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Abu Hijlih R, Sharaf B, Salah S, Bani Hani H, Nielsen SM, Heald B, Esplin ED, Ghanem R, Alzibdeh A, Al-Batsh T, Al-Masri Y, Abdel-Razeq H. Patterns and Frequency of Pathogenic Germline Variants Among Prostate Cancer Patients Utilizing Multi-Gene Panel Genetic Testing. World J Oncol 2024; 15:801-808. [PMID: 39328335 PMCID: PMC11424115 DOI: 10.14740/wjon1896] [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: 05/19/2024] [Accepted: 06/21/2024] [Indexed: 09/28/2024] Open
Abstract
Background Germline genetic testing (GGT) has significant implications in the management of patients with prostate cancer (PCa). Herein, we report on patterns and frequency of pathogenic/likely pathogenic germline variants (P/LPGVs) among newly diagnosed Arab patients with PCa. Methods Patients meeting the National Comprehensive Cancer Network (NCCN) eligibility criteria for GGT were offered a 19-gene PCa panel or an expanded 84-gene multi-cancer panel. Results During the study period, 231 patients were enrolled; 107 (46.3%) had metastatic disease at diagnosis. In total, 17 P/LPGVs were detected in 17 patients (7.4%). Among the 113 (48.9%) patients who underwent GGT with the 19-gene panel, eight (7.1%) had P/LPGVs, compared to nine (7.6%) of the 118 (51.1%) who did GGT through the expanded 84-gene panel (P = 0.88). Variant of uncertain significance (VUS) rate was higher (n = 73, 61.9%) among the group who underwent expanded 84-gene panel testing compared to those who underwent the 19-gene PCa panel (n = 35, 30.9%) (P = 0.001). P/LPGVs in DNA damage repair (DDR) genes, most frequently BRCA2, CHEK2 and TP53, were the most common P/LPGVs findings. Conclusion This study is the first to characterize the germline genetic profile of an Arab population with PCa. All detected P/LPGVs were potentially actionable, with most variants able to be detected with a PCa-specific panel.
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Affiliation(s)
- Ramiz Abu Hijlih
- Department of Radiation Oncology, King Hussein Cancer Center, Amman, Jordan
| | - Baha Sharaf
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Samer Salah
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Hira Bani Hani
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | | | | | | | - Rami Ghanem
- Department of Surgery, King Hussein Cancer Center, Amman, Jordan
| | - Abdulla Alzibdeh
- Department of Radiation Oncology, King Hussein Cancer Center, Amman, Jordan
| | - Tamer Al-Batsh
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Yosra Al-Masri
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
- School of Medicine, the University of Jordan, Amman, Jordan
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Gohlke J, Lindqvist J, Hourani Z, Heintzman S, Tonino P, Elsheikh B, Morales A, Vatta M, Burghes A, Granzier H, Roggenbuck J. Pathomechanisms of Monoallelic variants in TTN causing skeletal muscle disease. Hum Mol Genet 2024:ddae136. [PMID: 39277846 DOI: 10.1093/hmg/ddae136] [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: 04/29/2024] [Revised: 07/01/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024] Open
Abstract
Pathogenic variants in the titin gene (TTN) are known to cause a wide range of cardiac and musculoskeletal disorders, with skeletal myopathy mostly attributed to biallelic variants. We identified monoallelic truncating variants (TTNtv), splice site or internal deletions in TTN in probands with mild, progressive axial and proximal weakness, with dilated cardiomyopathy frequently developing with age. These variants segregated in an autosomal dominant pattern in 7 out of 8 studied families. We investigated the impact of these variants on mRNA, protein levels, and skeletal muscle structure and function. Results reveal that nonsense-mediated decay likely prevents accumulation of harmful truncated protein in skeletal muscle in patients with TTNtvs. Splice variants and an out-of-frame deletion induce aberrant exon skipping, while an in-frame deletion produces shortened titin with intact N- and C-termini, resulting in disrupted sarcomeric structure. All variant types were associated with genome-wide changes in splicing patterns, which represent a hallmark of disease progression. Lastly, RNA-seq studies revealed that GDF11, a member of the TGF-β superfamily, is upregulated in diseased tissue, indicating that it might be a useful therapeutic target in skeletal muscle titinopathies.
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Affiliation(s)
- Jochen Gohlke
- Department of Cellular and Molecular Medicine, University of Arizona, 1656 E. Mabel St., Tucson, AZ 85724, United States
| | - Johan Lindqvist
- Department of Cellular and Molecular Medicine, University of Arizona, 1656 E. Mabel St., Tucson, AZ 85724, United States
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, University of Arizona, 1656 E. Mabel St., Tucson, AZ 85724, United States
| | - Sarah Heintzman
- Department of Neurology, The Ohio State University Wexner Medical Center, 395 W. 12th Ave, Columbus, OH 43210, United States
| | - Paola Tonino
- Research, Innovation and Impact Core Facilities Department, University of Arizona, 1333 N. Martin Ave, Tucson, AZ 85719, United States
| | - Bakri Elsheikh
- Department of Neurology, The Ohio State University Wexner Medical Center, 395 W. 12th Ave, Columbus, OH 43210, United States
| | - Ana Morales
- Invitae Corporation, 1400 16th St., San Francisco, CA 94103, United States
| | - Matteo Vatta
- Invitae Corporation, 1400 16th St., San Francisco, CA 94103, United States
| | - Arthur Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, 370 W 9th Ave, Columbus, OH 43210, United States
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, 1656 E. Mabel St., Tucson, AZ 85724, United States
| | - Jennifer Roggenbuck
- Department of Neurology, The Ohio State University Wexner Medical Center, 395 W. 12th Ave, Columbus, OH 43210, United States
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Abdel-Razeq H, Bani Hani H, Sharaf B, Tamimi F, Khalil H, Abu Sheikha A, Alkyam M, Abdel-Razeq S, Ghatasheh T, Radaideh T, Khater S. Patterns and Frequency of Pathogenic Germline Mutations among Patients with Newly-Diagnosed Endometrial Cancer: The Jordanian Exploratory Cancer Genetics (Jo-ECAG) Endometrial Study. Cancers (Basel) 2024; 16:2543. [PMID: 39061183 PMCID: PMC11274358 DOI: 10.3390/cancers16142543] [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: 06/05/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Most of endometrial cancers are sporadic, with 5% or less being attributed to inherited pathogenic germline mutations and mostly related to the Lynch syndrome. To our knowledge, this is the first study to investigate patterns and frequencies of germline mutations in patients with endometrial cancer in an Arab region. Consecutive patients with endometrial cancer (n = 130), regardless of their age and family history, were enrolled. Germline genetic testing, using an 84-gene panel, was performed on all. Almost half of the patient population (n = 64, 49.2%) was tested based on international guidelines, while the remaining patients (n = 66, 50.8%) were tested as part of an ongoing universal germline genetic testing program. Among the whole group, 18 (13.8%) patients had positive pathogenic or likely pathogenic (P/LP) germline variants. The most common variants encountered were in MLH1 (n = 4, 22.2%), PMS2 (n = 3, 16.7%), ATM, MSH2, MUTYH, and BRCA2 (n = 2, 11.1% each). In addition, three (2.3%) patients were found to have an increased risk allele of the APC gene. P/LP variants were more common among patients with carcinosarcoma and clear cell carcinoma, younger patients (age ≤ 50 years), and in patients with a non-metastatic disease. We conclude that germline genetic variants, mostly in genes related to the Lynch syndrome, are relatively common among Arab patients with endometrial cancer.
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Affiliation(s)
- Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
- School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Hira Bani Hani
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Baha Sharaf
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Faris Tamimi
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Hanan Khalil
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Areej Abu Sheikha
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Mais Alkyam
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | | | - Tala Ghatasheh
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Tala Radaideh
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
| | - Suhaib Khater
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (H.B.H.); (B.S.); (F.T.); (H.K.); (A.A.S.); (M.A.); (T.G.); (T.R.); (S.K.)
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4
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Wyatt Castillo RB, Nielsen SM, Chen E, Heald B, Ellsworth RE, Esplin ED, Tomlinson GE. Disparate Rates of Germline Variants in Cancer Predisposition Genes in African American/Black Compared With Non-Hispanic White Individuals Between 2015 and 2022. JCO Precis Oncol 2024; 8:e2300715. [PMID: 38991178 DOI: 10.1200/po.23.00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
PURPOSE African American/Black (AA/B) individuals are under-represented in genomic databases and thus less likely to receive definitive information from germline genetic testing (GGT) than non-Hispanic White (NHW) individuals. With nearly 500,000 AA/B and NHW individuals having undergone multigene panel testing (MGPT) for hereditary cancer risk at a single commercial laboratory, to our knowledge, we present the largest study to date investigating cancer GGT results in AA/B and NHW individuals. METHODS MGPT results from a retrospective cohort of AA/B (n = 48,684) and NHW (n = 444,831) patients were evaluated. Frequencies of pathogenic germline variants (PGVs) and variants of uncertain significance (VUS) were compared between AA/B and NHW individuals. Changes in frequency of VUS over time were determined. Pearson's chi-squared test was used to compare categorical variables among groups. All significance tests were two-tailed, and P < .05 was considered statistically significant. RESULTS Between 2015 and 2022, rates of VUS decreased 2.3-fold in AA/B and 1.8-fold in NHW individuals; however, frequencies of VUS and PGV remained significantly higher (46% v 32%; P < .0001) and lower (9% v 13%; P < .0001) in AA/B compared with NHW individuals. Rates of VUS in ATM, BRCA1, BRCA2, PALB2, and PMS2 were significantly higher in AA/B compared with NHW individuals, whereas rates of PGV in BRCA1, BRCA2, and PALB2 were higher in AA/B compared with NHW individuals (P < .001). CONCLUSION Despite reductions in VUS frequencies over time, disparities in definitive GGT results persist. Increasing inclusion of AA/B populations in both testing and research will further increase knowledge of genetic variants across these racial groups.
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Affiliation(s)
- Rachel B Wyatt Castillo
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
| | | | | | | | | | | | - Gail E Tomlinson
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
- Mays Cancer Center, UT Health San Antonio, San Antonio, TX
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5
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Goanta EV, Vacarescu C, Tartea G, Ungureanu A, Militaru S, Muraretu A, Faur-Grigori AA, Petrescu L, Vătăsescu R, Cozma D. Unexpected Genetic Twists in Patients with Cardiac Devices. J Clin Med 2024; 13:3801. [PMID: 38999368 PMCID: PMC11242405 DOI: 10.3390/jcm13133801] [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: 05/31/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
Objective: To assess the frequency and types of genetic mutations in patients with arrhythmias who underwent cardiac device implantation. Methods: Retrospective observational study, including 38 patients with different arrhythmias and cardiac arrest as a first cardiac event. Treatment modalities encompass pacemakers, transvenous defibrillators, loop recorders, subcutaneous defibrillators, and cardiac resynchronization therapy. All patients underwent genetic testing, using commercially available panels (106-174 genes). Outcome measures include mortality, arrhythmia recurrence, and device-related complications. Results: Clinical parameters revealed a family history of sudden cardiac death in 19 patients (50%), who were predominantly male (58%) and had a mean age of 44.5 years and a mean left ventricle ejection fraction of 40.3%. Genetic testing identified mutations in various genes, predominantly TMEM43 (11%). In two patients (3%) with arrhythmogenic cardiomyopathy, complete subcutaneous defibrillator extraction with de novo transvenous implantable cardioverter-defibrillator implantation was needed. The absence of multiple associations among severe gene mutations was crucial for cardiac resynchronization therapy response. Mortality in this group was around 3% in titin dilated cardiomyopathy patients. Conclusions: Integration of genetic testing into the decision-making process for patients with electronic devices represents a paradigm shift in personalized medicine. By identifying genetic markers associated with arrhythmia susceptibility, heart failure etiology, and cardiac resynchronization therapy response, clinicians can tailor device choices to optimize patient outcomes.
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Affiliation(s)
- Emilia-Violeta Goanta
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Cardiology Department, Emergency County Hospital of Craiova, Tabaci Street, Nr. 1, 200642 Craiova, Romania; (G.T.); (A.U.); (A.M.)
| | - Cristina Vacarescu
- Department of Cardiology, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania; (L.P.); (D.C.)
- Institute of Cardiovascular Diseases Timisoara, 13A Gheorghe Adam Street, 300310 Timisoara, Romania;
- Research Center of the Institute of Cardiovascular Diseases Timisoara, 13A Gheorghe Adam Street, 300310 Timisoara, Romania
| | - Georgica Tartea
- Cardiology Department, Emergency County Hospital of Craiova, Tabaci Street, Nr. 1, 200642 Craiova, Romania; (G.T.); (A.U.); (A.M.)
- Department of Physiology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Adrian Ungureanu
- Cardiology Department, Emergency County Hospital of Craiova, Tabaci Street, Nr. 1, 200642 Craiova, Romania; (G.T.); (A.U.); (A.M.)
| | - Sebastian Militaru
- Department of Cardiology, Craiova University of Medicine and Pharmacy, 200349 Craiova, Romania;
| | - Alexandra Muraretu
- Cardiology Department, Emergency County Hospital of Craiova, Tabaci Street, Nr. 1, 200642 Craiova, Romania; (G.T.); (A.U.); (A.M.)
| | | | - Lucian Petrescu
- Department of Cardiology, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania; (L.P.); (D.C.)
| | - Radu Vătăsescu
- Cardiology Department, Clinical Emergency Hospital, 014461 Bucharest, Romania;
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Dragos Cozma
- Department of Cardiology, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania; (L.P.); (D.C.)
- Institute of Cardiovascular Diseases Timisoara, 13A Gheorghe Adam Street, 300310 Timisoara, Romania;
- Research Center of the Institute of Cardiovascular Diseases Timisoara, 13A Gheorghe Adam Street, 300310 Timisoara, Romania
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6
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Ceyhan-Birsoy O, Stadler ZK. Tumor-Only Sequencing: A Story Only Half Told. JCO Precis Oncol 2024; 8:e2400226. [PMID: 38810205 DOI: 10.1200/po.24.00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Germline testing and tumor sequencing are often both necessary for optimal cancer treatment and management.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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7
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Abu-Hijlih R, Sharaf B, Salah S, Bani Hani H, Alqaisieh M, Alzibdeh A, Ababneh L, Mahafdah S, Abdel-Razeq H. Germline Genetic Mutations in Adult Patients with Sarcoma: Insight into the Middle East Genetic Landscape. Cancers (Basel) 2024; 16:1668. [PMID: 38730621 PMCID: PMC11083501 DOI: 10.3390/cancers16091668] [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: 02/13/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Data on germline mutations in soft tissue and bone sarcomas are scarce. We sought to identify the prevalence of germline mutations in adult sarcoma patients treated at a tertiary cancer center. Newly diagnosed patients were offered germline genetic testing via an 84-gene panel. The prevalence of pathogenic germline variants (PGVs) and their association with disease-, and patient- related factors are reported. A total of 87 patients were enrolled, the median age was 48 (19-78) years, and 47 (54%) were females. Gastrointestinal stromal tumors (n = 12, 13.8%), liposarcoma (n = 10, 11.5%), and Ewing sarcoma (n = 10, 11.5%) were the main subtypes. A total of 20 PGVs were detected in 18 (20.7%) patients. Variants of uncertain significance, in the absence of PGVs, were detected in 40 (45.9%) patients. Young age (p = 0.031), presence of a second primary cancer (p = 0.019), and female gender (p = 0.042) were correlated with the presence of PGVs. All identified PGVs have potential clinical actionability and cascade testing, and eight (44.44%) suggested eligibility for a targeted therapy. Almost one in five adult patients with soft tissue and bone sarcomas harbor pathogenic or likely pathogenic variants. Many of these variants are potentially actionable, and almost all have implications on cancer screening and family counselling. In this cohort from the Middle East, younger age, presence of a second primary tumor, and female gender were significantly associated with higher PGVs rates. Larger studies able to correlate treatment outcomes with genetic variants are highly needed.
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Affiliation(s)
- Ramiz Abu-Hijlih
- Department of Radiation Oncology, King Hussein Cancer Center, Amman 11941, Jordan; (R.A.-H.); (A.A.)
| | - Baha Sharaf
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Samer Salah
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Hira Bani Hani
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Mohammad Alqaisieh
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Abdulla Alzibdeh
- Department of Radiation Oncology, King Hussein Cancer Center, Amman 11941, Jordan; (R.A.-H.); (A.A.)
| | - Layan Ababneh
- School of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Suleiman Mahafdah
- Department of Surgery, Royal Jordanian Medical Services, Amman 11855, Jordan;
| | - Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
- School of Medicine, The University of Jordan, Amman 11942, Jordan
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Neves Rebello Alves L, Valle dos Santos Silveira L, Silva dos Reis Trabach R, Dummer Meira D, de Vargas Wolfgramm dos Santos E, Drumond Louro I. PIGN c.776T>C (p.Phe259Ser) variant present in trans with a pathogenic variant for PIGN-congenital disorder of glycosylation: Bella-Noah syndrome. Heliyon 2024; 10:e27438. [PMID: 38509968 PMCID: PMC10951506 DOI: 10.1016/j.heliyon.2024.e27438] [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: 11/16/2023] [Revised: 12/12/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Glycosylation is the most common protein and lipid post-translational modification in humans. Congenital disorders of glycosylation (CDG) are characterized by both genetic and clinical heterogeneity, presenting multisystemic manifestations, and in most cases are autosomal recessive in inheritance. The PIGN gene is responsible for the addition of phosphoethanolamine to the first mannose in the glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway, a highly conserved process that enables proteins to bind to the cell surface membrane. Here, we report a family with two siblings pediatric cases with the exact same compound heterozygous variants in PIGN. The (c.776T > C) variant of uncertain significance (VUS) together with a known pathogenic variant (c.932T > G), resulting in clinical features compatible with PIGN-related conditions, more specific the CDG. This is the first time that PIGN variant c.776T > C is reported in literature in individuals with PIGN-congenital disorder of glycosylation (PIGN-CDG), and the current submission in ClinVar by Invitae® is specifically of our case. Detailed clinical information and molecular analyses are presented. Here, we show for the first time two affected siblings with one pathogenic variant (c.932T > G) and the c.776T > C VUS in trans. In honor of the family, we propose the name Bella-Noah Syndrome for disorder.
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Affiliation(s)
- Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Lívia Valle dos Santos Silveira
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória, 29090-040, ES, Brazil
| | - Raquel Silva dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
| | - Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Eldamária de Vargas Wolfgramm dos Santos
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
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9
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Voinescu OR, Ionescu BI, Militaru S, Afana AS, Sascau R, Vasiliu L, Onciul S, Dobrescu MA, Cozlac RA, Cozma D, Rancea R, Dragulescu B, Andreescu NI, Puiu M, Jurcut RO, Chirita-Emandi A. Genetic Characterization of Dilated Cardiomyopathy in Romanian Adult Patients. Int J Mol Sci 2024; 25:2562. [PMID: 38473809 DOI: 10.3390/ijms25052562] [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: 01/20/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Dilated cardiomyopathy (DCM) represents a group of disorders affecting the structure and function of the heart muscle, leading to a high risk of heart failure and sudden cardiac death (SCD). DCM frequently involves an underlying genetic etiology. Genetic testing is valuable for risk stratification, treatment decisions, and family screening. Romanian population data on the genetic etiology of DCM are lacking. We aimed to investigate the genetic causes for DCM among Romanian adult patients at tertiary referral centers across the country. Clinical and genetic investigations were performed on adult patients presenting to tertiary hospitals in Romania. The genetic investigations used next-generation sequencing panels of disease-associated DCM genes. A total of 122 patients with DCM underwent genetic testing. The mean age at DCM diagnosis was 41.6 ± 12.4 years. The genetic investigations identified pathogenic or likely pathogenic variants in 50.8% of participants, while 25.4% had variants of unknown significance. Disease-causing variants in 15 genes were identified in people with DCM, with 31 previously unreported variants. Variants in TTN, LMNA, and DSP explained 75% of genetic causes for DCM. In total, 52.4% of patients had a family history of DCM/SCD. Left ventricular ejection fraction of <35% was observed in 41.9% of patients with disease-causing variants and 55% with negative or uncertain findings. Further genotype-phenotype correlations were explored in this study population. The substantial percentage (50.8%) of disease-causing variants identified in patients with DCM acknowledges the importance of genetic investigations. This study highlights the genetic landscape in genes associated with DCM in the Romanian population.
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Affiliation(s)
- Oana Raluca Voinescu
- Department of Cardiology, Cardiology Discipline II, University of Medicine and Pharmacy "Victor Babeș", Eftimie Murgu Sq., 300041 Timișoara, Romania
| | - Bogdana Ioana Ionescu
- Department of Cardiology, University of Medicine and Pharmacy 'Carol Davila', Dionisie Lupu Street, no. 37, Sector 2, 4192910 Bucharest, Romania
- Expert Center for Rare Cardiac Genetic Diseases, Emergency Institute for Cardiovascular Diseases 'Prof.dr.C.C.Iliescu', Fundeni 258, 022328 Bucharest, Romania
| | - Sebastian Militaru
- Department of Cardiology, Craiova University of Medicine and Pharmacy, Petru Rareș Street no 2, 200349 Craiova, Romania
- Cardiomed Hospital, Craiova, Str. Spania, Nr. 35A, 200513 Craiova, Romania
| | - Andreea Sorina Afana
- Department of Cardiology, Craiova University of Medicine and Pharmacy, Petru Rareș Street no 2, 200349 Craiova, Romania
- Cardiomed Hospital, Craiova, Str. Spania, Nr. 35A, 200513 Craiova, Romania
| | - Radu Sascau
- Internal Medicine Department, "Grigore T. Popa" University of Medicine and Pharmacy, 16 Universitatii Street, 700503 Iași, Romania
- Cardiology Department, Cardiovascular Diseases Institute "Prof. Dr. George I. M. Georgescu", 50 Boulevard Carol I, 700503 Iași, Romania
| | - Laura Vasiliu
- Internal Medicine Department, "Grigore T. Popa" University of Medicine and Pharmacy, 16 Universitatii Street, 700503 Iași, Romania
- Cardiology Department, Cardiovascular Diseases Institute "Prof. Dr. George I. M. Georgescu", 50 Boulevard Carol I, 700503 Iași, Romania
| | - Sebastian Onciul
- Department of Cardiology, University of Medicine and Pharmacy 'Carol Davila', Dionisie Lupu Street, no. 37, Sector 2, 4192910 Bucharest, Romania
| | - Mihaela Amelia Dobrescu
- Genetics Department, Craiova University of Medicine and Pharmacy, Petru Rareș 2 Street, 200349 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
| | - Ramona Alina Cozlac
- Department of Cardiology, Cardiology Discipline II, University of Medicine and Pharmacy "Victor Babeș", Eftimie Murgu Sq., 300041 Timișoara, Romania
- Cardiology Department, Institute of Cardiovascular Diseases, Gheorghe Adam Street, 13A, 300310 Timișoara, Romania
| | - Dragos Cozma
- Department of Cardiology, Cardiology Discipline II, University of Medicine and Pharmacy "Victor Babeș", Eftimie Murgu Sq., 300041 Timișoara, Romania
- Cardiology Department, Institute of Cardiovascular Diseases, Gheorghe Adam Street, 13A, 300310 Timișoara, Romania
| | - Raluca Rancea
- Cardiology Department, Heart Institute Niculae Stăncioiu, 19-21 Motilor Street, 400001 Cluj-Napoca, Romania
| | - Bogdan Dragulescu
- Communications Department, Politehnica University Timisoara, sq Victoriei 2, 300006 Timișoara, Romania
| | - Nicoleta Ioana Andreescu
- Department of Microscopic Morphology, Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babeș" Timișoara, 2 Piaţa Eftimie Murgu Street, 300041 Timişoara, Romania
- Regional Center of Medical Genetics Timiș, Clinical Emergency Hospital for Children "Louis Țurcanu" Iosif Nemoianu Street N°2, 300011 Timișoara, Romania
| | - Maria Puiu
- Department of Microscopic Morphology, Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babeș" Timișoara, 2 Piaţa Eftimie Murgu Street, 300041 Timişoara, Romania
- Regional Center of Medical Genetics Timiș, Clinical Emergency Hospital for Children "Louis Țurcanu" Iosif Nemoianu Street N°2, 300011 Timișoara, Romania
| | - Ruxandra Oana Jurcut
- Department of Cardiology, University of Medicine and Pharmacy 'Carol Davila', Dionisie Lupu Street, no. 37, Sector 2, 4192910 Bucharest, Romania
- Expert Center for Rare Cardiac Genetic Diseases, Emergency Institute for Cardiovascular Diseases 'Prof.dr.C.C.Iliescu', Fundeni 258, 022328 Bucharest, Romania
| | - Adela Chirita-Emandi
- Department of Microscopic Morphology, Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babeș" Timișoara, 2 Piaţa Eftimie Murgu Street, 300041 Timişoara, Romania
- Regional Center of Medical Genetics Timiș, Clinical Emergency Hospital for Children "Louis Țurcanu" Iosif Nemoianu Street N°2, 300011 Timișoara, Romania
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10
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Morales A, Moretz C, Ren S, Smith E, Callis TE, Hall T, Hatchell KE, Nussbaum RL, Regalado E, Rojahn S, Vatta M, Esplin ED, Murillo J. Real-World Genetic Testing Utilization Among Patients With Cardiomyopathy. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004028. [PMID: 38088168 DOI: 10.1161/circgen.122.004028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Ana Morales
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Chad Moretz
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Sheng Ren
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
| | | | - Thomas E Callis
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Taryn Hall
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
| | - Kathryn E Hatchell
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Robert L Nussbaum
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Ellen Regalado
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Susan Rojahn
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Matteo Vatta
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Edward D Esplin
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Jaime Murillo
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
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11
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Zhunussova G, Omarbayeva N, Kaidarova D, Abdikerim S, Mit N, Kisselev I, Yergali K, Zhunussova A, Goncharova T, Abdrakhmanova A, Djansugurova L. Determination of genetic predisposition to early breast cancer in women of Kazakh ethnicity. Oncotarget 2023; 14:860-877. [PMID: 37791908 PMCID: PMC10549772 DOI: 10.18632/oncotarget.28518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer among women in Kazakhstan. To date, little data are available on the spectrum of genetic variation in Kazakh women with BC. We aimed to identify population-specific genetic markers associated with the risk of developing early-onset BC and test their association with clinical and prognostic factors. The study included 224 Kazakh women diagnosed with BC (≤40 age). Entire coding regions (>1700 exons) and the flanking noncoding regions of 94 cancer-associated genes were sequenced from blood DNA using MiSeq platform. We identified 38 unique pathogenic variants (PVs) in 13 different cancer-predisposing genes among 57 patients (25.4%), of which 6 variants were novel. In total, 12 of the 38 distinct PVs were detected recurrently, including BRCA1 c.5266dup, c.5278-2del, and c.2T>C, and BRCA2 c.9409dup and c.9253del that may be founder in this population. BRCA1 carriers were significantly more likely to develop triple-negative BC (OR = 6.61, 95% CI 2.44-17.91, p = 0.0002) and have family history of BC (OR = 3.17, 95% CI 1.14-8.76, p = 0.03) compared to non-carriers. This study allowed the identification of PVs specific to early-onset BC, which may be used as a foundation to develop regional expertise and diagnostic tools for early detection of BC in young Kazakh women.
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Affiliation(s)
- Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
| | - Nazgul Omarbayeva
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Dilyara Kaidarova
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Ilya Kisselev
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | | | - Aliya Abdrakhmanova
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
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12
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Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
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Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
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13
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Shore N, Gazi M, Pieczonka C, Heron S, Modh R, Cahn D, Belkoff LH, Berger A, Mazzarella B, Veys J, Idom C, Morris D, Jayram G, Engelman A, Bukkapatnam R, Dato P, Bevan-Thomas R, Cornell R, Wise DR, Hardwick MK, Hernandez RD, Rojahn S, Layman P, Hatchell KE, Heald B, Nussbaum RL, Nielsen SM, Esplin ED. Efficacy of National Comprehensive Cancer Network Guidelines in Identifying Pathogenic Germline Variants Among Unselected Patients with Prostate Cancer: The PROCLAIM Trial. Eur Urol Oncol 2023; 6:477-483. [PMID: 37574391 DOI: 10.1016/j.euo.2023.07.008] [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: 03/16/2023] [Revised: 06/07/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND Prostate cancer (PCa) patients with pathogenic/likely pathogenic germline variants (PGVs) in cancer predisposition genes may be eligible for U.S. Food and Drug Administration-approved targeted therapies, clinical trials, or enhanced screening. Studies suggest that eligible patients are missing genetics-informed care due to restrictive testing criteria. OBJECTIVE To establish the prevalence of actionable PGVs among prospectively accrued, unselected PCa patients, stratified by their guideline eligibility. DESIGN, SETTING, AND PARTICIPANTS Consecutive, unselected PCa patients were enrolled at 15 sites in the USA from October 2019 to August 2021, and had multigene cancer panel testing. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Correlates between the prevalence of PGVs and clinician-reported demographic and clinical characteristics were examined. RESULTS AND LIMITATIONS Among 958 patients (median [quartiles] age at diagnosis 65 [60, 71] yr), 627 (65%) had low- or intermediate-risk disease (grade group 1, 2, or 3). A total of 77 PGVs in 17 genes were identified in 74 patients (7.7%, 95% confidence interval [CI] 6.2-9.6%). No significant difference was found in the prevalence of PGVs among patients who met the 2019 National Comprehensive Cancer Network Prostate criteria (8.8%, 43/486, 95% CI 6.6-12%) versus those who did not (6.6%, 31/472, 95% CI 4.6-9.2%; odds ratio 1.38, 95% CI 0.85-2.23), indicating that these criteria would miss 42% of patients (31/74, 95% CI 31-53%) with PGVs. The criteria were less effective at predicting PGVs in patients from under-represented populations. Most PGVs (81%, 60/74) were potentially clinically actionable. Limitations include the inability to stratify analyses based on individual ethnicity due to low numbers of non-White patients with PGVs. CONCLUSIONS Our results indicate that almost half of PCa patients with PGVs are missed by current testing guidelines. Comprehensive germline genetic testing should be offered to all patients with PCa. PATIENT SUMMARY One in 13 patients with prostate cancer carries an inherited variant that may be actionable for the patient's current care or prevention of future cancer, and could benefit from expanded testing criteria.
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Affiliation(s)
- Neal Shore
- Carolina Urologic Research Center, Myrtle Beach, SC, USA.
| | - Mukaram Gazi
- University Urology Associates of New Jersey, Hamilton, NJ, USA
| | | | - Sean Heron
- Advanced Urology Institute, St. Petersburg, FL, USA
| | - Rishi Modh
- Advanced Urology Institute, St. Petersburg, FL, USA
| | | | | | - Aaron Berger
- Associated Urological Specialists, Chicago Ridge, IL, USA
| | | | | | | | | | | | | | | | - Paul Dato
- Genesis Healthcare Partners, San Diego, CA, USA
| | | | | | - David R Wise
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Robert L Nussbaum
- Invitae Corporation, San Francisco, CA, USA; Volunteer Faculty, University of California San Francisco, San Francisco, CA, USA
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14
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Sorscher S, LoPiccolo J, Heald B, Chen E, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder E, Lee H, Nussbaum RL, Martins R, Esplin ED. Rate of Pathogenic Germline Variants in Patients With Lung Cancer. JCO Precis Oncol 2023; 7:e2300190. [PMID: 37992258 PMCID: PMC10681406 DOI: 10.1200/po.23.00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Germline genetic testing (GGT) is now recommended for all patients diagnosed with ovarian or pancreatic cancer and for a large proportion of patients based solely on a diagnosis of colorectal or breast cancer. However, GGT is not yet recommended for all patients diagnosed with lung cancer (LC), primarily because of a lack of evidence that supports a significant frequency of identifying pathogenic germline variants (PGVs) in these patients. This study characterizes GGT results in a cohort of patients with LC. METHODS We reviewed deidentified data for 7,788 patients with GGT (2015-2022). PGV frequencies were compared to a control cohort of unaffected individuals. GGT results were stratified by genomic ancestry, history of cancer, and PGV clinical actionability per current guidelines. RESULTS Of all patients with LC, 14.9% (1,161/7,788) had PGVs. The rate was similar when restricted to patients with no cancer family history (FH) or personal history (PH) of other cancers (14.3%). PGVs were significantly enriched in BRCA2, ATM, CHEK2, BRCA1, and mismatch repair genes compared with controls. Patients of European (EUR) genomic ancestry had the highest PGV rate (18%) and variants of uncertain significance were significantly higher in patients of non-EUR genomic ancestry. Of the PGVs identified, 61.3% were in DNA damage repair (DDR) genes and 95% were clinically actionable. CONCLUSION This retrospective study shows a LC diagnosis identifies patients with a significant likelihood of having a cancer-predisposing PGV across genomic ancestries. Enrichment of PGVs in DDR genes suggests that these PGVs may contribute to LC cancer predisposition. The frequency of PGVs among patients with LC did not differ significantly according to FH or PH of other cancers.
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Affiliation(s)
| | - Jaclyn LoPiccolo
- Hematology/Oncology Division, Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | - Hayan Lee
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Renato Martins
- Hematology, Oncology and Palliative Care Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
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15
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Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn 2023; 25:411-427. [PMID: 37207865 DOI: 10.1016/j.jmoldx.2023.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023] Open
Abstract
Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.
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Affiliation(s)
- Kristy R Crooks
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Kelly D Farwell Hagman
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California
| | - Diana Mandelker
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni Santani
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; LetsGetChecked, PrivaPath Diagnostics, Dublin, Ireland; Veritas Genetics, Danvers, Massachusetts
| | - Ryan J Schmidt
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Stephen E Lincoln
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; InVitae, Bethesda, Maryland
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16
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Appelbaum PS, Burke W, Parens E, Roberts J, Berger S, Chung WK. Cases in Precision Medicine: Is There an Obligation to Return Reinterpreted Genetic Results to Former Patients? Ann Intern Med 2023; 176:563-567. [PMID: 36972543 PMCID: PMC10413009 DOI: 10.7326/m22-3682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Interpretation of many genetic test results can change over time as new data accumulate. Hence, physicians who order genetic tests may subsequently receive revised reports with important implications for patients' medical treatment-even for patients who are no longer in their care. Several of the ethical principles underlying medical practice suggest an obligation to reach out to former patients with this information. Discharging that obligation can be accomplished, at a minimum, by attempting to contact the former patient with their last known contact information.
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Affiliation(s)
- Paul S. Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center and NY State Psychiatric Institute, New York, NY
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA
| | | | - Jessica Roberts
- Health Law & Policy Institute, University of Houston Law Center, Houston, TX
| | - Sara Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY
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17
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Adam F, Fluri M, Scherz A, Rabaglio M. Occurrence of variants of unknown clinical significance in genetic testing for hereditary breast and ovarian cancer syndrome and Lynch syndrome: a literature review and analytical observational retrospective cohort study. BMC Med Genomics 2023; 16:7. [PMID: 36647026 PMCID: PMC9843935 DOI: 10.1186/s12920-023-01437-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND PURPOSE Over the last decade, the implementation of multigene panels for hereditary tumor syndrome has increased at our institution (Inselspital, University Hospital Berne, Switzerland). The aim of this study was to determine the prevalence of variants of unknown significance (VUS) in patients with suspected Lynch syndrome and suspected hereditary breast and ovarian cancer syndrome, the latter in connection with the trend toward ordering larger gene panels. RESULTS Retrospectively collected data from 1057 patients at our institution showed at least one VUS in 126 different cases (11.9%). In patients undergoing genetic testing for BRCA1/2, the prevalence of VUS was 6%. When < 10 additional genes were tested in addition to BRCA1/2, the prevalence increased to 13.8%, and 31.8% for > 10 additional genes, respectively. The gene most frequently affected with a VUS was ATM. 6% of our patients who were tested for Lynch syndrome had a VUS result in either MLH1, MSH2 or MSH6. CONCLUSIONS Our data demonstrate that panel testing statistically significantly increases VUS rates due to variants in non-BRCA genes. Good genetic counseling before and after obtaining results is therefore particularly important when conducting multigene panels to minimize patient uncertainty due to VUS results.
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Affiliation(s)
- Felicia Adam
- Medical Faculty of the University of Bern, Bern, Switzerland
| | - Muriel Fluri
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Amina Scherz
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Manuela Rabaglio
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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Ashkenazi Jewish and Other White APC I1307K Carriers Are at Higher Risk for Multiple Cancers. Cancers (Basel) 2022; 14:cancers14235875. [PMID: 36497357 PMCID: PMC9740723 DOI: 10.3390/cancers14235875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose: APC I1307K has a higher prevalence among Ashkenazi Jews (AJ), and a two-fold increased risk for colorectal cancer (CRC) compared to non-Jewish populations. We assessed CRC and extracolonic malignancies among I1307K carriers from AJ and non-AJ whites (NAW). Methods: We compared the rate of I1307K in cancer patients who underwent germline genetic testing via a multi-gene panel with healthy subjects retrieved from the gnomAD database. Cases undergoing testing were not selected and testing was undertaken through a commercial laboratory. Results: Overall, 586/7624 (7.6%) AJ with cancer carried I1307K compared to 342/4918 (6.9%) in the AJ control group (p = NS). In the NAW, 318/141,673 (0.2%) cancer patients and 73/58,918 (0.1%) controls carried the variant [OR = 1.8, (95% CI 1.41−2.35), p < 0.001]. I1307K in NAW was associated with an increased risk of CRC [OR = 1.95, (95% CI 1.39−2.73), p < 0.01], melanoma [OR = 2.54, (95% CI 1.57−3.98)], breast [females, OR = 1.73, (95% CI 1.18−2.65), p < 0.01], and prostate cancer [males, OR = 2.42, (95% CI 1.45−3.94), p < 0.01]. Among AJ, the variant increased the risk for CRC [OR = 1.67, (95% CI 1.36−2.05), p < 0.001] and renal cancer [OR = 1.64, (95% CI 1.04−2.47)]. AJ men had a higher risk for any cancer [OR = 1.32, (95% CI 1.05−1.66), p < 0.05] and melanoma [OR = 2.04, (95% CI 1.24−3.22); p < 0.05]. Conclusions: This is the most extensive study to date conducted on I1307K carriers, although it is amenable to selection bias. NAW carrying I1307K had a higher risk of any cancer and several specific cancer types, whereas AJ carrying the variant had a risk for only a few select cancers. Our data add to the research base on I1307 carriers concerning future risk management.
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Rojahn S, Hambuch T, Adrian J, Gafni E, Gileta A, Hatchell H, Johnson B, Kallman B, Karfilis K, Kautzer C, Kennemer M, Kirk L, Kvitek D, Lettes J, Macrae F, Mendez F, Paul J, Pellegrino M, Preciado R, Risinger J, Schultz M, Spurka L, Swamy S, Truty R, Usem N, Velenich A, Aradhya S. Scalable detection of technically challenging variants through modified next-generation sequencing. Mol Genet Genomic Med 2022; 10:e2072. [PMID: 36251442 PMCID: PMC9747563 DOI: 10.1002/mgg3.2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions). METHODS We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes. RESULTS Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats. CONCLUSIONS NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.
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20
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Johnson B, Ouyang K, Frank L, Truty R, Rojahn S, Morales A, Aradhya S, Nykamp K. Systematic use of phenotype evidence in clinical genetic testing reduces the frequency of variants of uncertain significance. Am J Med Genet A 2022; 188:2642-2651. [PMID: 35570716 PMCID: PMC9544038 DOI: 10.1002/ajmg.a.62779] [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: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 01/24/2023]
Abstract
Guidelines for variant interpretation include criteria for incorporating phenotype evidence, but this evidence is inconsistently applied. Systematic approaches to using phenotype evidence are needed. We developed a method for curating disease phenotypes as highly or moderately predictive of variant pathogenicity based on the frequency of their association with disease-causing variants. To evaluate this method's accuracy, we retrospectively reviewed variants with clinical classifications that had evolved from uncertain to definitive in genes associated with curated predictive phenotypes. To demonstrate the clinical validity and utility of this approach, we compared variant classifications determined with and without predictive phenotype evidence. The curation method was accurate for 93%-98% of eligible variants. Among variants interpreted using highly predictive phenotype evidence, the percentage classified as pathogenic or likely pathogenic was 80%, compared with 46%-54% had the evidence not been used. Positive results among individuals harboring variants with highly predictive phenotype-guided interpretations would have been missed in 25%-37% of diagnostic tests and 39%-50% of carrier screens had other approaches to phenotype evidence been used. In summary, predictive phenotype evidence associated with specific curated genes can be systematically incorporated into variant interpretation to reduce uncertainty and increase the clinical utility of genetic testing.
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Affiliation(s)
| | | | | | | | | | - Ana Morales
- Invitae CorporationSan FranciscoCaliforniaUSA
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21
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Dellefave-Castillo LM, Cirino AL, Callis TE, Esplin ED, Garcia J, Hatchell KE, Johnson B, Morales A, Regalado E, Rojahn S, Vatta M, Nussbaum RL, McNally EM. Assessment of the Diagnostic Yield of Combined Cardiomyopathy and Arrhythmia Genetic Testing. JAMA Cardiol 2022; 7:966-974. [PMID: 35947370 PMCID: PMC9366660 DOI: 10.1001/jamacardio.2022.2455] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Genetic testing can guide management of both cardiomyopathies and arrhythmias, but cost, yield, and uncertain results can be barriers to its use. It is unknown whether combined disease testing can improve diagnostic yield and clinical utility for patients with a suspected genetic cardiomyopathy or arrhythmia. Objective To evaluate the diagnostic yield and clinical management implications of combined cardiomyopathy and arrhythmia genetic testing through a no-charge, sponsored program for patients with a suspected genetic cardiomyopathy or arrhythmia. Design, Setting, and Participants This cohort study involved a retrospective review of DNA sequencing results for cardiomyopathy- and arrhythmia-associated genes. The study included 4782 patients with a suspected genetic cardiomyopathy or arrhythmia who were referred for genetic testing by 1203 clinicians; all patients participated in a no-charge, sponsored genetic testing program for cases of suspected genetic cardiomyopathy and arrhythmia at a single testing site from July 12, 2019, through July 9, 2020. Main Outcomes and Measures Positive gene findings from combined cardiomyopathy and arrhythmia testing were compared with findings from smaller subtype-specific gene panels and clinician-provided diagnoses. Results Among 4782 patients (mean [SD] age, 40.5 [21.3] years; 2551 male [53.3%]) who received genetic testing, 39 patients (0.8%) were Ashkenazi Jewish, 113 (2.4%) were Asian, 571 (11.9%) were Black or African American, 375 (7.8%) were Hispanic, 2866 (59.9%) were White, 240 (5.0%) were of multiple races and/or ethnicities, 138 (2.9%) were of other races and/or ethnicities, and 440 (9.2%) were of unknown race and/or ethnicity. A positive result (molecular diagnosis) was confirmed in 954 of 4782 patients (19.9%). Of those, 630 patients with positive results (66.0%) had the potential to inform clinical management associated with adverse clinical outcomes, increased arrhythmia risk, or targeted therapies. Combined cardiomyopathy and arrhythmia gene panel testing identified clinically relevant variants for 1 in 5 patients suspected of having a genetic cardiomyopathy or arrhythmia. If only patients with a high suspicion of genetic cardiomyopathy or arrhythmia had been tested, at least 137 positive results (14.4%) would have been missed. If testing had been restricted to panels associated with the clinician-provided diagnostic indications, 75 of 689 positive results (10.9%) would have been missed; 27 of 75 findings (36.0%) gained through combined testing involved a cardiomyopathy indication with an arrhythmia genetic finding or vice versa. Cascade testing of family members yielded 402 of 958 positive results (42.0%). Overall, 2446 of 4782 patients (51.2%) had only variants of uncertain significance. Patients referred for arrhythmogenic cardiomyopathy had the lowest rate of variants of uncertain significance (81 of 176 patients [46.0%]), and patients referred for catecholaminergic polymorphic ventricular tachycardia had the highest rate (48 of 76 patients [63.2%]). Conclusions and Relevance In this study, comprehensive genetic testing for cardiomyopathies and arrhythmias revealed diagnoses that would have been missed by disease-specific testing. In addition, comprehensive testing provided diagnostic and prognostic information that could have potentially changed management and monitoring strategies for patients and their family members. These results suggest that this improved diagnostic yield may outweigh the burden of uncertain results.
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Affiliation(s)
- Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Allison L Cirino
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts.,Institute of Health Professions, Massachusetts General Hospital, Boston
| | | | | | - John Garcia
- Invitae Corporation, San Francisco, California
| | | | | | - Ana Morales
- Invitae Corporation, San Francisco, California
| | | | | | | | | | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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22
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Nunziato M, Di Maggio F, Pensabene M, Esposito MV, Starnone F, De Angelis C, Calabrese A, D’Aiuto M, Botti G, De Placido S, D’Argenio V, Salvatore F. Multi-gene panel testing increases germline predisposing mutations’ detection in a cohort of breast/ovarian cancer patients from Southern Italy. Front Med (Lausanne) 2022; 9:894358. [PMID: 36035419 PMCID: PMC9403188 DOI: 10.3389/fmed.2022.894358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is the most common neoplasia in females worldwide, about 10% being hereditary/familial and due to DNA variants in cancer-predisposing genes, such as the highly penetrant BRCA1/BRCA2 genes. However, their variants explain up to 25% of the suspected hereditary/familial cases. The availability of NGS methodologies has prompted research in this field. With the aim to improve the diagnostic sensitivity of molecular testing, a custom designed panel of 44 genes, including also non-coding regions and 5’ and 3’ UTR regions, was set up. Here, are reported the results obtained in a cohort of 64 patients, including also few males, from Southern Italy. All patients had a positive personal and/or familial history for breast and other cancers, but tested negative to routine BRCA analysis. After obtaining their written informed consent, a genomic DNA sample/patient was used to obtain an enriched DNA library, then analyzed by NGS. Sequencing data analysis allowed the identification of pathogenic variants in 12 of tested patients (19%). Interestingly, MUTYH was the most frequently altered gene, followed by RNASEL, ATM, MSH6, MRE11A, and PALB2 genes. The reported resultsreinforce the need for enlarged molecular testing beyond BRCA genes, at least in patients with a personal and familial history, strongly suggestive for a hereditary/familial form. This gives also a hint to pursue more specific precision oncology therapy.
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Affiliation(s)
- Marcella Nunziato
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Federica Di Maggio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Matilde Pensabene
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Maria Valeria Esposito
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Flavio Starnone
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Alessandra Calabrese
- Division of Breast Surgery, Department of Breast Disease, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Massimiliano D’Aiuto
- Clinica Villa Fiorita, Aversa, Italy
- Division of Breast Oncology, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Gerardo Botti
- Scientific Directorate, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Valeria D’Argenio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy
- *Correspondence: Valeria D’Argenio,
| | - Francesco Salvatore
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Francesco Salvatore,
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23
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Heald B, Mokhtary S, Nielsen SM, Rojahn S, Yang S, Michalski ST, Esplin ED. Unexpected actionable genetic variants revealed by multigene panel testing of patients with uterine cancer. Gynecol Oncol 2022; 166:344-350. [PMID: 35691755 DOI: 10.1016/j.ygyno.2022.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/09/2022] [Accepted: 05/28/2022] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Hereditary uterine cancer (UC) is traditionally associated with pathogenic/likely pathogenic germline variants (PGVs) in Lynch syndrome genes or PTEN; however, growing evidence supports a role for other genes that may reveal new clinical management options. In this study we assessed the prevalence and potential clinical impact of PGVs identified in UC patients referred for comprehensive germline genetic testing that combined testing for Lynch syndrome, PTEN, and other cancer predisposition genes. METHODS Prevalence of PGVs in patients referred to a single clinical lab for germline genetic testing with an indication of uterine or endometrial cancer were retrospectively assessed and compared by syndrome type, patient age at testing, and self-reported ancestry. Potential clinical actionability of PGVs was based on established guidelines for clinical management, targeted therapies, and clinical trial eligibility. RESULTS PGVs were detected in 13.6% of the cohort (880/6490). PGVs were most frequently observed in Lynch syndrome genes (60.4%) and PTEN (1.5%), with 38.1% in another cancer predisposition gene (i.e., CHEK2, BRCA1/BRCA2). PGV prevalence was similar for patients <50 years and those ≥50 years (15.1% vs 13.2%). Nearly all PGVs (97.2%) were associated with guideline-recommended management, including cascade testing; 60.5% were associated with FDA-approved therapies; and 35.2% were associated with clinical trials. CONCLUSIONS Focusing germline testing on Lynch syndrome genes and PTEN and limiting testing to patients <50 years of age at diagnosis may overlook a substantial proportion of UC patients who harbor actionable PGVs. Universal comprehensive genetic testing of UC patients could benefit many patients and at-risk family members.
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Affiliation(s)
- Brandie Heald
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Sara Mokhtary
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Shan Yang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
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24
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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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/13/2022] [Accepted: 06/15/2022] [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
| | | | | | | | | | | | | | | | - 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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25
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Quinn J, Modell V, Johnson B, Poll S, Aradhya S, Orange JS, Modell F. Global Expansion of Jeffrey's Insights: Jeffrey Modell Foundation's Genetic Sequencing Program for Primary Immunodeficiency. Front Immunol 2022; 13:906540. [PMID: 35757720 PMCID: PMC9226364 DOI: 10.3389/fimmu.2022.906540] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic disorders that impair the immune system, known as Primary Immunodeficiencies (PI), include over 450 single-gene inborn errors of immunity. Timely and appropriate diagnosis and treatment is vital to quality of life (QOL) and sometimes survival, as patients are susceptible to frequent, persistent, severe, and sometimes life-threatening infections or autoimmunity. Suspected PI patients that do not have a genetic diagnosis often endure a prolonged, onerous, inefficient, and expensive experience, known as a diagnostic odyssey. The resulting diagnostic delay prohibits proper disease management and treatment, causing unnecessary distress and diminished QOL. Next-generation sequencing (NGS) offers relief from the distress of the diagnostic odyssey, but because of cost and barriers to access, it is regularly unobtainable. The Jeffrey Modell Foundation (JMF) introduced "Jeffrey's Insights", a no-charge genetic sequencing pilot program, in January 2019 for patients within the Jeffrey Modell Centers Network (JMCN) with an underlying PI, but no genetic diagnosis. Building on the success of the pilot program, JMF expanded it globally to more than 400 Centers in the JMCN in early 2020. The most current version of Invitae's PI Panel available was used for this program. All participating clinicians were invited to complete a brief questionnaire assessing prior impediments to access and post-sequencing alterations in disease management and treatment. A total of 1,398 patients were tested, with 20.3% receiving a molecular diagnosis and many more receiving helpful diagnostic leads. Results obtained from genetic sequencing led to an alteration of clinical diagnosis, disease management, treatment, and genetic counseling in 39%, 38%, 35%, and 53% of patients, respectively. The global expansion of this program further underscores the crucial need for NGS for PI, along with its efficiency and potential cost savings. The results of this program to date further define rationale for the availability of comprehensive diagnostic NGS for patients with PI when requisitioned by an expert immunologist.
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Affiliation(s)
- Jessica Quinn
- Jeffrey Modell Foundation, New York, NY, United States
| | - Vicki Modell
- Jeffrey Modell Foundation, New York, NY, United States
| | | | - Sarah Poll
- Invitae, San Francisco, CA, United States
| | | | | | - Fred Modell
- Jeffrey Modell Foundation, New York, NY, United States
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26
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Schmidlen TJ, Bristow SL, Hatchell KE, Esplin ED, Nussbaum RL, Haverfield EV. The Impact of Proband Indication for Genetic Testing on the Uptake of Cascade Testing Among Relatives. Front Genet 2022; 13:867226. [PMID: 35783293 PMCID: PMC9243226 DOI: 10.3389/fgene.2022.867226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although multiple factors can influence the uptake of cascade genetic testing, the impact of proband indication has not been studied. We performed a retrospective, cross-sectional study comparing cascade genetic testing rates among relatives of probands who received either diagnostic germline testing or non-indication-based proactive screening via next-generation sequencing (NGS)-based multigene panels for hereditary cancer syndromes (HCS) and/or familial hypercholesterolemia (FH). The proportion of probands with a medically actionable (positive) finding were calculated based on genes associated with Centers for Disease Control and Prevention (CDC) Tier 1 conditions, HCS genes, and FH genes. Among probands with a positive finding, cascade testing rates and influencing factors were assessed. A total of 270,715 probands were eligible for inclusion in the study (diagnostic n = 254,281,93.9%; proactive n = 16,434, 6.1%). A positive result in a gene associated with a CDC Tier 1 condition was identified in 10,520 diagnostic probands (4.1%) and 337 proactive probands (2.1%), leading to cascade testing among families of 3,305 diagnostic probands (31.4%) and 36 proactive probands (10.7%) (p < 0.0001). A positive result in an HCS gene was returned to 23,272 diagnostic probands (9.4%) and 970 proactive probands (6.1%), leading to cascade testing among families of 6,611 diagnostic probands (28.4%) and 89 proactive probands (9.2%) (p < 0.0001). Cascade testing due to a positive result in an HCS gene was more commonly pursued when the diagnostic proband was White, had a finding in a gene associated with a CDC Tier 1 condition, or had a personal history of cancer, or when the proactive proband was female. A positive result in an FH gene was returned to 1,647 diagnostic probands (25.3%) and 67 proactive probands (0.62%), leading to cascade testing among families of 360 diagnostic probands (21.9%) and 4 proactive probands (6.0%) (p < 0.01). Consistently higher rates of cascade testing among families of diagnostic probands may be due to a perceived urgency because of personal or family history of disease. Due to the proven clinical benefit of cascade testing, further research on obstacles to systematic implementation and uptake of testing for relatives of any proband with a medically actionable variant is warranted.
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Appelbaum PS, Burke W, Parens E, Zeevi DA, Arbour L, Garrison NA, Bonham VL, Chung WK. Is there a way to reduce the inequity in variant interpretation on the basis of ancestry? Am J Hum Genet 2022; 109:981-988. [PMID: 35659933 PMCID: PMC9247826 DOI: 10.1016/j.ajhg.2022.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The underrepresentation of non-European ancestry groups in current genomic databases complicates interpretation of their genetic test results, yielding a much higher prevalence of variants of uncertain significance (VUSs). Such VUS findings can frustrate the goals of genetic testing, create anxiety in patients, and lead to unnecessary medical interventions. Approaches to addressing underrepresentation of people with genetic ancestries other than European are being undertaken by broad-based recruitment efforts. However, some underrepresented groups have concerns that might preclude participation in such efforts. We describe here two initiatives aimed at meeting the needs of underrepresented ancestry groups in genomic datasets. The two communities, the Sephardi Jewish community in New York and First Peoples of Canada, have very different concerns about contributing to genomic research and datasets. Sephardi concerns focus on the possible negative effects of genetic findings on the marriage prospects of family members. Canadian Indigenous populations seek control over the research uses to which their genetic data would be put. Both cases involve targeted efforts to respond to the groups' concerns; these efforts include governance models aimed at ensuring that the data are used primarily to inform clinical test analyses and at achieving successful engagement and participation of community members. We suggest that these initiatives could provide models for other ancestral groups seeking to improve the accuracy and utility of clinical genetic testing while respecting the underlying preferences and values of community members with regard to the use of their genetic data.
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Affiliation(s)
- Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, and New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Erik Parens
- The Hastings Center, Garrison, NY 10524, USA
| | - David A Zeevi
- Dor Yeshorim, The Committee for the Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada; BC Children's Hospital Research Institute, Victoria, BC V8P 5C2, Canada
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095; Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA 9009, USA5
| | - Vence L Bonham
- Social and Behavioral Research Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
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28
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Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLB, Witkowski L, Zouk H, Weng C, Leppig KA, Sleiman PMA, Hakonarson H, Williams MS, Luo Y, Jarvik GP, Green RC, Chung WK, Gharavi AG, Lennon NJ, Rehm HL, Gibbs RA, Peterson JF, Roden DM, Wiesner GL, Denny JC. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. JAMA Oncol 2022; 8:835-844. [PMID: 35446370 PMCID: PMC9026237 DOI: 10.1001/jamaoncol.2022.0373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Knowledge about the spectrum of diseases associated with hereditary cancer syndromes may improve disease diagnosis and management for patients and help to identify high-risk individuals. Objective To identify phenotypes associated with hereditary cancer genes through a phenome-wide association study. Design, Setting, and Participants This phenome-wide association study used health data from participants in 3 cohorts. The Electronic Medical Records and Genomics Sequencing (eMERGEseq) data set recruited predominantly healthy individuals from 10 US medical centers from July 16, 2016, through February 18, 2018, with a mean follow-up through electronic health records (EHRs) of 12.7 (7.4) years. The UK Biobank (UKB) cohort recruited participants from March 15, 2006, through August 1, 2010, with a mean (SD) follow-up of 12.4 (1.0) years. The Hereditary Cancer Registry (HCR) recruited patients undergoing clinical genetic testing at Vanderbilt University Medical Center from May 1, 2012, through December 31, 2019, with a mean (SD) follow-up through EHRs of 8.8 (6.5) years. Exposures Germline variants in 23 hereditary cancer genes. Pathogenic and likely pathogenic variants for each gene were aggregated for association analyses. Main Outcomes and Measures Phenotypes in the eMERGEseq and HCR cohorts were derived from the linked EHRs. Phenotypes in UKB were from multiple sources of health-related data. Results A total of 214 020 participants were identified, including 23 544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12 611 women [53.6%]), 187 234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104 055 [55.6%] women), and 3242 in the HCR cohort (mean [SD] age, 52.5 [15.5] years; 2851 [87.9%] women). All 38 established gene-cancer associations were replicated, and 19 new associations were identified. These included the following 7 associations with neoplasms: CHEK2 with leukemia (odds ratio [OR], 3.81 [95% CI, 2.64-5.48]) and plasma cell neoplasms (OR, 3.12 [95% CI, 1.84-5.28]), ATM with gastric cancer (OR, 4.27 [95% CI, 2.35-7.44]) and pancreatic cancer (OR, 4.44 [95% CI, 2.66-7.40]), MUTYH (biallelic) with kidney cancer (OR, 32.28 [95% CI, 6.40-162.73]), MSH6 with bladder cancer (OR, 5.63 [95% CI, 2.75-11.49]), and APC with benign liver/intrahepatic bile duct tumors (OR, 52.01 [95% CI, 14.29-189.29]). The remaining 12 associations with nonneoplastic diseases included BRCA1/2 with ovarian cysts (OR, 3.15 [95% CI, 2.22-4.46] and 3.12 [95% CI, 2.36-4.12], respectively), MEN1 with acute pancreatitis (OR, 33.45 [95% CI, 9.25-121.02]), APC with gastritis and duodenitis (OR, 4.66 [95% CI, 2.61-8.33]), and PTEN with chronic gastritis (OR, 15.68 [95% CI, 6.01-40.92]). Conclusions and Relevance The findings of this genetic association study analyzing the EHRs of 3 large cohorts suggest that these new phenotypes associated with hereditary cancer genes may facilitate early detection and better management of cancers. This study highlights the potential benefits of using EHR data in genomic medicine.
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Affiliation(s)
- Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa A Bastarache
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ran Tao
- Department of Biostatistics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Scott Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Justin D Andujar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Sarah T Bland
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle
| | - Siddharth Pratap
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee
| | - Ayorinde Cooley
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Emma Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carrie L Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Leora Witkowski
- Centre Universitaire de Santé McGill, McGill University Health Centre, Montreal, Quebec, Canada
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Kathleen A Leppig
- Genetic Services and Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
| | - Robert C Green
- Brigham and Women's Hospital, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Heidi L Rehm
- Medical & Population Genetics Program and Genomics Platform, Broad Institute of MIT and Harvard Cambridge, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee.,Divisions of Cardiovascular Medicine and Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Lieberman KV, Chang AR, Block GA, Robinson K, Bristow SL, Morales A, Mitchell A, McCalley S, McKay J, Pollak MR, Aradhya S, Warady BA. The KIDNEYCODE Program: Diagnostic Yield and Clinical Features of Individuals with CKD. KIDNEY360 2022; 3:900-909. [PMID: 36128480 PMCID: PMC9438426 DOI: 10.34067/kid.0004162021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/14/2022] [Indexed: 01/10/2023]
Abstract
Background Despite increasing recognition that CKD may have underlyi ng genetic causes, genetic testing remains limited. This study evaluated the diagnostic yield and phenotypic spectrum of CKD in individuals tested through the KIDNEYCODE sponsored genetic testing program. Methods Unrelated individuals who received panel testing (17 genes) through the KIDNEYCODE sponsored genetic testing program were included. Individuals had to meet at least one of the following eligibility criteria: eGFR ≤90 ml/min per 1.73m2 and hematuria or a family history of kidney disease; or suspected/biopsy-confirmed Alport syndrome or FSGS in tested individuals or relatives. Results Among 859 individuals, 234 (27%) had molecular diagnoses in genes associated with Alport syndrome (n=209), FSGS (n=12), polycystic kidney disease (n=6), and other disorders (n=8). Among those with positive findings in a COL4A gene, the majority were in COL4A5 (n=157, 72 hemizygous male and 85 heterozygous female individuals). A positive family history of CKD, regardless of whether clinical features were reported, was more predictive of a positive finding than was the presence of clinical features alone. For the 248 individuals who had kidney biopsies, a molecular diagnosis was returned for 49 individuals (20%). Most (n=41) individuals had a molecular diagnosis in a COL4A gene, 25 of whom had a previous Alport syndrome clinical diagnosis, and the remaining 16 had previous clinical diagnoses including FSGS (n=2), thin basement membrane disease (n=9), and hematuria (n=1). In total, 491 individuals had a previous clinical diagnosis, 148 (30%) of whom received a molecular diagnosis, the majority (89%, n=131) of which were concordant. Conclusions Although skewed to identify individuals with Alport syndrome, these findings support the need to improve access to genetic testing for patients with CKD-particularly in the context of family history of kidney disease, hematuria, and hearing loss.
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Affiliation(s)
- Kenneth V Lieberman
- Division of Pediatric Nephrology, Joseph M. Sanzari Children's Hospital of the Hackensack Meridian Health Network, Hackensack, New Jersey
| | - Alexander R Chang
- Division of Nephrology, Geisinger Medical Center, Danville, Pennsylvania
| | - Geoffrey A Block
- Division of Clinical Research, Reata Pharmaceuticals, Inc., Plano, Texas
| | | | - Sara L Bristow
- Department of Clinical Genomics, Invitae, San Francisco, California
- Department of Medical Affairs, Invitae, San Francisco, California
| | - Ana Morales
- Department of Clinical Genomics, Invitae, San Francisco, California
- Department of Medical Affairs, Invitae, San Francisco, California
| | - Asia Mitchell
- Department of Clinical Genomics, Invitae, San Francisco, California
- Department of Medical Affairs, Invitae, San Francisco, California
| | - Stephen McCalley
- Division of Medical Affairs, Reata Pharmaceuticals, Inc., Plano, Texas
| | - Jim McKay
- Division of Medical Affairs, Reata Pharmaceuticals, Inc., Plano, Texas
| | - Martin R Pollak
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Swaroop Aradhya
- Department of Clinical Genomics, Invitae, San Francisco, California
- Department of Medical Affairs, Invitae, San Francisco, California
| | - Bradley A Warady
- Division of Pediatric Nephrology, Children's Mercy Kansas City, Kansas City, Missouri
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30
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Kwong A, Ho CYS, Shin VY, Au CH, Luk WP, Fung LH, Chan TL, Chan KKL, Ngan HYS, Ma ESK. Germline mutations in Chinese ovarian cancer with or without breast cancer. Mol Genet Genomic Med 2022; 10:e1940. [PMID: 35608067 PMCID: PMC9266594 DOI: 10.1002/mgg3.1940] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/08/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ovarian and breast cancers are known to have significant genetic components. Considering the differences in the mutation spectrum across ethnicity, it is important to identify hereditary breast and ovarian cancer (HBOC) genes mutation in Chinese for clinical management. METHODS Two cohorts of 451 patients with ovarian cancer only (OV) and 93 patients with both breast and ovarian (BROV) cancers were initially screened for BRCA1, BRCA2, TP53, and PTEN. 109 OV and 43 BROV patients with extensive clinical risk and were being tested negative, were then further characterized by 30-gene panel analysis. RESULTS Pathogenic BRCA1/2 variants were identified in 45 OV patients and 33 BROV patients, giving a prevalence of 10% and 35.5%, respectively. After the extended screening, mutations in other HBOC genes were identified in an additional 12.8% (14/109) of the OV cohort and 14% (6/43) in the BROV cohort. The most commonly mutated genes in the OV cohort were MSH2 (4.6%) while in the BROV cohort were MSH2 (4.7%) and PALB2 (4.7%). With this extended multigene testing strategy, pathogenic mutations were detected in 12.8% of OV patients (BRCAs: 10%; additional genes: 12.8%) and 40.9% (BRCAs: 35.5%; additional genes: 14%) of BROV patients. CONCLUSION Extended characterization of the contributions of HBOC genes to OV and BROV patients has significant impacts on further management in patients and their families, expanding the screening net for more asymptomatic individuals.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Pofulam, Hong Kong SAR.,Department of Surgery, University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Surgery, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR.,Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR
| | - Cecilia Yuen Sze Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Chun Hang Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Wing Pan Luk
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Ling Hiu Fung
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Karen Kar Loen Chan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Hextan Yuen Sheung Ngan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
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31
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Espinel W, Champine M, Hampel H, Jeter J, Sweet K, Pilarski R, Pearlman R, Shane K, Brock P, Westman JA, Kipnis L, Sotelo J, Chittenden A, Culver S, Stopfer JE, Schneider KA, Sacca R, Koeller DR, Gaonkar S, Vaccari E, Kane S, Michalski ST, Yang S, Nielsen SM, Bristow SL, Lincoln SE, Nussbaum RL, Esplin ED. Clinical Impact of Pathogenic Variants in DNA Damage Repair Genes beyond BRCA1 and BRCA2 in Breast and Ovarian Cancer Patients. Cancers (Basel) 2022; 14:2426. [PMID: 35626031 PMCID: PMC9139211 DOI: 10.3390/cancers14102426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Consensus guidelines for hereditary breast and ovarian cancer include management recommendations for pathogenic/likely pathogenic (P/LP) variants in ATM, CHEK2, PALB2, and other DNA damage repair (DDR) genes beyond BRCA1 or BRCA2. We report on clinical management decisions across three academic medical centers resulting from P/LP findings in DDR genes in breast/ovarian cancer patients. Among 2184 patients, 156 (7.1%) carried a P/LP variant in a DDR gene. Clinical follow-up information was available for 101/156 (64.7%) patients. Genetic test result-based management recommendations were made for 57.8% (n = 59) of patients and for 64.7% (n = 66) of patients' family members. Most recommendations were made for moderate-to-high risk genes and were consistent with guidelines. Sixty-six percent of patients (n = 39/59) implemented recommendations. This study suggests that P/LP variants in DDR genes beyond BRCA1 and BRCA2 can change clinical management recommendations for patients and their family members, facilitate identification of new at-risk carriers, and impact treatment decisions. Additional efforts are needed to improve the implementation rates of genetic-testing-based management recommendations for patients and their family members.
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Affiliation(s)
- Whitney Espinel
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (W.E.); (M.C.)
| | - Marjan Champine
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (W.E.); (M.C.)
| | - Heather Hampel
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Joanne Jeter
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Kevin Sweet
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Robert Pilarski
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Rachel Pearlman
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Kate Shane
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Pamela Brock
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Judith A. Westman
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Lindsay Kipnis
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Jilliane Sotelo
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Anu Chittenden
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Samantha Culver
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Jill E. Stopfer
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Katherine A. Schneider
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Rosalba Sacca
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Diane R. Koeller
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Shraddha Gaonkar
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Erica Vaccari
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Sarah Kane
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Scott T. Michalski
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Shan Yang
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Sarah M. Nielsen
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Sara L. Bristow
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Stephen E. Lincoln
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Robert L. Nussbaum
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Edward D. Esplin
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
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Czajkowski D, Szmyd R, Gee HE. Impact of DNA damage response defects in cancer cells on response to immunotherapy and radiotherapy. J Med Imaging Radiat Oncol 2022; 66:546-559. [PMID: 35460184 PMCID: PMC9321602 DOI: 10.1111/1754-9485.13413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022]
Abstract
The DNA damage response (DDR) is a complex set of downstream pathways triggered in response to DNA damage to maintain genomic stability. Many tumours exhibit mutations which inactivate components of the DDR, making them prone to the accumulation of DNA defects. These can both facilitate the development of tumours and provide potential targets for novel therapeutic interventions. The inhibition of the DDR has been shown to induce radiosensitivity in certain cancers, rendering them susceptible to treatment with radiotherapy and improving the therapeutic window. Moreover, DDR defects are a strong predictor of patient response to immune checkpoint inhibition (ICI). The ability to target the DDR selectively has the potential to expand the tumour neoantigen repertoire, thus increasing tumour immunogenicity and facilitating a CD8+ T and NK cell response against cancer cells. Combinatorial approaches, which seek to integrate DDR inhibition with radiotherapy and immunotherapy, have shown promise in early trials. Further studies are necessary to understand these synergies and establish reliable biomarkers.
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Affiliation(s)
| | - Radosław Szmyd
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
| | - Harriet E Gee
- University of Sydney, Sydney, New South Wales, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
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Ramos-Dávila EM, Garza-Garza LA, Villafuerte-de la Cruz R, Aguilar-Y-Mendez D, Morales-Garza HJ, Garza-Leon M, Ruiz-Lozano RE, Ancona-Lezama D. Novel RB1 germline mutation in a healthy man. Ophthalmic Genet 2022; 43:561-566. [PMID: 35410579 DOI: 10.1080/13816810.2022.2062390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Retinoblastoma (Rb) most frequently presents as a unilateral sporadic disease up to 40% of cases, however, arise from a monoallelic germline pathogenic variant. Only 10% of the germline mutations are inherited, and high penetrance is seen in up to 90% of these cases. As an effort to optimize counseling and screening, mutations are classified according to inheritance patterns. However, RB1 spectrum is highly heterogeneous, and information for unaffected carriers remains scarce. MATERIALS AND METHODS The Mexican family of a 5-month-old patient diagnosed with Rb was studied. The family consisted of five individuals (father, mother, and three siblings). Genetic testing using a next-generation sequencing assay targeting RB1 with oligonucleotide baits designed to capture its exons and 20 bases flanking intronic sequences was performed in every family member. Clinical history and a complete ophthalmological examination (best-corrected visual acuity, slit-lamp biomicroscopy, macular optical coherence tomography, fundus autofluorescence, optical coherence tomography angiography, and electrophysiological studies) were performed in members testing positive to RB1 mutation. RESULTS The father and her five-month-old daughter tested positive for a non-synonymous RB1 mutation c.459del (p.Lys154Serfs*21). The girl presented with bilateral retinoblastoma, successfully treated with cryotherapy and intravenous chemotherapy. The father had no relevant findings on imaging studies or ophthalmologic evaluation. CONCLUSIONS This report describes a rare case of a novel low-penetrance RB1 germline mutation. Long-term follow-up of the father will include periodic evaluation of the eyes and orbits, and surveillance for systemic sarcoma and secondary malignancies. Implications for unaffected individuals need to be further studied.
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Affiliation(s)
- Eugenia M Ramos-Dávila
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Lucas A Garza-Garza
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Rocío Villafuerte-de la Cruz
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Dione Aguilar-Y-Mendez
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Héctor J Morales-Garza
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Manuel Garza-Leon
- Departamento de Ciencias Clínicas de la División de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, México
| | - Raul E Ruiz-Lozano
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - David Ancona-Lezama
- Ocular Oncology Service, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
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Jasiewicz A, Rudnicka H, Kluźniak W, Gronwald W, Kluz T, Cybulski C, Jakubowska A, Lubiński J, Gronwald J. Frequency of BRCA1 and BRCA2 mutations in ovarian cancer patients in South-East Poland. Hered Cancer Clin Pract 2022; 20:12. [PMID: 35382848 PMCID: PMC8981954 DOI: 10.1186/s13053-022-00219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/16/2022] [Indexed: 12/01/2022] Open
Abstract
Background Mutations in BRCA1 and BRCA2 genes are well-established risk factors of breast and ovarian cancer. In our former study, we observed that approximately 6% of unselected ovarian cancer patients in the region of Podkarpacie (South-East Poland) carry BRCA1 causative founder variants, which is significantly lower than in other regions of Poland. Therefore, it is deeply justified to do research based on the sequencing of whole BRCA1 and BRCA2 genes. Methods We examined 158 consecutive unselected cases of ovarian cancer patients from the region of Podkarpacie. We performed BRCA1 and BRCA2 genes Next-Generation Sequencing study in all cases. Results Altogether, in 18 of 158 (11.4%) ovarian cancer patients with BRCA1 or BRCA2 pathogenic mutations were found. BRCA1 pathogenic variants were detected in 11 of the 158 (7.0%) ovarian cancer cases. 10 of 11 (91%) detected BRCA1 mutations were founder mutations, detectable with the standard test used in Poland. BRCA2 pathogenic variants were found in 7 of the 158 (4.4%) cases. No BRCA2 pathogenic variants were founder mutations. The median age of patients at the diagnosis of the 18 hereditary ovarian cancers was 57.5 years. Conclusions The frequency of BRCA1 or BRCA2 gene mutation carriers among patients with ovarian cancer from the Podkarpacie region is comparable to other regions of Poland. However, a significantly higher percentage of BRCA2 gene mutations was observed, that were not detectable with a standard test for detection of founder mutations. Diagnostics based only on testing the BRCA1/2 Polish founder mutations is characterized by relatively low sensitivity in the case of ovarian cancer patients from South-East Poland and should be supplemented by NGS study, in particular of the BRCA2 gene.
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Affiliation(s)
- Andrzej Jasiewicz
- Laboratory of Clinical Genetics, Molecular Biology of Cancer and Translational Research, Faculty of Medicine, Rzeszow University, 1a Warzywna St, 35-310, Rzeszów, Poland.,Genetic Counseling Center, Subcarpatian Oncological Hospital, 18 Bielawskiego St, 36-200, Brzozów, Poland
| | - Helena Rudnicka
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Wojciech Kluźniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Wojciech Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Tomasz Kluz
- Department of Obstetrics and Gynecology, Faculty of Medicine, Fryderyk Chopin University Hospital, Rzeszow University, No 1, 2 Szopena St, 35-055, Rzeszów, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 1 Unit Lubelskiej St, 71-252, Szczecin, Poland.
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Uson PLS, Riegert-Johnson D, Boardman L, Kisiel J, Mountjoy L, Patel N, Lizaola-Mayo B, Borad MJ, Ahn D, Sonbol MB, Jones J, Leighton JA, Gurudu S, Singh H, Klint M, Kunze KL, Golafshar MA, Esplin ED, Nussbaum RL, Stewart AK, Bekaii-Saab TS, Jewel Samadder N. Germline Cancer Susceptibility Gene Testing in Unselected Patients With Colorectal Adenocarcinoma: A Multicenter Prospective Study. Clin Gastroenterol Hepatol 2022; 20:e508-e528. [PMID: 33857637 DOI: 10.1016/j.cgh.2021.04.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Hereditary factors play a role in the development of colorectal cancer (CRC). Identification of germline predisposition can have implications on treatment and cancer prevention. This study aimed to determine the prevalence of pathogenic germline variants (PGVs) in CRC patients using a universal testing approach, association with clinical outcomes, and the uptake of family variant testing. METHODS We performed a prospective multisite study of germline sequencing using a more than 80-gene next-generation sequencing platform among CRC patients (not selected for age or family history) receiving care at Mayo Clinic Cancer Centers between April 1, 2018, and March 31, 2020. RESULTS Of 361 patients, the median age was 57 years (SD, 12.4 y), 43.5% were female, 82% were white, and 38.2% had stage IV disease. PGVs were found in 15.5% (n = 56) of patients, including 44 in moderate- and high-penetrance cancer susceptibility genes. Thirty-four (9.4%) patients had incremental clinically actionable findings that would not have been detected by practice guideline criteria or a CRC-specific gene panel. Only younger age at diagnosis was associated with the presence of PGVs (odds ratio, 1.99; 95% CI, 1.12-3.56). After a median follow-up period of 20.7 months, no differences in overall survival were seen between those with or without a PGV (P = .2). Eleven percent of patients had modifications in their treatment based on genetic findings. Family cascade testing was low (16%). CONCLUSIONS Universal multigene panel testing in CRC was associated with a modest, but significant, detection of heritable mutations over guideline-based testing. One in 10 patients had changes in their management based on test results. Uptake of cascade family testing was low, which is a concerning observation that warrants further study.
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Affiliation(s)
| | - Douglas Riegert-Johnson
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Jacksonville, Florida; Department of Clinical Genomics, Mayo Clinic; Center for Individualized Medicine, Mayo Clinic
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - John Kisiel
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Neej Patel
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Blanca Lizaola-Mayo
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Mitesh J Borad
- Division of Hematology and Medical Oncology; Center for Individualized Medicine, Mayo Clinic
| | - Daniel Ahn
- Division of Hematology and Medical Oncology
| | | | - Jeremy Jones
- Division of Hematology and Medical Oncology, Department of Medicine, Mayo Clinic, Jacksonville, Florida
| | - Jonathan A Leighton
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Suryakanth Gurudu
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Harminder Singh
- Department of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Katie L Kunze
- Department of Health Services Research, Mayo Clinic, Phoenix, Arizona
| | | | | | | | - A Keith Stewart
- Division of Hematology and Medical Oncology; Department of Clinical Genomics, Mayo Clinic; Center for Individualized Medicine, Mayo Clinic
| | | | - Niloy Jewel Samadder
- Department of Clinical Genomics, Mayo Clinic; Center for Individualized Medicine, Mayo Clinic; Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona.
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36
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Ramamurthy C, Nassar AH, Abou Alaiwi S, Adib E, Akl EW, Yang S, Esplin ED, Liss MA, Tomlinson GE, Sonpavde GP. Prevalence of pathogenic germline cancer risk variants in testicular cancer patients: Identifying high risk groups. Urol Oncol 2022; 40:113.e9-113.e15. [PMID: 35022142 DOI: 10.1016/j.urolonc.2021.12.014] [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: 06/18/2021] [Revised: 10/14/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Germline studies in testicular cancer have focused on unselected populations but so far have not led to recommendations for testicular cancer screening. OBJECTIVE Herein, we hypothesized that men with testicular cancer and an additional risk factor for hereditary cancer predisposition carry a higher rate of pathogenic variants than men with testicular cancer without another risk factor. METHODS AND RESULTS 187 patients with a personal history of testicular cancer underwent germline testing via Invitae. Patients were divided into low-risk and high-risk patients. Low-risk patients (n=83) had testicular cancer as their only primary malignancy without a family history of testicular cancer. High-risk patients (n=104) had additional primary malignancies and/or a family history of testicular cancer. 23.1% of patients harbored pathogenic germline variants with 19.6% carrying actionable variants. Among low-risk patients, 13.5% carried pathogenic variants versus 29.9% in the high-risk cohort. Of patients with a family history of non-testicular cancers and a personal history of additional primary malignancies, 32% harbored pathogenic variants. CONCLUSION High-risk patients are twice as likely to harbor pathogenic variants compared to low-risk patients. Importantly, patients with a family history of cancer and other primary malignancies represent a subset of patients that may benefit from genetic evaluation.
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Affiliation(s)
| | - Amin H Nassar
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elie W Akl
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Shan Yang
- Invitae Corporation, San Francisco, CL
| | | | - Michael A Liss
- Department of Medical Oncology, UT Health San Antonio, San Antonio, TX
| | - Gail E Tomlinson
- Department of Pediatrics, Division of Hematology and Oncology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Guru P Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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McKnight D, Bristow SL, Truty RM, Morales A, Stetler M, Westbrook MJ, Robinson K, Riethmaier D, Borlot F, Kellogg M, Hwang ST, Berg A, Aradhya S. Multigene Panel Testing in a Large Cohort of Adults With Epilepsy: Diagnostic Yield and Clinically Actionable Genetic Findings. Neurol Genet 2022; 8:e650. [PMID: 34926809 PMCID: PMC8678910 DOI: 10.1212/nxg.0000000000000650] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVES Although genetic testing among children with epilepsy has demonstrated clinical utility and become a part of routine testing, studies in adults are limited. This study reports the diagnostic yield of genetic testing in adults with epilepsy. METHODS Unrelated individuals aged 18 years and older who underwent diagnostic genetic testing for epilepsy using a comprehensive, next-generation sequencing-based, targeted gene panel (range 89-189 genes) were included in this cross-sectional study. Clinical information, provided at the discretion of the ordering clinician, was reviewed and analyzed. Diagnostic yield was calculated for all individuals including by age at seizure onset and comorbidities based on clinician-reported information. The proportion of individuals with clinically actionable genetic findings, including instances when a specific treatment would be indicated or contraindicated due to a diagnostic finding, was calculated. RESULTS Among 2,008 individuals, a diagnostic finding was returned for 218 adults (10.9%), with clinically actionable findings in 55.5% of diagnoses. The highest diagnostic yield was in adults with seizure onset during infancy (29.6%, 0-1 year), followed by in early childhood (13.6%, 2-4 years), late childhood (7.0%, 5-10 years), adolescence (2.4%, 11-17 years), and adulthood (3.7%, ≥18 years). Comorbid intellectual disability (ID) or developmental delay resulted in a high diagnostic yield (16.0%), most notably for females (19.6% in females vs 12.3% in males). Among individuals with pharmacoresistant epilepsy, 13.5% had a diagnostic finding, and of these, 57.4% were clinically actionable genetic findings. DISCUSSION These data reinforce the utility of genetic testing for adults with epilepsy, particularly for those with childhood-onset seizures, ID, and pharmacoresistance. This is an important consideration due to longer survival and the complexity of the transition from pediatric to adult care. In addition, more than half of diagnostic findings in this study were considered clinically actionable, suggesting that genetic testing could have a direct impact on clinical management and outcomes.
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Affiliation(s)
- Dianalee McKnight
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Sara L. Bristow
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Rebecca M. Truty
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Ana Morales
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Molly Stetler
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - M. Jody Westbrook
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Kristina Robinson
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Darlene Riethmaier
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Felippe Borlot
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Marissa Kellogg
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Sean T. Hwang
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Anne Berg
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
| | - Swaroop Aradhya
- From the Invitae (D.M., S.L.B., R.M.T., A.M., M.S., M.J.W., K.R., D.R., S.A.), San Francisco, CA; Alberta Children's Hospital Research Institute, Cumming School of Medicine, (F.B.) University of Calgary, Canada; Oregon Health & Science University Comprehensive Epilepsy Center (M.K.); Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell (S.T.H); Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago (A.B.); and Department of Neurology, Northwestern University-Feinberg School of Medicine (A.B.), Chicago, IL
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Rush ET, Johnson B, Aradhya S, Beltran D, Bristow SL, Eisenbeis S, Guerra NE, Krolczyk S, Miller N, Morales A, Ramesan P, Sarafrazi S, Truty R, Dahir K. Molecular Diagnoses of X-Linked and Other Genetic Hypophosphatemias: Results From a Sponsored Genetic Testing Program. J Bone Miner Res 2022; 37:202-214. [PMID: 34633109 PMCID: PMC9298723 DOI: 10.1002/jbmr.4454] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/27/2021] [Accepted: 10/02/2021] [Indexed: 12/20/2022]
Abstract
X-linked hypophosphatemia (XLH), a dominant disorder caused by pathogenic variants in the PHEX gene, affects both sexes of all ages and results in elevated serum fibroblast growth factor 23 (FGF23) and below-normal serum phosphate. In XLH, rickets, osteomalacia, short stature, and lower limb deformity may be present with muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Invitae and Ultragenyx collaborated to provide a no-charge sponsored testing program using a 13-gene next-generation sequencing panel to confirm clinical XLH or aid diagnosis of suspected XLH/other genetic hypophosphatemia. Individuals aged ≥6 months with clinical XLH or suspected genetic hypophosphatemia were eligible. Of 831 unrelated individuals tested between February 2019 and June 2020 in this cross-sectional study, 519 (62.5%) individuals had a pathogenic or likely pathogenic variant in PHEX (PHEX-positive). Among the 312 PHEX-negative individuals, 38 received molecular diagnoses in other genes, including ALPL, CYP27B1, ENPP1, and FGF23; the remaining 274 did not have a molecular diagnosis. Among 319 patients with a provider-reported clinical diagnosis of XLH, 88.7% (n = 283) had a reportable PHEX variant; 81.5% (n = 260) were PHEX-positive. The most common variant among PHEX-positive individuals was an allele with both the gain of exons 13-15 and c.*231A>G (3'UTR variant) (n = 66/519). Importantly, over 80% of copy number variants would have been missed by traditional microarray analysis. A positive molecular diagnosis in 41 probands (4.9%; 29 PHEX positive, 12 non-PHEX positive) resulted in at least one family member receiving family testing. Additional clinical or family member information resulted in variant(s) of uncertain significance (VUS) reclassification to pathogenic/likely pathogenic (P/LP) in 48 individuals, highlighting the importance of segregation and clinical data. In one of the largest XLH genetic studies to date, 65 novel PHEX variants were identified and a high XLH diagnostic yield demonstrated broad insight into the genetic basis of XLH. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Eric T Rush
- Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri - Kansas City School of Medicine, Kansas City, MO, USA.,Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | | | | | | | - Norma E Guerra
- Department of Pediatric Nephrology, Hospital General del Centro Médico Nacional «La Raza», Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | | | | | | | | | | | | | - Kathryn Dahir
- Program for Metabolic Bone Disorders, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
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Comprehensive Genetic Testing for Pediatric Hypertrophic Cardiomyopathy Reveals Clinical Management Opportunities and Syndromic Conditions. Pediatr Cardiol 2022; 43:616-623. [PMID: 34714385 PMCID: PMC8554517 DOI: 10.1007/s00246-021-02764-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) has historically been diagnosed phenotypically. Through genetic testing, identification of a molecular diagnosis (MolDx) is increasingly common but the impact on pediatric patients is unknown. This was a retrospective study of next-generation sequencing data for 602 pediatric patients with a clinician-reported history of HCM. Diagnostic yield was stratified by gene and self-reported race/ethnicity. A MolDx of HCM was identified in 242 (40%) individuals. Sarcomeric genes were the highest yielding, but pathogenic and/or likely pathogenic (P/LP) variants in syndromic genes were found in 36% of individuals with a MolDx, often in patients without documented clinical suspicion for a genetic syndrome. Among all MolDx, 73% were in genes with established clinical management recommendations and 2.9% were in genes that conferred eligibility for clinical trial enrollment. Black patients were the least likely to receive a MolDx. In the current era, genetic testing can impact management of HCM, beyond diagnostics or prognostics, through disease-specific guidelines or clinical trial eligibility. Genetic testing frequently can help identify syndromes in patients for whom syndromes may not be suspected. These findings highlight the importance of pursuing broad genetic testing, independent of suspicion based on phenotype. Lower rates of MolDx in Black patients may contribute to health inequities. Further research is needed evaluating the genetics of HCM in underrepresented/underserved populations. Additionally, research related to the impact of genetic testing on clinical management of other diseases is warranted.
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CDH1 germline variants are enriched in patients with colorectal cancer, gastric cancer, and breast cancer. Br J Cancer 2021; 126:797-803. [PMID: 34949788 PMCID: PMC8888603 DOI: 10.1038/s41416-021-01673-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background and aims CDH1 germline variants have been linked to heritability in diffuse gastric (DGC) and lobular breast cancer (LBC). Studies have not yet assessed whether CDH1 is a cancer-susceptibility gene in other cancers. Herein, we mapped the landscape of pathogenic and likely pathogenic (P/LP) germline variants in CDH1 across various cancers and ethnicities. Methods We evaluated CDH1 germline P/LP variants in 212,944 patients at one CLIA-certified laboratory (Invitae) and described their frequency in 7 cancer types. We screened for CDH1 variant enrichment in each cancer relative to a cancer-free population from The Genome Aggregation Database version 3 (gnomADv3). Results CDH1 P/LP variants were identified in 141 patients, most commonly in patients with DGC (27/408, 6.6%) followed by colorectal signet-ring cell cancer (CSRCC; 3/79, 3.8%), gastric cancer (56/2756, 2%), and LBC (22/6809, 0.3%). CDH1 P/LP variants were enriched in specific ethnic populations with breast cancer, gastric cancer, CRC, LBC, DGC, and CSRCC compared to matched ethnicities from gnomADv3. Conclusion We report for the first time the prevalence of P/LP CDH1 variants across several cancers and show significant enrichment in CDH1 P/LP variants for patients with CSRCC, DGC, and LBC across various ethnicities. Future prospective studies are warranted to validate these findings.
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Landry KK, Seward DJ, Dragon JA, Slavik M, Xu K, McKinnon WC, Colello L, Sweasy J, Wallace SS, Cuke M, Wood ME. Investigation of discordant sibling pairs from hereditary breast cancer families and analysis of a rare PMS1 variant. Cancer Genet 2021; 260-261:30-36. [PMID: 34852986 DOI: 10.1016/j.cancergen.2021.11.004] [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: 08/10/2021] [Revised: 10/12/2021] [Accepted: 11/11/2021] [Indexed: 11/02/2022]
Abstract
BACKGROUND It is likely that additional genes for hereditary breast cancer can be identified using a discordant sib pair design. Using this design we identified individuals harboring a rare PMS1 c.605G>A variant previously predicted to result in loss of function. OBJECTIVES A family-based design and predictive algorithms were used to prioritize candidate variants possibly associated with an increased risk of hereditary breast cancer. Functional analyses were performed for one of the candidate variants, PMS1 c.605G>A. METHODS 1) 14 discordant sister-pairs from hereditary breast cancer families were identified. 2) Whole exome sequencing was performed and candidate risk variants identified. 3) A rare PMS variant was identified in 2 unrelated affected sisters but no unaffected siblings. 4) Functional analysis of this variant was carried out using targeted mRNA sequencing. RESULTS Genotype-phenotype correlation did not demonstrate tracking of the variant with cancer in the family. Functional analysis revealed no difference in exon 6 incorporation, which was validated by analyzing PMS1 allele specific expression. CONCLUSIONS The PMS1 c.605G>A variant did not segregate with disease, and there was no variant-dependent impact on PMS1 exon 6 splicing, supporting this variant is likely benign. Functional analyses are imperative to understanding the clinical significance of predictive algorithms.
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Affiliation(s)
- K K Landry
- Department of Medicine Hematology-Oncology, UVM Medical Center, Burlington, VT, USA.
| | - D J Seward
- Department of Pathology and Laboratory Medicine, U-VM Larner College of Medicine, Burlington, VT, USA
| | - J A Dragon
- Department of Microbiology and Molecular Genetics, UVM Larner College of Medicine, Burlington, VT, USA
| | - M Slavik
- Department of Microbiology and Molecular Genetics, UVM Larner College of Medicine, Burlington, VT, USA
| | - K Xu
- Department of Pathology and Laboratory Medicine, U-VM Larner College of Medicine, Burlington, VT, USA
| | - W C McKinnon
- Department of Medicine Hematology-Oncology, UVM Medical Center, Burlington, VT, USA
| | - L Colello
- Department of Medicine Hematology-Oncology, UVM Medical Center, Burlington, VT, USA
| | - J Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - S S Wallace
- Department of Microbiology and Molecular Genetics, UVM Larner College of Medicine, Burlington, VT, USA
| | - M Cuke
- Department of Medicine Hematology-Oncology, UVM Medical Center, Burlington, VT, USA
| | - M E Wood
- Department of Medicine Hematology-Oncology, UVM Medical Center, Burlington, VT, USA
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Re-evaluating cancer risks associated with the CHEK2 p.Ser428Phe Ashkenazi Jewish founder pathogenic variant. Fam Cancer 2021; 21:305-308. [PMID: 34622392 DOI: 10.1007/s10689-021-00278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/28/2021] [Indexed: 01/13/2023]
Abstract
A missense variant (p.Ser428Phe [S428F]) in the CHEK2 gene is reportedly associated with a 2-3 fold increase in breast cancer risk in Ashkenazi Jews. This study aimed to re-evaluate cancer risks conferred by the CHEK2 S428F variant in Ashkenazi Jews. De-identified data from CHEK2 S428F variant carriers sequenced with multigene panels were analyzed. Overall, 486/341,531 (0.14%) cases of all ethnicities diagnosed with any cancer type were CHEK2 S428F carriers, of whom 243/9980 self-identified as Ashkenazi Jews and carried this risk variant only. Compared with ethnically matched non-cancer controls, across all cancer cases, this variant was not more prevalent (p = 0.271). Specifically, variant prevalence was not different in breast cancer cases compared with controls. Though the variant was shown to be enriched in pancreatic cancer cases (p = 0.008), sample size was small. The CHEK2 S428F variant was not overrepresented in Ashkenazi Jews with breast cancer and most other cancer types analyzed, except for pancreatic cancer, compared with ethnically matched non- cancer controls. These findings should prompt reevaluating ethnic-specific CHEK2 S428F cancer attributable risk.
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Mooney R, Espinel W, Elrick A, Kehoe K, Kohlmann W, Kaphingst KA. Uptake of genetic counseling and multi-gene panel testing among women in the Intermountain West with previous negative BRCA1 and BRCA2 results contacted for updated testing. J Genet Couns 2021; 31:470-478. [PMID: 34570943 PMCID: PMC9206233 DOI: 10.1002/jgc4.1513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Women with a personal history of breast or ovarian cancer who previously had BRCA1/2 testing now have the opportunity for additional genetic risk information through multi-gene panel testing. However, little is known about women's receptivity to further contact and uptake of genetic counseling and updated genetic testing. Utilizing a clinic database to identify potential participants, we prospectively contacted women in the United States with a personal and/or family history of breast or ovarian cancer who had negative BRCA1/2 testing, which was performed primarily between 2011 and 2018. Eligible and interested participants were scheduled for a genetic counseling appointment to discuss updated genetic testing using a multi-gene panel. We attempted to contact 455 participants, screened 203 (45%), and 103 (23%) completed a pre-test genetic counseling visit to discuss updated testing. Of these, 88 participants had updated multi-gene panel testing. Participants had an average age of 59 years, and most (78%) had breast cancer with an average age of 45 at diagnosis. The majority (97%) of participants were white. Of participants who underwent panel testing, 13% (n = 11) had at least one pathogenic variant identified. Most participants (86%) had an out-of-pocket cost of $100 or less for their panel. There is a sizable population of women with a personal and/or family history of breast or ovarian cancer and negative BRCA1/2 test results who would qualify for updated multi-gene panel testing. In our study, 59% of those reached who were eligible completed a pre-test genetic counseling visit. Clinics could consider an outreach program to offer genetic counseling and updated genetic testing. Supports for this type of effort may include coordinators and genetic counseling assistants and an available database with patients' contact information and prior genetic test results. Updated testing allows women more information about their risk and may expand the value of genetic counseling.
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Affiliation(s)
- Ryan Mooney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Whitney Espinel
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ashley Elrick
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Communication, University of Utah, Salt Lake City, Utah, USA
| | - Kelsey Kehoe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Kimberly A Kaphingst
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Communication, University of Utah, Salt Lake City, Utah, USA
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O'Neill SC, Hamilton JG, Conley CC, Peshkin BN, Sacca R, McDonnell GA, Isaacs C, Robson ME, Tercyak KP. Improving our model of cascade testing for hereditary cancer risk by leveraging patient peer support: a concept report. Hered Cancer Clin Pract 2021; 19:40. [PMID: 34565430 PMCID: PMC8474818 DOI: 10.1186/s13053-021-00198-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Consensus and evidence suggest that cascade testing is critical to achieve the promise of cancer genetic testing. However, barriers to cascade testing include effective family communication of genetic risk information and family members' ability to cope with genetic risk. These barriers are further complicated by the developmental needs of unaffected family members during critical windows for family communication and adaptation. Peer support could address these barriers. We provide two illustrative examples of ongoing BRCA1/2-related clinical trials that apply a peer support model to improve family communication and functioning. Peer support can augment currently available genetic services to facilitate adjustment to and effective use of cancer genetic risk information. Importantly, this scalable approach can address the presence of cancer risk within families across multiple developmental stages. This applies a family-centered perspective that accommodates all potentially at-risk relatives. This peer support model can be further applied to emerging topics in clinical genetics to expand reach and impact.
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Affiliation(s)
- Suzanne C O'Neill
- Georgetown Lombardi Comprehensive Cancer Center, Washington, D.C, USA.
| | | | - Claire C Conley
- Georgetown Lombardi Comprehensive Cancer Center, Washington, D.C, USA
| | - Beth N Peshkin
- Georgetown Lombardi Comprehensive Cancer Center, Washington, D.C, USA
| | - Rosalba Sacca
- Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - Claudine Isaacs
- Georgetown Lombardi Comprehensive Cancer Center, Washington, D.C, USA
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - Kenneth P Tercyak
- Georgetown Lombardi Comprehensive Cancer Center, Washington, D.C, USA
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Sturm AC, Truty R, Callis TE, Aguilar S, Esplin ED, Garcia S, Haverfield EV, Morales A, Nussbaum RL, Rojahn S, Vatta M, Rader DJ. Limited-Variant Screening vs Comprehensive Genetic Testing for Familial Hypercholesterolemia Diagnosis. JAMA Cardiol 2021; 6:902-909. [PMID: 34037665 PMCID: PMC8156154 DOI: 10.1001/jamacardio.2021.1301] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Question How many clinically significant variants for familial hypercholesterolemia would be missed by limited-variant screening conducted on microarrays? Findings In this cross-sectional review of comprehensive genetic test results for individuals with indications for familial hypercholesterolemia, a limited-variant screen was found to have a significantly lower detection rate (8.4%) than the comprehensive diagnostic test (27%). Meaning The results of this study suggest that clinically significant findings for familial hypercholesterolemia would be missed for two-thirds of affected individuals if limited-variant screening was used. Importance Familial hypercholesterolemia (FH) is the most common inherited cardiovascular disease and carries significant morbidity and mortality risks. Genetic testing can identify affected individuals, but some array-based assays screen only a small subset of known pathogenic variants. Objective To identify the number of clinically significant variants associated with FH that would be missed by an array-based, limited-variant screen when compared with next-generation sequencing (NGS)–based comprehensive testing. Design, Setting, and Participants This cross-sectional study compared comprehensive genetic test results for clinically significant variants associated with FH with results for a subset of 24 variants screened by a limited-variant array. Data were deidentified next-generation sequencing results from indication-based or proactive gene panels. Individuals receiving next-generation sequencing–based genetic testing, either for an FH indication between November 2015 and June 2020 or as proactive health screening between February 2016 and June 2020 were included. Ancestry was reported by clinicians who could select from preset options or enter free text on the test requisition form. Main Outcomes and Measures Number of pathogenic or likely pathogenic (P/LP) variants identified. Results This study included 4563 individuals who were referred for FH diagnostic testing and 6482 individuals who received next-generation sequencing of FH-associated genes as part of a proactive genetic test. Among individuals in the indication cohort, the median (interquartile range) age at testing was 49 (32-61) years, 55.4% (2528 of 4563) were female, and 63.6% (2902 of 4563) were self-reported White/Caucasian. In the indication cohort, the positive detection rate would have been 8.4% (382 of 4563) for a limited-variant screen compared with the 27.0% (1230 of 4563) observed with the next-generation sequencing–based comprehensive test. As a result, 68.9% (848 of 1230) of individuals with a P/LP finding in an FH-associated gene would have been missed by the limited screen. The potential for missed findings in the indication cohort varied by ancestry; among individuals with a P/LP finding, 93.7% (59 of 63) of self-reported Black/African American individuals and 84.7% (122 of 144) of Hispanic individuals would have been missed by the limited-variant screen, compared with 33.3% (4 of 12) of Ashkenazi Jewish individuals. In the proactive cohort, the prevalence of clinically significant FH variants was approximately 1:191 per the comprehensive test, and 61.8% (21 of 34) of individuals with an FH-associated P/LP finding would have been missed by a limited-variant screen. Conclusions and Relevance Limited-variant screens may falsely reassure the majority of individuals at risk for FH that they do not carry a disease-causing variant, especially individuals of self-reported Black/African American and Hispanic ancestry.
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Affiliation(s)
- Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | | | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia.,Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
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Affiliation(s)
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
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Nykamp K, Truty R, Riethmaier D, Wilkinson J, Bristow SL, Aguilar S, Neitzel D, Faulkner N, Aradhya S. Elucidating clinical phenotypic variability associated with the polyT tract and TG repeats in CFTR. Hum Mutat 2021; 42:1165-1172. [PMID: 34196078 PMCID: PMC9292755 DOI: 10.1002/humu.24250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 02/05/2023]
Abstract
Biallelic pathogenic variants in CFTR manifest as cystic fibrosis (CF) or other CFTR-related disorders (CFTR-RDs). The 5T allele, causing alternative splicing and reduced protein activity, is modulated by the adjacent TG repeat element, though previous data have been limited to small, selective cohorts. Here, the risk and spectrum of phenotypes associated with the CFTR TG-T5 haplotype variants (TG11T5, TG12T5, and TG13T5) in the absence of the p.Arg117His variant are evaluated. Individuals who received physician-ordered next-generation sequencing of CFTR were included. TG[11-13]T5 variant frequencies (biallelic or with another CF-causing variant [CFvar]) were calculated. Clinical information reported by the ordering provider or the individual was examined. Among 548,300 individuals, the T5 minor allele frequency (MAF) was 4.2% (TG repeat distribution: TG11 = 68.1%, TG12 = 29.5%, TG13 = 2.4%). When present with a CFvar, each TG[11-13]T5 variant was significantly enriched in individuals with a high suspicion of CF or CFTR-RD (personal/family history of CF/CFTR-RD) compared to those with a low suspicion for CF or CFTR-RD (hereditary cancer screening, CFTR not requisitioned). Compared to CFvar/CFvar individuals, those with TG[11-13]T5/CFvar generally had single-organ involvement, milder symptoms, variable expressivity, and reduced penetrance. These data improve our understanding of disease risks associated with TG[11-13]T5 variants and have important implications for reproductive genetic counseling.
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One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genet Med 2021; 23:1673-1680. [PMID: 34007000 PMCID: PMC8460443 DOI: 10.1038/s41436-021-01187-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. METHODS An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. RESULTS In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. CONCLUSION The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.
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Multigene Panel Testing for Hereditary Cancer and Genetic Counseling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33983594 DOI: 10.1007/978-981-32-9620-6_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
As sequencing technology and information of the genomic causes for cancer development expand, multi-gene panel testing for hereditary cancer is increasing in clinical practice. In this chapter, we reviewed the application of multi-gene panel with pre-/post- testing considerations and summarized genetic counseling based on panel testing results in clinical field. In addition, we introduce multi-gene panel for hereditary cancer developed in Seoul National University Hospital.
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Bowen BM, Truty R, Aradhya S, Bristow SL, Johnson BA, Morales A, Tan CA, Westbrook MJ, Winder TL, Chavez JC. SMA Identified: Clinical and Molecular Findings From a Sponsored Testing Program for Spinal Muscular Atrophy in More Than 2,000 Individuals. Front Neurol 2021; 12:663911. [PMID: 34025568 PMCID: PMC8134668 DOI: 10.3389/fneur.2021.663911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Spinal muscular atrophy (SMA) linked to chromosome 5q is an inherited progressive neuromuscular disorder with a narrow therapeutic window for optimal treatment. Although genetic testing provides a definitive molecular diagnosis that can facilitate access to effective treatments, limited awareness and other barriers may prohibit widespread testing. In this study, the clinical and molecular findings of SMA Identified—a no-charge sponsored next-generation sequencing (NGS)-based genetic testing program for SMA diagnosis—are reported. Methods: Between March 2018 and March 2020, unrelated individuals who had a confirmed or suspected SMA diagnosis or had a family history of SMA were eligible. All individuals underwent diagnostic genetic testing for SMA at clinician discretion. In total, 2,459 individuals were tested and included in this analysis. An NGS-based approach interrogated sequence and copy number of SMN1 and SMN2. Variants were confirmed by multiplex ligation-dependent probe amplification sequencing. Individuals were categorized according to genetic test results: diagnostic (two pathogenic SMN1 variants), nearly diagnostic (SMN1 exon-7 deletion with a variant of uncertain significance [VUS] in SMN1 or SMN2), indeterminate VUS (one VUS in SMN1 or SMN2), carrier (heterozygous SMN1 deletion only), or negative (no pathogenic variants or VUS in SMN1 or SMN2). Diagnostic yield was calculated. Genetic test results were analyzed based on clinician-reported clinical features and genetic modifiers (SMN2 copy number and SMN2 c.859G>C). Results: In total, 2,459 unrelated individuals (mean age 24.3 ± 23.0 years) underwent diagnostic testing. The diagnostic yield for diagnostic plus nearly diagnostic results was 31.3% (n = 771/2,459). Age of onset and clinical presentation varied considerably for individuals and was dependent on SMN2 copy number. Homozygous deletions represented the most common genetic etiology (96.2%), with sequence variants also observed in probands with clinical diagnoses of SMA. Conclusions: Using a high-yield panel test in a no-charge sponsored program early in the diagnostic odyssey may open the door for medical interventions in a substantial number of individuals with SMA. These findings have potential implications for clinical management of probands and their families.
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