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Drexler KA, Talati AN, Gilmore KL, Veazey RV, Powell BC, Weck KE, Davis EE, Vora NL. Association of deep phenotyping with diagnostic yield of prenatal exome sequencing for fetal brain abnormalities. Genet Med 2023; 25:100915. [PMID: 37326029 PMCID: PMC10580430 DOI: 10.1016/j.gim.2023.100915] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE To evaluate whether deep prenatal phenotyping of fetal brain abnormalities (FBAs) increases diagnostic yield of trio-exome sequencing (ES) compared with standard phenotyping. METHODS Retrospective exploratory analysis of a multicenter prenatal ES study. Participants were eligible if an FBA was diagnosed and subsequently found to have a normal microarray. Deep phenotyping was defined as phenotype based on targeted ultrasound plus prenatal/postnatal magnetic resonance imaging, autopsy, and/or known phenotypes of other affected family members. Standard phenotyping was based on targeted ultrasound alone. FBAs were categorized by major brain findings on prenatal ultrasound. Cases with positive ES results were compared with those that have negative results by available phenotyping, as well as diagnosed FBAs. RESULTS A total of 76 trios with FBAs were identified, of which 25 (33%) cases had positive ES results and 51 (67%) had negative results. Individual modalities of deep phenotyping were not associated with diagnostic ES results. The most common FBAs identified were posterior fossa anomalies and midline defects. Neural tube defects were significantly associated with receipt of a negative ES result (0% vs 22%, P = .01). CONCLUSION Deep phenotyping was not associated with increased diagnostic yield of ES for FBA in this small cohort. Neural tube defects were associated with negative ES results.
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Affiliation(s)
- Kathleen A Drexler
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Asha N Talati
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly L Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rachel V Veazey
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford C Powell
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen E Weck
- Department of Genetics, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erica E Davis
- Department of Pediatrics, Department of Cell and Developmental Biology, Feinberg School of Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University, Chicago, IL
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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3
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Patterson V, Ullah F, Bryant L, Griffin JN, Sidhu A, Saliganan S, Blaile M, Saenz MS, Smith R, Ellingwood S, Grange DK, Hu X, Mireguli M, Luo Y, Shen Y, Mulhern M, Zackai E, Ritter A, Izumi K, Hoefele J, Wagner M, Riedhammer KM, Seitz B, Robin NH, Goodloe D, Mignot C, Keren B, Cox H, Jarvis J, Hempel M, Gibson CF, Tran Mau-Them F, Vitobello A, Bruel AL, Sorlin A, Mehta S, Raymond FL, Gilmore K, Powell BC, Weck K, Li C, Vulto-van Silfhout AT, Giacomini T, Mancardi MM, Accogli A, Salpietro V, Zara F, Vora NL, Davis EE, Burdine R, Bhoj E. Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish. Sci Adv 2023; 9:eade0631. [PMID: 37126546 PMCID: PMC10132768 DOI: 10.1126/sciadv.ade0631] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
We report 21 families displaying neurodevelopmental differences and multiple congenital anomalies while bearing a series of rare variants in mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4). MAP4K4 has been implicated in many signaling pathways including c-Jun N-terminal and RAS kinases and is currently under investigation as a druggable target for multiple disorders. Using several zebrafish models, we demonstrate that these human variants are either loss-of-function or dominant-negative alleles and show that decreasing Map4k4 activity causes developmental defects. Furthermore, MAP4K4 can restrain hyperactive RAS signaling in early embryonic stages. Together, our data demonstrate that MAP4K4 negatively regulates RAS signaling in the early embryo and that variants identified in affected humans abrogate its function, establishing MAP4K4 as a causal locus for individuals with syndromic neurodevelopmental differences.
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Affiliation(s)
- Victoria Patterson
- Princeton University, Princeton, NJ 08544, USA
- Department of Biology, University of York, York, UK
| | - Farid Ullah
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura Bryant
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John N. Griffin
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Alpa Sidhu
- The Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | | | - Mackenzie Blaile
- University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA
| | - Margarita S. Saenz
- University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA
| | - Rosemarie Smith
- Maine Medical Center, 22 Bramhall St, Portland, ME 04102, USA
| | - Sara Ellingwood
- Maine Medical Center, 22 Bramhall St, Portland, ME 04102, USA
| | - Dorothy K. Grange
- St. Louis Children’s Hospital, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, USA
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Maimaiti Mireguli
- First Affiliated Hospital of Xinjiang Medical University, Department of Pediatrics, Xinjiang Uygur Autonomous Region, China
| | - Yanfei Luo
- First Affiliated Hospital of Xinjiang Medical University, Department of Pediatrics, Xinjiang Uygur Autonomous Region, China
| | - Yiping Shen
- Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Maternal and Child Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi, Nanning, China
| | - Maureen Mulhern
- Columbia University Irving Medical Center, 630 W. 168th St, New York, NY 10032, USA
| | - Elaine Zackai
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alyssa Ritter
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kosaki Izumi
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatrics, Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University Hospital of Munich, Ludwig Maximilians University, Munich, Germany
| | - Korbinian M. Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Nathaniel H. Robin
- University of Alabama at Birmingham, 1720 University Blvd, Birmingham, AL 35233, USA
| | - Dana Goodloe
- University of Alabama at Birmingham, 1720 University Blvd, Birmingham, AL 35233, USA
| | - Cyril Mignot
- APHP-Sorbonne Université, GH Pitié-Salpêtrière, Paris, France
| | - Boris Keren
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Helen Cox
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Joanna Jarvis
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Maja Hempel
- University Hospital Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | | | | | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | | | | | | | - Kelly Gilmore
- Department of Ob/Gyn, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chumei Li
- McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | | | - Thea Giacomini
- Unit of Child Neuropsychiatry, University of Genova, EpiCARE Network, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Science, University of L’Aquila, 67100 L’Aquila, Italy
| | - Federico Zara
- Department of Biotechnological and Applied Clinical Science, University of L’Aquila, 67100 L’Aquila, Italy
| | - Neeta L. Vora
- Department of Ob/Gyn, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erica E. Davis
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Elizabeth Bhoj
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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4
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Waltz M, Yan H, Cadigan RJ, Canter C, Bain L, Bensen JT, Conway C, Haldeman-Englert C, Farnan L, M Foreman AK, Grant TL, Leach B, Lin FC, Mahla M, O'Daniel JM, O'Neill SC, Smith G, Powell BC, Berg JS, Rini CM. Question prompt lists and caregiver question asking in pediatric specialty appointments: A randomized controlled trial. Patient Educ Couns 2023; 109:107620. [PMID: 36689884 PMCID: PMC9931668 DOI: 10.1016/j.pec.2022.107620] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/09/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVE Question prompt lists (QPLs) have been effective at increasing patient involvement and question asking in medical appointments, which is critical for shared decision making. We investigated whether pre-visit preparation (PVP), including a QPL, would increase question asking among caregivers of pediatric patients with undiagnosed, suspected genetic conditions. METHODS Caregivers were randomized to receive the PVP before their appointment (n = 59) or not (control, n = 53). Appointments were audio-recorded. Transcripts were analyzed to determine questions asked. RESULTS Caregivers in the PVP group asked more questions (MeanPVP = 4.36, SDPVP = 4.66 vs. Meancontrol = 2.83, SDcontrol = 3.03, p = 0.045), including QPL questions (MeanPVP = 1.05, SDPVP = 1.39 vs. Meancontrol = 0.36, SDcontrol = 0.81, p = 0.002). Caregivers whose child had insurance other than Medicaid in the PVP group asked more total and QPL questions than their counterparts in the control group (ps = 0.005 and 0.002); there was no intervention effect among caregivers of children with Medicaid or no insurance (ps = 0.775 and 0.166). CONCLUSION The PVP increased question asking but worked less effectively among traditionally underserved groups. Additional interventions, including provider-focused efforts, may be needed to promote engagement of underserved patients. PRACTICE IMPLICATIONS Patient/family-focused interventions may not be beneficial for all populations. Providers should be aware of potential implicit and explicit biases and encourage question asking to promote patient/family engagement.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA.
| | - Haoyang Yan
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - R Jean Cadigan
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Courtney Canter
- Department of Anthropology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Carol Conway
- Parent/Advocate, Parent Advocates for Adult Children with Intellectual &/or Developmental Disabilities in NC, Chapel Hill, NC, USA
| | | | - Laura Farnan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Tracey L Grant
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Barbara Leach
- Parent/Advocate, Family Support Program, School of Social Work, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Madeline Mahla
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Bradford C Powell
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Christine M Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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5
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Bowling KM, Thompson ML, Kelly MA, Scollon S, Slavotinek AM, Powell BC, Kirmse BM, Hendon LG, Brothers KB, Korf BR, Cooper GM, Greally JM, Hurst ACE. Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing. Genome Med 2022; 14:131. [PMID: 36414972 PMCID: PMC9682742 DOI: 10.1186/s13073-022-01139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The uptake of exome/genome sequencing has introduced unexpected testing results (incidental findings) that have become a major challenge for both testing laboratories and providers. While the American College of Medical Genetics and Genomics has outlined guidelines for laboratory management of clinically actionable secondary findings, debate remains as to whether incidental findings should be returned to patients, especially those representing pediatric populations. METHODS The Sequencing Analysis and Diagnostic Yield working group in the Clinical Sequencing Evidence-Generating Research Consortium has collected a cohort of pediatric patients found to harbor a genomic sequencing-identified non-ACMG-recommended incidental finding. The incidental variants were not thought to be associated with the indication for testing and were disclosed to patients and families. RESULTS In total, 23 "non-ACMG-recommended incidental findings were identified in 21 pediatric patients included in the study. These findings span four different research studies/laboratories and demonstrate differences in incidental finding return rate across study sites. We summarize specific cases to highlight core considerations that surround identification and return of incidental findings (uncertainty of disease onset, disease severity, age of onset, clinical actionability, and personal utility), and suggest that interpretation of incidental findings in pediatric patients can be difficult given evolving phenotypes. Furthermore, return of incidental findings can benefit patients and providers, but do present challenges. CONCLUSIONS While there may be considerable benefit to return of incidental genetic findings, these findings can be burdensome to providers and present risk to patients. It is important that laboratories conducting genomic testing establish internal guidelines in anticipation of detection. Moreover, cross-laboratory guidelines may aid in reducing the potential for policy heterogeneity across laboratories as it relates to incidental finding detection and return. However, future discussion is required to determine whether cohesive guidelines or policy statements are warranted.
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Affiliation(s)
- Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, LLC, HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anne M Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA, 94158, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian M Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Laura G Hendon
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kyle B Brothers
- Norton Children's Research Institute Affiliated with UofL School of Medicine, Louisville, KY, 40202, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 25294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 25294, USA.
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6
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Waltz M, Canter C, Bensen JT, Berg JS, Foreman AKM, Grant TL, Lich KH, Navas A, O’Daniel JM, Powell BC, Rini CM, Staley BS, Cadigan RJ. The Burden of COVID-19 on Caregivers of Children with Suspected Genetic Conditions: A Therapeutic Odyssey. Phys Occup Ther Pediatr 2022; 43:257-271. [PMID: 36310386 PMCID: PMC10079636 DOI: 10.1080/01942638.2022.2138734] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
AIMS Children with disabilities and rare or undiagnosed conditions and their families have faced numerous hardships of living during the COVID-19 pandemic. For those with undiagnosed conditions, the diagnostic odyssey can be long, expensive, and marked by uncertainty. We, therefore, sought to understand whether and how COVID-19 impacted the trajectory of children's care. METHODS We conducted semi-structured qualitative interviews with 25 caregivers who, prior to the pandemic, were on a diagnostic odyssey for their children. RESULTS Most caregivers did not report any interruptions to their child's diagnostic odyssey. The greatest impact was access to therapy services, including the suspension or loss of their child's in-person therapeutic care and difficulties with virtual therapies. This therapy gap caused caregivers to fear that their children were not making progress. CONCLUSION Although much has been written about the challenges of diagnostic odysseys for children and their families, this study illustrates the importance of expanding the focus of these studies to include therapeutic odysseys. Because therapeutic odysseys continue regardless of whether diagnoses are made, future research should investigate how to support caregivers through children's therapies within and outside of the COVID-19 context.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Courtney Canter
- Department of Anthropology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | - Tracey L. Grant
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Kristen Hassmiller Lich
- Department of Health Policy and Management, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Angelo Navas
- Department of Pediatrics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Julianne M. O’Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Christine M. Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brooke S. Staley
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - R. Jean Cadigan
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
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7
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Hunter JE, Jenkins CL, Bulkley JE, Gilmore MJ, Lee K, Pak CM, Wallace KE, Buchanan AH, Foreman AKM, Freed AS, Goehringer S, Manickam K, Meeks NJL, Ramos EM, Shah N, Steiner RD, Subramanian SL, Trotter T, Webber EM, Williams MS, Goddard KAB, Powell BC. ClinGen's Pediatric Actionability Working Group: Clinical actionability of secondary findings from genome-scale sequencing in children and adolescents. Genet Med 2022; 24:1328-1335. [PMID: 35341655 PMCID: PMC9156571 DOI: 10.1016/j.gim.2022.02.019] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Synthesis and curation of evidence regarding the clinical actionability of secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting of these findings. To assess actionability of SFs in children and adolescents, the Clinical Genome Resource established the Pediatric Actionability Working Group (AWG). METHODS The Pediatric AWG modified the framework of the existing Adult AWG, which included production of summary reports of actionability for genes and associated conditions and consensus actionability scores for specific outcome-intervention pairs. Modification of the adult framework for the pediatric setting included accounting for special considerations for reporting presymptomatic or predictive genetic findings in the pediatric context, such as maintaining future autonomy by not disclosing conditions not actionable until adulthood. The Pediatric AWG then applied this new framework to genes and associated conditions with putative actionability. RESULTS As of September 2021, the Pediatric AWG applied the new framework to 70 actionability topics representing 143 genes. Reports and scores are publicly available at www.clinicalgenome.org. CONCLUSION The Pediatric AWG continues to curate gene-condition topics and build an evidence-based resource, supporting clinical communities and decision-makers with policy development on the return of SFs in pediatric populations.
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Affiliation(s)
- Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, ResearchTriangle Park, NC.
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Marian J Gilmore
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Kristy Lee
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine M Pak
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Kathleen E Wallace
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amanda S Freed
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA
| | | | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH; The Ohio State University College of Medicine, Columbus, OH
| | - Naomi J L Meeks
- Section of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Erin M Ramos
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Neethu Shah
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Robert D Steiner
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | | | | | | | | | - Katrina A B Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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8
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Muenzen KD, Amendola LM, Kauffman TL, Mittendorf KF, Bensen JT, Chen F, Green R, Powell BC, Kvale M, Angelo F, Farnan L, Fullerton SM, Robinson JO, Li T, Murali P, Lawlor JM, Ou J, Hindorff LA, Jarvik GP, Crosslin DR. Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience. Human Genetics and Genomics Advances 2022; 3:100120. [PMID: 35707062 PMCID: PMC9190054 DOI: 10.1016/j.xhgg.2022.100120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Integrating data across heterogeneous research environments is a key challenge in multi-site, collaborative research projects. While it is important to allow for natural variation in data collection protocols across research sites, it is also important to achieve interoperability between datasets in order to reap the full benefits of collaborative work. However, there are few standards to guide the data coordination process from project conception to completion. In this paper, we describe the experiences of the Clinical Sequence Evidence-Generating Research (CSER) consortium Data Coordinating Center (DCC), which coordinated harmonized survey and genomic sequencing data from seven clinical research sites from 2020 to 2022. Using input from multiple consortium working groups and from CSER leadership, we first identify 14 lessons learned from CSER in the categories of communication, harmonization, informatics, compliance, and analytics. We then distill these lessons learned into 11 recommendations for future research consortia in the areas of planning, communication, informatics, and analytics. We recommend that planning and budgeting for data coordination activities occur as early as possible during consortium conceptualization and development to minimize downstream complications. We also find that clear, reciprocal, and continuous communication between consortium stakeholders and the DCC is equally important to maintaining a secure and centralized informatics ecosystem for pooling data. Finally, we discuss the importance of actively interrogating current approaches to data governance, particularly for research studies that straddle the research-clinical divide.
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9
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [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: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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10
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Spees LP, Hicklin K, Adams MC, Farnan L, Bensen JT, Gilleskie DB, Berg JS, Powell BC, Lich KH. Testing and extending strategies for identifying genetic disease-related encounters in pediatric patients. Genet Med 2022; 24:831-838. [PMID: 35034852 PMCID: PMC8995346 DOI: 10.1016/j.gim.2021.12.001] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE To better understand health care utilization and develop decision support tools, methods for identifying patients with suspected genetic diseases (GDs) are needed. Previous studies had identified inpatient-relevant International Classification of Diseases (ICD) codes that were possibly, probably, or definitely indicative of GDs. We assessed whether these codes identified GD-related inpatient, outpatient, and emergency department encounters among pediatric patients with suspected GDs from a previous study (the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing [NCGENES] study). METHODS Using the electronic medical records of 140 pediatric patients from the NCGENES study, we characterized the presence of ICD codes representing possible, probable, or definite GD-related diagnoses across encounter types. In addition, we examined codes from encounters for which initially no GD-related codes had been found and determined whether these codes were indicative of a GD. RESULTS Among NCGENES patients with visits between 2014 and 2017, 92% of inpatient, 75% of emergency department, and 63% of outpatient encounters included ≥1 GD-related code. Encounters with highly specific (ie, definite) GD codes had fewer low-specificity GD codes than encounters with only low-specificity GD codes. We identified an additional 32 ICD-9 and 56 ICD-10 codes possibly indicative of a GD. CONCLUSION Code-based strategies can be refined to assess health care utilization among pediatric patients and may contribute to a systematic approach to identify patients with suspected GDs.
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Affiliation(s)
- Lisa P Spees
- Department of Health Policy and Management, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Karen Hicklin
- Department of Industrial & Systems Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL
| | - Michael C Adams
- Division of Pediatric Genetics & Metabolism, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura Farnan
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jeannette T Bensen
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Donna B Gilleskie
- Department of Economics, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S Berg
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford C Powell
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kristen Hassmiller Lich
- Department of Health Policy and Management, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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11
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Filer DL, Kuo F, Brandt AT, Tilley CR, Mieczkowski PA, Berg JS, Robasky K, Li Y, Bizon C, Tilson JL, Powell BC, Bost DM, Jeffries CD, Wilhelmsen KC. Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing. BMC Bioinformatics 2021; 22:374. [PMID: 34284719 PMCID: PMC8293537 DOI: 10.1186/s12859-021-04246-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022] Open
Abstract
Background As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number variants (CNVs) often get overlooked or obscured by under-powered data collection. Many groups have developed methodology for detecting CNVs from ES, but existing methods often perform poorly for small CNVs and rely on large numbers of samples not always available to clinical laboratories. Furthermore, methods often rely on Bayesian approaches requiring user-defined priors in the setting of insufficient prior knowledge. This report first demonstrates the benefit of multiplexed exome capture (pooling samples prior to capture), then presents a novel detection algorithm, mcCNV (“multiplexed capture CNV”), built around multiplexed capture. Results We demonstrate: (1) multiplexed capture reduces inter-sample variance; (2) our mcCNV method, a novel depth-based algorithm for detecting CNVs from multiplexed capture ES data, improves the detection of small CNVs. We contrast our novel approach, agnostic to prior information, with the the commonly-used ExomeDepth. In a simulation study mcCNV demonstrated a favorable false discovery rate (FDR). When compared to calls made from matched genome sequencing, we find the mcCNV algorithm performs comparably to ExomeDepth. Conclusion Implementing multiplexed capture increases power to detect single-exon CNVs. The novel mcCNV algorithm may provide a more favorable FDR than ExomeDepth. The greatest benefits of our approach derive from (1) not requiring a database of reference samples and (2) not requiring prior information about the prevalance or size of variants. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04246-w.
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Affiliation(s)
- Dayne L Filer
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA. .,Renaissance Computing Institute, Chapel Hill, USA.
| | - Fengshen Kuo
- Renaissance Computing Institute, Chapel Hill, USA
| | - Alicia T Brandt
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA
| | | | | | - Jonathan S Berg
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA
| | - Kimberly Robasky
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA.,UNC School of Information and Library Science, Chapel Hill, USA
| | - Yun Li
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, USA
| | - Chris Bizon
- Renaissance Computing Institute, Chapel Hill, USA
| | | | - Bradford C Powell
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA
| | - Darius M Bost
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA
| | | | - Kirk C Wilhelmsen
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA.,Department of Neurology, UNC School of Medicine, Chapel Hill, USA
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12
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Filer DL, Mieczkowski PA, Brandt A, Gilmore KL, Powell BC, Berg JS, Wilhelmsen KC, Vora NL. Noninvasive prenatal exome sequencing diagnostic utility limited by sequencing depth and fetal fraction. Prenat Diagn 2021; 42:567-573. [PMID: 34265090 DOI: 10.1002/pd.6009] [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] [Received: 10/08/2020] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Sequencing cell-free DNA now allows detection of large chromosomal abnormalities and dominant Mendelian disorders in the prenatal period. Improving upon these methods would allow newborn screening programs to begin with prenatal genetics, ultimately improving the management of rare genetic disorders. METHODS As a pilot study, we performed exome sequencing on the cell-free DNA from three mothers with singleton pregnancies to assess the viability of broad sequencing modalities in a noninvasive prenatal setting. RESULTS We found poor resolution of maternal and fetal genotypes due to both sampling and technical issues. CONCLUSION We find broad sequencing modalities inefficient for noninvasive prenatal applications. Alternatively, we suggest a more targeted path forward for noninvasive prenatal genotyping.
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Affiliation(s)
- Dayne L Filer
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA.,Renaissance Computing Institute, Chapel Hill, NC, USA
| | - Piotr A Mieczkowski
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Kelly L Gilmore
- Department of Obstetrics & Gynecology, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA.,Renaissance Computing Institute, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Kirk C Wilhelmsen
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA.,Renaissance Computing Institute, Chapel Hill, NC, USA.,Department of Neurology, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Neeta L Vora
- Department of Genetics, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA.,Department of Obstetrics & Gynecology, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
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13
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Blatt J, Parekh P, Powell BC, Fedoriw Y, Reddy I, Montgomery ND. Rosai-Dorfman Disease and Exocrine Pancreatic Insufficiency in a Patient With a Germline SLC29A3 Mutation. J Pediatr Hematol Oncol 2021; 43:e689-e691. [PMID: 32769566 DOI: 10.1097/mph.0000000000001889] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/04/2020] [Indexed: 11/26/2022]
Abstract
Rosai-Dorfman disease (RDD) typically presents as bulky lymphadenopathy. Somatic mutations in RAS/MAP kinase pathway genes are common but germline mutations are rare. A patient with RDD and exocrine pancreatic insufficiency was found to have a homozygous germline mutation in SLC29A3, which has been associated with the Histiocytosis/Lymphadenopathy Plus Syndrome. His RDD also was positive for a somatic mutation in lymphoid enhancer binding factor 1 (LEF1). The concurrence of RDD and pancreatic insufficiency should raise consideration of SLC29A3 mutations. Other cases will be needed to confirm this observation and a possible contribution of LEF1 to the development of RDD.
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Affiliation(s)
- Julie Blatt
- Divisions of Pediatric Hematology Oncology
- The Lineberger Comprehensive Cancer Center
| | - Preeti Parekh
- UNC Rex Health, Hematopathology, The University of North Carolina at Chapel Hill, Chapel Hill
| | | | - Yuri Fedoriw
- Hematopathology
- The Lineberger Comprehensive Cancer Center
| | - Indira Reddy
- Raleigh Medical Group, Gastroenterology, Raleigh, NC
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14
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Staley BS, Milko LV, Waltz M, Griesemer I, Mollison L, Grant TL, Farnan L, Roche M, Navas A, Lightfoot A, Foreman AKM, O'Daniel JM, O'Neill SC, Lin FC, Roman TS, Brandt A, Powell BC, Rini C, Berg JS, Bensen JT. Evaluating the clinical utility of early exome sequencing in diverse pediatric outpatient populations in the North Carolina Clinical Genomic Evaluation of Next-generation Exome Sequencing (NCGENES) 2 study: a randomized controlled trial. Trials 2021; 22:395. [PMID: 34127041 PMCID: PMC8201439 DOI: 10.1186/s13063-021-05341-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/06/2021] [Accepted: 05/26/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Exome sequencing (ES) has probable utility for shortening the diagnostic odyssey of children with suspected genetic disorders. This report describes the design and methods of a study evaluating the potential of ES as a routine clinical tool for pediatric patients who have suspected genetic conditions and who are in the early stages of the diagnostic odyssey. METHODS The North Carolina Clinical Genomic Evaluation by Next-generation Exome Sequencing (NCGENES) 2 study is an interdisciplinary, multi-site Phase III randomized controlled trial of two interventions: educational pre-visit preparation (PVP) and offer of first-line ES. In this full-factorial design, parent-child dyads are randomly assigned to one of four study arms (PVP + usual care, ES + usual care, PVP + ES + usual care, or usual care alone) in equal proportions. Participants are recruited from Pediatric Genetics or Neurology outpatient clinics in three North Carolina healthcare facilities. Eligible pediatric participants are < 16 years old and have a first visit to a participating clinic, a suspected genetic condition, and an eligible parent/guardian to attend the clinic visit and complete study measures. The study oversamples participants from underserved and under-represented populations. Participants assigned to the PVP arms receive an educational booklet and question prompt list before clinical interactions. Randomization to offer of first-line ES is revealed after a child's clinic visit. Parents complete measures at baseline, pre-clinic, post-clinic, and two follow-up timepoints. Study clinicians provide phenotypic data and complete measures after the clinic visit and after returning results. Reportable study-related research ES results are confirmed in a CLIA-certified clinical laboratory. Results are disclosed to the parent by the clinical team. A community consultation team contributed to the development of study materials and study implementation methods and remains engaged in the project. DISCUSSION NCGENES 2 will contribute valuable knowledge concerning technical, clinical, psychosocial, and health economic issues associated with using early diagnostic ES to shorten the diagnostic odyssey of pediatric patients with likely genetic conditions. Results will inform efforts to engage diverse populations in genomic medicine research and generate evidence that can inform policy, practice, and future research related to the utility of first-line diagnostic ES in health care. TRIAL REGISTRATION ClinicalTrials.gov NCT03548779 . Registered on June 07, 2018.
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Affiliation(s)
- Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA.
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Margaret Waltz
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ida Griesemer
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lonna Mollison
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tracey L Grant
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura Farnan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Myra Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Angelo Navas
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra Lightfoot
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Suzanne C O'Neill
- Department of Oncology, Georgetown University, Washington, DC, 20007, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA
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15
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DeCristo DM, Milko LV, O'Daniel JM, Foreman AKM, Mollison LF, Powell BC, Powell CM, Berg JS. Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making. Genome Med 2021; 13:50. [PMID: 33781310 PMCID: PMC8008582 DOI: 10.1186/s13073-021-00867-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 08/18/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Newborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of precision medicine, genomic sequencing has been introduced to this area with the hopes of detecting variants related to a vastly expanded number of conditions. Though implementation of genomic sequencing for newborn screening in public health and clinical settings is limited, commercial laboratories have begun to offer genomic screening panels for neonates. METHODS We examined genes listed on four commercial laboratory genomic screening panels for neonates and assessed their clinical actionability using an established age-based semi-quantitative metric to categorize them. We identified genes that were included on multiple panels or distinct between panels. RESULTS Three hundred and nine genes appeared on one or more commercial panels: 74 (23.9%) genes were included in all four commercial panels, 45 (14.6%) were on only three panels, 76 (24.6%) were on only two panels, and 114 (36.9%) genes were listed on only one of the four panels. Eighty-two genes (26.5%) listed on one or more panels were assessed by our method to be inappropriate for newborn screening and to require additional parental decision-making. Conversely, 249 genes that we previously identified as being highly actionable were not listed on any of the four commercial laboratory genomic screening panels. CONCLUSIONS Commercial neonatal genomic screening panels have heterogeneous content and may contain some conditions with lower actionability than would be expected for public health newborn screening; conversely, some conditions with higher actionability may be omitted from these panels. The lack of transparency about how conditions are selected suggests a need for greater detail about panel content in order for parents to make informed decisions. The nuanced activity of gene list selection for genomic screening should be iteratively refined with evidence-based approaches to provide maximal benefit and minimal harm to newborns.
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Affiliation(s)
- Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Lonna F Mollison
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
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16
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Waltz M, Prince AER, O’Daniel JM, Foreman AKM, Powell BC, Berg JS. Referencing BRCA in hereditary cancer risk discussions: In search of an anchor in a sea of uncertainty. J Genet Couns 2020; 29:949-959. [PMID: 31967382 PMCID: PMC7374021 DOI: 10.1002/jgc4.1219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/01/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 01/14/2023]
Abstract
As panel testing and exome sequencing are increasingly incorporated into clinical care, clinicians must grapple with how to communicate the risks and treatment decisions surrounding breast cancer genes beyond BRCA1 and BRCA2. In this paper, we examine clinicians' practice of employing BRCA1 and BRCA2 to help contextualize less certain genetic information regarding cancer risk and the possible implications of this practice for patients within the context of an exome sequencing study, NCGENES. We audio-recorded return of results appointments for 14 women who participated in NCGENES, previously had breast cancer, and were suspected of having a hereditary cancer predisposition. These patients were also interviewed four weeks later regarding their understanding of their results. We found that BRCA1 and BRCA2 were held as the gold standard, where clinicians compared what is known about BRCA to the limited understanding of other breast cancer-related genes. BRCA1 and BRCA2 were used as anchors to shape patients' understandings of genetic knowledge, risk, and management, illustrating how the information clinicians provide to patients may work as an external anchor. Yet, presenting BRCA1 and BRCA2 as a means of scientific reassurance can run the risk of patients conflating knowledge about certainty of risk with degree of risk after receiving a result for a moderate penetrance gene. This can be further complicated by misperceptions of the precision of cancer predictability attributed to these or other described 'cancer genes' in public media.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Julianne M. O’Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M. Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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17
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Amendola LM, Muenzen K, Biesecker LG, Bowling KM, Cooper GM, Dorschner MO, Driscoll C, Foreman AKM, Golden-Grant K, Greally JM, Hindorff L, Kanavy D, Jobanputra V, Johnston JJ, Kenny EE, McNulty S, Murali P, Ou J, Powell BC, Rehm HL, Rolf B, Roman TS, Van Ziffle J, Guha S, Abhyankar A, Crosslin D, Venner E, Yuan B, Zouk H, Jarvik GP, Jarvik GP. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet 2020; 107:932-941. [PMID: 33108757 DOI: 10.1016/j.ajhg.2020.09.011] [Citation(s) in RCA: 39] [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: 08/03/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Harmonization of variant pathogenicity classification across laboratories is important for advancing clinical genomics. The two CLIA-accredited Electronic Medical Record and Genomics Network sequencing centers and the six CLIA-accredited laboratories and one research laboratory performing genome or exome sequencing in the Clinical Sequencing Evidence-Generating Research Consortium collaborated to explore current sources of discordance in classification. Eight laboratories each submitted 20 classified variants in the ACMG secondary finding v.2.0 genes. After removing duplicates, each of the 158 variants was annotated and independently classified by two additional laboratories using the ACMG-AMP guidelines. Overall concordance across three laboratories was assessed and discordant variants were reviewed via teleconference and email. The submitted variant set included 28 P/LP variants, 96 VUS, and 34 LB/B variants, mostly in cancer (40%) and cardiac (27%) risk genes. Eighty-six (54%) variants reached complete five-category (i.e., P, LP, VUS, LB, B) concordance, and 17 (11%) had a discordance that could affect clinical recommendations (P/LP versus VUS/LB/B). 21% and 63% of variants submitted as P and LP, respectively, were discordant with VUS. Of the 54 originally discordant variants that underwent further review, 32 reached agreement, for a post-review concordance rate of 84% (118/140 variants). This project provides an updated estimate of variant concordance, identifies considerations for LP classified variants, and highlights ongoing sources of discordance. Continued and increased sharing of variant classifications and evidence across laboratories, and the ongoing work of ClinGen to provide general as well as gene- and disease-specific guidance, will lead to continued increases in concordance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, Seattle, WA 98195, USA
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18
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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19
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Vora NL, Gilmore K, Brandt A, Gustafson C, Strande N, Ramkissoon L, Hardisty E, Foreman AKM, Wilhelmsen K, Owen P, Weck KE, Berg JS, Powell CM, Powell BC. Correction: An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genet Med 2020; 22:1426. [PMID: 32555414 DOI: 10.1038/s41436-020-0870-x] [Citation(s) in RCA: 3] [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] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Gustafson
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natasha Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillips Owen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen E Weck
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia M Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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20
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Vora NL, Gilmore K, Brandt A, Gustafson C, Strande N, Ramkissoon L, Hardisty E, Foreman AKM, Wilhelmsen K, Owen P, Weck KE, Berg JS, Powell CM, Powell BC. An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genet Med 2020; 22:954-961. [PMID: 31974414 PMCID: PMC7205580 DOI: 10.1038/s41436-020-0750-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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] [Received: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
PURPOSE We investigated the diagnostic and clinical performance of trio exome sequencing (ES) in parent-fetus trios where the fetus had sonographic abnormalities but normal karyotype, microarray and, in some cases, normal gene-specific sequencing. METHODS ES was performed from DNA of 102 anomalous fetuses and from peripheral blood from their parents. Parents provided consent for the return of diagnostic results in the fetus, medically actionable findings in the parents, and identification as carrier couple for significant autosomal recessive conditions. RESULTS In 21/102 (20.6%) fetuses, ES provided a positive-definitive or positive-probable diagnosis. In 10/102 (9.8%), ES provided an inconclusive-possible result. At least 2/102 (2.0%) had a repeat pregnancy during the study period and used the information from the study for prenatal diagnosis in the next pregnancy. Six of 204 (2.9%) parents received medically actionable results that affected their own health and 3/102 (2.9%) of couples received results that they were carriers for the same autosomal recessive condition. CONCLUSION ES has diagnostic utility in a select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy, variant interpretation, and various types of diagnostic results affecting both fetal and parental health must be addressed by highly tailored pre- and post-test genetic counseling.
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Affiliation(s)
- Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Gustafson
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natasha Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillips Owen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen E Weck
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia M Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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21
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Filer DL, Wilhelmsen KC, Gilmore KL, Powell BC, Powell CM, Vora NL. 784: Novel sequencing-based framework for non-invasive fetal genotyping. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.11.800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Kanavy DM, McNulty SM, Jairath MK, Brnich SE, Bizon C, Powell BC, Berg JS. Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. Genome Med 2019; 11:77. [PMID: 31783775 PMCID: PMC6884856 DOI: 10.1186/s13073-019-0683-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 06/14/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that "well-established" functional studies can be used as evidence in variant classification. These guidelines articulated key attributes of functional data, including that assays should reflect the biological environment and be analytically sound; however, details of how to evaluate these attributes were left to expert judgment. The Clinical Genome Resource (ClinGen) designates Variant Curation Expert Panels (VCEPs) in specific disease areas to make gene-centric specifications to the ACMG/AMP guidelines, including more specific definitions of appropriate functional assays. We set out to evaluate the existing VCEP guidelines for functional assays. METHODS We evaluated the functional criteria (PS3/BS3) of six VCEPs (CDH1, Hearing Loss, Inherited Cardiomyopathy-MYH7, PAH, PTEN, RASopathy). We then established criteria for evaluating functional studies based on disease mechanism, general class of assay, and the characteristics of specific assay instances described in the primary literature. Using these criteria, we extensively curated assay instances cited by each VCEP in their pilot variant classification to analyze VCEP recommendations and their use in the interpretation of functional studies. RESULTS Unsurprisingly, our analysis highlighted the breadth of VCEP-approved assays, reflecting the diversity of disease mechanisms among VCEPs. We also noted substantial variability between VCEPs in the method used to select these assays and in the approach used to specify strength modifications, as well as differences in suggested validation parameters. Importantly, we observed discrepancies between the parameters VCEPs specified as required for approved assay instances and the fulfillment of these requirements in the individual assays cited in pilot variant interpretation. CONCLUSIONS Interpretation of the intricacies of functional assays often requires expert-level knowledge of the gene and disease, and current VCEP recommendations for functional assay evidence are a useful tool to improve the accessibility of functional data by providing a starting point for curators to identify approved functional assays and key metrics. However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.
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Affiliation(s)
- Dona M Kanavy
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M McNulty
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meera K Jairath
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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23
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Milko LV, O’Daniel JM, DeCristo DM, Crowley SB, Foreman AKM, Wallace KE, Mollison LF, Strande NT, Girnary ZS, Boshe LJ, Aylsworth AS, Gucsavas-Calikoglu M, Frazier DM, Vora NL, Roche MI, Powell BC, Powell CM, Berg JS. An Age-Based Framework for Evaluating Genome-Scale Sequencing Results in Newborn Screening. J Pediatr 2019; 209:68-76. [PMID: 30851990 PMCID: PMC6535354 DOI: 10.1016/j.jpeds.2018.12.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/24/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To assess the performance of a standardized, age-based metric for scoring clinical actionability to evaluate conditions for inclusion in newborn screening and compare it with the results from other contemporary methods. STUDY DESIGN The North Carolina Newborn Exome Sequencing for Universal Screening study developed an age-based, semiquantitative metric to assess the clinical actionability of gene-disease pairs and classify them with respect to age of onset or timing of interventions. This categorization was compared with the gold standard Recommended Uniform Screening Panel and other methods to evaluate gene-disease pairs for newborn genomic sequencing. RESULTS We assessed 822 gene-disease pairs, enriched for pediatric onset of disease and suspected actionability. Of these, 466 were classified as having childhood onset and high actionability, analogous to conditions selected for the Recommended Uniform Screening Panel core panel. Another 245 were classified as having childhood onset and low to no actionability, 25 were classified as having adult onset and high actionability, 19 were classified as having adult onset and low to no actionability, and 67 were excluded due to controversial evidence and/or prenatal onset. CONCLUSIONS This study describes a novel method to facilitate decisions about the potential use of genomic sequencing for newborn screening. These categories may assist parents and physicians in making informed decisions about the disclosure of results from voluntary genomic sequencing in children.
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Affiliation(s)
| | | | | | | | | | | | | | - Natasha T. Strande
- Department of Genetics, UNC Chapel Hill,Department of Pathology and Laboratory Medicine, UNC Chapel Hill
| | - Zahra S. Girnary
- Department of Genetics, UNC Chapel Hill,current affiliation: Mission Fullerton Genetics Center, Asheville, NC
| | - Lacey J. Boshe
- Department of Genetics, UNC Chapel Hill,current affiliation: School of Medicine, UNC Chapel Hill
| | - Arthur S. Aylsworth
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Dianne M. Frazier
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, UNC Chapel Hill
| | - Myra I. Roche
- Department of Genetics, UNC Chapel Hill,Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Cynthia M. Powell
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
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Amendola LM, Berg JS, Horowitz CR, Angelo F, Bensen JT, Biesecker BB, Biesecker LG, Cooper GM, East K, Filipski K, Fullerton SM, Gelb BD, Goddard KA, Hailu B, Hart R, Hassmiller-Lich K, Joseph G, Kenny EE, Koenig BA, Knight S, Kwok PY, Lewis KL, McGuire AL, Norton ME, Ou J, Parsons DW, Powell BC, Risch N, Robinson M, Rini C, Scollon S, Slavotinek AM, Veenstra DL, Wasserstein MP, Wilfond BS, Hindorff LA, Plon SE, Jarvik GP, Jarvik GP. The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations. Am J Hum Genet 2018; 103:319-327. [PMID: 30193136 DOI: 10.1016/j.ajhg.2018.08.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/15/2018] [Indexed: 01/26/2023] Open
Abstract
The Clinical Sequencing Evidence-Generating Research (CSER) consortium, now in its second funding cycle, is investigating the effectiveness of integrating genomic (exome or genome) sequencing into the clinical care of diverse and medically underserved individuals in a variety of healthcare settings and disease states. The consortium comprises a coordinating center, six funded extramural clinical projects, and an ongoing National Human Genome Research Institute (NHGRI) intramural project. Collectively, these projects aim to enroll and sequence over 6,100 participants in four years. At least 60% of participants will be of non-European ancestry or from underserved settings, with the goal of diversifying the populations that are providing an evidence base for genomic medicine. Five of the six clinical projects are enrolling pediatric patients with various phenotypes. One of these five projects is also enrolling couples whose fetus has a structural anomaly, and the sixth project is enrolling adults at risk for hereditary cancer. The ongoing NHGRI intramural project has enrolled primarily healthy adults. Goals of the consortium include assessing the clinical utility of genomic sequencing, exploring medical follow up and cascade testing of relatives, and evaluating patient-provider-laboratory level interactions that influence the use of this technology. The findings from the CSER consortium will offer patients, healthcare systems, and policymakers a clearer understanding of the opportunities and challenges of providing genomic medicine in diverse populations and settings, and contribute evidence toward developing best practices for the delivery of clinically useful and cost-effective genomic sequencing in diverse healthcare settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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25
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Milko LV, Rini C, Lewis MA, Butterfield RM, Lin FC, Paquin RS, Powell BC, Roche MI, Souris KJ, Bailey DB, Berg JS, Powell CM. Evaluating parents' decisions about next-generation sequencing for their child in the NC NEXUS (North Carolina Newborn Exome Sequencing for Universal Screening) study: a randomized controlled trial protocol. Trials 2018; 19:344. [PMID: 29950170 PMCID: PMC6022715 DOI: 10.1186/s13063-018-2686-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 01/08/2018] [Accepted: 05/14/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Using next-generation sequencing (NGS) in newborn screening (NBS) could expand the number of genetic conditions detected pre-symptomatically, simultaneously challenging current precedents, raising ethical concerns, and extending the role of parental decision-making in NBS. The NC NEXUS (Newborn Exome Sequencing for Universal Screening) study seeks to assess the technical possibilities and limitations of NGS-NBS, devise and evaluate a framework to convey various types of genetic information, and develop best practices for incorporating NGS-NBS into clinical care. The study is enrolling both a healthy cohort and a cohort diagnosed with known disorders identified through recent routine NBS. It uses a novel age-based metric to categorize a priori the large amount of data generated by NGS-NBS and interactive online decision aids to guide parental decision-making. Primary outcomes include: (1) assessment of NGS-NBS sensitivity, (2) decision regret, and (3) parental decision-making about NGS-NBS, and, for parents randomized to have the option of requesting them, additional findings (diagnosed and healthy cohorts). Secondary outcomes assess parents' reactions to the study and to decision-making. METHODS/DESIGN Participants are parents and children in a well-child cohort recruited from a prenatal clinic and a diagnosed cohort recruited from pediatric clinics that treat children with disorders diagnosed through traditional NBS (goal of 200 children in each cohort). In phase 1, all parent participants use an online decision aid to decide whether to accept NGS-NBS for their child and provide consent for NGS-NBS. In phase 2, parents who consent to NGS-NBS are randomized to a decision arm or control arm (2:1 allocation) and learn their child's NGS-NBS results, which include conditions from standard (non-NGS) NBS plus other highly actionable childhood-onset conditions. Parents in the decision arm use a second decision aid to make decisions about additional results from their child's sequencing. In phase 3, decision arm participants learn additional results they have requested. Online questionnaires are administered at up to five time points. DISCUSSION NC NEXUS will use a rigorous interdisciplinary approach designed to collect rich data to inform policy, practice, and future research. TRIAL REGISTRATION clinicaltrials.gov, NCT02826694 . Registered on 11 July, 2016.
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Affiliation(s)
- Laura V. Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Christine Rini
- Department of Biomedical Research, Hackensack University Medical Center, Hackensack, NJ 07601 USA
| | - Megan A. Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709 USA
| | - Rita M. Butterfield
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599 USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Ryan S. Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709 USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Myra I. Roche
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599 USA
| | - Katherine J. Souris
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Donald B. Bailey
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, Research Triangle Park, NC 27709 USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Cynthia M. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599 USA
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26
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Rini C, Khan CM, Moore E, Roche MI, Evans JP, Berg JS, Powell BC, Corbie-Smith G, Foreman AKM, Griesemer I, Lee K, O'Daniel JM, Henderson GE. The who, what, and why of research participants' intentions to request a broad range of secondary findings in a diagnostic genomic sequencing study. Genet Med 2017; 20:760-769. [PMID: 29261173 PMCID: PMC5920790 DOI: 10.1038/gim.2017.176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
PURPOSE In a diagnostic exome sequencing study (the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing project, NCGENES), we investigated adult patients' intentions to request six categories of secondary findings (SFs) with low or no medical actionability and correlates of their intentions. METHODS At enrollment, eligible participants (n = 152) completed measures assessing their sociodemographic, clinical, and literacy-related characteristics. Prior to and during an in-person diagnostic result disclosure visit, they received education about categories of SFs they could request. Immediately after receiving education at the visit, participants completed measures of intention to learn SFs, interest in each category, and anticipated regret for learning and not learning each category. RESULTS Seventy-eight percent of participants intended to learn at least some SFs. Logistic regressions examined their intention to learn any or all of these findings (versus none) and interest in each of the six individual categories (yes/no). Results revealed little association between intentions and sociodemographic, clinical, or literacy-related factors. Across outcomes, participants who anticipated regret for learning SFs reported weaker intention to learn them (odds ratios (ORs) from 0.47 to 0.71), and participants who anticipated regret for not learning these findings reported stronger intention to learn them (OR 1.61-2.22). CONCLUSION Intentions to request SFs with low or no medical actionability may be strongly influenced by participants' desire to avoid regret.
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Affiliation(s)
- Christine Rini
- John Theuer Cancer Center, Hackensack University Medical Center, Hackensack, New Jersey, USA.
| | | | - Elizabeth Moore
- Blue Cross and Blue Shield of North Carolina, Durham, North Carolina, USA
| | - Myra I Roche
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James P Evans
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Giselle Corbie-Smith
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Center for Health Equity Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M Foreman
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ida Griesemer
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julianne M O'Daniel
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gail E Henderson
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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27
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Affiliation(s)
- James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill2Department of Medicine, University of North Carolina at Chapel Hill
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill
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28
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Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics 2017; 139:peds.2016-2252. [PMID: 28096516 PMCID: PMC5260149 DOI: 10.1542/peds.2016-2252] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.
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Affiliation(s)
| | - Pankaj B. Agrawal
- Divisions of Newborn Medicine and,Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Alan H. Beggs
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy M. Brower
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Julie A. Cakici
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | | | - Kee Chan
- Chicago School of Public Health, University of Illinois, Chicago, Illinois
| | | | - Robert J. Currier
- Genetic Disease Screening Program, California Department of Public Health, Sacramento, California
| | - Dmitry Dukhovny
- Department of Pediatrics and Division of Neonatology, Oregon Health & Science University, Portland, Oregon
| | | | | | - Ingrid A. Holm
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Galen Joseph
- Department of Anthropology, History, and Social Medicine
| | | | | | - Pui-Yan Kwok
- Institute for Human Genetics,,Cardiovascular Research Institute, and Department of Dermatology
| | - John Lantos
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, Missouri
| | - Steven J. Leeder
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, Missouri
| | - Megan A. Lewis
- RTI International, Research Triangle Park, North Carolina
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | | | | | - Richard B. Parad
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | - Joshua Petrikin
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, Missouri
| | | | - Cynthia M. Powell
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jennifer M. Puck
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Myra Roche
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Joseph T. Shieh
- Institute for Human Genetics,,Department of Pediatrics, Benioff Children’s Hospital, and
| | | | - Michael S. Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Laurel Willig
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, Missouri
| | - Timothy W. Yu
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tiina Urv
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
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29
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Saliba J, Zabriskie R, Ghosh R, Powell BC, Hicks S, Kimmel M, Meng Q, Ritter DI, Wheeler DA, Gibbs RA, Tsai FTF, Plon SE. Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs. Pharmacogenet Genomics 2016; 26:271-9. [PMID: 26906009 PMCID: PMC4853247 DOI: 10.1097/fpc.0000000000000208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Mutations or alterations in expression of the 5' nucleotidase gene family can lead to altered responses to treatment with nucleoside analogs. While investigating leukemia susceptibility genes, we discovered a very rare p.L254P NT5C1A missense variant in the substrate recognition motif. Given the paucity of cellular drug response data from the NT5C1A germline variation, we characterized p.L254P and eight rare variants of NT5C1A from genomic databases. MATERIALS AND METHODS Through lentiviral infection, we created HEK293 cell lines that stably overexpress wild-type NT5C1A, p.L254P, or eight NT5C1A variants reported in the National Heart Lung and Blood Institute Exome Variant Server (one truncating and seven missense). IC50 values were determined by cytotoxicity assays after exposure to chemotherapeutic nucleoside analogs (cladribine, gemcitabine, 5-fluorouracil). In addition, we used structure-based homology modeling to generate a three-dimensional model for the C-terminal region of NT5C1A. RESULTS The p.R180X (truncating), p.A214T, and p.L254P missense changes were the only variants that significantly impaired protein function across all nucleotide analogs tested (>5-fold difference vs. wild-type; P<0.05). Several of the remaining variants individually showed differential effects (both more and less resistant) across the analogs tested. The homology model provided a structural framework to understand the impact of NT5C1A mutants on catalysis and drug processing. The model predicted active site residues within NT5C1A motif III and we experimentally confirmed that p.K314 (not p.K320) is required for NT5C1A activity. CONCLUSION We characterized germline variation and predicted protein structures of NT5C1A. Individual missense changes showed considerable variation in response to the different nucleoside analogs tested, which may impact patients' responses to treatment.
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Affiliation(s)
- Jason Saliba
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ryan Zabriskie
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Rajarshi Ghosh
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Bradford C Powell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX
| | - Qingchang Meng
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Deborah I Ritter
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Francis T F Tsai
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
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30
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Berg JS, Foreman AKM, O'Daniel JM, Booker JK, Boshe L, Carey T, Crooks KR, Jensen BC, Juengst ET, Lee K, Nelson DK, Powell BC, Powell CM, Roche MI, Skrzynia C, Strande NT, Weck KE, Wilhelmsen KC, Evans JP. A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing. Genet Med 2015; 18:467-75. [PMID: 26270767 PMCID: PMC4752935 DOI: 10.1038/gim.2015.104] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 01/01/2023] Open
Abstract
PURPOSE As genome-scale sequencing is increasingly applied in clinical scenarios, a wide variety of genomic findings will be discovered as secondary or incidental findings, and there is debate about how they should be handled. The clinical actionability of such findings varies, necessitating standardized frameworks for a priori decision making about their analysis. METHODS We established a semiquantitative metric to assess five elements of actionability: severity and likelihood of the disease outcome, efficacy and burden of intervention, and knowledge base, with a total score from 0 to 15. RESULTS The semiquantitative metric was applied to a list of putative actionable conditions, the list of genes recommended by the American College of Medical Genetics and Genomics (ACMG) for return when deleterious variants are discovered as secondary/incidental findings, and a random sample of 1,000 genes. Scores from the list of putative actionable conditions (median = 12) and the ACMG list (median = 11) were both statistically different than the randomly selected genes (median = 7) (P < 0.0001, two-tailed Mann-Whitney test). CONCLUSION Gene-disease pairs having a score of 11 or higher represent the top quintile of actionability. The semiquantitative metric effectively assesses clinical actionability, promotes transparency, and may facilitate assessments of clinical actionability by various groups and in diverse contexts.Genet Med 18 5, 467-475.
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Affiliation(s)
- Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julianne M O'Daniel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jessica K Booker
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lacey Boshe
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy Carey
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy R Crooks
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian C Jensen
- Division of Cardiology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eric T Juengst
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy Lee
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel K Nelson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia M Powell
- Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Myra I Roche
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cecile Skrzynia
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Natasha T Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kirk C Wilhelmsen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James P Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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31
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Powell BC, Jiang L, Muzny DM, Treviño LR, Dreyer ZE, Strong LC, Wheeler DA, Gibbs RA, Plon SE. Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing. Pediatr Blood Cancer 2013; 60:E1-3. [PMID: 23255406 PMCID: PMC3926299 DOI: 10.1002/pbc.24417] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/03/2012] [Indexed: 11/10/2022]
Abstract
Although acute lymphocytic leukemia (ALL) is the most common childhood cancer, genetic predisposition to ALL remains poorly understood. Whole-exome sequencing was performed in an extended kindred in which five individuals had been diagnosed with leukemia. Analysis revealed a nonsense variant of TP53 which has been previously reported in families with sarcomas and other typical Li Fraumeni syndrome-associated cancers but never in a familial leukemia kindred. This unexpected finding enabled identification of an appropriate sibling bone marrow donor and illustrates that exome sequencing will reveal atypical clinical presentations of even well-studied genes.
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Affiliation(s)
- Bradford C. Powell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lichun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Lisa R. Treviño
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - ZoAnn E. Dreyer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
| | - Louise C. Strong
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX,Department of Pediatrics, Baylor College of Medicine, Houston, TX,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
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Cowin AJ, Adams DH, Strudwick XL, Chan H, Hooper JA, Sander GR, Rayner TE, Matthaei KI, Powell BC, Campbell HD. Flightless I deficiency enhances wound repair by increasing cell migration and proliferation. J Pathol 2007; 211:572-581. [PMID: 17326236 DOI: 10.1002/path.2143] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Wound healing disorders are a therapeutic problem of increasing clinical importance involving substantial morbidity, mortality, and rising health costs. Our studies investigating flightless I (FliI), a highly conserved actin-remodelling protein, now reveal that FliI is an important regulator of wound repair whose manipulation may lead to enhanced wound outcomes. We demonstrate that FliI-deficient + /- mice are characterized by improved wound healing with increased epithelial migration and enhanced wound contraction. In contrast, FliI-overexpressing mice have significantly impaired wound healing with larger less contracted wounds and reduced cellular proliferation. We show that FliI is secreted in response to wounding and that topical application of antibodies raised against the leucine-rich repeat domain of the FliI protein (FliL) significantly improves wound repair. These studies reveal that FliI affects wound repair via mechanisms involving cell migration and proliferation and that FliI might represent an effective novel therapeutic factor to improve conditions in which wound healing is impaired.
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Affiliation(s)
- A J Cowin
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
- Department of Paediatrics, University of Adelaide, South Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Australia
| | - D H Adams
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
| | - X L Strudwick
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
| | - H Chan
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
| | - J A Hooper
- Molecular Genetics and Evolution Group and Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, ACT, Australia
| | - G R Sander
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
- Department of Paediatrics, University of Adelaide, South Australia
| | - T E Rayner
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
| | - K I Matthaei
- Division of Molecular Bioscience, The John Curtin School of Medical Research, Canberra, ACT, Australia
| | - B C Powell
- Child Health Research Institute, 72 King William Road, North Adelaide, South Australia
- Department of Paediatrics, University of Adelaide, South Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Australia
| | - H D Campbell
- Molecular Genetics and Evolution Group and Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, ACT, Australia
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Crayton ME, Powell BC, Vision TJ, Giddings MC. Tracking the evolution of alternatively spliced exons within the Dscam family. BMC Evol Biol 2006; 6:16. [PMID: 16483367 PMCID: PMC1397879 DOI: 10.1186/1471-2148-6-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [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: 09/26/2005] [Accepted: 02/16/2006] [Indexed: 11/30/2022] Open
Abstract
Background The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17), potentially generating 38,016 protein isoforms. This degree of transcript diversity has not been found in mammalian homologs of Dscam. We examined the molecular evolution of exons within this gene family to locate the point of divergence for this alternative splicing pattern. Results Using the fruit fly Dscam exons 4, 6, 9 and 17 as seed sequences, we iteratively searched sixteen genomes for homologs, and then performed phylogenetic analyses of the resulting sequences to examine their evolutionary history. We found homologs in the nematode, arthropod and vertebrate genomes, including homologs in several vertebrates where Dscam had not been previously annotated. Among these, only the arthropods contain homologs arranged in tandem arrays indicative of mutually exclusive splicing. We found no homologs to these exons within the Arabidopsis, yeast, tunicate or sea urchin genomes but homologs to several constitutive exons from fly Dscam were present within tunicate and sea urchin. Comparing the rate of turnover within the tandem arrays of the insect taxa (fruit fly, mosquito and honeybee), we found the variants within exons 4 and 17 are well conserved in number and spatial arrangement despite 248–283 million years of divergence. In contrast, the variants within exons 6 and 9 have undergone considerable turnover since these taxa diverged, as indicated by deeply branching taxon-specific lineages. Conclusion Our results suggest that at least one Dscam exon array may be an ancient duplication that predates the divergence of deuterostomes from protostomes but that there is no evidence for the presence of arrays in the common ancestor of vertebrates. The different patterns of conservation and turnover among the Dscam exon arrays provide a striking example of how a gene can evolve in a modular fashion rather than as a single unit.
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Affiliation(s)
- Mack E Crayton
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Bradford C Powell
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Todd J Vision
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Morgan C Giddings
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Abstract
Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.
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Affiliation(s)
- Bradford C Powell
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clyde A Hutchison
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- J. Craig Venter Institute, Rockville, Maryland, USA
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Abstract
Several experimental approaches were used to construct a detailed transcriptional profile of the phylogenetically conserved ftsZ cell division gene cluster in both Mycoplasma genitalium and its closest relative, Mycoplasma pneumoniae. We determined initiation and termination points for the cluster, as well as an absolute steady-state RNA level for each gene. Transcription of this cluster in both these organisms was shown to be highly strand specific. While the four genes in this cluster are cotranscribed, their transcription unit also includes two genes of close proximity yet disparate function. A transcription initiation point immediately upstream of these two genes was detected in M. genitalium but not M. pneumoniae. In M. pneumoniae, transcription of the six genes terminates at a poly(U)-tailed hairpin. In M. genitalium, this transcription terminates at two closely spaced points by an unknown mechanism. Real-time reverse transcription-PCR analysis of this cluster in M. pneumoniae shows that mRNA levels for all six genes vary at most fivefold and form a gradient of decreasing quantity with increasing distance from the promoter at the beginning of the cluster. mRNA from coding regions was approximately 20- to 100-fold more abundant than that from intergenic regions. We estimated the most abundant mRNA we detected at 0.6 copy per cell. We conclude that groups of functionally related genes in M. genitalium and M. pneumoniae are often preceded by promoters but rarely followed by terminators. This causes functionally unrelated genes to be commonly cotranscribed in these organisms.
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Affiliation(s)
- Gwynedd A Benders
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Abstract
HOXC-13 has an important role in controlling hair formation through regulating keratin differentiation-specific genes. In this study, we describe the isolation and characterisation of the Hoxc-13 gene from sheep wool follicles and its expression in the skin. We show that the gene organisation of ovine Hoxc-13 is similar to other homeobox genes of the Abd-B type I Homeobox class with two exons split by an intron next to the homeobox. The gene spans 7.5 kilobases (kb) and has a relatively large intron, which divides an open reading frame of 2361 nucleotides. The predicted ovine Hoxc-13 protein of 330 amino acids has over 97% sequence identity with the human and mouse proteins. A second novel transcript was identified, which could produce a truncated Hoxc-13 protein lacking 15 amino acids from the N-terminus. A positionally conserved Hoxc-13 binding site in the Hoxc-13 proximal promoters of sheep, human, mouse and newt suggests that Hoxc-13 expression is autoregulatory. Positionally conserved motifs for LEF-1 and Whn/Foxn1 suggest that Hoxc-13 may be a downstream target of these transcription factors known to regulate hair growth. In addition to expression in the follicle, we detected Hoxc-13 in cells of the blood sinus surrounding vibrissal follicles and in scattered cells in the upper dermis of the skin. Thus, in addition to a role in controlling transcription of hair keratins, Hoxc-13 may have other roles in skin function.
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Affiliation(s)
- G R Sander
- Department of Animal Science, University of Adelaide, Australia.
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Abstract
BACKGROUND and aims: In neonates the gastrointestinal tract is exposed to food and bacterial antigens at a time when the gut mucosal immune system has not developed the ability to induce oral tolerance. This increases the risk for an inappropriate immune response to oral antigens. Transforming growth factor beta (TGF-beta) is an immunoregulatory cytokine present in high concentration in maternal milk. Interleukin 18 (IL-18) is a cytokine that mediates early immune events, and drives T cell development. We assessed the role of TGF-beta in mediating mucosal immune development and specifically the effect on endogenous IL-18. METHODS Rat pups were randomly assigned to the following groups, naturally suckled, maternal milk via cannula, and formula fed with and without physiological levels of TGF-beta2. A comparison of the immune response profile was then carried out. Cytokine profiles, dendritic cell, intestinal mast cell, and eosinophil numbers were assessed. RESULTS We show that feeding formula deficient in TGF-beta2 resulted in accumulated IL-18 protein release from intestinal epithelial cells and IL-18 mRNA up regulation. A proinflammatory cytokine profile resulted in the gut, along with increased numbers of activated dendritic cells, eosinophils, and mast cells. Supplementation of the formula with TGF-beta2 down regulated the proinflammatory cytokine mRNA as well as the number of activated lymphocytes, eosinophils, mast cells, CD80, and CD86 positive dendritic cells. CONCLUSION The data suggests an important role for maternal milk, in regulating immune responses after exposure to food antigens, which might otherwise induce deleterious immune responses in the intestine of suckling neonates. This regulation is potentially mediated by milk TGF-beta2, as well as endogenous IL-18.
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Affiliation(s)
- I A Penttila
- Child Health Research Institute, North Adelaide, SA 5006, Australia.
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Abstract
The past decade has seen a remarkable explosion in our knowledge of the size and diversity of the myosin superfamily. Since these actin-based motors are candidates to provide the molecular basis for many cellular movements, it is essential that motility researchers be aware of the complete set of myosins in a given organism. The availability of cDNA and/or draft genomic sequences from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Dictyostelium discoideum has allowed us to tentatively define and compare the sets of myosin genes in these organisms. This analysis has also led to the identification of several putative myosin genes that may be of general interest. In humans, for example, we find a total of 40 known or predicted myosin genes including two new myosins-I, three new class II (conventional) myosins, a second member of the class III/ninaC myosins, a gene similar to the class XV deafness myosin, and a novel myosin sharing at most 33% identity with other members of the superfamily. These myosins are in addition to the recently discovered class XVI myosin with N-terminal ankyrin repeats and two human genes with similarity to the class XVIII PDZ-myosin from mouse. We briefly describe these newly recognized myosins and extend our previous phylogenetic analysis of the myosin superfamily to include a comparison of the complete or nearly complete inventories of myosin genes from several experimentally important organisms.
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Affiliation(s)
- J S Berg
- Department of Cell and Molecular Physiology, CB#7545, University of North Carolina at Chapel Hill, 27599, USA
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Abstract
We have cloned ovine Barx2, a member of the Bar class of homeobox genes, and present the first description of Barx2 expression in wool follicle development. Barx2 is uniformly expressed in the embryonic ectoderm but is transiently downregulated during the initiation of follicle morphogenesis. Subsequently, Barx2 is expressed throughout the epithelial component of the developing follicle except for a small group of cells at the leading edge of the follicle placode. These Barx2-negative cells are destined to form the follicle bulb and are the progenitors of the inner root sheath and hair shaft. In adult follicles, Barx2 is expressed throughout the outer root sheath but not in the inner root sheath or hair shaft, or in dermal cells associated with the follicle. The pattern of Barx2 expression in follicle morphogenesis is similar to that of the cell adhesion molecule E-cadherin, a similarity that echoes Barx2 coexpression with the L1 cell adhesion molecule in other tissues during mouse embryogenesis. Barx2 is also expressed in tongue and esophagus, two other keratinizing tissues, and we speculate that Barx2 may have a general function in controlling adhesive processes in keratinizing epithelia.
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Affiliation(s)
- G Sander
- Department of Animal Science, University of Adelaide, Waite Campus, Glen Osmond, South Australia
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Liu SM, Mata G, Figliomeni S, Powell BC, Nesci A, Masters DG. Transsulfuration, protein synthesis rate and follicle mRNA in the skin of young Merino lambs in response to infusions of methionine and serine. Br J Nutr 2000; 83:401-9. [PMID: 10858698] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Methionine (Met) is usually the first limiting amino acid for sheep and supplements of Met may increase production of wool and meat. The wool response may be due to an increased supply of cysteine (Cys) from transsulfuration (TS) of Met. Met is catabolized through homocysteine to form Cys when the S from Met is transferred to serine (Ser). We hypothesized that providing additional Met would create a deficiency of Ser and that by simultaneously providing Met and Ser, TS and wool growth could be increased more than by providing Met alone. The effects of i.v. infusions of Met and Ser to young Merino lambs on TS, fractional synthesis rate (FSR) of protein in skin, follicle mRNA and wool growth were examined. Following 4 d of constant i.v. infusion of 3 g Met/d, or 10 g Ser/d or both, the isotope tracers: L-[3-(13)C]Cys, L-[ring-d5]phenylalanine (Phe) and L-[2,3,3-d3]Ser were infused over 8 h to allow for measurements of irreversible loss rate (ILR), and TS in whole body and skin. Skin biopsies were taken for measurement of FSR. Wool growth rate was measured using autoradiography. An infusion of Met significantly (P < 0.05) improved wool growth rate and increased skin FSR, Cys supply from TS and enhanced levels of follicle mRNA (from the K2.10 intermediate filament gene and three gene families encoding keratin associated proteins KAP1, KAP4 and KAP12). The extra Met lowered Ser ILR. The infusion of Ser doubled Ser ILR in the body and increased skin FSR calculated using the Cys tracer in plasma (P < 0.05). However, there were no significant (P > 0.05) changes in TS, skin FSR calculated using the Phe and Ser tracers, follicle mRNA or wool growth rate as a result of Ser infusion. While there were trends towards increased TS and FSR with Ser infusion, the overall lack of significant changes indicates a high capacity for the de novo synthesis of Ser.
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Affiliation(s)
- S M Liu
- Department of Animal Science, University of Adelaide, Glen Osmond, Australia.
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Dunn SM, Keough RA, Rogers GE, Powell BC. Regulation of hair gene expression. Exp Dermatol 1999; 8:341-2. [PMID: 10439262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- S M Dunn
- Department of Animal Science, University of Adelaide, Glen Osmond, South Australia
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Bawden CS, Powell BC, Walker SK, Rogers GE. Sheep transgenesis with keratin and non-keratin genes: expression in the wool follicle for modified fibre properties and growth rates. Exp Dermatol 1999; 8:342-3. [PMID: 10439263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- C S Bawden
- Department of Animal Science, University of Adelaide, Glen Osmond, South Australia
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Hynd PI, Nattrass G, Wilson N, Powell BC. Amino acid transport in wool and hair follicles. Exp Dermatol 1999; 8:325-6. [PMID: 10439252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- P I Hynd
- Department of Animal Science, University of Adelaide, Glen Osmond, SA
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Nancarrow MJ, Powell BC, Hynd PI. Expression of ornithine decarboxylase during embryonic development of wool follicles. Exp Dermatol 1999; 8:326-8. [PMID: 10439253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- M J Nancarrow
- Department of Animal Science, University of Adelaide, Glen Osmond, Australia
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Wilson N, Hynd PI, Powell BC. The role of BMP-2 and BMP-4 in follicle initiation and the murine hair cycle. Exp Dermatol 1999; 8:367-8. [PMID: 10439283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- N Wilson
- Department of Animal Science, University of Adelaide, Glen Osmond, South Australia
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Abstract
Ornithine decarboxylase (ODC) is the key enzyme in the synthesis of polyamines, small cationic molecules believed to have a role in many cellular processes such as cell migration, proliferation and differentiation. We show that ODC expression is associated with cell proliferation and commitment in hair follicle development and hair growth. In embryonic epidermis, ODC is expressed in ectodermal cells at sites where follicles develop, and persists in cells at the leading edge of the follicle placode. ODC is abundantly expressed in proliferating bulb cells of anagen follicles, except for a pocket of cells at the base of the bulb. Entry of the follicle into catagen is accompanied by a down-regulation of ODC expression, which is not resumed until a new follicle is initiated. In vibrissae, ODC expression is more complex. ODC is expressed not only in the bulb but also in the hair shaft, presenting a striking biphasic pattern. Additionally, ODC is expressed in a group of outer root sheath cells in the vicinity of the follicle bulge, the putative site of hair follicle stem cells.
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Affiliation(s)
- M J Nancarrow
- Department of Animal Science, University of Adelaide, South Australia, Australia.
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47
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Abstract
During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesise large amounts of hair keratin proteins. To identify some of the controls that specify expression of hair genes we have defined the minimal promoter of the wool keratin intermediate filament gene K2.10. The region of this gene spanning nucleotides −350 to +53 was sufficient to direct expression of the lacZ gene to the follicle cortex of transgenic mice but deletion of nucleotides −350 to −150 led to a complete loss of promoter activity. When a four base substitution mutation was introduced into the minimal functional promoter at the binding site for lymphoid enhancer factor 1 (LEF-1), promoter activity in transgenic mice was decreased but specificity was not affected. To investigate the interaction of trans-acting factors within the minimal K2.10 promoter we performed DNase I footprinting analyses and electrophoretic mobility shift assays. In addition to LEF-1, Sp1, AP2-like and NF1-like proteins bound to the promoter. The Sp1 and AP2-like proteins bound sequences flanking the LEF-1 binding site whereas the NF1-like proteins bound closer to the transcription start site. We conclude that the LEF-1 binding site is an enhancer element of the K2.10 promoter in the hair follicle cortex and that factors other than LEF-1 regulate promoter tissue- and differentiation-specificity.
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Affiliation(s)
- S M Dunn
- Department of Animal Science, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
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Whitbread LA, Powell BC. Expression of the intermediate filament keratin gene, K15, in the basal cell layers of epithelia and the hair follicle. Exp Cell Res 1998; 244:448-59. [PMID: 9806795 DOI: 10.1006/excr.1998.4217] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The intermediate filament keratin, K15, is present in variable abundance in stratified epithelia. In this study we have isolated and characterized the sheep K15 gene, focusing on its expression in the follicles of sheep and mice. We show that K15 is expressed throughout the hair cycle in the basal layer of the outer root sheath that envelops the follicle. Strikingly, however, in large medullated wool follicles, a small group of basal outer root sheath cells located in the region thought to contain hair follicle stem cells are K15-negative. In the follicle bulb K15 is expressed in cells situated next to the dermal papilla but not in the inner bulb cells. Elsewhere, K15 is expressed at a low, variable level in the basal layer of the epidermis and sebaceous gland, often in a punctate pattern. In the esophagus of the sheep K15 expression is restricted to the basal layer, in contrast to human esophagus where it is expressed throughout the epithelium. Transgenic mouse lines established with a 15-kb sheep K15 gene construct exhibited faithful expression and showed no phenotypic consequences of K15 overexpression. An investigation of transgene expression showed that K15 is continuously expressed in outer root sheath cells during the hair cycle. Given its expression in the mitotically active basal cell layers of diverse epithelia and the follicle, K15 expression appears to signal an early stage in the pathway of keratinocyte differentiation that precedes the decision of a cell to become epidermal or hair-like.
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Affiliation(s)
- L A Whitbread
- John Curtin School of Medical Research, Australian National University, Acton, ACT, 0200, Australia
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49
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Abstract
The Notch signalling pathway is an important mediator of cell fate selection whose involvement in epidermal appendage formation is now becoming recognised. Hair follicle development and hair formation involve the co-ordinated differentiation of several different cell types in which Notch appears to have a role. We report intricate expression patterns for the Notch-1 receptor and three ligands, Delta-1, Jagged-1 and Jagged-2 in the hair follicle. Notch-1 is expressed in ectodermal-derived cells of the follicle, in the inner cells of the embryonic placode and the follicle bulb, and in the suprabasal cells of the mature outer root sheath. Delta-1 is only expressed during embryonic follicle development and is exclusive to the mesenchymal cells of the pre-papilla located beneath the follicle placode. Expression of Jagged-1 or Jagged-2 overlaps Notch-1 expression at all stages. In mature follicles, Jagged-1 and Jagged-2 are expressed in complementary patterns in the follicle bulb and outer root sheath, Jagged-1 in suprabasal cells and Jagged-2 predominantly in basal cells. In the follicle bulb, Jagged-2 is localised to the inner (basal) bulb cells next to the dermal papilla which do not express Notch-1, whereas Jagged-1 expression in the upper follicle bulb overlaps Notch-1 expression and correlates with bulb cell differentiation into hair shaft cortical and cuticle keratinocytes.
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Affiliation(s)
- B C Powell
- Department of Animal Science, University of Adelaide, Waite Campus, Glen Osmond, 5064, Australia.
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50
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Abstract
Alteration of the protein composition of the wool fibre via transgenesis with sheep wool keratin and keratin associated protein (KAP) genes may lead to production of fibre types with improved processing and wearing qualities. Using this approach, we have demonstrated that high level cortical-specific expression of a wool type II intermediate filament (IF) keratin gene, K2.10, leads to marked alterations in both the microstructure and macrostructure of the wool fibres, which have higher lustre and reduced crimp. Analysis of mRNA found reduced levels of transcripts from endogenous cortical type I (p < 0.05) and type II (p < 0.01) keratin IF genes and from the KAP8 (p < 0.001) and KAP2 (p < 0.01) gene families. Examination of protein composition revealed an altered ratio in the keratin type II protein family of the wool fibre cortex. Whilst the over-expressed K2.10 transgene product constituted the majority of keratin type II IF protein, it appeared unable to form heterodimers with much of the expressed endogenous keratin type I IF. In comparison with non-transgenic sheep, fewer IF microfibrils were visible in the cortical cells of fibres from transgenics. The combined effect on fibre structure was disruption of the formation of orthocortical and paracortical cells in the fibre cortex, a factor which could account for the reduction in fibre crimp. No effects upon transcript or protein levels, or fibre microstructure or macrostructure were observed in transgenic sheep expressing the transgene at lower levels, indicating that subtle changes to the gene expression profile in sheep wool follicles can be tolerated. The data here also illustrate that control over endogenous transcript levels in the cortex results when factors acting on the endogenous keratin type I, keratin type II and KAP gene sequences are sequestered by the active K2.10 transgene locus. Moreover, interference to a transcriptional hierarchy shared by keratin and KAP genes may occur prior to establishment of the orthocortical and paracortical compartments of the follicle cortex, at the level of the chromatin.
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Affiliation(s)
- C S Bawden
- Department of Animal Science, University of Adelaide, Glen Osmond, South Australia
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