1
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Maron JL, Kingsmore S, Gelb BD, Vockley J, Wigby K, Bragg J, Stroustrup A, Poindexter B, Suhrie K, Kim JH, Diacovo T, Powell CM, Trembath A, Guidugli L, Ellsworth KA, Reed D, Kurfiss A, Breeze JL, Trinquart L, Davis JM. Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder. JAMA 2023; 330:161-169. [PMID: 37432431 PMCID: PMC10336625 DOI: 10.1001/jama.2023.9350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 11/30/2022] [Accepted: 05/12/2023] [Indexed: 07/12/2023]
Abstract
Importance Genomic testing in infancy guides medical decisions and can improve health outcomes. However, it is unclear whether genomic sequencing or a targeted neonatal gene-sequencing test provides comparable molecular diagnostic yields and times to return of results. Objective To compare outcomes of genomic sequencing with those of a targeted neonatal gene-sequencing test. Design, Setting, and Participants The Genomic Medicine for Ill Neonates and Infants (GEMINI) study was a prospective, comparative, multicenter study of 400 hospitalized infants younger than 1 year of age (proband) and their parents, when available, suspected of having a genetic disorder. The study was conducted at 6 US hospitals from June 2019 to November 2021. Exposure Enrolled participants underwent simultaneous testing with genomic sequencing and a targeted neonatal gene-sequencing test. Each laboratory performed an independent interpretation of variants guided by knowledge of the patient's phenotype and returned results to the clinical care team. Change in clinical management, therapies offered, and redirection of care was provided to families based on genetic findings from either platform. Main Outcomes and Measures Primary end points were molecular diagnostic yield (participants with ≥1 pathogenic variant or variant of unknown significance), time to return of results, and clinical utility (changes in patient care). Results A molecular diagnostic variant was identified in 51% of participants (n = 204; 297 variants identified with 134 being novel). Molecular diagnostic yield of genomic sequencing was 49% (95% CI, 44%-54%) vs 27% (95% CI, 23%-32%) with the targeted gene-sequencing test. Genomic sequencing did not report 19 variants found by the targeted neonatal gene-sequencing test; the targeted gene-sequencing test did not report 164 variants identified by genomic sequencing as diagnostic. Variants unidentified by the targeted genomic-sequencing test included structural variants longer than 1 kilobase (25.1%) and genes excluded from the test (24.6%) (McNemar odds ratio, 8.6 [95% CI, 5.4-14.7]). Variant interpretation by laboratories differed by 43%. Median time to return of results was 6.1 days for genomic sequencing and 4.2 days for the targeted genomic-sequencing test; for urgent cases (n = 107) the time was 3.3 days for genomic sequencing and 4.0 days for the targeted gene-sequencing test. Changes in clinical care affected 19% of participants, and 76% of clinicians viewed genomic testing as useful or very useful in clinical decision-making, irrespective of a diagnosis. Conclusions and Relevance The molecular diagnostic yield for genomic sequencing was higher than a targeted neonatal gene-sequencing test, but the time to return of routine results was slower. Interlaboratory variant interpretation contributes to differences in molecular diagnostic yield and may have important consequences for clinical management.
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Affiliation(s)
- Jill L. Maron
- Women and Infants Hospital of Rhode Island, Providence
| | - Stephen Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jerry Vockley
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, San Diego
| | - Jennifer Bragg
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Annemarie Stroustrup
- Division of Neonatology, Department of Pediatrics, Cohen Children’s Medical Center at Northwell Health, New Hyde Park, New York, New York
| | - Brenda Poindexter
- Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kristen Suhrie
- Indiana University School of Medicine, Department of Pediatrics and Medical and Molecular Genetics, Indianapolis
| | - Jae H. Kim
- Perinatal Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Thomas Diacovo
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cynthia M. Powell
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Andrea Trembath
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | | | - Dallas Reed
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Anne Kurfiss
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Janis L. Breeze
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Ludovic Trinquart
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Jonathan M. Davis
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
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2
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Owen MJ, Batalov S, Ellsworth KA, Wright M, Breeding S, Hugh K, Kingsmore SF, Ding Y. Rapid Whole Genome Sequencing for Diagnosis of Single Locus Genetic Diseases in Critically Ill Children. Methods Mol Biol 2023; 2621:217-239. [PMID: 37041447 DOI: 10.1007/978-1-0716-2950-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Upon admission to intensive care units (ICU), the differential diagnosis of almost all infants with diseases of unclear etiology includes single locus genetic diseases. Rapid whole genome sequencing (rWGS), including sample preparation, short-read sequencing-by-synthesis, informatics pipelining, and semiautomated interpretation, can now identify nucleotide and structural variants associated with most genetic diseases with robust analytic and diagnostic performance in as little as 13.5 h. Early diagnosis of genetic diseases transforms medical and surgical management of infants in ICUs, minimizing both the duration of empiric treatment and the delay to start of specific treatment. Both positive and negative rWGS tests have clinical utility and can improve outcomes. Since first described 10 years ago, rWGS has evolved considerably. Here we describe our current methods for routine diagnostic testing for genetic diseases by rWGS in as little as 18 h.
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Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Katarzyna A Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sylvia Breeding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kwon Hugh
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
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3
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Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [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: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
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Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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4
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Yang JH, Friederich MW, Ellsworth KA, Frederick A, Foreman E, Malicki D, Dimmock D, Lenberg J, Prasad C, Yu AC, Rupar CA, Hegele RA, Manickam K, Koboldt DC, Crist E, Choi SS, Farhan SM, Harvey H, Sattar S, Karp N, Wong T, Haas R, Van Hove JL, Wigby K. Expanding the phenotypic and molecular spectrum of NFS1-related disorders that cause functional deficiencies in mitochondrial and cytosolic iron-sulfur cluster containing enzymes. Hum Mutat 2022; 43:305-315. [PMID: 35026043 PMCID: PMC8863643 DOI: 10.1002/humu.24330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/11/2021] [Accepted: 01/10/2022] [Indexed: 11/11/2022]
Abstract
Iron-sulfur cluster proteins are involved in critical functions for gene expression regulation and mitochondrial bioenergetics including the oxidative phosphorylation system. The c.215G>A p.(Arg72Gln) variant in NFS1 has been previously reported to cause infantile mitochondrial complex II and III deficiency. We describe three additional unrelated patients with the same missense variant. Two infants with the same homozygous variant presented with hypotonia, weakness and lactic acidosis, and one patient with compound heterozygous p.(Arg72Gln) and p.(Arg412His) variants presented as a young adult with gastrointestinal symptoms and fatigue. Skeletal muscle biopsy from patients 1 and 3 showed abnormal mitochondrial morphology, and functional analyses demonstrated decreased activity in respiratory chain complex II and variably in complexes I and III. We found decreased mitochondrial and cytosolic aconitase activities but only mildly affected lipoylation of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase enzymes. Our studies expand the phenotypic spectrum and provide further evidence for the pathogenicity and functional sequelae of NFS1-related disorders with disturbances in both mitochondrial and cytosolic iron-sulfur cluster containing enzymes.
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Affiliation(s)
- Jennifer H. Yang
- Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA,Division of Child Neurology, Rady Children’s Hospital, San Diego, CA 92123, USA,These authors contributed equally to this work
| | - Marisa W. Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA,Department of Pathology and Laboratory Medicine, Children’s Hospital Colorado, 13121 East 16th Avenue, Aurora, CO 80045, USA,These authors contributed equally to this work
| | | | - Aliya Frederick
- Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA,Division of Child Neurology, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Emily Foreman
- Division of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Denise Malicki
- Department of Pathology, University of California San Diego, San Diego, CA 92093, USA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jerica Lenberg
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Chitra Prasad
- Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada,Department of Pediatrics, Division of Medical Genetics, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5K8, Canada
| | - Andrea C. Yu
- Division of Metabolics and Newborn Screening, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, ON, K1H 8L1, Canada
| | - C. Anthony Rupar
- Department of Pathology, London Health Science Centre, London, Ontario N6A 5A5, Canada,London Health Sciences Centre, Children’s Health Research Institute London, Ontario N6C 2V5, Canada
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5K8, Canada,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Kandamurugu Manickam
- Division of Genetics and Genomics, Nationwide Children’s Hospital, Columbus, OH 43205 USA
| | - Daniel C. Koboldt
- The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Erin Crist
- The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Samantha S. Choi
- The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Sali M.K. Farhan
- Departments of Neurology and Neurosurgery, and Human Genetics, the Montreal Neurological Institute and Hospital, McGill University, 3801 Rue University, Montréal, QC H3A 2B4, Canada
| | - Helen Harvey
- Division of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Shifteh Sattar
- Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA,Division of Child Neurology, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Natalya Karp
- Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada,Department of Pediatrics, Division of Medical Genetics, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5K8, Canada
| | - Terence Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Richard Haas
- Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA,Division of Child Neurology, Rady Children’s Hospital, San Diego, CA 92123, USA,These authors contributed equally to this work
| | - Johan L.K. Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA,Department of Pathology and Laboratory Medicine, Children’s Hospital Colorado, 13121 East 16th Avenue, Aurora, CO 80045, USA,These authors contributed equally to this work
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Division of Pediatrics, University of California San Diego, San Diego, CA 92093, USA,These authors contributed equally to this work
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5
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Woodring TS, Mirza MH, Benavides V, Ellsworth KA, Wright MS, Javed MJ, Ramiro S. Uncertain, Not Unimportant: Callosal Dysgenesis and Variants of Uncertain Significance in ROBO1. Pediatrics 2021; 148:e2020019000. [PMID: 34193621 DOI: 10.1542/peds.2020-019000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Congenital anomalies affect 3% to 5% of births and remain the leading cause of infant death in the United States. As whole exome and genome sequencing are increasingly used to diagnose underlying genetic disease, the patient's clinical presentation remains the most important context for interpreting sequencing results, including frequently reported variants of uncertain significance (VUS). Classification of a variant as VUS acknowledges limits on evidence to establish whether a variant can be classified as pathogenic or benign according to the American College of Medical Genetics guidelines. Importantly, the VUS designation reflects limits on the breadth of evidence linking the genetic variant to a disease. However, available evidence, although limited, may be surprisingly relevant in an individual patient's case. Accordingly, a VUS result should be approached neither as nondiagnostic genetic result nor as automatically "uncertain" in its potential to guide clinical decision-making. In this article, we discuss a case of an infant born at 29 weeks 4 days without a corpus callosum, whose whole genome sequencing yielded compound heterozygous variants both classified as VUS in ROBO1, a gene encoding for a receptor involved in a canonical signaling mechanism that guides axons across midline. Approaching the VUS result as potentially pathogenic, we found the infant ultimately had pituitary dysfunction and renal anomalies consistent with other reported ROBO1 variants and basic science literature. Accordingly, we highlight resources for variant interpretation available to clinicians to evaluate VUS results, particularly as they inform the diagnosis of individually rare but collectively common rare diseases.
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Affiliation(s)
- Therese S Woodring
- University of Wisconsin Hospital and Clinics, Madison, Wisconsin
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | - Mohammed H Mirza
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | | | | | | | - M Jawad Javed
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
| | - Susan Ramiro
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
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6
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James KN, Lau M, Shayan K, Lenberg J, Mardach R, Ignacio R, Halbach J, Choi L, Kumar S, Ellsworth KA. Expanding the genotypic spectrum of ACTG2-related visceral myopathy. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006085. [PMID: 33883208 PMCID: PMC8208046 DOI: 10.1101/mcs.a006085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Visceral myopathies (VMs) encompass a spectrum of disorders characterized by chronic disruption of gastrointestinal function, with or without urinary system involvement. Pathogenic missense variation in smooth muscle γ-actin gene (ACTG2) is associated with autosomal dominant VM. Whole-genome sequencing of an infant presenting with chronic intestinal pseudo-obstruction revealed a homozygous 187 bp (c.589_613 + 163del188) deletion spanning the exon 6–intron 6 boundary within ACTG2. The patient's clinical course was marked by prolonged hospitalizations, multiple surgeries, and intermittent total parenteral nutrition dependence. This case supports the emerging understanding of allelic heterogeneity in ACTG2-related VM, in which both biallelic and monoallelic variants in ACTG2 are associated with gastrointestinal dysfunction of similar severity and overlapped clinical presentation. Moreover, it illustrates the clinical utility of rapid whole-genome sequencing, which can comprehensively and precisely detect different types of genomic variants including small deletions, leading to guidance of clinical care decisions.
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Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Megan Lau
- UC San Diego School of Medicine, La Jolla, California 92093, USA
| | - Katayoon Shayan
- Pathology Department, Hepatology and Nutrition, Rady Children's Hospital, San Diego, California 92123, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Rebecca Mardach
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Romeo Ignacio
- Division of Pediatric Surgery, Hepatology and Nutrition, Rady Children's Hospital, San Diego, California 92123, USA
| | - Jonathan Halbach
- Division of Pediatric Surgery, Hepatology and Nutrition, Rady Children's Hospital, San Diego, California 92123, USA
| | - Lillian Choi
- Division of Gastroenterology, Hepatology and Nutrition, Rady Children's Hospital, San Diego, California 92123, USA
| | - Soma Kumar
- Division of Gastroenterology, Hepatology and Nutrition, Rady Children's Hospital, San Diego, California 92123, USA
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7
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Chandrasekar I, Tourney A, Loo K, Carmichael J, James K, Ellsworth KA, Dimmock D, Joseph M. Hemimegalencephaly and intractable seizures associated with the NPRL3 gene variant in a newborn: A case report. Am J Med Genet A 2021; 185:2126-2130. [PMID: 33749980 DOI: 10.1002/ajmg.a.62185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/02/2021] [Accepted: 02/24/2021] [Indexed: 01/24/2023]
Abstract
Hemimegalencephaly (HME) is a rare hamartomatous congenital malformation of the brain characterized by dysplastic overgrowth of either one of the cerebral hemispheres. HME is associated with early onset seizures, abnormal neurological findings, and with subsequent cognitive and behavioral disabilities. Seizures associated with HME are often refractory to antiepileptic medications. Hemispherectomy is usually necessary to provide effective seizure control. The exact etiology of HME is not fully understood, but involves a disturbance in early brain development and likely involves genes responsible for patterning and symmetry of the brain. We present a female newborn who had refractory seizures due to HME. Whole genome sequencing revealed a novel, likely pathogenic, maternally inherited, 3Kb deletion encompassing exon 5 of the NPRL3 gene (chr16:161898-164745x1). The NPRL3 gene encodes for a nitrogen permease regulator 3-like protein, a subunit of the GATOR complex, which regulates the mTOR signaling pathway. A trial of mTOR inhibitor drug, Sirolimus, did not improve her seizure control. Functional hemispherectomy at 3 months of age resulted in total abatement of clinical seizures.
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Affiliation(s)
- Indira Chandrasekar
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Anne Tourney
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Kamela Loo
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Jason Carmichael
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Kiely James
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Katarzyna A Ellsworth
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - David Dimmock
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Maries Joseph
- Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
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8
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Simon MT, Eftekharian SS, Ferdinandusse S, Tang S, Naseri T, Reupena MS, McGarvey ST, Minster RL, Weeks DE, Nguyen DD, Lee S, Ellsworth KA, Vaz FM, Dimmock D, Pitt J, Abdenur JE. ECHS1 disease in two unrelated families of Samoan descent: Common variant - rare disorder. Am J Med Genet A 2021; 185:157-167. [PMID: 33112498 PMCID: PMC7746601 DOI: 10.1002/ajmg.a.61936] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/12/2020] [Accepted: 10/03/2020] [Indexed: 01/30/2023]
Abstract
Mutations in the short-chain enoyl-CoA hydratase (SCEH) gene, ECHS1, cause a rare autosomal recessive disorder of valine catabolism. Patients usually present with developmental delay, regression, dystonia, feeding difficulties, and abnormal MRI with bilateral basal ganglia involvement. We present clinical, biochemical, molecular, and functional data for four affected patients from two unrelated families of Samoan descent with identical novel compound heterozygous mutations. Family 1 has three affected boys while Family 2 has an affected daughter, all with clinical and MRI findings of Leigh syndrome and intermittent episodes of acidosis and ketosis. WES identified a single heterozygous variant in ECHS1 at position c.832G > A (p.Ala278Thr). However, western blot revealed significantly reduced ECHS1 protein for all affected family members. Decreased SCEH activity in fibroblasts and a mild increase in marker metabolites in urine further supported ECHS1 as the underlying gene defect. Additional investigations at the DNA (aCGH, WGS) and RNA (qPCR, RT-PCR, RNA-Seq, RNA-Array) level identified a silent, common variant at position c.489G > A (p.Pro163=) as the second mutation. This substitution, present at high frequency in the Samoan population, is associated with decreased levels of normally spliced mRNA. To our understanding, this is the first report of a novel, hypomorphic allele c.489G > A (p.Pro163=), associated with SCEH deficiency.
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Affiliation(s)
- Mariella T. Simon
- Division of Metabolic DisordersCHOC Children's HospitalOrangeCaliforniaUSA
- Department of Human GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Shaya S. Eftekharian
- Division of Metabolic DisordersCHOC Children's HospitalOrangeCaliforniaUSA
- College of Osteopathic MedicineWestern University of Health SciencesPomonaCaliforniaUSA
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMCUniversity of Amsterdam, Amsterdam Gastroenterology and MetabolismAmsterdamThe Netherlands
| | - Sha Tang
- Department of Clinical GenomicsAmbry GeneticsCaliforniaUSA
| | | | | | - Stephen T. McGarvey
- Department of EpidemiologyInternational Health Institute, Brown University School of Public HealthProvidenceRhode IslandUSA
| | - Ryan L. Minster
- Department of Human GeneticsGraduate School of Public Health, University of PittsburghPittsburghPennsylvaniaUSA
| | - Daniel E. Weeks
- Department of Human GeneticsGraduate School of Public Health, University of PittsburghPittsburghPennsylvaniaUSA
- Department of BiostatisticsGraduate School of Public Health, University of PittsburghPittsburghPennsylvaniaUSA
| | | | - Daniel D. Nguyen
- Division of Metabolic DisordersCHOC Children's HospitalOrangeCaliforniaUSA
- Department of BiochemistryCalifornia State University Long BeachLong BeachCaliforniaUSA
| | - Sansan Lee
- Hawaii Community GeneticsHawai'i Pacific HealthHonoluluHawaiiUSA
| | | | - Frédéric M. Vaz
- Department of PaediatricsUniversity of Melbourne, Victorian Clinical Genetics Services, Murdoch Childrens Research InstituteMelbourneVictoriaAustralia
| | - David Dimmock
- Rady Children's Institute for Genomic MedicineSan DiegoCaliforniaUSA
| | - James Pitt
- Department of PaediatricsUniversity of Melbourne, Victorian Clinical Genetics Services, Murdoch Childrens Research InstituteMelbourneVictoriaAustralia
| | - Jose E. Abdenur
- Division of Metabolic DisordersCHOC Children's HospitalOrangeCaliforniaUSA
- Department of PediatricsUniversity of California IrvineOrangeCaliforniaUSA
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9
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Sanford E, Wong T, Ellsworth KA, Ingulli E, Kingsmore SF. Clinical utility of ultra-rapid whole-genome sequencing in an infant with atypical presentation of WT1-associated nephrotic syndrome type 4. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005470. [PMID: 32843431 PMCID: PMC7476414 DOI: 10.1101/mcs.a005470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022] Open
Abstract
Relatively little is known about phenotypic variability in nonsyndromic nephropathy associated with the gene encoding the WT1 transcription factor. We report a 12-mo-old female who presented with vomiting, diarrhea, and fatigue in the setting of renal failure and malignant hypertension. Trio ultra-rapid whole-genome sequencing identified a novel, likely pathogenic, de novo missense variant (c.485T > A, p.Val162Asp) in WT1 in 46 h, consistent with a diagnosis of nephrotic syndrome type 4 (NPHS4; OMIM 256370). This disorder typically presents with nephrotic syndrome (gross proteinuria, hypoalbuminemia, and edema). Rapid diagnosis had an immediate impact on her clinical management in the pediatric intensive care unit. Diagnostic renal biopsy was avoided, and placement of permanent dialysis access, a gastrostomy tube, and bilateral nephrectomy were accelerated. This report expands the presenting phenotype of nonsyndromic nephrotic syndrome and/or renal failure due to heterozygous variants in WT1 (NPHS4). It also highlights the relationship between time to genomic diagnosis and clinical utility in critically ill infants.
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Affiliation(s)
- Erica Sanford
- Rady Children's Institute of Genomic Medicine, Rady Children's Hospital–San Diego, San Diego, California 92123, USA;,Division of Pediatric Intensive Care Medicine, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Terence Wong
- Rady Children's Institute of Genomic Medicine, Rady Children's Hospital–San Diego, San Diego, California 92123, USA
| | - Katarzyna A. Ellsworth
- Rady Children's Institute of Genomic Medicine, Rady Children's Hospital–San Diego, San Diego, California 92123, USA
| | - Elizabeth Ingulli
- Division of Pediatric Nephrology, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Stephen F. Kingsmore
- Rady Children's Institute of Genomic Medicine, Rady Children's Hospital–San Diego, San Diego, California 92123, USA
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10
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Rabin R, Radmanesh A, Glass IA, Dobyns WB, Aldinger KA, Shieh JT, Romoser S, Bombei H, Dowsett L, Trapane P, Bernat JA, Baker J, Mendelsohn NJ, Popp B, Siekmeyer M, Sorge I, Sansbury FH, Watts P, Foulds NC, Burton J, Hoganson G, Hurst JA, Menzies L, Osio D, Kerecuk L, Cobben JM, Jizi K, Jacquemont S, Bélanger SA, Löhner K, Veenstra-Knol HE, Lemmink HH, Keller-Ramey J, Wentzensen IM, Punj S, McWalter K, Lenberg J, Ellsworth KA, Radtke K, Akbarian S, Pappas J. Genotype-phenotype correlation at codon 1740 of SETD2. Am J Med Genet A 2020; 182:2037-2048. [PMID: 32710489 DOI: 10.1002/ajmg.a.61724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 10/24/2019] [Revised: 03/10/2020] [Accepted: 05/08/2020] [Indexed: 11/06/2022]
Abstract
The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2.
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Affiliation(s)
- Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA
| | - Alireza Radmanesh
- Division of Pediatric Neuroradiology, Department of Radiology, NYU School of Medicine, New York, New York, USA
| | - Ian A Glass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA.,Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joseph T Shieh
- Institute for Human Genetics, Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, California, USA
| | - Shelby Romoser
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Hannah Bombei
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Leah Dowsett
- Kapi'olani Medical Specialists and Department of Pediatrics, University of Hawai'i John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Pamela Trapane
- Division of Pediatric Genetics, Department of Pediatrics, University of Florida College of Medicine-Jacksonville, Jacksonville, Florida, USA
| | - John A Bernat
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Janice Baker
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | | | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Ina Sorge
- Department of Pediatric Radiology, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Francis Hugh Sansbury
- All Wales Medical Genomics Service, Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Patrick Watts
- Department of Ophthalmology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Services, Southampton University Hospital NHS Foundation Trust, Southampton, UK
| | - Jennifer Burton
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - George Hoganson
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Jane A Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Deborah Osio
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Larissa Kerecuk
- Renal Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Jan M Cobben
- North West Thames Regional Genetic Services, Northwick Park Hospitals NHS Foundation Trust, London, UK.,Emma Children Hospital, Amsterdam, The Netherlands
| | - Khadijé Jizi
- CHU Sainte-Justine Hospital, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stacey A Bélanger
- Development Clinic, CHU Sainte-Justine Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | | | | | - Jerica Lenberg
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, California, USA
| | | | - Kelly Radtke
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA.,Clinical Genetics, NYU Orthopedic Hospital, New York, New York, USA
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11
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Ellsworth KA, Eckloff BW, Li L, Moon I, Fridley BL, Jenkins GD, Carlson E, Brisbin A, Abo R, Bamlet W, Petersen G, Wieben ED, Wang L. Contribution of FKBP5 genetic variation to gemcitabine treatment and survival in pancreatic adenocarcinoma. PLoS One 2013; 8:e70216. [PMID: 23936393 PMCID: PMC3731355 DOI: 10.1371/journal.pone.0070216] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/17/2013] [Indexed: 01/06/2023] Open
Abstract
PURPOSE FKBP51, (FKBP5), is a negative regulator of Akt. Variability in FKBP5 expression level is a major factor contributing to variation in response to chemotherapeutic agents including gemcitabine, a first line treatment for pancreatic cancer. Genetic variation in FKBP5 could influence its function and, ultimately, treatment response of pancreatic cancer. EXPERIMENTAL DESIGN We set out to comprehensively study the role of genetic variation in FKBP5 identified by Next Generation DNA resequencing on response to gemcitabine treatment of pancreatic cancer by utilizing both tumor and germline DNA samples from 43 pancreatic cancer patients, including 19 paired normal-tumor samples. Next, genotype-phenotype association studies were performed with overall survival as well as with FKBP5 gene expression in tumor using the same samples in which resequencing had been performed, followed by functional genomics studies. RESULTS In-depth resequencing identified 404 FKBP5 single nucleotide polymorphisms (SNPs) in normal and tumor DNA. SNPs with the strongest associations with survival or FKBP5 expression were subjected to functional genomic study. Electromobility shift assay showed that the rs73748206 "A(T)" SNP altered DNA-protein binding patterns, consistent with significantly increased reporter gene activity, possibly through its increased binding to Glucocorticoid Receptor (GR). The effect of rs73748206 was confirmed on the basis of its association with FKBP5 expression by affecting the binding to GR in lymphoblastoid cell lines derived from the same patients for whom DNA was used for resequencing. CONCLUSION This comprehensive FKBP5 resequencing study provides insights into the role of genetic variation in variation of gemcitabine response.
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Affiliation(s)
- Katarzyna A. Ellsworth
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Bruce W. Eckloff
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Liang Li
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Irene Moon
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Brooke L. Fridley
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gregory D. Jenkins
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Erin Carlson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Abra Brisbin
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Ryan Abo
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - William Bamlet
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gloria Petersen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric D. Wieben
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Liewei Wang
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
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12
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Ellsworth KA, Eckloff BW, Li L, Moon I, Fridley BL, Jenkins GD, Carlson E, Brisbin A, Abo R, Bamlet W, Petersen G, Wieben ED, Wang L. Abstract 2209: Contribution of FKBP5 genetic variation to gemcitabine treatment and survival in pancreatic cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The FKBP5 gene encodes the FKBP51 immunophilin, a negative regulator of AKT. Variability in level of FKBP5 expression is a major factor contributing to variation in response to several classes of chemotherapeutic agents including gemcitabine, first line treatment for pancreatic cancer. Genetic variation of FKBP5 could influence its expression, function, and, ultimately, treatment response of pancreatic cancer. We set out to comprehensively study the role of genetic variation in FKBP5 identified by Next Generation DNA resequencing in response to gemcitabine treatment of pancreatic cancer by utilizing both tumor and germline DNA samples from 43 pancreatic cancer patients, including 19 paired tumor-normal samples. Genotype-phenotype association studies with overall survival (in tumor only) as well as with FKBP5 gene expression were performed using the same samples in which Next Generation DNA resequencing had been performed, followed by functional genomic studies of top selected single nucleotide polymorphisms (SNPs). In-depth resequencing identified 404 FKBP5 SNPs in both normal and tumor DNA patient samples. SNPs with the smallest p-values for association with FKBP5 survival or expression were subjected to functional genomic studies. Electromobility shift assay (EMSA) showed that the rs73748206 “T” allele altered DNA-protein binding patterns, consistent with a significantly increased reporter gene activity. The effect of rs73748206 was also confirmed by mRNA expression studies using lymphoblastoid cell lines (LCL) derived from the same patients from whom DNA used for resequencing had been obtained. This comprehensive FKBP5 resequencing study provides insight into the role of inheritance in variation in response to gemcitabine therapy of pancreatic cancer.
Citation Format: Katarzyna A. Ellsworth, Bruce W. Eckloff, Liang Li, Irene Moon, Brooke L. Fridley, Greg D. Jenkins, Erin Carlson, Abra Brisbin, Ryan Abo, William Bamlet, Gloria Petersen, Eric D. Wieben, Liewei Wang. Contribution of FKBP5 genetic variation to gemcitabine treatment and survival in pancreatic cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2209. doi:10.1158/1538-7445.AM2013-2209
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13
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Brisbin A, Jenkins GD, Ellsworth KA, Wang L, Fridley BL. Localization of association signal from risk and protective variants in sequencing studies. Front Genet 2012; 3:173. [PMID: 22973297 PMCID: PMC3434438 DOI: 10.3389/fgene.2012.00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 05/15/2012] [Accepted: 08/19/2012] [Indexed: 11/13/2022] Open
Abstract
Aggregating information across multiple variants in a gene or region can improve power for rare variant association testing. Power is maximized when the aggregation region contains many causal variants and few neutral variants. In this paper, we present a method for the localization of the association signal in a region using a sliding-window based approach to rare variant association testing in a region. We first introduce a novel method for analysis of rare variants, the Difference in Minor Allele Frequency test (DMAF), which allows combined analysis of common and rare variants, and makes no assumptions about the direction of effects. In whole-region analyses of simulated data with risk and protective variants, DMAF and other methods which pool data across individuals were found to outperform methods which pool data across variants. We then implement a sliding-window version of DMAF, using a step-down permutation approach to control type I error with the testing of multiple windows. In simulations, the sliding-window DMAF improved power to detect a causal sub-region, compared to applying DMAF to the whole region. Sliding-window DMAF was also effective in localizing the causal sub-region. We also applied the DMAF sliding-window approach to test for an association between response to the drug gemcitabine and variants in the gene FKBP5 sequenced in 91 lymphoblastoid cell lines derived from white non-Hispanic individuals. The application of the sliding-window test procedure detected an association in a sub-region spanning an exon and two introns, when rare and common variants were analyzed together.
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Affiliation(s)
- Abra Brisbin
- Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
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14
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Wang L, Ellsworth KA, Moon I, Pelleymounter LL, Eckloff BW, Martin YN, Fridley BL, Jenkins GD, Batzler A, Suman VJ, Ravi S, Dixon JM, Miller WR, Wieben ED, Buzdar A, Weinshilboum RM, Ingle JN. Functional genetic polymorphisms in the aromatase gene CYP19 vary the response of breast cancer patients to neoadjuvant therapy with aromatase inhibitors. Cancer Res 2010; 70:319-28. [PMID: 20048079 DOI: 10.1158/0008-5472.can-09-3224] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aromatase (CYP19) is a critical enzyme in estrogen biosynthesis and aromatase inhibitors (AI) are employed widely for endocrine therapy in postmenopausal women with breast cancer. We hypothesized that single nucleotide polymorphisms (SNPs) in the CYP19 gene may alter the effectiveness of AI therapy in the neoadjuvant setting. Genomic DNA was obtained for sequencing from 52 women pre-AI and post-AI treatment in this setting. Additionally, genomic DNA obtained from 82 samples of breast cancer and 19 samples of normal breast tissue was subjected to resequencing. No differences in CYP19 sequence were observed between tumor and germ-line DNA in the same patient. A total of 48 SNPs were identified including 4 novel SNPs when compared with previous resequencing data. For genotype-phenotype association studies, we determined the levels of aromatase activity, estrone, estradiol, and tumor size in patients pre-AI and post-AI treatment. We defined two tightly linked SNPs (rs6493497 and rs7176005 in the 5'-flanking region of CYP19 exon 1.1) that were significantly associated with a greater change in aromatase activity after AI treatment. In a follow-up study of 200 women with early-stage breast cancer who were treated with adjuvant anastrozole, these same two SNPs were also associated with higher plasma estradiol levels in patients pre-AI and post-AI treatment. Electrophoretic mobility shift and reporter gene assays confirmed likely functional effects of these two SNPs on transcription of CYP19. Our findings indicate that two common genetic polymorphisms in the aromatase gene CYP19 vary the response of breast cancer patients to aromatase inhibitors.
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Affiliation(s)
- Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA.
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15
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Grebb JA, Ellsworth KA, Freed WJ. Differences between calcium channel inhibitors in their effects on phencyclidine-induced behavioral stimulation in mice. Pharmacol Biochem Behav 1985; 23:613-8. [PMID: 4070337 DOI: 10.1016/0091-3057(85)90426-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Sixteen calcium channel inhibitors (CCI's) were tested in a model utilizing phencyclidine (PCP)-induced behavioral stimulation in mice. There were marked differences in the effects of CCI's both within subclasses and between subclasses of CCI's. All of the dihydropyridines and possibly flunarizine were effective in blocking PCP-induced behavioral stimulation. Papaverine derivatives, including verapamil, and several other CCI's, were ineffective.
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