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Lim E, Borden C, Mehta S, Roberts MB, Mazzola S, Zhao F, Wang X. Reclassification of Variants Following Renal Genetics Testing: Uncommon Yet Impactful for Diagnosis and Management. Kidney Int Rep 2024; 9:1441-1450. [PMID: 38707809 PMCID: PMC11068948 DOI: 10.1016/j.ekir.2024.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Genetic testing is increasingly utilized in nephrology practice, but limited real-world data exist on variant reclassification following renal genetics testing. Methods A cohort of patients at the Cleveland Clinic Renal Genetics Clinic who underwent genetic testing through clinical laboratories was assessed with their clinical and laboratory data analyzed. Results Between January 2019 and June 2023, 425 new patients with variable kidney disorders from 413 pedigrees completed genetic testing through 10 clinical laboratories, including 255 (60%) females with median (25th, 75th percentiles) age of 36 (22-54) years. Multigene panel was the most frequently used modality followed by single-gene testing, exome sequencing (ES), chromosomal microarray (CMA), and genome sequencing (GS). At initial report, 52% of patients had ≥1 variants of uncertain significance (VUS) with or without concurrent pathogenic variant(s). Twenty amendments were issued across 19 pedigrees involving 19 variants in 17 genes. The overall variant reclassification rate was 5%, with 63% being upgrades and 32% downgrades. Of the reclassified variants, 79% were initially reported as VUS. The median time-to-amendments from initial reports was 8.4 (4-27) months. Following the variant reclassifications, 60% of the patients received a new diagnosis or a change in diagnosis. Among these, 67% of patients received significant changes in clinical management. Conclusion Variant reclassification following genetic testing is infrequent but important for diagnosis and management of patients with suspected genetic kidney disease. The majority of variant reclassifications involve VUS and are upgrades in clinically issued amended reports. Further studies are needed to investigate the predictors of such events.
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Affiliation(s)
- Euyn Lim
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Chloe Borden
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Seysha Mehta
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary-Beth Roberts
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Fang Zhao
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Xiangling Wang
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
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Takahashi K, Yachida N, Tamura R, Adachi S, Kondo S, Abé T, Umezu H, Nyuzuki H, Okuda S, Nakaoka H, Yoshihara K. Clonal origin and genomic diversity in Lynch syndrome-associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p.L582H. Genes Chromosomes Cancer 2024; 63:e23231. [PMID: 38459936 DOI: 10.1002/gcc.23231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
Lynch syndrome-associated endometrial cancer patients often present multiple synchronous tumors and this assessment can affect treatment strategies. We present a case of a 27-year-old woman with tumors in the uterine corpus, cervix, and ovaries who was diagnosed with endometrial cancer and exhibited cervical invasion and ovarian metastasis. Her family history suggested Lynch syndrome, and genetic testing identified a variant of uncertain significance, MLH1 p.L582H. We conducted immunohistochemical staining, microsatellite instability analysis, and Sanger sequencing for Lynch syndrome-associated cancers in three generations of the family and identified consistent MLH1 loss. Whole-exome sequencing for the corpus, cervical, and ovarian tumors of the proband identified a copy-neutral loss of heterozygosity (LOH) occurring at the MLH1 position in all tumors. This indicated that the germline variant and the copy-neutral LOH led to biallelic loss of MLH1 and was the cause of cancer initiation. All tumors shared a portion of somatic mutations with high mutant allele frequencies, suggesting a common clonal origin. There were no mutations shared only between the cervix and ovary samples. The profiles of mutant allele frequencies shared between the corpus and cervix or ovary indicated that two different subclones originating from the corpus independently metastasized to the cervix or ovary. Additionally, all tumors presented unique mutations in endometrial cancer-associated genes such as ARID1A and PIK3CA. In conclusion, we demonstrated clonal origin and genomic diversity in a Lynch syndrome-associated endometrial cancer, suggesting the importance of evaluating multiple sites in Lynch syndrome patients with synchronous tumors.
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Affiliation(s)
- Kotaro Takahashi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shuhei Kondo
- Division of Pathology, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Tatsuya Abé
- Division of Oral Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hajime Umezu
- Division of Pathology, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Hiromi Nyuzuki
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Division of bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Pleasant V. A Public Health Emergency: Breast Cancer Among Black Communities in the United States. Obstet Gynecol Clin North Am 2024; 51:69-103. [PMID: 38267132 DOI: 10.1016/j.ogc.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
While Black people have a similar incidence of breast cancer compared to White people, they have a 40% increased death rate. Black people are more likely to be diagnosed with aggressive subtypes such as triple-negative breast cancer. However, despite biological factors, systemic racism and social determinants of health create delays in care and barriers to treatment. While genetic testing holds incredible promise for Black people, uptake remains low and results may be challenging to interpret. There is a need for more robust, multidisciplinary, and antiracist interventions to reverse breast cancer-related racial disparities.
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Affiliation(s)
- Versha Pleasant
- Department of Obstetrics and Gynecology, Cancer Genetics & Breast Health Clinic, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA.
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4
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Fillman C, Anantharajah A, Marmelstein B, Dillon M, Horton C, Peterson C, Lopez J, Tondon R, Brannan T, Katona BW. Combining clinical and molecular characterization of CDH1: a multidisciplinary approach to reclassification of a splicing variant. Fam Cancer 2023; 22:521-526. [PMID: 37540482 DOI: 10.1007/s10689-023-00346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
Pathogenic germline variants (PGVs) in the CDH1 gene are associated with diffuse gastric and lobular breast cancer syndrome (DGLBC) and can increase the lifetime risk for both diffuse gastric cancer and lobular breast cancer. Given the risk for diffuse gastric cancer among individuals with CDH1 PGVs is up to 30-40%, prophylactic total gastrectomy is often recommended to affected individuals. Therefore, accurate interpretation of CDH1 variants is of the utmost importance for proper clinical decision-making. Herein we present a 45-year-old female, with lobular breast cancer and a father with gastric cancer of unknown pathology at age 48, who was identified to have an intronic variant of uncertain significance in the CDH1 gene, specifically c.833-9 C > G. Although the proband did not meet the International Gastric Cancer Linkage Consortium (IGCLC) criteria for gastric surveillance, she elected to pursue an upper endoscopy where non-targeted gastric biopsies identified a focus of signet ring cell carcinoma (SRCC). The proband then underwent a total gastrectomy, revealing numerous SRCC foci, but no invasive diffuse gastric cancer. Simultaneously, a genetic testing laboratory performed RNA sequencing to further analyze the CDH1 intronic variant, identifying an abnormal transcript from a novel acceptor splice site. The RNA analysis in conjunction with the patient's gastric foci of SRCC and family history was sufficient evidence for reclassification of the variant from uncertain significance to likely pathogenic. In conclusion, we report the first case of the CDH1 c.833-9 C > G intronic variant being associated with DGLBC and illustrate how collaboration among clinicians, laboratory personnel, and patients is crucial for variant resolution.
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Affiliation(s)
- Corrine Fillman
- Cancer Risk and Genetics Program, St. Luke's University Health Network, Bethlehem, PA, USA
| | | | - Briana Marmelstein
- Cancer Risk and Genetics Program, St. Luke's University Health Network, Bethlehem, PA, USA
| | - Monica Dillon
- Cancer Risk and Genetics Program, St. Luke's University Health Network, Bethlehem, PA, USA
| | | | | | - Joseph Lopez
- Cancer Risk and Genetics Program, St. Luke's University Health Network, Bethlehem, PA, USA
| | - Rashmi Tondon
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Bryson W Katona
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd. 751 South Pavilion, Philadelphia, PA, 19104, USA.
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Nesic K, Krais JJ, Vandenberg CJ, Wang Y, Patel P, Cai KQ, Kwan T, Lieschke E, Ho GY, Barker HE, Bedo J, Casadei S, Farrell A, Radke M, Shield-Artin K, Penington JS, Geissler F, Kyran E, Zhang F, Dobrovic A, Olesen I, Kristeleit R, Oza A, Ratnayake G, Traficante N, DeFazio A, Bowtell DDL, Harding TC, Lin K, Swisher EM, Kondrashova O, Scott CL, Johnson N, Wakefield MJ. BRCA1 secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287465. [PMID: 36993400 PMCID: PMC10055590 DOI: 10.1101/2023.03.20.23287465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
BRCA1 splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out the mutation-containing exon, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi. BRCA1 exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary BRCA1 splice site mutations (SSMs), predicted in silico to drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots and BRCA1 minigene modelling. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials. We demonstrate that SSMs drive BRCA1 exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.
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Affiliation(s)
- Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | | | | | - Tanya Kwan
- Clovis Oncology Inc., San Francisco, CA, USA
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gwo-Yaw Ho
- School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Bedo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Andrew Farrell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marc Radke
- University of Washington, Seattle, WA, USA
| | - Kristy Shield-Artin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jocelyn S. Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Franziska Geissler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Fan Zhang
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Inger Olesen
- The Andrew Love Cancer Centre, Barwon Health, Geelong, Victoria, Australia
| | - Rebecca Kristeleit
- Department of Oncology, Guys and St Thomas’ NHS Foundation Trust, London, UK
- National Institute for Health Research, University College London Hospitals Clinical Research Facility, London, UK
| | - Amit Oza
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Nadia Traficante
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Anna DeFazio
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council New South Wales, Sydney, New South Wales, Australia
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynecological Oncology, Westmead Hospital, Western Sydney Local Health District, New South Wales, Australia
| | - David D. L. Bowtell
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Kevin Lin
- Clovis Oncology Inc., San Francisco, CA, USA
| | | | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
| | | | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
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6
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Henkel J, Laner A, Locher M, Wohlfrom T, Neitzel B, Becker K, Neuhann T, Abicht A, Steinke-Lange V, Holinski-Feder E. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 2023; 31:925-930. [PMID: 37188824 PMCID: PMC10400578 DOI: 10.1038/s41431-023-01380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/18/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
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Affiliation(s)
- Jan Henkel
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | | | | | | | | | | | - Angela Abicht
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Germany
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, München, Germany.
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany.
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7
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Diquigiovanni C, Rizzardi N, Kampmeier A, Liparulo I, Bianco F, De Nicolo B, Cataldi-Stagetti E, Cuna E, Severi G, Seri M, Bertrand M, Haack TB, Marina AD, Braun F, Fato R, Kuechler A, Bergamini C, Bonora E. Mutant SPART causes defects in mitochondrial protein import and bioenergetics reversed by Coenzyme Q. Open Biol 2023; 13:230040. [PMID: 37433330 DOI: 10.1098/rsob.230040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Pathogenic variants in SPART cause Troyer syndrome, characterized by lower extremity spasticity and weakness, short stature and cognitive impairment, and a severe mitochondrial impairment. Herein, we report the identification of a role of Spartin in nuclear-encoded mitochondrial proteins. SPART biallelic missense variants were detected in a 5-year-old boy with short stature, developmental delay and muscle weakness with impaired walking distance. Patient-derived fibroblasts showed an altered mitochondrial network, decreased mitochondrial respiration, increased mitochondrial reactive oxygen species and altered Ca2+ versus control cells. We investigated the mitochondrial import of nuclear-encoded proteins in these fibroblasts and in another cell model carrying a SPART loss-of-function mutation. In both cell models the mitochondrial import was impaired, leading to a significant decrease in different proteins, including two key enzymes involved in CoQ10 (CoQ) synthesis, COQ7 and COQ9, with a severe reduction in CoQ content, versus control cells. CoQ supplementation restored cellular ATP levels to the same extent shown by the re-expression of wild-type SPART, suggesting CoQ treatment as a promising therapeutic approach for patients carrying mutations in SPART.
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Affiliation(s)
- Chiara Diquigiovanni
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna 40138, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Antje Kampmeier
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen 45122, Germany
| | - Irene Liparulo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Francesca Bianco
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Department of Veterinary Sciences, University of Bologna, Bologna 40064, Italy
| | - Bianca De Nicolo
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Erica Cataldi-Stagetti
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Elisabetta Cuna
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Giulia Severi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Marco Seri
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- Center for Rare Diseases, University of Tübingen, Tübingen 72076, Germany
| | - Adela Della Marina
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen 45122, Germany
| | - Frederik Braun
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen 45122, Germany
| | - Romana Fato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen 45122, Germany
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
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8
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Muir SM, Reagle R. Characterization of variant reclassification and patient re-contact in a cancer genetics clinic. J Genet Couns 2022; 31:1261-1272. [PMID: 35763673 DOI: 10.1002/jgc4.1600] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/14/2022] [Accepted: 05/30/2022] [Indexed: 12/14/2022]
Abstract
Expanded genetic testing guidelines for hereditary cancers, increased utilization of large multigene panels, and improved methods for reclassifying variants have led to a greater need to understand how variant reclassification and patient re-contact are managed. This study aimed to describe the process of variant reclassification and subsequent patient re-contact at a comprehensive cancer genetic counseling service in a large metropolitan medical center with several statewide satellite locations. A retrospective chart review was performed to identify reclassified variants between 1/1/1997 and 12/1/2020. In total, 8.4% (211/2503) of variants were reclassified over the 24-year period, which includes multiple cases involving the same unique variant. Several variants underwent more than one reclassification, resulting in 232 total reclassifications among 194 individuals. Nearly all reclassifications were prompted by the laboratory (99.1%; 230/232) rather than the genetics clinic staff. Overall, 10.3% (24/232) of all reclassifications were upgrades, but only 9.1% (21/232) led to a change in management recommendations. The median time for variant reclassification was 1.7 years (interquartile range [IQR] = 0.8-3.2 years). There was no statistically significant difference in the time to reclassification for White patients (median = 1.6 years; IQR = 0.8-2.8 years) compared to non-White patients (median = 2.0 years; IQR = 0.9-3.7 years; Mann-Whitney U = 4,764.0, p = 0.066). Patient re-contact was attempted for 97.4% (226/232) of variants and was always performed by a genetic counselor, most often through a mailed letter (85.8%, 194/226). Specifically for reclassifications that led to a change in management recommendations, re-contact was always attempted, most often through combined telephone and mailed letter (95.2%; 20/21). Overall, the median time from reclassification to attempted patient re-contact was 13 days (range: 0-589 days). The characterization of this clinic's reclassification and re-contact procedures can serve as an example for other genetics clinics trying to incorporate re-contact into their workflow.
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Affiliation(s)
- Sarah M Muir
- Genetic Counseling Program, Wayne State University, Detroit, Michigan, USA
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9
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García S. A, Costa M, Leon A, Pastor O. The challenge of managing the evolution of genomics data over time: a conceptual model-based approach. BMC Bioinformatics 2022; 23:472. [PMID: 36352353 PMCID: PMC9648044 DOI: 10.1186/s12859-022-04944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Precision medicine is a promising approach that has revolutionized disease prevention and individualized treatment. The DELFOS oracle is a model-driven genomics platform that aids clinicians in identifying relevant variations that are associated with diseases. In its previous version, the DELFOS oracle did not consider the high degree of variability of genomics data over time. However, changes in genomics data have had a profound impact on clinicians' work and pose the need for changing past, present, and future clinical actions. Therefore, our objective in this work is to consider changes in genomics data over time in the DELFOS oracle. METHODS Our objective has been achieved through three steps. First, we studied the characteristics of each database from which the DELFOS oracle extracts data. Second, we characterized which genomics concepts of the conceptual schema that supports the DELFOS oracle change over time. Third, we updated the DELFOS Oracle so that it can manage the temporal dimension. To validate our approach, we carried out a use case to illustrate how the new version of the DELFOS oracle handles the temporal dimension. RESULTS Three events can change genomics data, namely, the addition of a new variation, the addition of a new link between a variation and a phenotype, and the update of a link between a variation and a phenotype. These events have been linked to the entities of the conceptual model that are affected by them. Finally, a new version of the DELFOS oracle that can deal with the temporal dimension has been implemented. CONCLUSION Huge amounts of genomics data that is associated with diseases change over time, impacting patients' diagnosis and treatment. Including this information in the DELFOS oracle added an extra layer of complexity, but using a model-driven based approach mitigated the cost of implementing the needed changes. The new version handles the temporal dimension appropriately and eases clinicians' work.
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Affiliation(s)
- Alberto García S.
- PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
| | - Mireia Costa
- PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
| | - Ana Leon
- PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
| | - Oscar Pastor
- PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
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10
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Mighton C, Shickh S, Aguda V, Krishnapillai S, Adi-Wauran E, Bombard Y. From the patient to the population: Use of genomics for population screening. Front Genet 2022; 13:893832. [PMID: 36353115 PMCID: PMC9637971 DOI: 10.3389/fgene.2022.893832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/26/2022] [Indexed: 10/22/2023] Open
Abstract
Genomic medicine is expanding from a focus on diagnosis at the patient level to prevention at the population level given the ongoing under-ascertainment of high-risk and actionable genetic conditions using current strategies, particularly hereditary breast and ovarian cancer (HBOC), Lynch Syndrome (LS) and familial hypercholesterolemia (FH). The availability of large-scale next-generation sequencing strategies and preventive options for these conditions makes it increasingly feasible to screen pre-symptomatic individuals through public health-based approaches, rather than restricting testing to high-risk groups. This raises anew, and with urgency, questions about the limits of screening as well as the moral authority and capacity to screen for genetic conditions at a population level. We aimed to answer some of these critical questions by using the WHO Wilson and Jungner criteria to guide a synthesis of current evidence on population genomic screening for HBOC, LS, and FH.
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Affiliation(s)
- Chloe Mighton
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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11
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Ossa Gomez CA, Achatz MI, Hurtado M, Sanabria-Salas MC, Sullcahuaman Y, Chávarri-Guerra Y, Dutil J, Nielsen SM, Esplin ED, Michalski ST, Bristow SL, Hatchell KE, Nussbaum RL, Pineda-Alvarez DE, Ashton-Prolla P. Germline Pathogenic Variant Prevalence Among Latin American and US Hispanic Individuals Undergoing Testing for Hereditary Breast and Ovarian Cancer: A Cross-Sectional Study. JCO Glob Oncol 2022; 8:e2200104. [PMID: 35867948 PMCID: PMC9812461 DOI: 10.1200/go.22.00104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To report on pathogenic germline variants detected among individuals undergoing genetic testing for hereditary breast and/or ovarian cancer (HBOC) from Latin America and compare them with self-reported Hispanic individuals from the United States. METHODS In this cross-sectional study, unrelated individuals with a personal/family history suggestive of HBOC who received clinician-ordered germline multigene sequencing were grouped according to the location of the ordering physician: group A, Mexico, Central America, and the Caribbean; group B, South America; and group C, United States with individuals who self-reported Hispanic ethnicity. Relatives who underwent cascade testing were analyzed separately. RESULTS Among 24,075 unrelated probands across all regions, most were female (94.9%) and reported a personal history suggestive of HBOC (range, 65.0%-80.6%); the mean age at testing was 49.1 ± 13.1 years. The average number of genes analyzed per patient was highest in group A (A 63 ± 28, B 56 ± 29, and C 40 ± 28). Between 9.1% and 18.7% of patients had pathogenic germline variants in HBOC genes (highest yield in group A), with the majority associated with high HBOC risk. Compared with US Hispanics individuals the overall yield was significantly higher in both Latin American regions (A v C P = 1.64×10-9, B v C P < 2.2×10-16). Rates of variants of uncertain significance were similar across all three regions (33.7%-42.6%). Cascade testing uptake was low in all regions (A 6.6%, B 4.5%, and C 1.9%). CONCLUSION This study highlights the importance of multigene panel testing in Latin American individuals with newly diagnosed or history of HBOC, who can benefit from medical management changes including targeted therapies, eligibility to clinical trials, risk-reducing surgeries, surveillance and prevention of secondary malignancy, and genetic counseling and subsequent cascade testing of at-risk relatives.
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Affiliation(s)
| | - Maria Isabel Achatz
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | - Mabel Hurtado
- Instituto Oncológico, Fundación Arturo López Pérez, Santiago, Chile
| | | | - Yasser Sullcahuaman
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru,Instituto de Investigación Genomica, Lima, Peru
| | - Yanin Chávarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Pone, Puerto Rico
| | | | | | | | | | | | | | - Daniel E. Pineda-Alvarez
- Invitae, San Francisco, CA,Daniel E. Pineda-Alvarez, MD, Medical Affairs, Invitae Corporation, 1400 16th Street, San Francisco, CA, 94103; e-mail:
| | - Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil,Serviço de Genética Médica e Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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12
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Tallis E, Scollon S, Ritter DI, Plon SE. Evolution of germline TP53 variant classification in children with cancer. Cancer Genet 2022; 264-265:29-32. [PMID: 35306447 PMCID: PMC9133135 DOI: 10.1016/j.cancergen.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 12/13/2022]
Abstract
Li-Fraumeni syndrome, caused by germline pathogenic variants in TP53, results in susceptibility to multiple cancers. Variants of uncertain significance (VUS) and reclassification of variants over time pose management concerns given improved survival with cancer surveillance for LFS patients. We describe the experience of TP53 variant reclassification at a pediatric cancer center. METHODS We reviewed medical records (2010-2019) of 756 patients seen in Texas Children's Cancer Genetics Clinic. We noted initial TP53 classification and any reclassifications. We then classified TP53 variants following ClinGen TP53 variant curation expert panel recommendations using data from ClinVar, medical literature and IARC database. RESULTS Of 234 patients tested for TP53, 27 (11.5%) reports contained pathogenic/likely pathogenic (P/LP) variants and 7 (3)% contained VUS. By January 2022, 4 of 6 unique VUS and 2 of 16 unique P/LP variants changed interpretations in ClinVar. Reinterpretation of these 4 VUS in ClinVar matched clinical decision at the time of initial report. Applying TP53 VCEP specifications classified 3 VUS to P/LP/benign, and one pathogenic variant to likely benign. CONCLUSIONS Planned review of variant significance is essential, especially for patients with high probability of LFS.
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Affiliation(s)
- E Tallis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - S Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, United States
| | - D I Ritter
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, United States
| | - S E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, United States.
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13
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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14
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Franke K, Vagher J, Boyle J, Hall A, Smith‐Simmer K. Rare variant in the fumarate hydratase gene found in patients with clinical features of hereditary leiomyomatosis and renal cell cancer (HLRCC): A case series. Clin Case Rep 2022; 10:e05513. [PMID: 35251648 PMCID: PMC8886725 DOI: 10.1002/ccr3.5513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/07/2022] [Accepted: 02/16/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Keith Franke
- Master of Genetic Counselor Studies Program, Department of Pediatrics University of Wisconsin School of Medicine and Public Health Madison Wisconsin USA
| | - Jennie Vagher
- Huntsman Cancer Institute at the University of Utah Salt Lake City Utah USA
| | - Julie Boyle
- Huntsman Cancer Institute at the University of Utah Salt Lake City Utah USA
| | - April Hall
- Master of Genetic Counselor Studies Program, Department of Pediatrics University of Wisconsin School of Medicine and Public Health Madison Wisconsin USA
- Center for Human Genomics and Precision Medicine University of Wisconsin School of Medicine and Public Health Madison Wisconsin USA
| | - Kelcy Smith‐Simmer
- Master of Genetic Counselor Studies Program, Department of Pediatrics University of Wisconsin School of Medicine and Public Health Madison Wisconsin USA
- Oncology Genetics, University of Wisconsin Carbone Cancer Center UW Health Madison Wisconsin USA
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15
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Bellcross CA. Hereditary Breast and Ovarian Cancer. Obstet Gynecol Clin North Am 2022; 49:117-147. [DOI: 10.1016/j.ogc.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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He WB, Xiao WJ, Dai CL, Wang YR, Li XR, Gong F, Meng LL, Tan C, Zeng SC, Lu GX, Lin G, Tan YQ, Hu H, Du J. RNA splicing analysis contributes to reclassifying variants of uncertain significance and improves the diagnosis of monogenic disorders. J Med Genet 2022; 59:1010-1016. [PMID: 35121647 DOI: 10.1136/jmedgenet-2021-108013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/06/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Numerous variants of uncertain significance (VUSs) have been identified by whole exome sequencing in clinical practice. However, VUSs are not currently considered medically actionable. OBJECTIVE To assess the splicing patterns of 49 VUSs in 48 families identified clinically to improve genetic counselling and family planning. METHODS Forty-nine participants with 49 VUSs were recruited from the Reproductive and Genetic Hospital of CITIC-Xiangya. Bioinformatic analysis was performed to preliminarily predict the splicing effects of these VUSs. RT-PCR and minigene analysis were used to assess the splicing patterns of the VUSs. According to the results obtained, couples opted for different methods of reproductive interventions to conceive a child, including prenatal diagnosis and preimplantation genetic testing (PGT). RESULTS Eleven variants were found to alter pre-mRNA splicing and one variant caused nonsense-mediated mRNA decay, which resulted in the reclassification of these VUSs as likely pathogenic. One couple chose to undergo in vitro fertilisation with PGT treatment; a healthy embryo was transferred and the pregnancy is ongoing. Three couples opted for natural pregnancy with prenatal diagnosis. One couple terminated the pregnancy because the fetus was affected by short-rib thoracic dysplasia and harboured the related variant. The infants of the other two couples were born and were healthy at their last recorded follow-up. CONCLUSION RNA splicing analysis is an important method to assess the impact of sequence variants on splicing in clinical practice and can contribute to the reclassification of a significant proportion of VUSs. RNA splicing analysis should be considered for genetic disease diagnostics.
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Affiliation(s)
- Wen-Bin He
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Wen-Juan Xiao
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Cong-Ling Dai
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Yu-Rong Wang
- Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Xiu-Rong Li
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Fei Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Lan-Lan Meng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Si-Cong Zeng
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Guang-Xiu Lu
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Hao Hu
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China .,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China .,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
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17
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Zouk H, Yu W, Oza A, Hawley M, Vijay Kumar PK, Koch C, Mahanta LM, Harley JB, Jarvik GP, Karlson EW, Leppig KA, Myers MF, Prows CA, Williams MS, Weiss ST, Lebo MS, Rehm HL. Reanalysis of eMERGE phase III sequence variants in 10,500 participants and infrastructure to support the automated return of knowledge updates. Genet Med 2022; 24:454-462. [PMID: 34906510 PMCID: PMC10128874 DOI: 10.1016/j.gim.2021.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The clinical genomics knowledgebase is dynamic with variant classifications changing as newly identified cases, additional population data, and other evidence become available. This is a challenge for the clinical laboratory because of limited resource availability for variant reassessment. METHODS Throughout the Electronic Medical Records and Genomics phase III program, clinical sites associated with the Mass General Brigham/Broad sequencing center received automated, real-time notifications when reported variants were reclassified. In this study, we summarized the nature of these reclassifications and described the proactive reassessment framework we used for the Electronic Medical Records and Genomics program data set to identify variants most likely to undergo reclassification. RESULTS Reanalysis of 1855 variants led to the reclassification of 2% (n = 45) of variants, affecting 0.6% (n = 67) of participants. Of these reclassifications, 78% (n = 35) were high-impact changes affecting reportability, with 8 variants downgraded from likely pathogenic/pathogenic to variants of uncertain significance (VUS) and 27 variants upgraded from VUS to likely pathogenic/pathogenic. Most upgraded variants (67%) were initially classified as VUS-Favor Pathogenic, highlighting the benefit of VUS subcategorization. The most common reason for reclassification was new published case data and/or functional evidence. CONCLUSION Our results highlight the importance of periodic sequence variant reevaluation and the need for automated approaches to advance routine implementation of variant reevaluations in clinical practice.
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Affiliation(s)
- Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Prathik K Vijay Kumar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - John B Harley
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH; US Department of Veteran Affairs Medical Center, Cincinnati, OH
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Scott T Weiss
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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18
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Aksoy F, Tezcan Unlu H, Cecener G, Guney Eskiler G, Egeli U, Tunca B, Efendi Erdem E, Senol K, Gokgoz MS. Identification of CHEK2 germline mutations in BRCA1/2 and PALB2 negative breast and ovarian cancer patients. Hum Hered 2022; 87:000521369. [PMID: 34991090 DOI: 10.1159/000521369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The CHEK2 gene is known to be an important signal transducer involved in DNA repair, apoptosis, or cell cycle arrest in response to DNA damage. The mutations in this gene have been associated with a wide range of cancers, both sporadic and hereditary. Germline CHEK2 mutations are linked to an increased risk of breast cancer. Therefore, the aim of this study was to identify the prevalence of CHEK2 variants in BRCA1/2 and PALB2 negative early-onset patients with breast cancer and/or ovarian cancer in a Turkish population for the first time. METHODS The study included 95 patients with BRCA1/2 and PALB2 negative early-onset breast cancer and/or ovarian cancer and also 60 unaffected women. All the intron/exon boundaries and coding exons of CHEK2 were subjected to mutational analysis by heteroduplex analysis and DNA sequencing. RESULTS A total of 16 CHEK2 variants were found in breast cancer patients within the Turkish population. CHEK2 c.1100delC mutation studied in the CHEK2 gene most frequently was not detected in our study. The prevalence of variants of uncertain significance in CHEK2 was found to be 7.3% (n= 7) in BRCA1/2 and PALB2 mutation negative Turkish patients with early-onset breast and/or ovarian cancer. DISCUSSION/CONCLUSION The present study may shed light on alternative variations that could be significant for understanding the prevalence and clinical suitability of the CHEK2 gene.
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Matsui K, Yamamoto K, Tashiro S, Ibuki T. A systematic approach to the disclosure of genomic findings in clinical practice and research: a proposed framework with colored matrix and decision-making pathways. BMC Med Ethics 2021; 22:168. [PMID: 34953504 PMCID: PMC8709972 DOI: 10.1186/s12910-021-00738-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Whether and how to disclose genomic findings obtained in the course of genomic clinical practice and medical research has been a controversial global bioethical issue over the past two decades. Although several recommendations and judgment tools for the disclosure of genomic findings have been proposed, none are sufficiently systematic or inclusive or even consistent with each other. In order to approach the disclosure/non-disclosure practice in an ethical manner, optimal and easy-to-use tools for supporting the judgment of physicians/researchers in genomic medicine are necessary. Methods The bioethics literature on this topic was analyzed to parse and deconstruct the somewhat overlapping and therefore ill-defined key concepts of genomic findings, such as incidental, primary, secondary, and other findings. Based on the deconstruction and conceptual analyses of these findings, we then defined key parameters from which to identify the strength of duty to disclose (SDD) for a genomic finding. These analyses were then applied to develop a framework with the SDD matrix and systematic decision-making pathways for the disclosure of genomic findings. Results The following six major parameters (axes), along with sub-axes, were identified: Axis 1 (settings and institutions where findings emerge); Axis 2 (presence or absence of intention and anticipatability in discovery); Axis 3 (maximal actionability at the time of discovery); Axis 4 (net medical importance); Axis 5 (expertise of treating physician/researcher); and Axis 6 (preferences of individual patients/research subjects for disclosure). For Axes 1 to 4, a colored SDD matrix for genomic findings was developed in which levels of obligation for disclosing a finding can be categorized. For Axes 5 and 6, systematic decision-making pathways were developed via the SDD matrix. Conclusion We analyzed the SDD of genomic findings and developed subsequent systematic decision-making pathways of whether and how to disclose genomic findings to patients/research subjects and their relatives in an ethical manner. Our comprehensive framework may help physicians and researchers in genomic medicine make consistent ethical judgments regarding the disclosure of genomic findings.
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Affiliation(s)
- Kenji Matsui
- Division of Bioethics and Healthcare Law, The Institute for Cancer Control, The National Cancer Center Japan, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Keiichiro Yamamoto
- Office of Bioethics, The Center for Clinical Sciences, The National Center for Global Health and Medicine, Tokyo, Japan
| | - Shimon Tashiro
- Department of Sociology, Graduate School of Arts and Letters, Tohoku University, Sendai, Japan
| | - Tomohide Ibuki
- Institute of Arts and Sciences, Tokyo University of Science, Noda-shi, Japan
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20
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Margolin A, Helm BM, Treat K, Prucka SK, Halverson CME. Assessing parental understanding of variant reclassification in pediatric neurology and developmental pediatrics clinics. J Community Genet 2021; 12:663-670. [PMID: 34558037 DOI: 10.1007/s12687-021-00552-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/16/2021] [Indexed: 11/24/2022] Open
Abstract
Improvements in technology used for genetic testing have yielded an increased numbers of variants that are identified, each with a potential to return uninformative results. While some genetics providers may expect patients to be responsible for staying abreast of updates to their genetic testing results, it is unknown whether patients are even aware of the possibility of variant reclassification. Little research has assessed the comprehension and attitudes of parents of pediatric patients regarding reclassification of variants of uncertain significance (VUS). Semi-structured telephone interviews were conducted with parents (n = 15) whose children received a VUS from genetic testing in either the pediatric neurogenetics or developmental pediatrics clinics at Riley Hospital for Children in Indianapolis, Indiana. Most participants expressed understanding of the uncertainty surrounding their child's VUS test result. However, nearly half of participants shared that they had no prior knowledge of its potential reclassification. When asked whose responsibility it is to keep informed about changes to their child's VUS status, some participants stated that it belonged solely to healthcare providers - a distinctive finding of our study - whereas others felt that it was a joint responsibility between providers and the parents. We additionally found that some patients desire a support group for individuals with VUS. These results provide insight into the importance of pretest genetic counseling and the need for increased social and informational support for parents of children who receive inconclusive genetic testing results. We conclude that relying solely on the patient or guardian to manage uncertain results may be insufficient.
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Affiliation(s)
- Amy Margolin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sandra K Prucka
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Colin M E Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Indiana University School of Medicine, 410 W. 10th St., HITS 3131, Indianapolis, IN, 46202, USA.
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21
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An ethical analysis of divergent clinical approaches to the application of genetic testing for autism and schizophrenia. Hum Genet 2021; 141:1069-1084. [PMID: 34453583 DOI: 10.1007/s00439-021-02349-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022]
Abstract
Genetic testing to identify genetic syndromes and copy number variants (CNVs) via whole genome platforms such as chromosome microarray (CMA) or exome sequencing (ES) is routinely performed clinically, and is considered by a variety of organizations and societies to be a "first-tier" test for individuals with developmental delay (DD), intellectual disability (ID), or autism spectrum disorder (ASD). However, in the context of schizophrenia, though CNVs can have a large effect on risk, genetic testing is not typically a part of routine clinical care, and no clinical practice guidelines recommend testing. This raises the question of whether CNV testing should be similarly performed for individuals with schizophrenia. Here we consider this proposition in light of the history of genetic testing for ID/DD and ASD, and through the application of an ethical analysis designed to enable robust, accountable and justifiable decision-making. Using a systematic framework and application of relevant bioethical principles (beneficence, non-maleficence, autonomy, and justice), our examination highlights that while CNV testing for the indication of ID has considerable benefits, there is currently insufficient evidence to suggest that overall, the potential harms are outweighed by the potential benefits of CNV testing for the sole indications of schizophrenia or ASD. However, although the application of CNV tests for children with ASD or schizophrenia without ID/DD is, strictly speaking, off-label use, there may be clinical utility and benefits substantive enough to outweigh the harms. Research is needed to clarify the harms and benefits of testing in pediatric and adult contexts. Given that genetic counseling has demonstrated benefits for schizophrenia, and has the potential to mitigate many of the potential harms from genetic testing, any decisions to implement genetic testing for schizophrenia should involve high-quality evidence-based genetic counseling.
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22
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Zavala VA, Bracci PM, Carethers JM, Carvajal-Carmona L, Coggins NB, Cruz-Correa MR, Davis M, de Smith AJ, Dutil J, Figueiredo JC, Fox R, Graves KD, Gomez SL, Llera A, Neuhausen SL, Newman L, Nguyen T, Palmer JR, Palmer NR, Pérez-Stable EJ, Piawah S, Rodriquez EJ, Sanabria-Salas MC, Schmit SL, Serrano-Gomez SJ, Stern MC, Weitzel J, Yang JJ, Zabaleta J, Ziv E, Fejerman L. Cancer health disparities in racial/ethnic minorities in the United States. Br J Cancer 2021; 124:315-332. [PMID: 32901135 PMCID: PMC7852513 DOI: 10.1038/s41416-020-01038-6] [Citation(s) in RCA: 431] [Impact Index Per Article: 143.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/16/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023] Open
Abstract
There are well-established disparities in cancer incidence and outcomes by race/ethnicity that result from the interplay between structural, socioeconomic, socio-environmental, behavioural and biological factors. However, large research studies designed to investigate factors contributing to cancer aetiology and progression have mainly focused on populations of European origin. The limitations in clinicopathological and genetic data, as well as the reduced availability of biospecimens from diverse populations, contribute to the knowledge gap and have the potential to widen cancer health disparities. In this review, we summarise reported disparities and associated factors in the United States of America (USA) for the most common cancers (breast, prostate, lung and colon), and for a subset of other cancers that highlight the complexity of disparities (gastric, liver, pancreas and leukaemia). We focus on populations commonly identified and referred to as racial/ethnic minorities in the USA-African Americans/Blacks, American Indians and Alaska Natives, Asians, Native Hawaiians/other Pacific Islanders and Hispanics/Latinos. We conclude that even though substantial progress has been made in understanding the factors underlying cancer health disparities, marked inequities persist. Additional efforts are needed to include participants from diverse populations in the research of cancer aetiology, biology and treatment. Furthermore, to eliminate cancer health disparities, it will be necessary to facilitate access to, and utilisation of, health services to all individuals, and to address structural inequities, including racism, that disproportionally affect racial/ethnic minorities in the USA.
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Affiliation(s)
- Valentina A Zavala
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John M Carethers
- Departments of Internal Medicine and Human Genetics, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Luis Carvajal-Carmona
- University of California Davis Comprehensive Cancer Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA, USA
- Genome Center, University of California Davis, Davis, CA, USA
| | | | - Marcia R Cruz-Correa
- Department of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Melissa Davis
- Division of Breast Surgery, Department of Surgery, NewYork-Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rena Fox
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kristi D Graves
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Scarlett Lin Gomez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Llera
- Laboratorio de Terapia Molecular y Celular, IIBBA, Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lisa Newman
- Division of Breast Surgery, Department of Surgery, NewYork-Presbyterian/Weill Cornell Medical Center, New York, NY, USA
- Interdisciplinary Breast Program, New York-Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - Tung Nguyen
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - Nynikka R Palmer
- Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, CA, USA
| | - Eliseo J Pérez-Stable
- Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Office of the Director, National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Sorbarikor Piawah
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Erik J Rodriquez
- Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Silvia J Serrano-Gomez
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Mariana C Stern
- Departments of Preventive Medicine and Urology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey Weitzel
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jovanny Zabaleta
- Department of Pediatrics and Stanley S. Scott Cancer Center LSUHSC, New Orleans, LA, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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23
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How geneticists think about Differences/Disorders of Sexual Development (DSD): A conversation. J Pediatr Urol 2020; 16:760-767. [PMID: 32893165 DOI: 10.1016/j.jpurol.2020.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
A multidisciplinary DSD clinic offers the opportunity for different specialties to learn from each other, as each provides their own perspective and expertise to the management of these complex patients, leading to collaborative care. For the patient, a multi-disciplinary clinic can improve access to care and decrease stress, as patients see all of the specialists on one day. For urologists seeing patients with DSD within a multi-disciplinary DSD clinic as well as independently, understanding what other specialists provide can help facilitate care and referral. Medical genetics is part of a multi-disciplinary DSD clinic. Given the recent advances in genetic diagnostics, many of the offered tests may be less familiar to the pediatric urologist. Therefore, this conversation reviews the clinical presentations and genetic testing options including chromosomal microarray, genetic testing panel, whole exome sequencing, and whole genome sequencing and how these can be helpful in the diagnosis and management of patients with DSD conditions.
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24
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Roberts JL, Foulkes AL. GENETIC DUTIES. WILLIAM AND MARY LAW REVIEW 2020; 62:143-211. [PMID: 37654734 PMCID: PMC10471136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Most of our genetic information does not change, yet the results of our genetic tests might. Labs reclassify genetic variants in response to advances in genetic science. As a result, a person who took a test in 2010 could take the same test with the same lab in 2020 and get a different result. However, no legal duty requires labs or physicians to inform patients when a lab reclassifies a variant, even if the reclassification communicates clinically actionable information. This Article considers the need for such duties and their potential challenges. In so doing, it offers much-needed guidance to physicians and labs, who may face liability, and to courts, which will hear these cases.
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25
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Sokolova AO, Shirts BH, Konnick EQ, Tsai GJ, Goulart BHL, Montgomery B, Pritchard CC, Yu EY, Cheng HH. Complexities of Next-Generation Sequencing in Solid Tumors: Case Studies. J Natl Compr Canc Netw 2020; 18:1150-1155. [PMID: 32886903 DOI: 10.6004/jnccn.2020.7569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 03/31/2020] [Indexed: 11/17/2022]
Abstract
With the promise and potential of clinical next-generation sequencing for tumor and germline testing to impact treatment and outcomes of patients with cancer, there are also risks of oversimplification, misinterpretation, and missed opportunities. These issues risk limiting clinical benefit and, at worst, perpetuating false conclusions that could lead to inappropriate treatment selection, avoidable toxicity, and harm to patients. This report presents 5 case studies illustrating challenges and opportunities in clinical next-generation sequencing interpretation and clinical application in solid tumor oncologic care. First is a case that dissects the origin of an ATM mutation as originating from a hematopoietic clone rather than the tumor. Second is a case illustrating the potential for tumor sequencing to suggest germline variants associated with a hereditary cancer syndrome. Third are 2 cases showing the potential for variant reclassification of a germline variant of uncertain significance when considered alongside family history and tumor sequencing results. Finally, we describe a case illustrating challenges with using microsatellite instability for predicting tumor response to immune checkpoint inhibitors. The common theme of the case studies is the importance of examining clinical context alongside expert review and interpretation, which together highlight an expanding role for contextual examination and multidisciplinary expert review through molecular tumor boards.
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Affiliation(s)
- Alexandra O Sokolova
- 1Department of Medicine, University of Washington.,2Clinical Research Division, Fred Hutchinson Cancer Research Center.,4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Brian H Shirts
- 4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Eric Q Konnick
- 4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Ginger J Tsai
- 4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Bernardo H L Goulart
- 1Department of Medicine, University of Washington.,2Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Bruce Montgomery
- 1Department of Medicine, University of Washington.,2Clinical Research Division, Fred Hutchinson Cancer Research Center.,4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Colin C Pritchard
- 4Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Evan Y Yu
- 1Department of Medicine, University of Washington.,2Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Heather H Cheng
- 1Department of Medicine, University of Washington.,2Clinical Research Division, Fred Hutchinson Cancer Research Center
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26
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Gene panel screening for insight towards breast cancer susceptibility in different ethnicities. PLoS One 2020; 15:e0238295. [PMID: 32866190 PMCID: PMC7458311 DOI: 10.1371/journal.pone.0238295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 08/13/2020] [Indexed: 11/19/2022] Open
Abstract
African American breast cancer genetics is less understood compared to European American breast cancer susceptibility. Despite the many advantages of gene panel screening, studies investigating African American inherited breast cancer risk and comparing variant contributions between ethnicities are infrequent. Thus, 97 breast cancer-affected individuals of African and European descent from the Alabama Hereditary Cancer Cohort were screened using the research-based gene-panel, B.O.P. (Breast, Ovarian, and Prostate cancer). Upon sequencing and bioinformatic processing, rare coding variants in 14 cancer susceptibility genes were categorized according to the American College of Medical Genetics guidelines and compared between ethnicities. Overall, 107 different variants were identified, the majority of which were benign/likely benign. A pathogenic/likely pathogenic variant was detected in 8.6% and 6.5% of African American and European American cases, respectively, which was not statistically significant. However, African Americans were more likely to have at least one variant of uncertain significance (VUS; p-value 0.006); they also had significantly more VUSs in BRCA1/2 compared to European Americans (p-value 0.015). Additionally, 51.4% of African Americans and 32.3% of European Americans harbored multiple rare variants, and African Americans were more likely to have at least one VUS and one benign/likely benign variant (p-value 0.032), as well as multiple benign/likely benign variants (p-value 0.089). Moreover, of the 15 variants detected in multiple breast cancer cases, ATM c.2289T>C (p.F763L), a VUS, along with two likely benign variants, BRCA2 c.2926_2927delinsAT (p.S976I) and RAD51D c.251T>A (p.L84H), were determined to be associated with African American breast cancer risk when compared to ethnic-specific controls. Ultimately, B.O.P. screening provides essential insight towards the variant contributions in clinically relevant cancer susceptibility genes and differences between ethnicities, stressing the need for future research to elucidate inherited breast cancer risk.
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27
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Zhang J, Yao Y, He H, Shen J. Clinical Interpretation of Sequence Variants. CURRENT PROTOCOLS IN HUMAN GENETICS 2020; 106:e98. [PMID: 32176464 PMCID: PMC7431429 DOI: 10.1002/cphg.98] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.
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Affiliation(s)
- Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yanyi Yao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Haixian He
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, China
| | - Jun Shen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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28
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Schienda J, Stopfer J. Cancer Genetic Counseling-Current Practice and Future Challenges. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036541. [PMID: 31548230 DOI: 10.1101/cshperspect.a036541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer genetic counseling practice is rapidly evolving, with services being provided in increasingly novel ways. Pretest counseling for cancer patients may be abbreviated from traditional models to cover the elements of informed consent in the broadest of strokes. Genetic testing may be ordered by a cancer genetics professional, oncology provider, or primary care provider. Increasingly, direct-to-consumer testing options are available and utilized by consumers anxious to take control of their genetic health. Finally, genetic information is being used to inform oncology care, from surgical decision-making to selection of chemotherapeutic agent. This review provides an overview of the current and evolving practice of cancer genetic counseling as well as opportunities and challenges for a wide variety of indications in both the adult and pediatric setting.
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Affiliation(s)
- Jaclyn Schienda
- Division of Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jill Stopfer
- Division of Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
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29
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Halverson CME, Connors LM, Wessinger BC, Clayton EW, Wiesner GL. Patient perspectives on variant reclassification after cancer susceptibility testing. Mol Genet Genomic Med 2020; 8:e1275. [PMID: 32329193 PMCID: PMC7336756 DOI: 10.1002/mgg3.1275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Little is known about the impact of reclassification on patients' perception of medical uncertainty or trust in genetics-based clinical care. METHODS Semistructured telephone interviews were conducted with 20 patients who had received a reclassified genetic test result related to hereditary cancer. All participants had undergone genetic counseling and testing for cancer susceptibility at Vanderbilt-Ingram Cancer Center Hereditary Cancer Clinic within the last six years. RESULTS Most of the participants did not express distress related to the variant reclassification and only a minority expressed a decrease in trust in medical genetics. However, recall of the new interpretation was limited, even though all participants were recontacted by letter, phone, or clinic visit. CONCLUSION Reclassification of genetic tests is an important issue in modern healthcare because changes in interpretation have the potential to alter previously recommended management. Participants in this study did not express strong feelings of mistrust or doubt about their genetic evaluation. However, there was a low level of comprehension and information retention related to the updated report. Future research can build on this study to improve communication with patients about their reclassified results.
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Affiliation(s)
- Colin M E Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA.,Regenstrief Institute, Indianapolis, IN, USA
| | | | | | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,School of Law, Vanderbilt University, Nashville, TN, USA
| | - Georgia L Wiesner
- Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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30
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Wu D, Luo X, Feurstein S, Kesserwan C, Mohan S, Pineda-Alvarez DE, Godley LA. How I curate: applying American Society of Hematology-Clinical Genome Resource Myeloid Malignancy Variant Curation Expert Panel rules for RUNX1 variant curation for germline predisposition to myeloid malignancies. Haematologica 2020; 105:870-887. [PMID: 32165484 PMCID: PMC7109758 DOI: 10.3324/haematol.2018.214221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/21/2019] [Indexed: 01/30/2023] Open
Abstract
The broad use of next-generation sequencing and microarray platforms in research and clinical laboratories has led to an increasing appreciation of the role of germline mutations in genes involved in hematopoiesis and lineage differentiation that contribute to myeloid neoplasms. Despite implementation of the American College of Medical Genetics and Genomics and Association for Molecular Pathology 2015 guidelines for sequence variant interpretation, the number of variants deposited in ClinVar, a genomic repository of genotype and phenotype data, and classified as having uncertain significance or being discordantly classified among clinical laboratories remains elevated and contributes to indeterminate or inconsistent patient care. In 2018, the American Society of Hematology and the Clinical Genome Resource co-sponsored the Myeloid Malignancy Variant Curation Expert Panel to develop rules for classifying gene variants associated with germline predisposition to myeloid neoplasia. Herein, we demonstrate application of our rules developed for the RUNX1 gene to variants in six examples to show how we would classify them within the proposed framework.
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Affiliation(s)
- David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Simone Feurstein
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Chimene Kesserwan
- Albert Einstein College of Medicine, Department of Pathology, New York, NY
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, Chicago, IL .,Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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Rubinstein JC, Nicolson NG, Rottmann D, Morotti R, Korah R, Carling T, Christison-Lagay ER. Choice of control tissue impacts designation of germline variants in a cohort of papillary thyroid carcinoma patients. Ann Oncol 2020; 31:815-821. [PMID: 32165204 DOI: 10.1016/j.annonc.2020.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 02/26/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The term germline is commonly used to refer to any non-tumor control sample analyzed in tumor-normal paired sequencing experiments. Blood is the most commonly utilized control, and variants found in both tumor and blood are considered germline. However, somatic variants accumulate within an organism from embryogenesis throughout life. The resultant mosaicism is extensive and calls into question the assumption that blood, or any somatic tissue, represents the germline. Misclassification of germline and somatic variants has critical consequences for individual patient care and enormous impact on our health care system, given potential screening, counseling, and treatment implications of misidentifying germline variants. PATIENTS AND METHODS Whole-exome sequencing was performed on six separate specimens from each of two patients with papillary thyroid carcinoma, and three specimens each from eight additional patients forming a validation cohort. Tumor variants were compared with each individual non-tumor control and with composite control sets generated as approximations of true germline. For the index patient, parental blood was also sequenced to assess whether patient-only samples could approximate a trio-derived germline. RESULTS Using different non-tumor control tissues results in altered germline-somatic designation of tumor variants. In patient 1, 82% of variants are labeled germline using blood control, compared with 75.8%, 61.5%, and 49.6% using lymph node, thyroid, and thymus, respectively. In patient 2, the thyroid control resulted in the greatest percentage of germline calls (70.0%), followed by thymus (56.0%), lymph node (50.1%), and blood (44.1%). Composite control sets built from multiple samples can approximate the germline, even in the absence of parental DNA. CONCLUSIONS Misclassification of germline-somatic origin has potential consequences for patient care, informing screening, trial eligibility, prophylactic interventions, and family planning. This study demonstrates the need for caution in interpreting germline-somatic designation if these data are to inform clinical decisions and suggests that improved design of controls can overcome current limitations.
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Affiliation(s)
- J C Rubinstein
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - N G Nicolson
- Division of Surgical Oncology, Department of General Surgery, Yale School of Medicine, New Haven, USA
| | - D Rottmann
- Department of Pathology, Yale School of Medicine, New Haven, USA
| | - R Morotti
- Department of Pathology, Yale School of Medicine, New Haven, USA
| | - R Korah
- Division of Surgical Oncology, Department of General Surgery, Yale School of Medicine, New Haven, USA
| | - T Carling
- Division of Surgical Oncology, Department of General Surgery, Yale School of Medicine, New Haven, USA
| | - E R Christison-Lagay
- Division of Pediatric Surgery, Department of General Surgery, Yale School of Medicine, New Haven, USA.
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Achatz MI, Caleffi M, Guindalini R, Marques RM, Nogueira-Rodrigues A, Ashton-Prolla P. Recommendations for Advancing the Diagnosis and Management of Hereditary Breast and Ovarian Cancer in Brazil. JCO Glob Oncol 2020; 6:439-452. [PMID: 32155091 PMCID: PMC7113069 DOI: 10.1200/jgo.19.00170] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The objective of this review was to address the barriers limiting access to genetic cancer risk assessment and genetic testing for individuals with suspected hereditary breast and ovarian cancer (HBOC) through a review of the diagnosis and management steps of HBOC. METHODS A selected panel of Brazilian experts in fields related to HBOC was provided with a series of relevant questions to address before the multiday conference. During this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion, until a consensus was achieved. RESULTS The authors propose specific and realistic recommendations for improving access to early diagnosis, risk management, and cancer care of HBOC specific to Brazil. Moreover, in creating these recommendations, the authors strived to address all the barriers and impediments mentioned in this article. CONCLUSION There is a great need to expand hereditary cancer testing and counseling in Brazil, and changing current policies is essential to accomplishing this goal. Increased knowledge and awareness, together with regulatory actions to increase access to this technology, have the potential to improve patient care and prevention and treatment efforts for patients with cancer across the country.
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Affiliation(s)
| | - Maira Caleffi
- Nucleo Mama Porto Alegre and Associação Hospitalar Moinhos de Vento, Porto Alegre, Brazil
| | - Rodrigo Guindalini
- Oncologia D’or, Rede D’or São Luiz, Brazil
- Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Renato Moretti Marques
- Programa da Saúde da Mulher, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Centro de Oncologia e Hematologia, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Angelica Nogueira-Rodrigues
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Grupo Brasileiro de Oncologia Ginecológica, Belo Horizonte, Brazil
- DOM Oncologia, Minas Gerais, Brazil
| | - Patricia Ashton-Prolla
- Departmento de Genética, Universidade Federal do Rio Grande do Sul
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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Health Disparities in Germline Genetic Testing for Cancer Susceptibility. CURRENT BREAST CANCER REPORTS 2020. [DOI: 10.1007/s12609-020-00354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Impact of proactive high-throughput functional assay data on BRCA1 variant interpretation in 3684 patients with breast or ovarian cancer. J Hum Genet 2020; 65:209-220. [PMID: 31907386 DOI: 10.1038/s10038-019-0713-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/08/2022]
Abstract
The clinical utility of BRCA1/2 genotyping was recently extended from the selection of subjects at high risk for hereditary breast and ovary cancer to the identification of candidates for poly (ADP-ribose) polymerase (PARP) inhibitor treatment. This underscores the importance of accurate interpretation of BRCA1/2 genetic variants and of reducing the number of variants of uncertain significance (VUSs). Two recent studies by Findlay et al. and Starita et al. introduced high-throughput functional assays, and proactively analyzed variants in specific regions regardless of whether they had been previously observed. We retrospectively reviewed all BRCA1 and BRCA2 germline genetic test reports from patients with breast or ovarian cancer examined at Asan Medical Center (Seoul, Korea) between September 2011 and December 2018. Variants were assigned pathogenic or benign strong evidence codes according to the functional classification and were reclassified according to the ACMG/AMP 2015 guidelines. Among 3684 patients with available BRCA1 and BRCA2 germline genetic test reports, 429 unique variants (181 from BRCA1) were identified. Of 34 BRCA1 variants intersecting with the data reported by Findlay et al., three missense single-nucleotide variants from four patients (0.11%, 4/3684) were reclassified from VUSs to likely pathogenic variants. Four variants scored as functional were reclassified into benign or likely benign variants. Three variants that overlapped with the data reported by Starita et al. could not be reclassified. In conclusion, proactive high-throughput functional study data are useful for the reclassification of clinically observed VUSs. Integrating additional evidence, including functional assay results, may help reduce the number of VUSs.
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