet Metab 2008; 93:7-14. [PMID: 17933574 PMCID: PMC2692509 DOI: 10.1016/j.ymgme.2007.08.123] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2007] [Revised: 08/19/2007] [Accepted: 08/19/2007] [Indexed: 10/22/2022]
Abstract
The urea cycle exists for the removal of excess nitrogen from the body. Six separate enzymes comprise the urea cycle, and a deficiency in any one of them causes a urea cycle disorder (UCD) in humans. Arginase is the only urea cycle enzyme with an alternate isoform, though no known human disorder currently exists due to a deficiency in the second isoform. While all of the UCDs usually present with hyperammonemia in the first few days to months of life, most disorders are distinguished by a characteristic profile of plasma amino acid alterations that can be utilized for diagnosis. While enzyme assay is possible, an analysis of the underlying mutation is preferable for an accurate diagnosis. Mouse models for each of the urea cycle disorders exist (with the exception of NAGS deficiency), and for almost all of them, their clinical and biochemical phenotypes rather closely resemble the phenotypes seen in human patients. Consequently, all of the current mouse models are highly useful for future research into novel pharmacological and dietary treatments and gene therapy protocols for the management of urea cycle disorders.
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Affiliation(s)
- Joshua L. Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
- The Mental Retardation Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Stephen D. Cederbaum
- Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA
- The Mental Retardation Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Wayne W. Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA
- The Mental Retardation Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA
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Deignan JL, Livesay JC, Shantz LM, Pegg AE, O'Brien WE, Iyer RK, Cederbaum SD, Grody WW. Polyamine homeostasis in arginase knockout mice. Am J Physiol Cell Physiol 2007; 293:C1296-301. [PMID: 17686999 DOI: 10.1152/ajpcell.00393.2006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of ornithine decarboxylase (ODC) in polyamine metabolism has long been established, but the exact source of ornithine has always been unclear. The arginase enzymes are capable of producing ornithine for the production of polyamines and may hold important regulatory functions in the maintenance of this pathway. Utilizing our unique set of arginase single and double knockout mice, we analyzed polyamine levels in the livers, brains, kidneys, and small intestines of the mice at 2 wk of age, the latest timepoint at which all of them are still alive, to determine whether tissue polyamine levels were altered in response to a disruption of arginase I (AI) and II (AII) enzymatic activity. Whereas putrescine was minimally increased in the liver and kidneys from the AII knockout mice, spermidine and spermine were maintained. ODC activity was not greatly altered in the knockout animals and did not correlate with the fluctuations in putrescine. mRNA levels of ornithine aminotransferase (OAT), antizyme 1 (AZ1), and spermidine/spermine-N(1)-acetyltransferase (SSAT) were also measured and only minor alterations were seen, most notably an increase in OAT expression seen in the liver of AI knockout and double knockout mice. It appears that putrescine catabolism may be affected in the liver when AI is disrupted and ornithine levels are highly reduced. These results suggest that endogenous arginase-derived ornithine may not directly contribute to polyamine homeostasis in mice. Alternate sources such as diet may provide sufficient polyamines for maintenance in mammalian tissues.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1732, USA
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Deignan JL, Livesay JC, Yoo PK, Goodman SI, O'Brien WE, Iyer RK, Cederbaum SD, Grody WW. Ornithine deficiency in the arginase double knockout mouse. Mol Genet Metab 2006; 89:87-96. [PMID: 16753325 DOI: 10.1016/j.ymgme.2006.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 04/13/2006] [Indexed: 10/24/2022]
Abstract
Knockout mouse models have been created to study the consequences of deficiencies in arginase AI and AII, both individually and combined. The AI knockout animals die by 14 days of age from hyperammonemia, while the AII knockout has no obvious phenotype. The double knockout (AI(-/-)/AII(-/-)) exhibits the phenotype of the AI-deficient mice, with the additional absence of AII not exacerbating the observed phenotype of the AI knockout animals. Plasma amino acid measurements in the double knockout have shown arginine levels increased roughly 100-fold and ornithine decreased roughly 10-fold as compared to wildtype. Liver ornithine levels were reduced to 2% of normal in the double knockout with arginine very highly elevated. Arginine and ornithine were also altered in other tissues in the double knockout mice, such as kidney, brain, and small intestine. This is the first demonstration that the fatal hyperammonemia in the AI knockout mouse is almost certainly due to ornithine deficiency, the amino acid needed to drive the urea cycle. Others have shown that the expression of ornithine aminotransferase (OAT) rapidly decreases in the intestine at the same age when the AI-deficient animals die, indicating that this enzyme is critical to the maintenance of ornithine homeostasis, at least at this early stage of mouse development. Although most human AI-deficient patients have no symptomatic hyperammonemia at birth, it is possible that clinically significant ornithine deficiency is already present.
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Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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