1
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Shephard VK, Brown ML, Thompson BA, Harpur A, McAlary L. Rapid classification of a novel ALS-causing I149S variant in superoxide dismutase-1. Amyotroph Lateral Scler Frontotemporal Degener 2024:1-7. [PMID: 38742757 DOI: 10.1080/21678421.2024.2351177] [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: 01/30/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
Variants of the oxygen free radical scavenging enzyme superoxide dismutase-1 (SOD1) are associated with the neurodegenerative disease amyotrophic lateral sclerosis (ALS). These variants occur in roughly 20% of familial ALS cases, and 1% of sporadic ALS cases. Here, we identified a novel SOD1 variant in a patient in their 50s who presented with movement deficiencies and neuropsychiatric features. The variant was heterozygous and resulted in the isoleucine at position 149 being substituted with a serine (I149S). In silico analysis predicted the variant to be destabilizing to the SOD1 protein structure. Expression of the SOD1I149S variant with a C-terminal EGFP tag in neuronal-like NSC-34 cells resulted in extensive inclusion formation and reduced cell viability. Immunoblotting revealed that the intramolecular disulphide between Cys57 and Cys146 was fully reduced for SOD1I149S. Furthermore, SOD1I149S was highly susceptible to proteolytic digestion, suggesting a large degree of instability to the protein fold. Finally, fluorescence correlation spectroscopy and native-PAGE of cell lysates showed that SOD1I149S was monomeric in solution in comparison to the dimeric SOD1WT. This experimental data was obtained within 3 months and resulted in the rapid re-classification of the variant from a variant of unknown significance (VUS) to a clinically actionable likely pathogenic variant.
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Affiliation(s)
- Victoria K Shephard
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Mikayla L Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Bryony A Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC, Australia, and
| | - Alisha Harpur
- Department of Genomic Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
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2
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Luo X, Maciaszek JL, Thompson BA, Leong HS, Dixon K, Sousa S, Anderson M, Roberts ME, Lee K, Spurdle AB, Mensenkamp AR, Brannan T, Pardo C, Zhang L, Pesaran T, Wei S, Fasaye GA, Kesserwan C, Shirts BH, Davis JL, Oliveira C, Plon SE, Schrader KA, Karam R. Optimising clinical care through CDH1-specific germline variant curation: improvement of clinical assertions and updated curation guidelines. J Med Genet 2022; 60:568-575. [PMID: 36600593 DOI: 10.1136/jmg-2022-108807] [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: 07/06/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Germline pathogenic variants in CDH1 are associated with increased risk of diffuse gastric cancer and lobular breast cancer. Risk reduction strategies include consideration of prophylactic surgery, thereby making accurate interpretation of germline CDH1 variants critical for physicians deciding on these procedures. The Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel (VCEP) developed specifications for CDH1 variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations and continues to update these specifications. METHODS CDH1 variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen and expert knowledge from ongoing CDH1 variant curations. The CDH1 VCEP reviewed 273 variants using updated CDH1 specifications and incorporated published and unpublished data provided by diagnostic laboratories. RESULTS Updated CDH1-specific interpretation guidelines include 11 major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36 of 37) of variants with ClinVar conflicting interpretations were resolved to benign, likely benign, likely pathogenic or pathogenic, and 35% (15 of 43) of VUS were resolved to benign or likely benign. Overall, 88% (239 of 273) of curated variants had non-VUS classifications. To date, variants classified as pathogenic are either nonsense, frameshift, splicing, or affecting the translation initiation codon, and the only missense variants classified as pathogenic or likely pathogenic have been shown to affect splicing. CONCLUSIONS The development and evolution of CDH1-specific criteria by the expert panel resulted in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene, which can ultimately lead to more effective clinical management recommendations.
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Affiliation(s)
- Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Jamie L Maciaszek
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bryony A Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Katherine Dixon
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sónia Sousa
- Instituto de Investigação e Inovação em Saúde - (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology - (IPATIMUP), University of Porto, Porto, Portugal
| | | | | | - Kristy Lee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Liying Zhang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | | | - Sainan Wei
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Grace-Ann Fasaye
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Brian H Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jeremy L Davis
- Surgical Oncology Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Carla Oliveira
- Instituto de Investigação e Inovação em Saúde - (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology - (IPATIMUP), University of Porto, Porto, Portugal.,Department of Pathology, University of Porto, Porto, Portugal
| | - Sharon E Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Kasmintan A Schrader
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia, Canada
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3
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Tudini E, Andrews J, Lawrence DM, King-Smith SL, Baker N, Baxter L, Beilby J, Bennetts B, Beshay V, Black M, Boughtwood TF, Brion K, Cheong PL, Christie M, Christodoulou J, Chong B, Cox K, Davis MR, Dejong L, Dinger ME, Doig KD, Douglas E, Dubowsky A, Ellul M, Fellowes A, Fisk K, Fortuno C, Friend K, Gallagher RL, Gao S, Hackett E, Hadler J, Hipwell M, Ho G, Hollway G, Hooper AJ, Kassahn KS, Krishnaraj R, Lau C, Le H, San Leong H, Lundie B, Lunke S, Marty A, McPhillips M, Nguyen LT, Nones K, Palmer K, Pearson JV, Quinn MC, Rawlings LH, Sadedin S, Sanchez L, Schreiber AW, Sigalas E, Simsek A, Soubrier J, Stark Z, Thompson BA, U J, Vakulin CG, Wells AV, Wise CA, Woods R, Ziolkowski A, Brion MJ, Scott HS, Thorne NP, Spurdle AB. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. Am J Hum Genet 2022; 109:1960-1973. [PMID: 36332611 PMCID: PMC9674965 DOI: 10.1016/j.ajhg.2022.10.006] [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: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
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Affiliation(s)
- Emma Tudini
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - James Andrews
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M. Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Sarah L. King-Smith
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Naomi Baker
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | | | - John Beilby
- PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Victoria Beshay
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Michael Black
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Tiffany F. Boughtwood
- Australian Genomics, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | | | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia,University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - John Christodoulou
- Australian Genomics, Melbourne, VIC 3052, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Kathy Cox
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Mark R. Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Lucas Dejong
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kenneth D. Doig
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Dubowsky
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Melissa Ellul
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | | | - Song Gao
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Emma Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Johanna Hadler
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael Hipwell
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Georgina Hollway
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia,Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda J. Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia,School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
| | - Karin S. Kassahn
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Rahul Krishnaraj
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Chiyan Lau
- Pathology Queensland, Brisbane, QLD 4006, Australia,The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huong Le
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Ben Lundie
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony Marty
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Mary McPhillips
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Lan T. Nguyen
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia
| | - Katia Nones
- Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristen Palmer
- Genomics Statewide Services, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - John V. Pearson
- Genome Informatics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael C.J. Quinn
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia
| | - Lesley H. Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Louisa Sanchez
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andreas W. Schreiber
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Emanouil Sigalas
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Aygul Simsek
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Julien Soubrier
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Bryony A. Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - James U
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | | | - Amanda V. Wells
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Cheryl A. Wise
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Rick Woods
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Andrew Ziolkowski
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Marie-Jo Brion
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Hamish S. Scott
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Natalie P. Thorne
- Australian Genomics, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia,Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia
| | - Amanda B. Spurdle
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia,Corresponding author
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4
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Clark KA, Paquette A, Tao K, Bell R, Boyle JL, Rosenthal J, Snow AK, Stark AW, Thompson BA, Unger J, Gertz J, Varley KE, Boucher KM, Goldgar DE, Foulkes WD, Thomas A, Tavtigian SV. Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions. Am J Hum Genet 2022; 109:1153-1174. [PMID: 35659930 PMCID: PMC9247830 DOI: 10.1016/j.ajhg.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein-truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a mammalian two-hybrid assay. Downstream of the laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data, such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that 15%-20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 45 with concordant computational and functional assay evidence in favor of pathogenicity plus 223 with concordant evidence in favor of benignity; these are particularly likely to be classified as likely pathogenic and likely benign, respectively, once human observational data become available.
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Affiliation(s)
- Kathleen A Clark
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew Paquette
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kayoko Tao
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Russell Bell
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Julie L Boyle
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Judith Rosenthal
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Angela K Snow
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Alex W Stark
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bryony A Thompson
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Joshua Unger
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Katherine E Varley
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kenneth M Boucher
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - David E Goldgar
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - William D Foulkes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Research Institute McGill University Health Center, Montreal, QC H3T 1E2, Canada; Departments of Medicine, Human Genetics, and Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Alun Thomas
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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5
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Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [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: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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6
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Peters S, Thompson BA, Perrin M, James P, Zentner D, Kalman JM, Vandenberg JI, Fatkin D. Arrhythmic Phenotypes Are a Defining Feature of Dilated Cardiomyopathy-Associated SCN5A Variants: A Systematic Review. Circ Genom Precis Med 2022; 15:e003432. [PMID: 34949099 DOI: 10.1161/circgen.121.003432] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Variants in the SCN5A gene, that encodes the cardiac sodium channel, Nav1.5, are associated with a highly arrhythmogenic form of dilated cardiomyopathy (DCM). Our aim was to review the phenotypes, natural history, functional effects, and treatment outcomes of DCM-associated rare SCN5A variants. METHODS A systematic review of reported DCM-associated rare SCN5A variants was undertaken using PubMed and Embase. RESULTS Eighteen SCN5A rare variants in 29 families with DCM (173 affected individuals) were identified. Eleven variants had undergone experimental evaluation, with 7 of these resulting in increased sustained current flow during the action potential (eg, increased window current) and at resting membrane potentials (eg, creation of a new gating pore current). These variants were located in transmembrane voltage-sensing domains and had a consistent phenotype characterized by frequent multifocal narrow and broad complex ventricular premature beats (VPB; 72% of affected relatives), ventricular arrhythmias (33%), atrial arrhythmias (32%), sudden cardiac death (13%), and DCM (56%). This VPB-predominant phenotype was not seen with 1 variant that increased late sodium current, or with variants that reduced peak current density or had mixed effects. In the latter groups, affected individuals mainly showed sinus node dysfunction, conduction defects, and atrial arrhythmias, with infrequent VPB and ventricular arrhythmias. DCM did not occur in the absence of arrhythmias for any variant. Twelve studies (23 total patients) reported treatment success in the VPB-predominant cardiomyopathy using sodium channel-blocking drug therapy. CONCLUSIONS SCN5A variants can present with a diverse spectrum of primary arrhythmic features. A majority of DCM-associated variants cause a multifocal VPB-predominant cardiomyopathy that is reversible with sodium channel blocking drug therapy. Early recognition of the distinctive phenotype and prompt genetic testing to identify variant carriers are needed. Our findings have implications for interpretation and management of SCN5A variants found in DCM patients with and without arrhythmias.
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Affiliation(s)
- Stacey Peters
- Department of Cardiology (S.P., M.P., D.Z., J.M.K.), Royal Melbourne Hospital
- Department of Genomic Medicine (S.P., B.A.T., M.P., P.J., D.Z.), Royal Melbourne Hospital
- Department of Medicine, University of Melbourne (S.P., P.J., D.Z., J.M.K.)
| | - Bryony A Thompson
- Department of Genomic Medicine (S.P., B.A.T., M.P., P.J., D.Z.), Royal Melbourne Hospital
- Department of Pathology (B.A.T.), Royal Melbourne Hospital
| | - Mark Perrin
- Department of Genomic Medicine (S.P., B.A.T., M.P., P.J., D.Z.), Royal Melbourne Hospital
| | - Paul James
- Department of Genomic Medicine (S.P., B.A.T., M.P., P.J., D.Z.), Royal Melbourne Hospital
- Department of Medicine, University of Melbourne (S.P., P.J., D.Z., J.M.K.)
- Familial Cancer Centre, Peter MacCallum Centre, Melbourne, Victoria (P.J.)
| | - Dominica Zentner
- Department of Genomic Medicine (S.P., B.A.T., M.P., P.J., D.Z.), Royal Melbourne Hospital
- Department of Medicine, University of Melbourne (S.P., P.J., D.Z., J.M.K.)
| | - Jonathan M Kalman
- Department of Medicine, University of Melbourne (S.P., P.J., D.Z., J.M.K.)
| | - Jamie I Vandenberg
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute (J.I.V., D.F.)
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney (J.I.V., D.F.)
| | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute (J.I.V., D.F.)
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney (J.I.V., D.F.)
- Cardiology Department, St. Vincent's Hospital, Sydney, New South Wales, Australia (D.F.)
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7
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Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V, Boggs K, Bojadzieva J, Brown NJ, Bryen SJ, Buckley MF, Chong B, Davis MR, Dawes R, Delatycki M, Donaldson L, Downie L, Edwards C, Edwards M, Engel A, Ewans LJ, Faiz F, Fennell A, Field M, Freckmann ML, Gallacher L, Gear R, Goel H, Goh S, Goodwin L, Hanna B, Harraway J, Higgins M, Ho G, Hopper BK, Horton AE, Hunter MF, Huq AJ, Josephi-Taylor S, Joshi H, Kirk E, Krzesinski E, Kumar KR, Lemckert F, Leventer RJ, Lindsey-Temple SE, Lunke S, Ma A, Macaskill S, Mallawaarachchi A, Marty M, Marum JE, McCarthy HJ, Menezes MP, McLean A, Milnes D, Mohammad S, Mowat D, Niaz A, Palmer EE, Patel C, Patel SG, Phelan D, Pinner JR, Rajagopalan S, Regan M, Rodgers J, Rodrigues M, Roxburgh RH, Sachdev R, Roscioli T, Samarasekera R, Sandaradura SA, Savva E, Schindler T, Shah M, Sinnerbrink IB, Smith JM, Smith RJ, Springer A, Stark Z, Strom SP, Sue CM, Tan K, Tan TY, Tantsis E, Tchan MC, Thompson BA, Trainer AH, van Spaendonck-Zwarts K, Walsh R, Warwick L, White S, White SM, Williams MG, Wilson MJ, Wong WK, Wright DC, Yap P, Yeung A, Young H, Jones KJ, Bennetts B, Cooper ST. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genet Med 2021; 24:130-145. [PMID: 34906502 DOI: 10.1016/j.gim.2021.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/18/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). METHODS A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. RESULTS Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. CONCLUSION RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.
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Affiliation(s)
- Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Lisa G Riley
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lesley Ades
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lauren S Akesson
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Mohammad Al-Shinnag
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia
| | - Stephen I Alexander
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison D Archibald
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Yemima Berman
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Northern Clinical School, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Victoria Beshay
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Australian Genomics Health Alliance, Parkville, Victoria, Australia; Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Jasmina Bojadzieva
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | | | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Martin Delatycki
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Liz Donaldson
- The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Lilian Downie
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Caitlin Edwards
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Matthew Edwards
- Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia
| | - Amanda Engel
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Lisa J Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Fathimath Faiz
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Andrew Fennell
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | | | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Himanshu Goel
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia
| | - Shuxiang Goh
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Linda Goodwin
- Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Bernadette Hanna
- Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - James Harraway
- Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Gladys Ho
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Ari E Horton
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Monash Heart and Monash Children's Hospital, Monash Health, Clayton, Victoria, Australia; Monash Cardiovascular Research Centre, Clayton, Victoria, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Aamira J Huq
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Edwin Kirk
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Translational Genomics, Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, New South Wales, Australia
| | - Frances Lemckert
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Suzanna E Lindsey-Temple
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sebastian Lunke
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Alan Ma
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Melanie Marty
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Justine E Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Hugh J McCarthy
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Manoj P Menezes
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison McLean
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shekeeb Mohammad
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - David Mowat
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Aram Niaz
- Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Elizabeth E Palmer
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shilpan G Patel
- School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Jason R Pinner
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sulekha Rajagopalan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Jonathan Rodgers
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Miriam Rodrigues
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | | | - Rani Sachdev
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia, University of New South Wales, Randwick, New South Wales, Australia
| | - Ruvishani Samarasekera
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sarah A Sandaradura
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tim Schindler
- School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia; Newborn Care, Royal Hospital for Women, Randwick, New South Wales, Australia
| | - Margit Shah
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ingrid B Sinnerbrink
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Janine M Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Amanda Springer
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Kenneth Tan
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia
| | - Tiong Y Tan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Esther Tantsis
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michel C Tchan
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Rebecca Walsh
- NSW Health Pathology, Randwick, New South Wales, Australia
| | - Linda Warwick
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Stephanie White
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark G Williams
- Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia
| | - Meredith J Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Wui Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Dale C Wright
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Patrick Yap
- Northern Hub, Genetic Health Service NZ, Auckland, New Zealand
| | - Alison Yeung
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Helen Young
- Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bruce Bennetts
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The Children's Medical Research Institute, Westmead, New South Wales, Australia.
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8
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Stark Z, Foulger RE, Williams E, Thompson BA, Patel C, Lunke S, Snow C, Leong IUS, Puzriakova A, Daugherty LC, Leigh S, Boustred C, Niblock O, Rueda-Martin A, Gerasimenko O, Savage K, Bellamy W, Lin VSK, Valls R, Gordon L, Brittain HK, Thomas ERA, Taylor Tavares AL, McEntagart M, White SM, Tan TY, Yeung A, Downie L, Macciocca I, Savva E, Lee C, Roesley A, De Fazio P, Deller J, Deans ZC, Hill SL, Caulfield MJ, North KN, Scott RH, Rendon A, Hofmann O, McDonagh EM. Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution. Am J Hum Genet 2021; 108:1551-1557. [PMID: 34329581 PMCID: PMC8456155 DOI: 10.1016/j.ajhg.2021.06.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/27/2021] [Indexed: 02/02/2023] Open
Abstract
Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Rebecca E Foulger
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Eleanor Williams
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bryony A Thompson
- University of Melbourne, Melbourne, VIC 3010, Australia; Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catherine Snow
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ivone U S Leong
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Arina Puzriakova
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Louise C Daugherty
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher Boustred
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Olivia Niblock
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Antonio Rueda-Martin
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oleg Gerasimenko
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kevin Savage
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - William Bellamy
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Victor San Kho Lin
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Roman Valls
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lavinia Gordon
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Helen K Brittain
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ellen R A Thomas
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Guy's and St Thomas's NHS Trust, London SE1 9RS, UK
| | | | - Meriel McEntagart
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; St George's University Hospitals NHS Trust, London SW17 0QT, UK
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lilian Downie
- University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Jane Deller
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Zandra C Deans
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Sue L Hill
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kathryn N North
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ellen M McDonagh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Open Targets and European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
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9
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Thompson BA, Dear K, Donaldson E, Nixon R, Winship IM. A novel candidate gene in autosomal dominant facial pruritus. Clin Exp Dermatol 2021; 47:184-186. [PMID: 34386996 DOI: 10.1111/ced.14883] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 12/01/2022]
Abstract
Pruritus is a common and often debilitating symptom that is associated with dermatological conditions including eczema, allergic contact dermatitis, urticaria, some drug eruptions and less commonly systemic diseases and neuropathic causes1 . We report here an unusual familial centrofacial pruritus without any history or clinical findings of a rash, affecting three siblings and their father. The index patient (ll-1; Figure 1a) was a 62-year-old female with a 20-year history of severe localised pruritus of the nose. Her predominant symptom was debilitating itch on the surface of the skin around her nasal bridge, nasal septum and the nasal alae. She had no associated nasal congestion, rhinorrhea, skin changes nor rash and there was no relation to seasons, being outdoors, time of day, occupation, or food intake. Possible triggers included a warm environment and exercise.
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Affiliation(s)
- B A Thompson
- Department of Pathology, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Genomic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - K Dear
- Occupational Dermatology Research and Education Centre, Skin Health Institute, Carlton, VIC, Australia
| | - E Donaldson
- Department of Genomic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - R Nixon
- Occupational Dermatology Research and Education Centre, Skin Health Institute, Carlton, VIC, Australia
| | - I M Winship
- Department of Genomic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Medicine, University of Melbourne, Parkville, VIC, Australia
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10
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Thompson BA, Snow AK, Koptiuch C, Kohlmann WK, Mooney R, Johnson S, Huff CD, Yu Y, Teerlink CC, Feng BJ, Neklason DW, Cannon-Albright LA, Tavtigian SV. A novel ribosomal protein S20 variant in a family with unexplained colorectal cancer and polyposis. Clin Genet 2021; 97:943-944. [PMID: 32424863 DOI: 10.1111/cge.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan Mooney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Sara Johnson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, Utah, USA
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Lisa A Cannon-Albright
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Research and Development Service, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
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11
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Cannon-Albright LA, Teerlink CC, Stevens J, Snow AK, Thompson BA, Bell R, Nguyen KN, Sargent NR, Kohlmann WK, Neklason DW, Tavtigian SV. FANCM c5791C>T stopgain mutation (rs144567652) is a familial colorectal cancer risk factor. Mol Genet Genomic Med 2020; 8:e1532. [PMID: 33118316 PMCID: PMC7767553 DOI: 10.1002/mgg3.1532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/09/2020] [Accepted: 09/25/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose While familial aggregation of colorectal cancer (CRC) is recognized, the majority of the germline predisposition factors remain unidentified, and many high‐risk CRC pedigrees remain unexplained by known risk variants. Fanconi Anemia genes have been recognized to be associated with cancer risk. Notably, FANCM (OMIM 609644) variants have been reported to confer risk for CRC and breast cancer. Methods Exome sequencing of CRC‐affected cousins in a set of 47 independent extended high‐risk CRC pedigrees identified a candidate set of rare, shared variants. Variants were tested for association with risk in 744 Utah CRC cases and 1525 controls, and for segregation with CRC in affected relatives. Results A FANCM stopgain variant was observed in two CRC‐affected cousin pairs, each from an independent Utah high‐risk pedigree, and yielded a nonsignificant, but elevated OR = 2.05 in a set of Utah cases and controls. Segregation of the variant to other related CRC‐affected cases was observed in the two extended pedigrees. Conclusion A rare stopgain variant in FANCM (rs144567652) that is recognized as a breast cancer predisposition variant, and that has previously been proposed, but not confirmed, as a CRC predisposition variant, is validated here as a risk factor for familial CRC.
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Affiliation(s)
- Lisa A Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jeffrey Stevens
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia
| | - Russell Bell
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kim N Nguyen
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Nykole R Sargent
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Deborah W Neklason
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA
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12
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Thompson BA, Walters R, Parsons MT, Dumenil T, Drost M, Tiersma Y, Lindor NM, Tavtigian SV, de Wind N, Spurdle AB. Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation. Front Genet 2020; 11:798. [PMID: 32849802 PMCID: PMC7398121 DOI: 10.3389/fgene.2020.00798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/03/2020] [Indexed: 12/25/2022] Open
Abstract
Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected: 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants.
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Affiliation(s)
- Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rhiannon Walters
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael T Parsons
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Troy Dumenil
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, United States
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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13
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Baderna V, Schultz J, Kearns LS, Fahey M, Thompson BA, Ruddle JB, Huq A, Maltecca F. A novel AFG3L2 mutation close to AAA domain leads to aberrant OMA1 and OPA1 processing in a family with optic atrophy. Acta Neuropathol Commun 2020; 8:93. [PMID: 32600459 PMCID: PMC7325028 DOI: 10.1186/s40478-020-00975-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Autosomal dominant optic atrophy (ADOA) is a neuro-ophthalmic condition characterized by bilateral degeneration of the optic nerves. Although heterozygous mutations in OPA1 represent the most common genetic cause of ADOA, a significant number of cases remain undiagnosed. Here, we describe a family with a strong ADOA history with most family members spanning three generation having childhood onset of visual symptoms. The proband, in addition to optic atrophy, had neurological symptoms consistent with relapsing remitting multiple sclerosis. Clinical exome analysis detected a novel mutation in the AFG3L2 gene (NM_006796.2:c.1010G > A; p.G337E), which segregated with optic atrophy in family members. AFG3L2 is a metalloprotease of the AAA subfamily which exerts quality control in the inner mitochondrial membrane. Interestingly, the identified mutation localizes close to the AAA domain of AFG3L2, while those localized in the proteolytic domain cause dominant spinocerebellar ataxia type 28 (SCA28) or recessive spastic ataxia with epilepsy (SPAX5). Functional studies in patient fibroblasts demonstrate that the p.G337E AFG3L2 mutation strongly destabilizes the long isoforms of OPA1 via OMA hyper-activation and leads to mitochondrial fragmentation, thus explaining the family phenotype. This study widens the clinical spectrum of neurodegenerative diseases caused by AFG3L2 mutations, which shall be considered as genetic cause of ADOA.
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14
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Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. Bioinformatics 2020; 35:2315-2317. [PMID: 30475984 PMCID: PMC6596880 DOI: 10.1093/bioinformatics/bty960] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 10/29/2018] [Accepted: 11/22/2018] [Indexed: 02/02/2023] Open
Abstract
Summary Assessing the pathogenicity of genetic variants can be a complex and challenging task. Spliceogenic variants, which alter mRNA splicing, may yield mature transcripts that encode non-functional protein products, an important predictor of Mendelian disease risk. However, most variant annotation tools do not adequately assess spliceogenicity outside the native splice site and thus the disease-causing potential of variants in other intronic and exonic regions is often overlooked. Here, we present a plugin for the Ensembl Variant Effect Predictor that packages MaxEntScan and extends its functionality to provide splice site predictions using a maximum entropy model. The plugin incorporates a sliding window algorithm to predict splice site loss or gain for any variant that overlaps a transcript feature. We also demonstrate the utility of the plugin by comparing our predictions to two mRNA splicing datasets containing several cancer-susceptibility genes. Availability and implementation Source code is freely available under the Apache License, Version 2.0: https://github.com/Ensembl/VEP_plugins. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jannah Shamsani
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Stephen H Kazakoff
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Will McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Bryony A Thompson
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne VIC, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
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15
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Li S, Qian D, Thompson BA, Gutierrez S, Wu S, Pesaran T, LaDuca H, Lu HM, Chao EC, Black MH. Tumour characteristics provide evidence for germline mismatch repair missense variant pathogenicity. J Med Genet 2019; 57:62-69. [PMID: 31391288 DOI: 10.1136/jmedgenet-2019-106096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Pathogenic variants in mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2) increase risk for Lynch syndrome and related cancers. We quantified tumour characteristics to assess variant pathogenicity for germline MMR genes. METHODS Among 4740 patients with cancer with microsatellite instability (MSI) and immunohistochemical (IHC) results, we tested MMR pathogenic variant association with MSI/IHC status, and estimated likelihood ratios which we used to compute a tumour characteristic likelihood ratio (TCLR) for each variant. Predictive performance of TCLR in combination with in silico predictors, and a multifactorial variant prediction (MVP) model that included allele frequency, co-occurrence, co-segregation, and clinical and family history information was assessed. RESULTS Compared with non-carriers, carriers of germline pathogenic/likely pathogenic (P/LP) variants were more likely to have abnormal MSI/IHC status (p<0.0001). Among 150 classified missense variants, 73.3% were accurately predicted with TCLR alone. Models leveraging in silico scores as prior probabilities accurately classified >76.7% variants. Adding TCLR as quantitative evidence in an MVP model (MVP +TCLR Pred) increased the proportion of accurately classified variants from 88.0% (MVP alone) to 98.0% and generated optimal performance statistics among all models tested. Importantly, MVP +TCLR Pred resulted in the high yield of predicted classifications for missense variants of unknown significance (VUS); among 193 VUS, 62.7% were predicted as P/PL or benign/likely benign (B/LB) when assessed according to American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. CONCLUSION Our study demonstrates that when used separately or in conjunction with other evidence, tumour characteristics provide evidence for germline MMR missense variant assessment, which may have important implications for genetic testing and clinical management.
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Affiliation(s)
- Shuwei Li
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Dajun Qian
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Bryony A Thompson
- Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Sitao Wu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Tina Pesaran
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Holly LaDuca
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Mary Helen Black
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
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16
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Young EL, Thompson BA, Neklason DW, Firpo MA, Werner T, Bell R, Berger J, Fraser A, Gammon A, Koptiuch C, Kohlmann WK, Neumayer L, Goldgar DE, Mulvihill SJ, Cannon-Albright LA, Tavtigian SV. Pancreatic cancer as a sentinel for hereditary cancer predisposition. BMC Cancer 2018; 18:697. [PMID: 29945567 PMCID: PMC6020441 DOI: 10.1186/s12885-018-4573-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) predisposition have been shown to play a role in pancreatic cancer susceptibility. Growing evidence suggests that pancreatic cancer may be useful as a sentinel cancer to identify families that could benefit from HBOC or CRC surveillance, but to date pancreatic cancer is only considered an indication for genetic testing in the context of additional family history. METHODS Preliminary data generated at the Huntsman Cancer Hospital (HCH) included variants identified on a custom 34-gene panel or 59-gene panel including both known HBOC and CRC genes for respective sets of 66 and 147 pancreatic cancer cases, unselected for family history. Given the strength of preliminary data and corresponding literature, 61 sequential pancreatic cancer cases underwent a custom 14-gene clinical panel. Sequencing data from HCH pancreatic cancer cases, pancreatic cancer cases of the Cancer Genome Atlas (TCGA), and an unselected pancreatic cancer screen from the Mayo Clinic were combined in a meta-analysis to estimate the proportion of carriers with pathogenic and high probability of pathogenic variants of uncertain significance (HiP-VUS). RESULTS Approximately 8.6% of unselected pancreatic cancer cases at the HCH carried a variant with potential HBOC or CRC screening recommendations. A meta-analysis of unselected pancreatic cancer cases revealed that approximately 11.5% carry a pathogenic variant or HiP-VUS. CONCLUSION With the inclusion of both HBOC and CRC susceptibility genes in a panel test, unselected pancreatic cancer cases act as a useful sentinel cancer to identify asymptomatic at-risk relatives who could benefit from relevant HBOC and CRC surveillance measures.
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Affiliation(s)
- Erin L. Young
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Bryony A. Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Deborah W. Neklason
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Matthew A. Firpo
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Theresa Werner
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Oncology, Department of Medicine, University of Utah, Salt Lake City, United States
| | - Russell Bell
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Justin Berger
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Alison Fraser
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Amanda Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Wendy K. Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Leigh Neumayer
- Department of Surgery and Arizona Cancer Center, University of Arizona, Tucson, United States
| | - David E. Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, United States
| | - Sean J. Mulvihill
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Lisa A. Cannon-Albright
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
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17
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Li J, Li H, Makunin I, Thompson BA, Tao K, Young EL, Lopez J, Camp NJ, Tavtigian SV, John EM, Andrulis IL, Khanna KK, Goldgar D, Chenevix-Trench G. Panel sequencing of 264 candidate susceptibility genes and segregation analysis in a cohort of non-BRCA1, non-BRCA2 breast cancer families. Breast Cancer Res Treat 2017; 166:937-949. [PMID: 28840378 DOI: 10.1007/s10549-017-4469-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022]
Abstract
PURPOSE The main aim of this study was to screen epigenetic modifier genes and known breast cancer driver genes for germline mutations in non-BRCA1/2 (BRCAx) breast cancer families in order to identify novel susceptibility genes of moderate-high penetrance. METHODS We screened 264 candidate susceptibility genes in 656 index cases from non-BRCA1/2 families. Potentially pathogenic candidate mutations were then genotyped in all available family members for the assessment of co-segregation of the variant with disease in the family in order to estimate the breast cancer risks associated with these mutations. For 11 of the candidate susceptibility genes, we screened an additional 800 non-BRCA1/2 breast cancer cases and 787 controls. RESULTS Only two genes, CHD8 and USH2A showed any evidence of an increased risk of breast cancer (RR = 2.40 (95% CI 1.0-7.32) and 2.48 (95% CI 1.11-6.67), respectively). CONCLUSIONS We found no convincing evidence that epigenetic modifier and known breast cancer driver genes carry germline mutations that increase breast cancer risk. USH2A is no longer regarded as a breast cancer driver gene and seems an implausible candidate given its association with Usher syndrome. However, somatic mutations in CHD8 have been recently reported, making it an even more promising candidate, but further analysis of CHD8 in very large cohorts of families or case-control studies would be required to determine if it is a moderate-risk breast cancer susceptibility gene.
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Affiliation(s)
- Jun Li
- QIMR Berghofer, Brisbane, QLD, 4006, Australia
| | - Hongyan Li
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Igor Makunin
- QIMR Berghofer, Brisbane, QLD, 4006, Australia.,Research Computing Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Kayoko Tao
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Erin L Young
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Jacqueline Lopez
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, 94538, USA.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1X5, Canada
| | | | - David Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA.,Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
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18
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Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dámaso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, Valencia A, Holinski-Feder E, Brunet J, Feliubadaló L, Lázaro C, Navarro M, Pineda M, Capellá G. Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis. Int J Cancer 2017; 141:1365-1380. [PMID: 28577310 DOI: 10.1002/ijc.30820] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 12/07/2016] [Revised: 05/06/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022]
Abstract
In a proportion of patients presenting mismatch repair (MMR)-deficient tumors, no germline MMR mutations are identified, the so-called Lynch-like syndrome (LLS). Recently, MMR-deficient tumors have been associated with germline mutations in POLE and MUTYH or double somatic MMR events. Our aim was to elucidate the molecular basis of MSH2-deficient LS-suspected cases using a comprehensive analysis of colorectal cancer (CRC)-associated genes at germline and somatic level. Fifty-eight probands harboring MSH2-deficient tumors were included. Germline mutational analysis of MSH2 (including EPCAM deletions) and MSH6 was performed. Pathogenicity of MSH2 variants was assessed by RNA analysis and multifactorial likelihood calculations. MSH2 cDNA and methylation of MSH2 and MSH6 promoters were studied. Matched blood and tumor DNA were analyzed using a customized next generation sequencing panel. Thirty-five individuals were carriers of pathogenic or probably pathogenic variants in MSH2 and EPCAM. Five patients harbored 4 different MSH2 variants of unknown significance (VUS) and one had 2 novel MSH6 promoter VUS. Pathogenicity assessment allowed the reclassification of the 4 MSH2 VUS and 6 probably pathogenic variants as pathogenic mutations, enabling a total of 40 LS diagnostics. Predicted pathogenic germline variants in BUB1, SETD2, FAN1 and MUTYH were identified in 5 cases. Three patients had double somatic hits in MSH2 or MSH6, and another 2 had somatic alterations in other MMR genes and/or proofreading polymerases. In conclusion, our comprehensive strategy combining germline and somatic mutational status of CRC-associated genes by means of a subexome panel allows the elucidation of up to 86% of MSH2-deficient suspected LS tumors.
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Affiliation(s)
- Gardenia M Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Àngela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
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19
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González-Acosta M, Del Valle J, Navarro M, Thompson BA, Iglesias S, Sanjuan X, Paúles MJ, Padilla N, Fernández A, Cuesta R, Teulé À, Plotz G, Cadiñanos J, de la Cruz X, Balaguer F, Lázaro C, Pineda M, Capellá G. Elucidating the clinical significance of two PMS2 missense variants coexisting in a family fulfilling hereditary cancer criteria. Fam Cancer 2017; 16:501-507. [PMID: 28365877 DOI: 10.1007/s10689-017-9981-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The clinical spectrum of germline mismatch repair (MMR) gene variants continues increasing, encompassing Lynch syndrome, Constitutional MMR Deficiency (CMMRD), and the recently reported MSH3-associated polyposis. Genetic diagnosis of these hereditary cancer syndromes is often hampered by the presence of variants of unknown significance (VUS) and overlapping phenotypes. Two PMS2 VUS, c.2149G>A (p.V717M) and c.2444C>T (p.S815L), were identified in trans in one individual diagnosed with early-onset colorectal cancer (CRC) who belonged to a family fulfilling clinical criteria for hereditary cancer. Clinico-pathological data, multifactorial likelihood calculations and functional analyses were used to refine their clinical significance. Likelihood analysis based on cosegregation and tumor data classified the c.2444C>T variant as pathogenic, which was supported by impaired MMR activity associated with diminished protein expression in functional assays. Conversely, the c.2149G>A variant displayed MMR proficiency and protein stability. These results, in addition to the conserved PMS2 expression in normal tissues and the absence of germline microsatellite instability (gMSI) in the biallelic carrier ruled out a CMMRD diagnosis. The use of comprehensive strategies, including functional and clinico-pathological information, is mandatory to improve the clinical interpretation of naturally occurring MMR variants. This is critical for appropriate clinical management of cancer syndromes associated to MMR gene mutations.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - María José Paúles
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Raquel Cuesta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Guido Plotz
- Medical Clinic 1, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain.
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20
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Tricarico R, Kasela M, Mareni C, Thompson BA, Drouet A, Staderini L, Gorelli G, Crucianelli F, Ingrosso V, Kantelinen J, Papi L, De Angioletti M, Berardi M, Gaildrat P, Soukarieh O, Turchetti D, Martins A, Spurdle AB, Nyström M, Genuardi M. Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants. Hum Mutat 2016; 38:64-77. [PMID: 27629256 DOI: 10.1002/humu.23117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 04/26/2016] [Revised: 09/04/2016] [Accepted: 09/09/2016] [Indexed: 01/15/2023]
Abstract
Pathogenicity assessment of DNA variants in disease genes to explain their clinical consequences is an integral component of diagnostic molecular testing. The International Society for Gastrointestinal Hereditary Tumors (InSiGHT) has developed specific criteria for the interpretation of mismatch repair (MMR) gene variants. Here, we performed a systematic investigation of 24 MLH1 and MSH2 variants. The assessments were done by analyzing population frequency, segregation, tumor molecular characteristics, RNA effects, protein expression levels, and in vitro MMR activity. Classifications were confirmed for 15 variants and changed for three, and for the first time determined for six novel variants. Overall, based on our results, we propose the introduction of some refinements to the InSiGHT classification rules. The proposed changes have the advantage of homogenizing the InSIGHT interpretation criteria with those set out by the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium for the BRCA1/BRCA2 genes. We also observed that the addition of only few clinical data was sufficient to obtain a more stable classification for variants considered as "likely pathogenic" or "likely nonpathogenic." This shows the importance of obtaining as many as possible points of evidence for variant interpretation, especially from the clinical setting.
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Affiliation(s)
- Rossella Tricarico
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mariann Kasela
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | | | - Bryony A Thompson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Aurélie Drouet
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Lucia Staderini
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Greta Gorelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Francesca Crucianelli
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Valentina Ingrosso
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Jukka Kantelinen
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Maria De Angioletti
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy.,ICCOM-CNR, Sesto Fiorentino, Italy
| | - Margherita Berardi
- Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy
| | - Pascaline Gaildrat
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Omar Soukarieh
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Daniela Turchetti
- Medical Genetics, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alexandra Martins
- Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Minna Nyström
- Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.,Institute of Genomic Medicine, A. Gemelli School of Medicine, Medical Genetics Unit, Catholic University of the Sacred Heart, Rome, Italy
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21
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Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
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22
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van der Velde KJ, Kuiper J, Thompson BA, Plazzer J, van Valkenhoef G, de Haan M, Jongbloed JD, Wijmenga C, de Koning TJ, Abbott KM, Sinke R, Spurdle AB, Macrae F, Genuardi M, Sijmons RH, Swertz MA. Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization. Hum Mutat 2015; 36:712-9. [PMID: 25871441 PMCID: PMC4973827 DOI: 10.1002/humu.22798] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/30/2015] [Indexed: 12/02/2022]
Abstract
Next-generation sequencing in clinical diagnostics is providing valuable genomic variant data, which can be used to support healthcare decisions. In silico tools to predict pathogenicity are crucial to assess such variants and we have evaluated a new tool, Combined Annotation Dependent Depletion (CADD), and its classification of gene variants in Lynch syndrome by using a set of 2,210 DNA mismatch repair gene variants. These had already been classified by experts from InSiGHT's Variant Interpretation Committee. Overall, we found CADD scores do predict pathogenicity (Spearman's ρ = 0.595, P < 0.001). However, we discovered 31 major discrepancies between the InSiGHT classification and the CADD scores; these were explained in favor of the expert classification using population allele frequencies, cosegregation analyses, disease association studies, or a second-tier test. Of 751 variants that could not be clinically classified by InSiGHT, CADD indicated that 47 variants were worth further study to confirm their putative pathogenicity. We demonstrate CADD is valuable in prioritizing variants in clinically relevant genes for further assessment by expert classification teams.
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Affiliation(s)
- K. Joeri van der Velde
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Joël Kuiper
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Bryony A. Thompson
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - John‐Paul Plazzer
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
| | - Gert van Valkenhoef
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Mark de Haan
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Jan D.H. Jongbloed
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Cisca Wijmenga
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Tom J. de Koning
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Kristin M. Abbott
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Richard Sinke
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Finlay Macrae
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
- Department of MedicineThe Royal Melbourne HospitalUniversity of MelbourneMelbourneAustralia
| | - Maurizio Genuardi
- Institute of Medical Genetics“A. Gemelli” School of MedicineCatholic University of the Sacred HeartRomeItaly
| | - Rolf H. Sijmons
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Morris A. Swertz
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - InSiGHT Group
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
- Department of MedicineThe Royal Melbourne HospitalUniversity of MelbourneMelbourneAustralia
- Institute of Medical Genetics“A. Gemelli” School of MedicineCatholic University of the Sacred HeartRomeItaly
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23
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014; 6:32. [PMID: 25530820 PMCID: PMC4272815 DOI: 10.1186/s13148-014-0032-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Splicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries. FINDINGS Nucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy. CONCLUSION Nucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
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Pineda M, González-Acosta M, Thompson BA, Sánchez R, Gómez C, Martínez-López J, Perea J, Caldés T, Rodríguez Y, Landolfi S, Balmaña J, Lázaro C, Robles L, Capellá G, Rueda D. Detailed characterization of MLH1 p.D41H and p.N710D variants coexisting in a Lynch syndrome family with conserved MLH1 expression tumors. Clin Genet 2014; 87:543-8. [PMID: 25060679 DOI: 10.1111/cge.12467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 12/26/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant cancer-susceptibility disease caused by inactivating germline mutations in mismatch repair (MMR) genes. Variants of unknown significance (VUS) are often detected in mutational analysis of MMR genes. Here we describe a large family fulfilling Amsterdam I criteria carrying two rare VUS in the MLH1 gene: c.121G > C (p.D41H) and c.2128A > G (p.N710D). Collection of clinico-pathological data, multifactorial analysis, in silico predictions, and functional analyses were used to elucidate the clinical significance of the identified MLH1 VUS. Only the c.121G > C variant cosegregated with LS-associated tumors in the family. Diagnosed colorectal tumors were microsatellite unstable although immunohistochemical staining revealed no loss of MMR proteins expression. Multifactorial likelihood analysis classified c.2128A > G as a non-pathogenic variant and c.121G > C as pathogenic. In vitro functional tests revealed impaired MMR activity and diminished expression of c.121G > C. Accordingly, the N710 residue is located in the unconserved MLH1 C-terminal domain, whereas D41 is highly conserved and located in the ATPase domain. The obtained results will enable adequate genetic counseling of c.121G > C and c.2128A > G variant carriers and their families. Furthermore, they exemplify how cumulative data and comprehensive analyses are mandatory to refine the classification of MMR variants.
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Affiliation(s)
- M Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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25
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Buchanan DD, Tan YY, Walsh MD, Clendenning M, Metcalf AM, Ferguson K, Arnold ST, Thompson BA, Lose FA, Parsons MT, Walters RJ, Pearson SA, Cummings M, Oehler MK, Blomfield PB, Quinn MA, Kirk JA, Stewart CJ, Obermair A, Young JP, Webb PM, Spurdle AB. Reply to J. Moline et al. J Clin Oncol 2014; 32:2278-9. [PMID: 24912891 DOI: 10.1200/jco.2014.55.8213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Daniel D Buchanan
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Yen Y Tan
- Queensland Institute of Medical Research Berghofer Medical Research Institute; The University of Queensland School of Medicine, Brisbane, Queensland, Australia
| | - Michael D Walsh
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Clendenning
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alexander M Metcalf
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kaltin Ferguson
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sven T Arnold
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bryony A Thompson
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Felicity A Lose
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michael T Parsons
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rhiannon J Walters
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sally-Ann Pearson
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Margaret Cummings
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Martin K Oehler
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | | | | | - Judy A Kirk
- Westmead Institute for Cancer Research, Westmead Millennium Institute, University of Sydney, New South Wales, Australia
| | - Colin J Stewart
- PathWest, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Andreas Obermair
- Queensland Centre for Gynaecological Oncology, University of Queensland, Brisbane, Queensland, Australia
| | - Joanne P Young
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Penelope M Webb
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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26
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014. [DOI: 10.1186/preaccept-1571082317134727] [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: 11/10/2022] Open
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27
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 342] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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28
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Buchanan DD, Tan YY, Walsh MD, Clendenning M, Metcalf AM, Ferguson K, Arnold ST, Thompson BA, Lose FA, Parsons MT, Walters RJ, Pearson SA, Cummings M, Oehler MK, Blomfield PB, Quinn MA, Kirk JA, Stewart CJ, Obermair A, Young JP, Webb PM, Spurdle AB. Tumor mismatch repair immunohistochemistry and DNA MLH1 methylation testing of patients with endometrial cancer diagnosed at age younger than 60 years optimizes triage for population-level germline mismatch repair gene mutation testing. J Clin Oncol 2013; 32:90-100. [PMID: 24323032 DOI: 10.1200/jco.2013.51.2129] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Clinicopathologic data from a population-based endometrial cancer cohort, unselected for age or family history, were analyzed to determine the optimal scheme for identification of patients with germline mismatch repair (MMR) gene mutations. PATIENTS AND METHODS Endometrial cancers from 702 patients recruited into the Australian National Endometrial Cancer Study (ANECS) were tested for MMR protein expression using immunohistochemistry (IHC) and for MLH1 gene promoter methylation in MLH1-deficient cases. MMR mutation testing was performed on germline DNA of patients with MMR-protein deficient tumors. Prediction of germline mutation status was compared for combinations of tumor characteristics, age at diagnosis, and various clinical criteria (Amsterdam, Bethesda, Society of Gynecologic Oncology, ANECS). RESULTS Tumor MMR-protein deficiency was detected in 170 (24%) of 702 cases. Germline testing of 158 MMR-deficient cases identified 22 truncating mutations (3% of all cases) and four unclassified variants. Tumor MLH1 methylation was detected in 99 (89%) of 111 cases demonstrating MLH1/PMS2 IHC loss; all were germline MLH1 mutation negative. A combination of MMR IHC plus MLH1 methylation testing in women younger than 60 years of age at diagnosis provided the highest positive predictive value for the identification of mutation carriers at 46% versus ≤ 41% for any other criteria considered. CONCLUSION Population-level identification of patients with MMR mutation-positive endometrial cancer is optimized by stepwise testing for tumor MMR IHC loss in patients younger than 60 years, tumor MLH1 methylation in individuals with MLH1 IHC loss, and germline mutations in patients exhibiting loss of MSH6, MSH2, or PMS2 or loss of MLH1/PMS2 with absence of MLH1 methylation.
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Affiliation(s)
- Daniel D Buchanan
- Daniel D. Buchanan, Yen Y. Tan, Michael D. Walsh, Mark Clendenning, Alexander M. Metcalf, Kaltin Ferguson, Sven T. Arnold, Bryony A. Thompson, Felicity A. Lose, Michael T. Parsons, Rhiannon J. Walters, Sally-Ann Pearson, Joanne P. Young, Penelope M. Webb, and Amanda B. Spurdle, QIMR Berghofer Medical Research Institute, Herston; Yen Y. Tan and Andreas Obermair, University of Queensland School of Medicine, Brisbane; Margaret Cummings, University of Queensland Centre for Clinical Research, Herston, Queensland; Martin K. Oehler, Royal Adelaide Hospital, Adelaide, South Australia; Michael A. Quinn, Royal Women's Hospital, Melbourne, Victoria; Judy A. Kirk, Westmead Institute for Cancer Research, Westmead Millennium Institute, University of Sydney, Sydney, New South Wales; Colin J. Stewart, King Edward Memorial Hospital, Perth, Western Australia, Australia; and Penelope B. Blomfield, Royal Hobart Hospital, Hobart, Tasmania
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29
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Parsons MT, Whiley PJ, Beesley J, Drost M, de Wind N, Thompson BA, Marquart L, Hopper JL, Jenkins MA, Brown MA, Tucker K, Warwick L, Buchanan DD, Spurdle AB. Consequences of germline variation disrupting the constitutional translational initiation codon start sites of MLH1 and BRCA2: Use of potential alternative start sites and implications for predicting variant pathogenicity. Mol Carcinog 2013; 54:513-22. [PMID: 24302565 DOI: 10.1002/mc.22116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/03/2013] [Accepted: 11/07/2013] [Indexed: 12/21/2022]
Abstract
Variants that disrupt the translation initiation sequences in cancer predisposition genes are generally assumed to be deleterious. However, few studies have validated these assumptions with functional and clinical data. Two cancer syndrome gene variants likely to affect native translation initiation were identified by clinical genetic testing: MLH1:c.1A>G p.(Met1?) and BRCA2:c.67+3A>G. In vitro GFP-reporter assays were conducted to assess the consequences of translation initiation disruption on alternative downstream initiation codon usage. Analysis of MLH1:c.1A>G p.(Met1?) showed that translation was mostly initiated at an in-frame position 103 nucleotides downstream, but also at two ATG sequences downstream. The protein product encoded by the in-frame transcript initiating from position c.103 showed loss of in vitro mismatch repair activity comparable to known pathogenic mutations. BRCA2:c.67+3A>G was shown by mRNA analysis to result in an aberrantly spliced transcript deleting exon 2 and the consensus ATG site. In the absence of exon 2, translation initiated mostly at an out-of-frame ATG 323 nucleotides downstream, and to a lesser extent at an in-frame ATG 370 nucleotides downstream. Initiation from any of the downstream alternative sites tested in both genes would lead to loss of protein function, but further clinical data is required to confirm if these variants are associated with a high cancer risk. Importantly, our results highlight the need for caution in interpreting the functional and clinical consequences of variation that leads to disruption of the initiation codon, since translation may not necessarily occur from the first downstream alternative start site, or from a single alternative start site.
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Affiliation(s)
- Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Phillip J Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Niels de Wind
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Louise Marquart
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - John L Hopper
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia.,School of Public Health, Seoul National University, Seoul, Korea
| | - Mark A Jenkins
- Centre for MEGA Epidemiology, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | | | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, Sydney, Australia
| | - Linda Warwick
- ACT Genetics Service, The Canberra Hospital, Canberra, Australia
| | - Daniel D Buchanan
- Department of Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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30
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Nowaczyk MJM, Thompson BA, Zeesman S, Moog U, Sanchez-Lara PA, Magoulas PL, Falk RE, Hoover-Fong JE, Batista DAS, Amudhavalli SM, White SM, Graham GE, Rauen KA. Deletion of MAP2K2/MEK2: a novel mechanism for a RASopathy? Clin Genet 2013; 85:138-46. [PMID: 23379592 DOI: 10.1111/cge.12116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 11/29/2022]
Abstract
RASopathies are a class of genetic syndromes caused by germline mutations in genes encoding Ras/mitogen-activated protein kinase (Ras/MAPK) pathway components. Cardio-facio-cutaneous (CFC) syndrome is a RASopathy characterized by distinctive craniofacial features, skin and hair abnormalities, and congenital heart defects caused by activating mutations of BRAF, MEK1, MEK2, and KRAS. We define the phenotype of seven patients with de novo deletions of chromosome 19p13.3 including MEK2; they present with a distinct phenotype but have overlapping features with CFC syndrome. Phenotypic features of all seven patients include tall forehead, thick nasal tip, underdeveloped cheekbones, long midface, sinuous upper vermilion border, tall chin, angular jaw, and facial asymmetry. Patients also have developmental delay, hypotonia, heart abnormalities, failure to thrive, obstructive sleep apnea, gastroesophageal reflux and integument abnormalities. Analysis of epidermal growth factor-stimulated fibroblasts revealed that P-MEK1/2 was ∼50% less abundant in cells carrying the MEK2 deletion compared to the control. Significant differences in total MEK2 and Sprouty1 abundance were also observed. Our cohort of seven individuals with MEK2 deletions has overlapping features associated with RASopathies. This is the first report suggesting that, in addition to activating mutations, MEK2 haploinsufficiency can lead to dysregulation of the MAPK pathway.
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Affiliation(s)
- M J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada; Department of Pediatrics, McMaster University, Hamilton, Canada
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31
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Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RMW, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat 2012; 34:255-65. [PMID: 22949387 DOI: 10.1002/humu.22214] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/26/2012] [Indexed: 11/11/2022]
Abstract
Classification of rare missense substitutions observed during genetic testing for patient management is a considerable problem in clinical genetics. The Bayesian integrated evaluation of unclassified variants is a solution originally developed for BRCA1/2. Here, we take a step toward an analogous system for the mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) that confer colon cancer susceptibility in Lynch syndrome by calibrating in silico tools to estimate prior probabilities of pathogenicity for MMR gene missense substitutions. A qualitative five-class classification system was developed and applied to 143 MMR missense variants. This identified 74 missense substitutions suitable for calibration. These substitutions were scored using six different in silico tools (Align-Grantham Variation Grantham Deviation, multivariate analysis of protein polymorphisms [MAPP], MutPred, PolyPhen-2.1, Sorting Intolerant From Tolerant, and Xvar), using curated MMR multiple sequence alignments where possible. The output from each tool was calibrated by regression against the classifications of the 74 missense substitutions; these calibrated outputs are interpretable as prior probabilities of pathogenicity. MAPP was the most accurate tool and MAPP + PolyPhen-2.1 provided the best-combined model (R(2) = 0.62 and area under receiver operating characteristic = 0.93). The MAPP + PolyPhen-2.1 output is sufficiently predictive to feed as a continuous variable into the quantitative Bayesian integrated evaluation for clinical classification of MMR gene missense substitutions.
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Affiliation(s)
- Bryony A Thompson
- Queensland Institute of Medical Research, Herston, Brisbane, Australia
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32
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Thompson BA, Goldgar DE, Paterson C, Clendenning M, Walters R, Arnold S, Parsons MT, Michael D W, Gallinger S, Haile RW, Hopper JL, Jenkins MA, Lemarchand L, Lindor NM, Newcomb PA, Thibodeau SN, Young JP, Buchanan DD, Tavtigian SV, Spurdle AB. A multifactorial likelihood model for MMR gene variant classification incorporating probabilities based on sequence bioinformatics and tumor characteristics: a report from the Colon Cancer Family Registry. Hum Mutat 2012; 34:200-9. [PMID: 22949379 DOI: 10.1002/humu.22213] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 08/22/2012] [Indexed: 01/04/2023]
Abstract
Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ~12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia; School of Medicine, University of Queensland, Brisbane, Australia
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Whiley PJ, Guidugli L, Walker LC, Healey S, Thompson BA, Lakhani SR, Da Silva LM, Tavtigian SV, Goldgar DE, Brown MA, Couch FJ, Spurdle AB. Splicing and multifactorial analysis of intronic BRCA1 and BRCA2 sequence variants identifies clinically significant splicing aberrations up to 12 nucleotides from the intron/exon boundary. Hum Mutat 2011; 32:678-87. [PMID: 21394826 DOI: 10.1002/humu.21495] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 02/22/2011] [Indexed: 12/12/2022]
Abstract
Clinical management of breast cancer families is complicated by identification of BRCA1 and BRCA2 sequence alterations of unknown significance. Molecular assays evaluating the effect of intronic variants on native splicing can help determine their clinical relevance. Twenty-six intronic BRCA1/2 variants ranging from the consensus dinucleotides in the splice acceptor or donor to 53 nucleotides into the intron were identified in multiple-case families. The effect of the variants on splicing was assessed using HSF matrices, MaxEntScan and NNsplice, followed by analysis of mRNA from lymphoblastoid cell lines. A total of 12 variants were associated with splicing aberrations predicted to result in production of truncated proteins, including a variant located 12 nucleotides into the intron. The posterior probability of pathogenicity was estimated using a multifactorial likelihood approach, and provided a pathogenic or likely pathogenic classification for seven of the 12 spliceogenic variants. The apparent disparity between experimental evidence and the multifactorial predictions is likely due to several factors, including a paucity of likelihood information and a nonspecific prior probability applied for intronic variants outside the consensus dinucleotides. Development of prior probabilities of pathogenicity incorporating bioinformatic prediction of splicing aberrations should improve identification of functionally relevant variants and enhance multifactorial likelihood analysis of intronic variants.
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Walker LC, Whiley PJ, Couch FJ, Farrugia DJ, Healey S, Eccles DM, Lin F, Butler SA, Goff SA, Thompson BA, Lakhani SR, Da Silva LM, Tavtigian SV, Goldgar DE, Brown MA, Spurdle AB. Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: implications for prediction of pathogenicity. Hum Mutat 2010; 31:E1484-505. [PMID: 20513136 DOI: 10.1002/humu.21267] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Missense substitutions in high-risk cancer susceptibility genes create clinical uncertainty in the genetic counseling process. Multifactorial likelihood classification approaches and in vitro assays are useful for the classification of exonic sequence variants in BRCA1 and BRCA2, but these currently rely on the assumption that changes in protein function are the major biological mechanism of pathogenicity. This study investigates the potentially pathogenic role of aberrant splicing for exonic variants predicted to encode missense substitutions using patient-derived RNA. No splicing aberrations were identified for BRCA1c.5054C>T and BRCA2c.7336A>G, c.8839G>A, and c.9154C>T. However, RT-PCR analysis identified a major splicing aberration for BRCA1c.4868C>G(p.Ala1623Gly), a variant encoding a missense substitution considered likely to be neutral. Splicing aberrations were also observed for BRCA2c.7988A>T(p.Glu2663Val) and c.8168A>G(p.Asp2723Gly), but both variant and wildtype alleles were shown to be present in full-length mRNA transcripts, suggesting that variant protein may be translated. BRCA2 protein function assays indicated that BRCA2p.Glu2663Val, p.Asp2723Gly and p.Arg3052Trp missense proteins have abrogated function consistent with pathogenicity. Multifactorial likelihood analysis provided evidence for pathogenicity for BRCA1 c.5054C>T(p.Thr1685Ile) and BRCA2c.7988A>T(p.Glu2663Val), c.8168A>G(p.Asp2723Gly) and c.9154C>T(p.Arg3052Trp), supporting experimentally derived evidence. These findings highlight the need for improved bioinformatic prediction of splicing aberrations and to refine multifactorial likelihood models used to assess clinical significance.
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Affiliation(s)
- Logan C Walker
- Queensland Institute of Medical Research, Brisbane, Australia
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Neer JA, Carlson JK, Thompson BA. Standard oxygen consumption of seasonally acclimatized cownose rays, Rhinoptera bonasus (Mitchill 1815), in the northern Gulf of Mexico. Fish Physiol Biochem 2006; 32:67-71. [PMID: 20035481 DOI: 10.1007/s10695-006-7312-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/03/2006] [Indexed: 05/28/2023]
Abstract
Standard oxygen consumption rate (MO(2)) was determined for 19 cownose rays (Rhinoptera bonasus) using flow-through respirometry. Rays ranged in size from 0.4 to 8.25 kg (350-790 mm DW). Respirometry experiments were conducted on seasonally acclimatized rays at temperatures from 19.0 to 28.8 degrees C. Estimates of mass-dependent MO(2) ranged from 55.88 mg O(2) kg(-1) h(-1) for an 8.25 kg ray to 332.75 mg O(2) kg(-1) h(-1) for a 2.2 kg animal at 22-25 degrees C. Multiple regression analysis examining the effect of temperature, salinity, and mass on standard mass-independent MO(2) found temperature (P < 0.01), and mass (P < 0.0001) to have a significant effect on oxygen consumption, whereas salinity did not (P > 0.05). Q (10) was calculated as 2.33 (19-28 degrees C), falling between the estimates determined for two other batoid species, the bull ray (Myliobatos aquila; Q (10) = 1.87) and the bat ray (Myliobatis californica; Q (10) = 3.00). The difference in the Q (10) estimates may be attributed to the use of seasonally acclimatized as opposed to laboratory-acclimated animals.
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Affiliation(s)
- J A Neer
- Coastal Fisheries Institute, Louisiana State University, Baton Rouge, Louisiana, 70803-7503, USA,
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Sherer JL, Grant B, Mangone C, Thompson BA. Human resources: vested interests. Hosp Health Netw 1994; 68:44, 46, 48 passim. [PMID: 7951440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Thompson BA, Blount BW, Krumholz TS. Treatment approaches to bruxism. Am Fam Physician 1994; 49:1617-22. [PMID: 8184796] [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: 01/29/2023]
Abstract
Bruxism, or the grinding and clenching of teeth, occurs in approximately 15 percent of children and in as many as 96 percent of adults. The etiology of bruxism is unclear, but the condition has been associated with stress, occlusal disorders, allergies and sleep positioning. Because of its nonspecific pathology, bruxism may be difficult to diagnose. In addition to complaints from sleep partners, signs of teeth grinding include masticatory pain or fatigue, headaches, tooth sensitivity and attrition, oral infection and temporomandibular joint disorders. Signs of bruxism include tooth wear and mobility, as well as tender or hypertrophied masticatory muscles and joints. Children with bruxism are usually managed with observation and reassurance. Adults may be managed with stress reduction therapy, alteration of sleep positioning, drug therapy, biofeedback training, physical therapy and dental evaluation. If significant tooth attrition, mobility or fracture occurs, dental referral is mandatory.
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Affiliation(s)
- B A Thompson
- Womack Army Medical Center, Fort Bragg, North Carolina
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Thompson BA, Huston JL. How to break down tasks so they don't break you: coping with overwhelming demands on your time. Health Care Superv 1994; 12:39-43. [PMID: 10132241] [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] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Everyone, in every profession, seems to have too much to do and too little time to do it all. This seems to be even more true in the health care setting, where change is constant. Health care supervisors can become so overwhelmed with tasks that are expected of them that they have no idea of where to even begin. Rather than thinking about everything that must be done, the one single task strategy describes how you can break down your overwhelming tasks into manageable steps.
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Affiliation(s)
- B A Thompson
- Cabinet for Natural Resources and Environmental Protection, Commonwealth of Kentucky, Frankfort
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Olson MO, Rivers ZM, Thompson BA, Kao WY, Case ST. Interaction of nucleolar phosphoprotein C23 with cloned segments of rat ribosomal deoxyribonucleic acid. Biochemistry 1983; 22:3345-51. [PMID: 6311246 DOI: 10.1021/bi00283a007] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein C23, a predominant nucleolar phosphoprotein and a putative nucleolus organizer protein, was analyzed for its general DNA binding characteristics and for its selectivity in binding plasmid DNAs containing cloned fragments of the genes that code for ribosomal RNA (rDNA). By use of nitrocellulose filter disk assays, the protein bound saturably to nuclear DNA with a relatively high affinity. Binding was maximal at low ionic strength (0-0.1 M KCl) with progressively decreasing binding at or above 0.2 M. In competition assays protein C23 showed a marked preference for linear single-stranded vs. double-stranded DNA and little or no affinity for ribosomal RNA. The relative affinities of rDNA sequences for protein C23 were determined with cloned fragments spanning 15.8 kilobases (kb) of DNA starting approximately 3.7 kb upstream from the initiation site for 45S preribosomal RNA to near the 3' end of the sequence coding for 28S RNA. Of the five linearized plasmids tested, only one (pKW1) was an effective competitor for 32P-labeled nuclear DNA. As measured by the concentration of competing DNA required to achieve 50% competition, pKW1 was approximately 20-fold more effective than the second best competitor. The DNA insert in pKW1 is a 3.5-kb sequence which is located in the nontranscribed spacer region less than 0.5 kb upstream from the initiation site for 45S preribosomal RNA. These results suggest that protein C23 has a preference for binding DNA sequences in the nontranscribed spacer of rDNA.
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Thompson BA. Why be a nurse? Zambia Nurse J 1972; 4:13-4. [PMID: 4481102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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