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White JA, Kaninjing ET, Adeniji KA, Jibrin P, Obafunwa JO, Ogo CN, Mohammed F, Popoola A, Fatiregun OA, Oluwole OP, Thorpe RJ, Karanam B, Elhussin I, Ambs S, Tang W, Davis M, Polak P, Campbell MJ, Brignole KR, Rotimi SO, Dean-Colomb W, Odedina FT, Yates C. Whole-exome sequencing of Nigerian benign prostatic hyperplasia reveals increased alterations in apoptotic pathways. Prostate 2024; 84:460-472. [PMID: 38192023 PMCID: PMC10922327 DOI: 10.1002/pros.24662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Through whole-exome sequencing of 60 formalin-fixed paraffin-embedded Nigerian (NGRn) benign prostatic hyperplasia (BPH) samples, we identified germline and somatic alterations in apoptotic pathways impacting BPH development and progression. Prostate enlargement is a common occurrence in male aging; however, this enlargement can lead to lower urinary tract symptoms that negatively impact quality of life. This impact is disproportionately present in men of African ancestry. BPH pathophysiology is poorly understood and studies examining non-European populations are lacking. METHODS In this study, NGRn BPH, normal prostate, and prostate cancer (PCa) tumor samples were sequenced and compared to characterize genetic alterations in NGRn BPH. RESULTS Two hundred and two nonbenign, ClinVar-annotated germline variants were present in NGRn BPH samples. Six genes [BRCA1 (92%), HSD3B1 (85%), TP53 (37%), PMS2 (23%), BARD1 (20%), and BRCA2 (17%)] were altered in at least 10% of samples; however, compared to NGRn normal and tumor, the frequency of alterations in BPH samples showed no significant differences at the gene or variant level. BRCA2_rs11571831 and TP53_rs1042522 germline alterations had a statistically significant co-occurrence interaction in BPH samples. In at least two BPH samples, 173 genes harbored somatic variants known to be clinically actionable. Three genes (COL18A1, KIF16B, and LRP1) showed a statistically significant (p < 0.05) higher frequency in BPH. NGRn BPH also had five gene pairs (PKD1/KIAA0100, PKHD1/PKD1, DNAH9/LRP1B, NWD1/DCHS2, and TCERG1/LMTK2) with statistically significant co-occurring interactions. Two hundred and seventy-nine genes contained novel somatic variants in NGRn BPH. Three genes (CABP1, FKBP1C, and RP11-595B24.2) had a statistically significant (p < 0.05) higher alteration frequency in NGRn BPH and three were significantly higher in NGRn tumor (CACNA1A, DMKN, and CACNA2D2). Pairwise Fisher's exact tests showed 14 gene pairs with statistically significant (p < 0.05) interactions and four interactions approaching significance (p < 0.10). Mutational patterns in NGRn BPH were similar to COSMIC (Catalog of Somatic Mutations in Cancer) signatures associated with aging and dysfunctional DNA damage repair. CONCLUSIONS NGRn BPH contained significant germline alteration interactions (BRCA2_rs11571831 and TP53_rs1042522) and increased somatic alteration frequencies (LMTK2, LRP1, COL18A1, CABP1, and FKBP1C) that impact apoptosis. Normal prostate development is maintained by balancing apoptotic and proliferative activity. Dysfunction in either mechanism can lead to abnormal prostate growth. This work is the first to examine genomic sequencing in NGRn BPH and provides data that fill known gaps in the understanding BPH and how it impacts men of African ancestry.
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Affiliation(s)
- Jason A White
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama, USA
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Genetics, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Ernest T Kaninjing
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- School of Health and Human Performance, Georgia College & State University, Milledgeville, Georgia, USA
| | - Kayode A Adeniji
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- College of Health Sciences, University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Paul Jibrin
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- College of Health Sciences, National Hospital Abuja, Abuja, Federal Capital Territory, Nigeria
| | - John O Obafunwa
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Chidiebere N Ogo
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Surgery, Federal Medical Centre, Abeokuta, Ogun State, Nigeria
| | - Faruk Mohammed
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Pathology, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Ademola Popoola
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- College of Health Sciences, University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Omolara A Fatiregun
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Clinical Oncology, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, Abuja, Federal Capital Territory, Nigeria
| | - Roland J Thorpe
- Center for Health Disparities Solutions, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Balasubramanyam Karanam
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama, USA
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
| | - Isra Elhussin
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama, USA
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Brady Urological Institute, Baltimore, Maryland, USA
| | - Stefan Ambs
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Melissa Davis
- Department of Genetics, Morehouse School of Medicine, Atlanta, Georgia, USA
- Department of Surgery, New York Presbyterian-Weill Cornell Medicine, New York, New York, USA
| | - Paz Polak
- Quest Diagnostics, Secaucus, New Jersey, USA
| | - Moray J Campbell
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathryn R Brignole
- Lineberger Comprehensive Cancer Center, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Solomon O Rotimi
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Biochemistry and Covenant Applied Informatics and Communication Africa Centre of Excellence, Covenant University, Ota, Nigeria
| | - Windy Dean-Colomb
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama, USA
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Piedmont Medical Oncology-Newnan, Newnan, Georgia, USA
| | - Folake T Odedina
- Center for Health Equity and Community Engagement Research, Mayo Clinic, Jacksonville, Florida, USA
| | - Clayton Yates
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama, USA
- Prostate Cancer Transatlantic Consortium (CaPTC), Abuja, Wuse Zone 1, Nigeria
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Brady Urological Institute, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Carton RJ, Doyle MG, Kearney H, Steward CA, Lench NJ, Rogers A, Heinzen EL, McDonald S, Fay J, Lacey A, Beausang A, Cryan J, Brett F, El-Naggar H, Widdess-Walsh P, Costello D, Kilbride R, Doherty CP, Sweeney KJ, O'Brien DF, Henshall DC, Delanty N, Cavalleri GL, Benson KA. Somatic variants as a cause of drug-resistant epilepsy including mesial temporal lobe epilepsy with hippocampal sclerosis. Epilepsia 2024. [PMID: 38491957 DOI: 10.1111/epi.17943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE The contribution of somatic variants to epilepsy has recently been demonstrated, particularly in the etiology of malformations of cortical development. The aim of this study was to determine the diagnostic yield of somatic variants in genes that have been previously associated with a somatic or germline epilepsy model, ascertained from resected brain tissue from patients with multidrug-resistant focal epilepsy. METHODS Forty-two patients were recruited across three categories: (1) malformations of cortical development, (2) mesial temporal lobe epilepsy with hippocampal sclerosis, and (3) nonlesional focal epilepsy. Participants were subdivided based on histopathology of the resected brain. Paired blood- and brain-derived DNA samples were sequenced using high-coverage targeted next generation sequencing to high depth (585× and 1360×, respectively). Variants were identified using Genome Analysis ToolKit (GATK4) MuTect-2 and confirmed using high-coverage Amplicon-EZ sequencing. RESULTS Sequence data on 41 patients passed quality control. Four somatic variants were validated following amplicon sequencing: within CBL, ALG13, MTOR, and FLNA. The diagnostic yield across 41 patients was 10%, 9% in mesial temporal lobe epilepsy with hippocampal sclerosis and 20% in malformations of cortical development. SIGNIFICANCE This study provides novel insights into the etiology of mesial temporal lobe epilepsy with hippocampal sclerosis, highlighting a potential pathogenic role of somatic variants in CBL and ALG13. We also report candidate diagnostic somatic variants in FLNA in focal cortical dysplasia, while providing further insight into the importance of MTOR and related genes in focal cortical dysplasia. This work demonstrates the potential molecular diagnostic value of variants in both germline and somatic epilepsy genes.
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Affiliation(s)
- Robert J Carton
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael G Doyle
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
- Strategic Academic Recruitment Doctor of Medicine Programme, Royal College of Surgeons in Ireland in collaboration with Blackrock Clinic, Dublin, Ireland
| | - Hugh Kearney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | | | | | - Anthony Rogers
- Congenica Limited, BioData Innovation Centre, Cambridge, UK
| | - Erin L Heinzen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Seamus McDonald
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanna Fay
- Royal College of Surgeons in Ireland Biobanking Service, Dublin, Ireland
| | - Austin Lacey
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Hany El-Naggar
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Peter Widdess-Walsh
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Daniel Costello
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, Cork University Hospital, Cork, Ireland
| | - Ronan Kilbride
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Colin P Doherty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, St. James's Hospital, Dublin, Ireland
| | - Kieron J Sweeney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Donncha F O'Brien
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - David C Henshall
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine A Benson
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
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Segura-Tudela A, López-Nevado M, Nieto-López C, García-Jiménez S, Díaz-Madroñero MJ, Delgado Á, Cabrera-Marante O, Pleguezuelo D, Morales P, Paz-Artal E, Gil-Niño J, Marco FM, Serrano C, González-Granado LI, Quesada-Espinosa JF, Allende LM. Enrichment of Immune Dysregulation Disorders in Adult Patients with Human Inborn Errors of Immunity. J Clin Immunol 2024; 44:61. [PMID: 38363452 PMCID: PMC10873437 DOI: 10.1007/s10875-024-01664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Human inborn errors of immunity (IEI) comprise a group of diseases resulting from molecular variants that compromise innate and adaptive immunity. Clinical features of IEI patients are dominated by susceptibility to a spectrum of infectious diseases, as well as autoimmune, autoinflammatory, allergic, and malignant phenotypes that usually appear in childhood, which is when the diagnosis is typically made. However, some IEI patients are identified in adulthood due to symptomatic delay of the disease or other reasons that prevent the request for a molecular study. The application of next-generation sequencing (NGS) as a diagnostic technique has given rise to an ever-increasing identification of IEI-monogenic causes, thus improving the diagnostic yield and facilitating the possibility of personalized treatment. This work was a retrospective study of 173 adults with IEI suspicion that were sequenced between 2005 and 2023. Sanger, targeted gene-panel, and whole exome sequencing were used for molecular diagnosis. Disease-causing variants were identified in 44 of 173 (25.43%) patients. The clinical phenotype of these 44 patients was mostly related to infection susceptibility (63.64%). An enrichment of immune dysregulation diseases was found when cohorts with molecular diagnosis were compared to those without. Immune dysregulation disorders, group 4 from the International Union of Immunological Societies Expert Committee (IUIS), were the most prevalent among these adult patients. Immune dysregulation as a new item in the Jeffrey Model Foundation warning signs for adults significantly increases the sensitivity for the identification of patients with an IEI-producing molecular defect.
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Affiliation(s)
- Alejandro Segura-Tudela
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Marta López-Nevado
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Celia Nieto-López
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Sandra García-Jiménez
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - María J Díaz-Madroñero
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
| | - Ángeles Delgado
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
| | - Oscar Cabrera-Marante
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Daniel Pleguezuelo
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Pablo Morales
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
| | - Estela Paz-Artal
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Gil-Niño
- Department of Internal Medicine, University Hospital, 12 de Octubre, Madrid, Spain
| | - Francisco M Marco
- Unit of Immunology, University Hospital General Dr Balmis, Alicante, Spain
| | - Cristina Serrano
- Department of Immunology, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Luis I González-Granado
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- Unit of Immunodeficiencies, Department of Pediatrics, University Hospital, 12 de Octubre, Madrid, Spain
| | - Juan F Quesada-Espinosa
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain
- Department of Genetics, University Hospital, 12 de Octubre, Madrid, Spain
| | - Luis M Allende
- Department of Immunology, University Hospital, 12 de Octubre, Avda. de Andalucía S/N, 28041, Madrid, Spain.
- Research Institute Hospital, 12 Octubre (imas12), Madrid, Spain.
- School of Medicine, Complutense University of Madrid, Madrid, Spain.
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White G, Nonaka D, Chung TT, Oakey RJ, Izatt L. Somatic EPAS1 Variants in Pheochromocytoma and Paraganglioma in Patients With Sickle Cell Disease. J Clin Endocrinol Metab 2023; 108:3302-3310. [PMID: 37285480 PMCID: PMC10655516 DOI: 10.1210/clinem/dgad311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
CONTEXT Somatic EPAS1 variants account for 5% to 8% of all pheochromocytoma and paragangliomas (PPGL) but are detected in over 90% of PPGL in patients with congenital cyanotic heart disease, where hypoxemia may select for EPAS1 gain-of-function variants. Sickle cell disease (SCD) is an inherited hemoglobinopathy associated with chronic hypoxia and there are isolated reports of PPGL in patients with SCD, but a genetic link between the conditions has yet to be established. OBJECTIVE To determine the phenotype and EPAS1 variant status of patients with PPGL and SCD. METHODS Records of 128 patients with PPGL under follow-up at our center from January 2017 to December 2022 were screened for SCD diagnosis. For identified patients, clinical data and biological specimens were obtained, including tumor, adjacent non-tumor tissue and peripheral blood. Sanger sequencing of exons 9 and 12 of EPAS1, followed by amplicon next-generation sequencing of identified variants was performed on all samples. RESULTS Four patients with both PPGL and SCD were identified. Median age at PPGL diagnosis was 28 years. Three tumors were abdominal paragangliomas and 1 was a pheochromocytoma. No germline pathogenic variants in PPGL-susceptibility genes were identified in the cohort. Genetic testing of tumor tissue detected unique EPAS1 variants in all 4 patients. Variants were not detected in the germline, and 1 variant was detected in lymph node tissue of a patient with metastatic disease. CONCLUSION We propose that somatic EPAS1 variants may be acquired through exposure to chronic hypoxia in SCD and drive PPGL development. Future work is needed to further characterize this association.
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Affiliation(s)
- Gemma White
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Clinical Genetics, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 9RT, UK
| | - Daisuke Nonaka
- Department of Pathology, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 7EH, UK
- Department of Cellular Pathology, King's College London, London, SE1 1UL, UK
| | - Teng-Teng Chung
- Department of Endocrinology, University College London Hospital NHS Foundation Trust, London, NW1 2BU, UK
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Louise Izatt
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Clinical Genetics, Guy's and St Thomas’ NHS Foundation Trust, London, SE1 9RT, UK
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Ambayya A, Razali R, Sulong S, Zulkefli ES, Yap YY, Sathar J, Hassan R. Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing. Cancers (Basel) 2023; 15. [PMID: 36900179 DOI: 10.3390/cancers15051386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Characterising genomic variants is paramount in understanding the pathogenesis and heterogeneity of normal-karyotype acute myeloid leukaemia (AML-NK). In this study, clinically significant genomic biomarkers were ascertained using targeted DNA sequencing and RNA sequencing on eight AML-NK patients' samples collected at disease presentation and after complete remission. In silico and Sanger sequencing validations were performed to validate variants of interest, and they were followed by the performance of functional and pathway enrichment analyses for overrepresentation analysis of genes with somatic variants. Somatic variants involving 26 genes were identified and classified as follows: 18/42 (42.9%) as pathogenic, 4/42 (9.5%) as likely pathogenic, 4/42 (9.5%) as variants of unknown significance, 7/42 (16.7%) as likely benign and 9/42 (21.4%) as benign. Nine novel somatic variants were discovered, of which three were likely pathogenic, in the CEBPA gene with significant association with its upregulation. Transcription misregulation in cancer tops the affected pathways involving upstream genes (CEBPA and RUNX1) that were deregulated in most patients during disease presentation and were closely related to the most enriched molecular function gene ontology category, DNA-binding transcription activator activity RNA polymerase II-specific (GO:0001228). In summary, this study elucidated putative variants and their gene expression profiles along with functional and pathway enrichment in AML-NK patients.
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Gudmundsson S, Carlston CM, O'Donnell-Luria A. Interpreting variants in genes affected by clonal hematopoiesis in population data. Hum Genet 2023:10.1007/s00439-023-02526-4. [PMID: 36739343 PMCID: PMC10400727 DOI: 10.1007/s00439-023-02526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Reference population databases like the Genome Aggregation Database (gnomAD) have improved our ability to interpret the human genome. Variant frequencies and frequency-derived tools (such as depletion scores) have become fundamental to variant interpretation and the assessment of variant-gene-disease relationships. Clonal hematopoiesis (CH) obstructs variant interpretation as somatic variants that provide proliferative advantage will affect variant frequencies, depletion scores, and downstream filtering. Further, default filtering of variants or genes associated with CH risks filtering bona fide germline variants as variants associated with CH can also cause Mendelian conditions. Here, we provide our insights on interpreting population variant data in genes affected by clonal hematopoiesis, as well as recommendations for careful review of 36 established CH genes associated with neurodevelopmental conditions.
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Affiliation(s)
- Sanna Gudmundsson
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Colleen M Carlston
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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7
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Van Horebeek L, Dedoncker N, Dubois B, Goris A. Frequent somatic mosaicism in T lymphocyte subsets in individuals with and without multiple sclerosis. Front Immunol 2022; 13:993178. [PMID: 36618380 PMCID: PMC9817019 DOI: 10.3389/fimmu.2022.993178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Background Somatic variants are variations in an individual's genome acquired after the zygotic stadium and result from mitotic errors or not (fully) repaired DNA damage. Objectives To investigate whether somatic mosaicism in T lymphocyte subsets is enriched early in multiple sclerosis (MS). Methods We identified somatic variants with variant allele fractions ≥1% across the whole exome in CD4+ and CD8+ T lymphocytes of 21 treatment-naive MS patients with <5 years of disease duration and 16 partially age-matched healthy controls. We investigated the known somatic STAT3 variant p.Y640F in peripheral blood in a larger cohort of 446 MS patients and 259 controls. Results All subjects carried 1-142 variants in CD4+ or CD8+ T lymphocytes. Variants were more common, more abundant, and increased with age in CD8+ T lymphocytes. Somatic variants were common in the genes DNMT3A and especially STAT3. Overall, the presence or abundance of somatic variants, including the STAT3 p.Y640F variant, did not differ between MS patients and controls. Conclusions Somatic variation in T lymphocyte subsets is widespread in both control individuals and MS patients. Somatic mosaicism in T lymphocyte subsets is not enriched in early MS and thus unlikely to contribute to MS risk, but future research needs to address whether a subset of variants influences disease susceptibility.
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Affiliation(s)
- Lies Van Horebeek
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Nina Dedoncker
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Bénédicte Dubois
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium,Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - An Goris
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium,*Correspondence: An Goris,
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8
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Carli D, Resta N, Ferrero GB, Ruggieri M, Mussa A. Mosaic RASopathies: A review of disorders caused by somatic pathogenic variants in the genes of the RAS/MAPK pathway. Am J Med Genet C Semin Med Genet 2022; 190:520-529. [PMID: 36461154 DOI: 10.1002/ajmg.c.32021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 12/04/2022]
Abstract
Mosaic RASopathies are a heterogeneous group of diseases characterized by the presence at birth or early onset of congenital anomalies, cutaneous and vascular anomalies, segmental overgrowth, and increased cancer risk. They are caused by somatic pathogenic variants of the genes belonging the RAt Sarcoma Mitogen-activated protein kinase (RAS/MAPK) pathway causing its hyperactivation. Here, we review the clinical and molecular characteristics of this heterogeneous group of diseases, including the possibilities of molecular diagnosis and new therapeutic perspectives.
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Affiliation(s)
- Diana Carli
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy.,Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Nicoletta Resta
- Division of Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | | | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy.,Pediatric Clinical Genetics Unit, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Torino, Italy
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9
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Lai D, Gade M, Yang E, Koh HY, Lu J, Walley NM, Buckley AF, Sands TT, Akman CI, Mikati MA, McKhann GM, Goldman JE, Canoll P, Alexander AL, Park KL, Von Allmen GK, Rodziyevska O, Bhattacharjee MB, Lidov HGW, Vogel H, Grant GA, Porter BE, Poduri AH, Crino PB, Heinzen EL. Somatic variants in diverse genes leads to a spectrum of focal cortical malformations. Brain 2022; 145:2704-2720. [PMID: 35441233 PMCID: PMC9612793 DOI: 10.1093/brain/awac117] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
Post-zygotically acquired genetic variants, or somatic variants, that arise during cortical development have emerged as important causes of focal epilepsies, particularly those due to malformations of cortical development. Pathogenic somatic variants have been identified in many genes within the PI3K-AKT-mTOR-signalling pathway in individuals with hemimegalencephaly and focal cortical dysplasia (type II), and more recently in SLC35A2 in individuals with focal cortical dysplasia (type I) or non-dysplastic epileptic cortex. Given the expanding role of somatic variants across different brain malformations, we sought to delineate the landscape of somatic variants in a large cohort of patients who underwent epilepsy surgery with hemimegalencephaly or focal cortical dysplasia. We evaluated samples from 123 children with hemimegalencephaly (n = 16), focal cortical dysplasia type I and related phenotypes (n = 48), focal cortical dysplasia type II (n = 44), or focal cortical dysplasia type III (n = 15). We performed high-depth exome sequencing in brain tissue-derived DNA from each case and identified somatic single nucleotide, indel and large copy number variants. In 75% of individuals with hemimegalencephaly and 29% with focal cortical dysplasia type II, we identified pathogenic variants in PI3K-AKT-mTOR pathway genes. Four of 48 cases with focal cortical dysplasia type I (8%) had a likely pathogenic variant in SLC35A2. While no other gene had multiple disease-causing somatic variants across the focal cortical dysplasia type I cohort, four individuals in this group had a single pathogenic or likely pathogenic somatic variant in CASK, KRAS, NF1 and NIPBL, genes previously associated with neurodevelopmental disorders. No rare pathogenic or likely pathogenic somatic variants in any neurological disease genes like those identified in the focal cortical dysplasia type I cohort were found in 63 neurologically normal controls (P = 0.017), suggesting a role for these novel variants. We also identified a somatic loss-of-function variant in the known epilepsy gene, PCDH19, present in a small number of alleles in the dysplastic tissue from a female patient with focal cortical dysplasia IIIa with hippocampal sclerosis. In contrast to focal cortical dysplasia type II, neither focal cortical dysplasia type I nor III had somatic variants in genes that converge on a unifying biological pathway, suggesting greater genetic heterogeneity compared to type II. Importantly, we demonstrate that focal cortical dysplasia types I, II and III are associated with somatic gene variants across a broad range of genes, many associated with epilepsy in clinical syndromes caused by germline variants, as well as including some not previously associated with radiographically evident cortical brain malformations.
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Affiliation(s)
- Dulcie Lai
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meethila Gade
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hyun Yong Koh
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jinfeng Lu
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole M Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne F Buckley
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Tristan T Sands
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA.,Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Cigdem I Akman
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Mohamad A Mikati
- Department of Neurobiology, Duke University, Durham, NC 27708, USA.,Division of Pediatric Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guy M McKhann
- Department of Neurosurgery, Columbia University, New York Presbyterian Hospital, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allyson L Alexander
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristen L Park
- Department of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gretchen K Von Allmen
- Department of Neurology, McGovern Medical School, Houston, TX 77030, USA.,Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX 77030, USA
| | - Olga Rodziyevska
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX 77030, USA
| | | | - Hart G W Lidov
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Gerald A Grant
- Department of Neurosurgery, Lucile Packard Children's Hospital at Stanford, School of Medicine, Stanford, CA 94305, USA
| | - Brenda E Porter
- Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Annapurna H Poduri
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Erin L Heinzen
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Herzog H, Dogan S, Aktas B, Nel I. Targeted Sequencing of Plasma-Derived vs. Urinary cfDNA from Patients with Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:4101. [PMID: 36077638 PMCID: PMC9454533 DOI: 10.3390/cancers14174101] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
In breast cancer, the genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use. In contrast, only a few studies were performed investigating urinary cfDNA. In this pilot study, we analyzed plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical triple-negative breast cancer patients. We used a targeted next-generation sequencing approach to identify and compare genetic alterations in both body fluids. The cfDNA concentration was higher in urine compared to plasma, but there was no significant correlation between matched samples. Bioinformatical analysis revealed a total of 3339 somatic breast-cancer-related variants (VAF ≥ 3%), whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 shared variants were found in both body fluids. Throughout the cohort, the recovery rate of plasma-derived mutations in matching urinary cfDNA was 47% and even 63% for pathogenic variants only. The most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Notably, a pathogenic CHEK2 (T519M) variant was found in all 30 samples. Taken together, our results indicated that body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile.
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Affiliation(s)
- Henrike Herzog
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Senol Dogan
- Soft Matter Physics Division, Peter-Debye-Institute, University of Leipzig, 04103 Leipzig, Germany
| | - Bahriye Aktas
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Ivonne Nel
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
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11
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Flores-López BA, Ayala-Madrigal MDLL, Moreno-Ortiz JM, Peregrina-Sandoval J, Trujillo-Rojas MÁ, Venegas-Rodríguez JL, Hernández-Ramírez R, Fernández-Galindo MA, Gutiérrez-Angulo M. Molecular Profiling of Tumor Tissue in Mexican Patients with Colorectal Cancer. Curr Issues Mol Biol 2022; 44:3770-3778. [PMID: 36005154 PMCID: PMC9406459 DOI: 10.3390/cimb44080258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Colorectal cancer is a heterogeneous disease with multiple genomic changes that influence the clinical management of patients; thus, the search for new molecular targets remains necessary. The aim of this study was to identify genetic variants in tumor tissues from Mexican patients with colorectal cancer, using massive parallel sequencing. A total of 4813 genes were analyzed in tumoral DNA from colorectal cancer patients, using the TruSight One Sequencing panel. From these, 192 variants with clinical associations were found distributed in 168 different genes, of which 46 variants had not been previous reported in the literature or databases, although genes harboring those variants had already been described in colorectal cancer. Enrichment analysis of the affected genes was performed using Reactome software; pathway over-representation showed significance for disease, signal transduction, and immune system subsets in all patients, while exclusive subsets such as DNA repair, autophagy, and RNA metabolism were also found. Those characteristics, whether individual or shared, could give tumors specific capabilities for survival, aggressiveness, or response to treatment. Our results can be useful for future investigations targeting specific characteristics of tumors in colorectal cancer patients. The identification of exclusive or common pathways in colorectal cancer patients could be important for better diagnosis and personalized cancer treatment.
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Affiliation(s)
- Beatriz Armida Flores-López
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - María de la Luz Ayala-Madrigal
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Miguel Moreno-Ortiz
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Jorge Peregrina-Sandoval
- Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara 45200, Jalisco, Mexico
| | - Miguel Ángel Trujillo-Rojas
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Luis Venegas-Rodríguez
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Rosario Hernández-Ramírez
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Alejandra Fernández-Galindo
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Melva Gutiérrez-Angulo
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Correspondence:
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12
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Wong AM, Ding X, Wong AM, Xu M, Zhang L, Leung HH, Chan AW, Song QX, Kwong J, Chan LK, Man M, He M, Chen J, Zhang Z, You W, Lau C, Yu A, Wei Y, Yuan Y, Lai PB, Zhao J, Man K, Yu J, Kahn M, Wong N. Unique molecular characteristics of NAFLD-associated liver cancer accentuate β-catenin/TNFRSF19-mediated immune evasion. J Hepatol 2022; 77:410-23. [PMID: 35351523 DOI: 10.1016/j.jhep.2022.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/07/2022] [Accepted: 03/01/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS The hepatic manifestation of the metabolic syndrome, non-alcoholic fatty liver disease (NAFLD), can lead to the development of hepatocellular carcinoma (HCC). Despite a strong causative link, NAFLD-HCC is often underrepresented in systematic genome explorations. METHODS Herein, tumor-normal pairs from 100 patients diagnosed with NAFLD-HCC were subject to next-generation sequencing. Bioinformatic analyses were performed to identify key genomic, epigenomic and transcriptomic events associated with the pathogenesis of NAFLD-HCC. Establishment of primary patient-derived NAFLD-HCC culture was used as a representative human model for downstream in vitro investigations of the underlying CTNNB1 S45P driver mutation. A syngeneic immunocompetent mouse model was used to further test the involvement of CTNNB1mutand TNFRSF19 in reshaping the tumor microenvironment. RESULTS Mutational processes operative in the livers of patients with NAFLD inferred susceptibility to tumor formation through defective DNA repair pathways. Dense promoter mutations and dysregulated transcription factors accentuated activated transcriptional regulation in NAFLD-HCC, in particular the enrichment of MAZ-MYC activities. Somatic events common in HCCs arising from NAFLD and viral hepatitis B infection underscore similar driver pathways, although an incidence shift highlights CTNNB1mut dominance in NAFLD-HCC (33%). Immune exclusion correlated evidently with CTNNB1mut. Chromatin immunoprecipitation-sequencing integrated with transcriptome and immune profiling revealed a unique transcriptional axis, wherein CTNNB1mut leads to an upregulation of TNFRSF19 which subsequently represses senescence-associated secretory phenotype-like cytokines (including IL6 and CXCL8). This phenomenon could be reverted by the Wnt-modulator ICG001. CONCLUSIONS The unique mutational processes in the livers of patients with NAFLD and NAFLD-HCC allude to a "field effect" involving a gain-of-function role of CTNNB1 mutations in immune exclusion. LAY SUMMARY The increasing prevalence of metabolic syndrome in adult populations means that NAFLD is poised to be the major cause of liver cancer in the 21st century. We showed a strong "field effect" in the livers of patients with NAFLD, wherein activated β-catenin was involved in reshaping the tumor-immune microenvironment.
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13
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Abstract
Synonymous single nucleotide variants (sSNVs) are often considered functionally silent, but a few cases of cancer-causing sSNVs have been reported. From available databases, we collected four categories of sSNVs: germline, somatic in normal tissues, somatic in cancerous tissues, and putative cancer drivers. We found that screening sSNVs for recurrence among patients, conservation of the affected genomic position, and synVep prediction (synVep is a machine learning-based sSNV effect predictor) recovers cancer driver variants (termed proposed drivers) and previously unknown putative cancer genes. Of the 2.9 million somatic sSNVs found in the COSMIC database, we identified 2111 proposed cancer driver sSNVs. Of these, 326 sSNVs could be further tagged for possible RNA splicing effects, RNA structural changes, and affected RBP motifs. This list of proposed cancer driver sSNVs provides computational guidance in prioritizing the experimental evaluation of synonymous mutations found in cancers. Furthermore, our list of novel potential cancer genes, galvanized by synonymous mutations, may highlight yet unexplored cancer mechanisms.
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Affiliation(s)
- Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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14
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Azzollini J, Vingiani A, Agnelli L, Tamborini E, Perrone F, Conca E, Capone I, Busico A, Peissel B, Rosina E, Ducceschi M, Mantiero M, Lopez S, Raspagliesi F, Niger M, Duca M, Damian S, Proto C, de Braud F, Pruneri G, Manoukian S. Management of BRCA Tumour Testing in an Integrated Molecular Tumour Board Multidisciplinary Model. Front Oncol 2022; 12:857515. [PMID: 35463374 PMCID: PMC9026437 DOI: 10.3389/fonc.2022.857515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Tumour testing of the BRCA1/2 genes is routinely performed in patients with different cancer histological subtypes. To accurately identify patients with tumour-detected germline pathogenic variants (PVs) is a relevant issue currently under investigation. This study aims at evaluating the performance of the tumour-to-germline diagnostic flowchart model defined at our Institutional Molecular Tumour Board (MTB). Results from tumour BRCA sequencing of 641 consecutive unselected cancer patients were discussed during weekly MTB meetings with the early involvement of clinical geneticists for appropriate referral to genetic counselling. The overall tumour detection rate of BRCA1/2 PVs was 8.7% (56/641), ranging from 24.4% (31/127) in high-grade ovarian cancer to 3.9% (12/304) in tumours not associated with germline BRCA1/2 PVs. Thirty-seven patients with PVs (66%) were evaluated by a clinical geneticist, and in 24 of them (64.9%), germline testing confirmed the presence of the PV in blood. Nine of these patients (37.5%) were not eligible for germline testing according to the criteria in use at our institution. Cascade testing was subsequently performed on 18 relatives. The tumour-to-germline diagnostic pipeline, developed in the framework of our institutional MTB, compared with guideline-based germline testing following genetic counselling, proved to be effective in identifying a higher number of germline BRCA PVs carriers.
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Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Erica Rosina
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monika Ducceschi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Mantiero
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Lopez
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesco Raspagliesi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Duca
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Damian
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo de Braud
- Oncology and Hemato-oncology Department, University of Milan, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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15
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Salvo M, González-Feliú E, Toro J, Gallegos I, Maureira I, Miranda-González N, Barajas O, Bustamante E, Ahumada M, Colombo A, Armisén R, Villamán C, Ibañez C, Bravo ML, Sanhueza V, Spencer ML, de Toro G, Morales E, Bizama C, García P, Carrasco AM, Gutiérrez L, Bermejo JL, Verdugo RA, Marcelain K. Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America. J Pers Med 2021; 11:jpm11090899. [PMID: 34575676 PMCID: PMC8472524 DOI: 10.3390/jpm11090899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/29/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing (NGS) is progressively being used in clinical practice. However, several barriers preclude using this technology for precision oncology in most Latin American countries. To overcome some of these barriers, we have designed a 25-gene panel that contains predictive biomarkers for most current and near-future available therapies in Chile and Latin America. Library preparation was optimized to account for low DNA integrity observed in formalin-fixed paraffin-embedded tissue. The workflow includes an automated bioinformatic pipeline that accounts for the underrepresentation of Latin Americans in genome databases. The panel detected small insertions, deletions, and single nucleotide variants down to allelic frequencies of 0.05 with high sensitivity, specificity, and reproducibility. The workflow was validated in 272 clinical samples from several solid tumor types, including gallbladder (GBC). More than 50 biomarkers were detected in these samples, mainly in BRCA1/2, KRAS, and PIK3CA genes. In GBC, biomarkers for PARP, EGFR, PIK3CA, mTOR, and Hedgehog signaling inhibitors were found. Thus, this small NGS panel is an accurate and sensitive method that may constitute a more cost-efficient alternative to multiple non-NGS assays and costly, large NGS panels. This kind of streamlined assay with automated bioinformatics analysis may facilitate the implementation of precision medicine in Latin America.
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Affiliation(s)
- Mauricio Salvo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Evelin González-Feliú
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Jessica Toro
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Iván Gallegos
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Pathology, Hospital Clínico de la Universidad de Chile, Santiago 8380456, Chile
| | - Ignacio Maureira
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Medical Technology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile
| | - Nicolás Miranda-González
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Internal Medicine, Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
- Fundación Arturo López Pérez, Santiago 7500921, Chile; (E.B.); (A.M.C.)
| | - Eva Bustamante
- Fundación Arturo López Pérez, Santiago 7500921, Chile; (E.B.); (A.M.C.)
| | - Mónica Ahumada
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Internal Medicine, Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | - Alicia Colombo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Pathology, Hospital Clínico de la Universidad de Chile, Santiago 8380456, Chile
| | - Ricardo Armisén
- Center for Genetics and Genomics, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Camilo Villamán
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Carolina Ibañez
- Department of Hematology & Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile (PUC), Santiago 3580000, Chile; (C.I.); (M.L.B.)
| | - María Loreto Bravo
- Department of Hematology & Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile (PUC), Santiago 3580000, Chile; (C.I.); (M.L.B.)
| | - Verónica Sanhueza
- Department of Pathology, Hospital Padre Hurtado, Santiago 8710022, Chile;
| | - M. Loreto Spencer
- Department of Pathology, Hospital Clínico Regional Guillermo Grant Benavente, Concepción 4070038, Chile;
| | - Gonzalo de Toro
- School of Medical Technology, Universidad Austral de Chile at Puerto Montt, Puerto Montt 5110566, Chile;
| | - Erik Morales
- Department of Pathology, Hospital Regional de Talca, Talca 3460000, Chile;
- Department of Preclinical Sciences, Faculty of Medicine, Universidad Católica del Maule, Talca 3460000, Chile
| | - Carolina Bizama
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 3580000, Chile; (C.B.); (P.G.)
| | - Patricia García
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 3580000, Chile; (C.B.); (P.G.)
| | | | - Lorena Gutiérrez
- Department of Pathology, Hospital San Juan de Dios, Santiago 8320000, Chile;
| | | | - Ricardo A. Verdugo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Human Genetics Program, ICBM, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile
- Correspondence: (R.A.V.); (K.M.); Tel.: +56-22978-9527 (R.A.V.); +56-22978-9562 (K.M.)
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Correspondence: (R.A.V.); (K.M.); Tel.: +56-22978-9527 (R.A.V.); +56-22978-9562 (K.M.)
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16
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Abstract
Copy number variants (CNVs) have been implicated in neuropsychiatric disorders, with rare-inherited and de novo CNVs (dnCNVs) having large effects on disease liability. Recent studies started exploring a class of dnCNVs that occur post-zygotically, and are therefore present in some but not all cells of the body. Analogous to conditional mutations in animal models, the presence of risk mutations in a fraction of cells has the potential to enlighten how damaging mutations affect cell-type/cell-circuit specific pathologies leading to neuropsychiatric manifestations. Although mosaic CNVs appear to contribute to a modest fraction of risk (0.3-0.5%), expanding our insights about them with more sensitive experimental and statistical methods, has the potential to help clarify mechanisms of neuropsychiatric disease.
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Affiliation(s)
- Eduardo A Maury
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Bioinformatics & Integrative Genomics Program and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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van der Made CI, Potjewijd J, Hoogstins A, Willems HPJ, Kwakernaak AJ, de Sevaux RGL, van Daele PLA, Simons A, Heijstek M, Beck DB, Netea MG, van Paassen P, Elizabeth Hak A, van der Veken LT, van Gijn ME, Hoischen A, van de Veerdonk FL, Leavis HL, Rutgers A. Adult-onset autoinflammation caused by somatic mutations in UBA1: A Dutch case series of patients with VEXAS. J Allergy Clin Immunol 2021; 149:432-439.e4. [PMID: 34048852 DOI: 10.1016/j.jaci.2021.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND A novel autoinflammatory syndrome was recently described in male patients who harbored somatic mutations in the X-chromosomal UBA1 gene. These patients were characterized by adult-onset, treatment-refractory inflammation with fever, cytopenia, dysplastic bone marrow, vacuoles in myeloid and erythroid progenitor cells, cutaneous and pulmonary inflammation, chondritis, and vasculitis, which is abbreviated as VEXAS. OBJECTIVE This study aimed to (retrospectively) diagnose VEXAS in patients who had previously been registered as having unclassified autoinflammation. We furthermore aimed to describe clinical experiences with this multifaceted, complex disease. METHODS A systematic reanalysis of whole-exome sequencing data from a cohort of undiagnosed patients with autoinflammation from academic hospitals in The Netherlands was performed. When no sequencing data were available, targeted Sanger sequencing was applied in cases with high clinical suspicion of VEXAS. RESULTS A total of 12 male patients who carried mutations in UBA1 were identified. These patients presented with adult-onset (mean age 67 years, range 47-79 years) autoinflammation with systemic symptoms, elevated inflammatory parameters, and multiorgan involvement, most typically involving the skin and bone marrow. Novel features of VEXAS included interstitial nephritis, cardiac involvement, stroke, and intestinal perforation related to treatment with tocilizumab. Although many types of treatment were initiated, most patients became treatment-refractory, with a high mortality rate of 50%. CONCLUSION VEXAS should be considered in the differential diagnosis of males with adult-onset autoinflammation characterized by systemic symptoms and multiorgan involvement. Early diagnosis can prevent unnecessary diagnostic procedures and provide better prognostic information and more suitable treatment options, including stem cell transplantation.
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Affiliation(s)
- Caspar I van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judith Potjewijd
- Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Annemiek Hoogstins
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Huub P J Willems
- Department of Internal Medicine, Maxima Medisch Centrum, Eindhoven, The Netherlands
| | - Arjan J Kwakernaak
- Department of Internal Medicine and Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, location AMC/Meibergdreef, Amsterdam, The Netherlands
| | - Ruud G L de Sevaux
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul L A van Daele
- Department of Internal Medicine and Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marloes Heijstek
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Md
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pieter van Paassen
- Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - A Elizabeth Hak
- Department of Internal Medicine and Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, location AMC/Meibergdreef, Amsterdam, The Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Abraham Rutgers
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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18
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Min YK, Lee YK, Nam SH, Kim JK, Park KS, Kim JW. Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential. Clin Chem 2021; 66:832-841. [PMID: 32395759 DOI: 10.1093/clinchem/hvaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Because next-generation sequencing (NGS) for detecting somatic mutations has been adopted in clinical fields, both qualitative and quantitative QC of the somatic variants through whole coding regions detected by NGS is crucial. However, specific applications or guidelines, especially for quantitative QC, are currently insufficient. Our goal was to devise a practical approach for both quantitative and qualitative QC using an example of detecting clonal hematopoiesis of indeterminate potential (CHIP). METHODS We applied the QC scheme using commercial reference materials and in-house QC materials (IQCM) composed of haplotype map and cancer cell lines for monitoring CHIP. RESULTS This approach efficiently validated a customized CHIP NGS assay. Accuracy, analytical sensitivity, analytical specificity, qualitative precision (concordance), and limit of detection achieved were 99.87%, 98.53%, 100.00%, 100.00%, and 1.00%, respectively. The quantitative precision analysis also had a higher CV percentage at a lower alternative read depth (R2 = 0.749∼0.858). Use of IQCM ensured more than 100-fold reduction in the cost per run compared with that achieved using commercial reference materials. CONCLUSION Our approach determined the general analytical performance of NGS for detecting CHIP and recognized limitations such as lower precision at a lower level of variant burden. This approach could also be theoretically expanded to a general NGS assay for detecting somatic variants. Considering the reliable NGS results and cost-effectiveness, we propose the use of IQCM for QC of NGS assays at clinical laboratories.
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Affiliation(s)
- Young Kyu Min
- Department of Biomedical Laboratory Science, Dankook University, Chungnam, Korea
| | - Young Kee Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
| | | | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, Dankook University, Chungnam, Korea
| | - Kyung Sun Park
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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19
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Koppolu A, Maksym RB, Paskal W, Machnicki M, Rak B, Pępek M, Garbicz F, Pełka K, Kuśmierczyk Z, Jacko J, Rydzanicz M, Banach-Orłowska M, Stokłosa T, Płoski R, Malejczyk J, Włodarski PK. Epithelial Cells of Deep Infiltrating Endometriosis Harbor Mutations in Cancer Driver Genes. Cells 2021; 10:749. [PMID: 33805315 PMCID: PMC8065889 DOI: 10.3390/cells10040749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Endometriosis is an inflammatory condition manifested by the presence of endometrial-like tissue outside of the uterine cavity. The most common clinical presentations of endometriosis are dysmenorrhea, infertility, and severe pelvic pain. Few hypotheses attempt to explain the pathogenesis of endometriosis; however, none of the theories have been fully confirmed or considered universal. We examined somatic mutations in eutopic endometrium samples, deep endometriotic nodules and peripheral blood from 13 women with deep endometriosis of the rectovaginal space. Somatic variants were identified in laser microdissected samples using next-generation sequencing. A custom panel of 1296 cancer-related genes was employed, and selected genes representing cancer drivers and non-drivers for endometrial and ovarian cancer were thoroughly investigated. All 59 detected somatic variants were of low mutated allele frequency (<10%). In deep ectopic lesions, detected variants were significantly more often located in cancer driver genes, whereas in eutopic endometrium, there was no such distribution. Our results converge with other reports, where cancer-related mutations were found in endometriosis without cancer, particularly recurrent KRAS mutations. Genetic alterations located in ectopic endometriotic nodules could contribute to their formation; nevertheless, to better understand the pathogenesis of this disease, more research in this area must be performed.
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Affiliation(s)
- Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
| | - Radosław B. Maksym
- Department of Reproductive Health, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland
| | - Wiktor Paskal
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Marcin Machnicki
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Beata Rak
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
| | - Monika Pępek
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Filip Garbicz
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, 02-781 Warsaw, Poland
| | - Kacper Pełka
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Zofia Kuśmierczyk
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Joanna Jacko
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
| | - Magdalena Banach-Orłowska
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
| | - Tomasz Stokłosa
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
| | - Jacek Malejczyk
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
- Laboratory for Experimental Immunology, Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
| | - Paweł K. Włodarski
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
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20
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Tian T, Cao X, Chen Y, Jin L, Li Z, Han X, Lin Y, Wlodarczyk BJ, Finnell RH, Yuan Z, Wang L, Ren A, Lei Y. Somatic and de novo Germline Variants of MEDs in Human Neural Tube Defects. Front Cell Dev Biol 2021; 9:641831. [PMID: 33748132 PMCID: PMC7969791 DOI: 10.3389/fcell.2021.641831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 02/05/2023] Open
Abstract
Background Neural tube defects (NTDs) are among the most common and severe congenital defects in humans. Their genetic etiology is complex and remains poorly understood. The Mediator complex (MED) plays a vital role in neural tube development in animal models. However, no studies have yet examined the role of its human homolog in the etiology of NTDs. Methods In this study, 48 pairs of neural lesion site and umbilical cord tissues from NTD and 21 case-parent trios were involved in screening for NTD-related somatic and germline de novo variants. A series of functional cell assays were performed. We generated a Med12 p.Arg1784Cys knock-in mouse using CRISPR/Cas9 technology to validate the human findings. Results One somatic variant, MED12 p.Arg1782Cys, was identified in the lesion site tissue from an NTD fetus. This variant was absent in any other normal tissue from different germ layers of the same case. In 21 case-parent trios, one de novo stop-gain variant, MED13L p.Arg1760∗, was identified. Cellular functional studies showed that MED12 p.Arg1782Cys decreased MED12 protein level and affected the regulation of MED12 on the canonical-WNT signaling pathway. The Med12 p.Arg1784Cys knock-in mouse exhibited exencephaly and spina bifida. Conclusion These findings provide strong evidence that functional variants of MED genes are associated with the etiology of some NTDs. We demonstrated a potentially important role for somatic variants in the occurrence of NTDs. Our study is the first study in which an NTD-related variant identified in humans was validated in mice using CRISPR/Cas9 technology.
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Affiliation(s)
- Tian Tian
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xuanye Cao
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Yongyan Chen
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Lei Jin
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiwen Li
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xiao Han
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Ying Lin
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Bogdan J Wlodarczyk
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Richard H Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States.,Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Linlin Wang
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Aiguo Ren
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yunping Lei
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
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21
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van Rooij J, Mol MO, Melhem S, van der Wal P, Arp P, Paron F, Donker Kaat L, Seelaar H, Miedema SSM, Oshima T, Eggen BJL, Uitterlinden A, van Meurs J, van Kesteren RE, Smit AB, Buratti E, van Swieten JC. Somatic TARDBP variants as a cause of semantic dementia. Brain 2021; 143:3827-3841. [PMID: 33155043 PMCID: PMC7805802 DOI: 10.1093/brain/awaa317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/13/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
The aetiology of late-onset neurodegenerative diseases is largely unknown. Here we investigated whether de novo somatic variants for semantic dementia can be detected, thereby arguing for a more general role of somatic variants in neurodegenerative disease. Semantic dementia is characterized by a non-familial occurrence, early onset (<65 years), focal temporal atrophy and TDP-43 pathology. To test whether somatic variants in neural progenitor cells during brain development might lead to semantic dementia, we compared deep exome sequencing data of DNA derived from brain and blood of 16 semantic dementia cases. Somatic variants observed in brain tissue and absent in blood were validated using amplicon sequencing and digital PCR. We identified two variants in exon one of the TARDBP gene (L41F and R42H) at low level (1-3%) in cortical regions and in dentate gyrus in two semantic dementia brains, respectively. The pathogenicity of both variants is supported by demonstrating impaired splicing regulation of TDP-43 and by altered subcellular localization of the mutant TDP-43 protein. These findings indicate that somatic variants may cause semantic dementia as a non-hereditary neurodegenerative disease, which might be exemplary for other late-onset neurodegenerative disorders.
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Affiliation(s)
- Jeroen van Rooij
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shamiram Melhem
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pelle van der Wal
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pascal Arp
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Francesca Paron
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Laura Donker Kaat
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Suzanne S M Miedema
- Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Takuya Oshima
- Department of Biomedical Sciences of Cells and Systems, section Molecular Neurobiology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells and Systems, section Molecular Neurobiology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - André Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ronald E van Kesteren
- Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - August B Smit
- Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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22
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Gu HY, Lin LL, Zhang C, Yang M, Zhong HC, Wei RX. The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study. Front Oncol 2020; 10:1317. [PMID: 32850416 PMCID: PMC7396489 DOI: 10.3389/fonc.2020.01317] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Low response rates to immunotherapy have been reported in soft tissue sarcoma (STS). There are few predictive biomarkers of response, and the tumor immune microenvironment associated with progression and prognosis remains unclear in STS. Gene expression data from the Cancer Genome Atlas were used to identify the immune-related prognostic genes (IRPGs) and construct the immune gene-related prognostic model (IGRPM). The tumor immune microenvironment was characterized to reveal differences between patients with different prognoses. Furthermore, somatic mutation data and DNA methylation data were analyzed to understand the underlying mechanism leading to different prognoses. The IGRPM was constructed using five IRPGs (IFIH1, CTSG, STC2, SECTM1, and BIRC5). Two groups (high- and low-risk patients) were identified based on the risk score. Low-risk patients with higher overall survival time had higher immune scores, more immune cell infiltration (e.g., CD8 T cell and activated natural killer cells), higher expression of immune-stimulating molecules, higher stimulating cytokines and corresponding receptors, higher innate immunity molecules, and stronger antigen-presenting capacity. However, inhibition of immunity was observed in low-risk patients owing to the higher expression of immune checkpoint molecules and inhibiting cytokines. High-risk patients had high tumor mutation burden, which did not significantly influence survival. Gene set enrichment analysis further revealed that pathways of cell cycle and cancers were activated in high-risk patients. DNA methylation analysis indicated that relative high methylation was associated with better overall survival. Finally, the age, mitotic counts, and risk scores were independent prognostic factors for STS. Five IRPGs performed well in risk stratification of patients and are candidate biomarkers for predicting response to immunotherapy. Differences observed through the multi-omic study of patients with different prognoses may reveal the underlying mechanism of the development and progression of STS, and thereby improve treatment.
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Affiliation(s)
- Hui-Yun Gu
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lu-Lu Lin
- Department of Pathology and Pathophysiology, School of Basic Medicine, Wuhan University, Wuhan, China
| | - Chao Zhang
- Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Min Yang
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hou-Cheng Zhong
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ren-Xiong Wei
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
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23
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Li MM, Chao E, Esplin ED, Miller DT, Nathanson KL, Plon SE, Scheuner MT, Stewart DR; ACMG Professional Practice and Guidelines Committee. Points to consider for reporting of germline variation in patients undergoing tumor testing: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1142-8. [PMID: 32321997 DOI: 10.1038/s41436-020-0783-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 02/08/2023] Open
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24
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Zhang Z, Gao K, Liu Q, Zhou J, Li X, Lang N, Liu M, Wang T, Zhang J, Wang H, Dong Y, Ji T, Wang S, Liu X, Jiang Y, Cai L, Wu Y. Somatic variants in new candidate genes identified in focal cortical dysplasia type II. Epilepsia 2020; 61:667-678. [PMID: 32216069 DOI: 10.1111/epi.16481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Focal cortical dysplasia type II (FCDII) is a malformation of cortex development commonly found in children with drug-resistant epilepsy. FCDII has been associated with somatic mutations in mammalian target of rapamycin (mTOR)-related pathway genes and an upregulation of mTOR. Somatic mutations were found in 10%-63% of FCDII samples; the frequency of the mutant allele was 0.93%-33.5%. This study aimed to find new candidate genes involved in FCDII. METHODS We collected resected FCD lesions, perilesional brain tissues, and peripheral blood from 17 children with pathologically confirmed FCDII. We performed whole exome sequencing and followed a set of screening and analysis strategies to identify potentially deleterious somatic variants (PDSVs) in brain-expressed genes. We performed site-specific amplicon sequencing to validate the results. We also performed an in vitro functional study on an IRS1 variant. RESULTS In six of 17 samples, we identified seven PDSVs in seven genes, including two frameshift variants and five missense variants. The frequencies of the variant allele were 1.29%-5.50%. The genes were MTOR, TSC2, IRS1, RAB6B, RALA, HTR6, and ZNF337. PDSVs in IRS1, RAB6B, ZNF337, RALA, and HTR6 had not been previously associated with FCD. In one lesion, two PDSVs were found in two genes. In a transfected cell line, we demonstrated that the c.1791dupG (identified in FCDII from Patient 1) led to a truncated IRS1 and significant mTOR hyperactivation compared to cells that carried wild-type IRS1. mTOR was also activated in FCDII tissue from Patient 1. SIGNIFICANCE Seven PDSVs were identified in FCDII lesions in six of 17 children. Five variant genes had not been previously associated with cortical malformations. We demonstrated that the IRS1 variant led to mTOR hyperactivation in vitro. Although functional experiments are needed, the results provide evidence for novel candidate genes in the pathogenesis of FCDII.
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Affiliation(s)
- Zhongbin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Kai Gao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qingzhu Liu
- Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Jiapeng Zhou
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiyuan Li
- Institute of Computing Technology, Chinese Academy of Science, Beijing, China
| | - Na Lang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ming Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Tianshuang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hui Wang
- Department of Pathology, Peking University First Hospital, Beijing, China
| | - Ying Dong
- Department of Pathology, Peking University First Hospital, Beijing, China
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Shuang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Xiaoyan Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Lixin Cai
- Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
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25
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Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S. A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Nat Cancer 2020; 1:249-263. [PMID: 32118208 PMCID: PMC7048622 DOI: 10.1038/s43018-020-0027-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses.
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Affiliation(s)
- Andrea Degasperi
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tauanne Dias Amarante
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Czarnecki
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Scott Shooter
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xueqing Zou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dominik Glodzik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sandro Morganella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Arjun S Nanda
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Cherif Badja
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gene Koh
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie E Momen
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | | | - João M L Dias
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jamie Young
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Davies
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Serena Nik-Zainal
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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26
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Van Horebeek L, Dubois B, Goris A. Somatic Variants: New Kids on the Block in Human Immunogenetics. Trends Genet 2019; 35:935-947. [PMID: 31668909 DOI: 10.1016/j.tig.2019.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 01/21/2023]
Abstract
Somatic variants are not inherited but acquired during an individual's lifetime, and individuals are increasingly considered as complex mosaics of genetically distinct cells. Whereas this concept is long-recognized in cancer, this review focuses on the growing role of somatic variants in immune cells in nonmalignant immune-related disorders, such as primary immunodeficiency and autoimmune diseases. Older case reports described somatic variants early in development, leading to large numbers of affected cells and severe phenotypes. Thanks to technological evolution, it is now feasible to detect somatic variants occurring later in life and affecting fewer cells. Hence, only recently is the scale at which somatic variants contribute to monogenic diseases being uncovered and is their contribution to complex diseases being explored systematically.
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Affiliation(s)
- L Van Horebeek
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute, 3000 Leuven, Belgium
| | - B Dubois
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute, 3000 Leuven, Belgium; University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
| | - A Goris
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute, 3000 Leuven, Belgium.
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27
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Tanimoto K, Muramatsu T, Inazawa J. Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas. Cancer Med 2019; 8:7372-7384. [PMID: 31631560 PMCID: PMC6885893 DOI: 10.1002/cam4.2619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022] Open
Abstract
Owing to the development of next-generation sequencing (NGS) technologies, a large number of somatic variants have been identified in various types of cancer. However, the functional significance of most somatic variants remains unknown. Somatic variants that occur in exonic splicing enhancer (ESE) regions are thought to prevent serine and arginine-rich (SR) proteins from binding to ESE sequence motifs, which leads to exon skipping. We computationally identified somatic variants in ESEs by compiling numerous open-access datasets from The Cancer Genome Atlas (TCGA). Using somatic variants and RNA-seq data from 9635 patients across 32 TCGA projects, we identified 646 ESE-disrupting variants. The false positive rate of our method, estimated using a permutation test, was approximately 1%. Of these ESE-disrupting variants, approximately 71% were located in the binding motifs of four classical SR proteins. ESE-disrupting variants occurred in proportion to the number of somatic variants, but not necessarily in the specific genes associated with the biological processes of cancer. Existing bioinformatics tools could not predict the pathogenicity of ESE-disrupting variants identified in this study, although these variants could cause exon skipping. We demonstrated that ESE-disrupting nonsense variants tended to escape nonsense-mediated decay surveillance. Using integrated analyses of open access data, we could specifically identify ESE-disrupting variants. We have generated a powerful tool, which can handle datasets without normal samples or raw data, and thus contribute to reducing variants of uncertain significance because our statistical approach only uses the exon-junction read counts from the tumor samples.
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Affiliation(s)
- Kousuke Tanimoto
- Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Genomics Research Support Unit, Research Core, Tokyo Medical and Dental University (TMDU), Japan, Tokyo, Japan
| | - Tomoki Muramatsu
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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28
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Yip S, Christofides A, Banerji S, Downes MR, Izevbaye I, Lo B, MacMillan A, McCuaig J, Stockley T, Yousef GM, Spatz A. A Canadian guideline on the use of next-generation sequencing in oncology. Curr Oncol 2019; 26:e241-e254. [PMID: 31043833 PMCID: PMC6476432 DOI: 10.3747/co.26.4731] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.
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Affiliation(s)
- S Yip
- Cancer Genetics and Genomics Lab, BC Cancer, Vancouver, BC
| | | | - S Banerji
- Department of Medical Oncology, CancerCare Manitoba, Winnipeg, MB
| | - M R Downes
- Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON
| | - I Izevbaye
- Division of Molecular Pathology, Laboratory Medicine and Pathology, University of Alberta Hospital, Edmonton, AB
| | - B Lo
- Molecular Diagnostics, The Ottawa Hospital, Ottawa, ON
| | - A MacMillan
- Provincial Medical Genetics Program, St. John's, NL
| | - J McCuaig
- Princess Margaret Cancer Centre, Toronto, ON
| | - T Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, Toronto, ON
| | - G M Yousef
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON
| | - A Spatz
- Departments of Pathology and Oncology, McGill University, McGill University Health Centre and Lady Davis Institute, Montreal, QC
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29
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Liu KX, Lamba N, Hwang WL, Niemierko A, DuBois SG, Haas-Kogan DA. Risk stratification by somatic mutation burden in Ewing sarcoma. Cancer 2019; 125:1357-1364. [PMID: 30602061 DOI: 10.1002/cncr.31919] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022]
Abstract
BACKGROUND Up to one-third of patients with localized Ewing sarcoma (ES) develop recurrent disease, but current biomarkers do not accurately identify this high-risk group. Therefore, the objective of this study was to determine the utility of mutational burden in predicting outcomes in patients with localized ES. METHODS Clinical and genomic data from 99 patients with ES, of whom 63 had localized disease at diagnosis, were obtained from the cBioPortal for Cancer Genomics. Genomic data included the type and number of somatic mutations using cBioPortal mutation calling. Primary endpoints were overall survival (OS) and the time to progression (TTP). RESULTS Patients had a median number of 11 somatic mutations. Patients were stratified according to whether they had a lower or higher mutational burden if they had ≤11 or >11 mutations, respectively. Higher mutational burden was significantly associated with inferior OS and TTP, a finding that was confirmed by univariate and multivariable analyses. In patients who had localized disease at diagnosis, higher mutational burden was the only variable significantly associated with inferior OS and TTP. The presence of a mutation in either stromal antigen 2 (STAG2) or tumor protein 53 (TP53), both of which were correlated previously with shorter OS in patients with ES, were significantly associated with higher mutational burden. Upon stratifying patients who had localized disease based on a standard panel of cancer genes, higher risk stratification was correlated significantly with inferior TTP and trended toward significance with inferior OS. CONCLUSIONS Patients who have localized ES and a higher mutational burden have inferior OS and TTP compared with those who have lower mutation burden. The current findings suggest that the somatic mutation burden can be used to better risk stratify these patients and to guide clinical decision making.
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Affiliation(s)
- Kevin X Liu
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Nayan Lamba
- Harvard Medical School, Boston, Massachusetts
| | - William L Hwang
- Harvard Radiation Oncology Program, Harvard Medical School, Boston, Massachusetts
| | - Andrzej Niemierko
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven G DuBois
- Harvard Medical School, Boston, Massachusetts.,Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Daphne A Haas-Kogan
- Harvard Medical School, Boston, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham & Women's Hospital, Boston Children's Hospital, Boston, Massachusetts
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30
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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31
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Maresca L, Lodovichi S, Lorenzoni A, Cervelli T, Monaco R, Spugnesi L, Tancredi M, Falaschi E, Zavaglia K, Landucci E, Roncella M, Congregati C, Gadducci A, Naccarato AG, Caligo MA, Galli A. Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development. Front Genet 2018; 9:397. [PMID: 30283497 PMCID: PMC6156519 DOI: 10.3389/fgene.2018.00397] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/31/2018] [Indexed: 01/07/2023] Open
Abstract
In this study, we determined if BRCA1 partners involved in DNA double-strand break (DSB) and mismatch repair (MMR) may contribute to breast and ovarian cancer development. Taking advantage the functional conservation of DNA repair pathways between yeast and human, we expressed several BRCA1 missense variants in DNA repair yeast mutants to identify functional interaction between BRCA1 and DNA repair in BRCA1-induced genome instability. The pathogenic p.C61G, pA1708E, p.M775R, and p.I1766S, and the neutral pS1512I BRCA1 variants increased intra-chromosomal recombination in the DNA-repair proficient strain RSY6. In the mre11, rad50, rad51, and msh6 deletion strains, the BRCA1 variants p.C61G, pA1708E, p.M775R, p.I1766S, and pS1215I did not increase intra-chromosomal recombination suggesting that a functional DNA repair pathway is necessary for BRCA1 variants to determine genome instability. The pathogenic p.C61G and p.I1766S and the neutral p.N132K, p.Y179C, and p.N550H variants induced a significant increase of reversion in the msh2Δ strain; the neutral p.Y179C and the pathogenic p.I1766S variant induced gene reversion also, in the msh6Δ strain. These results imply a functional interaction between MMR and BRCA1 in modulating genome instability. We also performed a somatic mutational screening of MSH6, RAD50, MRE11A, and RAD51 genes in tumor samples from 34 patients and identified eight pathogenic or predicted pathogenic rare missense variants: four in MSH6, one in RAD50, one in MRE11A, and two in RAD51. Although we found no correlation between BRCA1 status and these somatic DNA repair variants, this study suggests that somatic missense variants in DNA repair genes may contribute to breast and ovarian tumor development.
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Affiliation(s)
- Luisa Maresca
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy.,PhD Program in Clinical and Translational Sciences, University of Pisa, Pisa, Italy
| | - Alessandra Lorenzoni
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Rossella Monaco
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Laura Spugnesi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Elisabetta Falaschi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Katia Zavaglia
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | | | | | - Caterina Congregati
- Department of Clinical and Experimental Medicine, Division of Internal Medicine, University Hospital of Pisa, Pisa, Italy
| | - Angiolo Gadducci
- Department of Clinical and Experimental Medicine, Division of Gynecology and Obstetrics, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
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32
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Min JW, Koh Y, Kim DY, Kim HL, Han JA, Jung YJ, Yoon SS, Choi SS. Identification of Novel Functional Variants of SIN3A and SRSF1 among Somatic Variants in Acute Myeloid Leukemia Patients. Mol Cells 2018; 41:465-475. [PMID: 29764005 PMCID: PMC5974623 DOI: 10.14348/molcells.2018.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/25/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022] Open
Abstract
The advent of massively parallel sequencing, also called next-generation sequencing (NGS), has dramatically influenced cancer genomics by accelerating the identification of novel molecular alterations. Using a whole genome sequencing (WGS) approach, we identified somatic coding and noncoding variants that may contribute to leukemogenesis in 11 adult Korean acute myeloid leukemia (AML) patients, with serial tumor samples (primary and relapse) available for 5 of them; somatic variants were identified in 187 AML-related genes, including both novel (SIN3A, C10orf53, PTPRR, and RERGL) and well-known (NPM1, RUNX1, and CEPBA) AML-related genes. Notably, SIN3A expression shows prognostic value in AML. A newly designed method, referred to as "hot-zone" analysis, detected two putative functional noncoding variants that can alter transcription factor binding affinity near PPP1R10 and SRSF1. Moreover, the functional importance of the SRSF1 noncoding variant was further investigated by luciferase assays, which showed that the variant is critical for the regulation of gene expression leading to leukemogenesis. We expect that further functional investigation of these coding and noncoding variants will contribute to a more in-depth understanding of the underlying molecular mechanisms of AML and the development of targeted anti-cancer drugs.
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Affiliation(s)
- Jae-Woong Min
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341,
Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080,
Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080,
Korea
| | - Dae-Yoon Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080,
Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Woman’s University, Seoul 03760,
Korea
| | - Jeong A Han
- Department of Biochemistry and Molecular Biology, School of Medicine, Kangwon National University, Chuncheon 24341,
Korea
| | - Yu-Jin Jung
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341,
Korea
| | - Sung-Soo Yoon
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080,
Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080,
Korea
| | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341,
Korea
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Rabizadeh S, Garner C, Sanborn JZ, Benz SC, Reddy S, Soon-Shiong P. Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer. Oncotarget 2018; 9:19223-19232. [PMID: 29721196 PMCID: PMC5922390 DOI: 10.18632/oncotarget.24973] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
A CMS approved test for lung cancer is based on tumor-only analysis of a targeted 35 gene panel, specifically excluding the use of the patient's normal germline tissue. However, this tumor-only approach increases the risk of mistakenly identifying germline single nucleotide polymorphisms (SNPs) as somatically-derived cancer driver mutations (false positives). 621 patients with 30 different cancer types, including lung cancer, were studied to compare the precision of tumor somatic variant calling in 35 genes using tumor-only DNA sequencing versus tumor-normal DNA plus RNA sequencing. When sequencing of lung cancer was performed using tumor genomes alone without normal germline controls, 94% of variants identified were SNPs and thus false positives. Filtering for common SNPs still resulted in as high as 48% false positive variant calling. With tumor-only sequencing, 29% of lung cancer patients had a false positive variant call in at least one of twelve genes with directly targetable drugs. RNA analysis showed 18% of true somatic variants were not expressed. Thus, sequencing and analysis of both normal germline and tumor genomes is necessary for accurate identification of molecular targets. Treatment decisions based on tumor-only analysis may result in the administration of ineffective therapies while also increasing the risk of negative drug-related side effects.
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Affiliation(s)
| | | | | | | | | | - Patrick Soon-Shiong
- NantOmics, LLC, Culver City, CA, USA.,NantHealth, Inc., Culver City, CA, USA
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34
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Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, Mccoy M, Griffith M, Griffith OL, Mcgarvey P, Kulkarni S. ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research. Pac Symp Biocomput 2018; 23:247-258. [PMID: 29218886 PMCID: PMC5728662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients (1). In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing (2). The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning (3). To achieve truly personalized medicine in oncology, it is critical to catalog cancer sequence variants from MolDx testing for their clinical relevance along with treatment information and patient outcomes, and to do so in a way that supports large-scale data aggregation and new hypothesis generation. One critical challenge to encoding variant data is adopting a standard of annotation of those variants that are clinically actionable. Through the NIH-funded Clinical Genome Resource (ClinGen) (4), in collaboration with NLM's ClinVar database and >50 academic and industry based cancer research organizations, we developed the Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations (5). We are currently involved in collaborative efforts to align the MVLD framework with parallel, complementary sequence variants interpretation clinical guidelines from the Association of Molecular Pathologists (AMP) for clinical labs (6). In order to truly democratize access to MolDx data for care and research needs, these standards must be harmonized to support sharing of clinical cancer variants. Here we describe the processes and methods developed within the ClinGen's Somatic WG in collaboration with over 60 cancer care and research organizations as well as CLIA-certified, CAP-accredited clinical testing labs to develop standards for cancer variant interpretation and sharing.
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Affiliation(s)
- Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington D.C., USA
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35
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Coffee B, Cox HC, Kidd J, Sizemore S, Brown K, Manley S, Mancini-DiNardo D. Detection of somatic variants in peripheral blood lymphocytes using a next generation sequencing multigene pan cancer panel. Cancer Genet 2017; 211:5-8. [PMID: 28279308 DOI: 10.1016/j.cancergen.2017.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%. Overall, 137 (0.06%) individuals were identified as carrying likely somatic PVs, most commonly in TP53 (73), CHEK2 (27), and ATM (20). Among this group, a second PV with a NGS read frequency consistent with a germline variant within the same gene or a different gene on the panel was detected in 21 individuals (15.3%), which is similar to the detection rate in our general testing population. Likely somatic PVs accounted for 38.8% of all PVs in TP53. In comparison, likely somatic PVs accounted for <1% of PVs in most other genes. Likely somatic PVs were more frequently identified in older individuals (p < 0.001). Additional studies are ongoing to further investigate the incidence and clinical implications of somatic variants, enabling the appropriate medical management for these patients.
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Affiliation(s)
- Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - John Kidd
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Scott Sizemore
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Krystal Brown
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Susan Manley
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
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36
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Krishnan N, Gupta S, Palve V, Varghese L, Pattnaik S, Jain P, Khyriem C, Hariharan A, Dhas K, Nair J, Pareek M, Prasad V, Siddappa G, Suresh A, Kekatpure V, Kuriakose M, Panda B. Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence. F1000Res 2015; 4:1215. [PMID: 26834999 PMCID: PMC4706066 DOI: 10.12688/f1000research.7302.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/25/2022] Open
Abstract
Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
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Affiliation(s)
- Neeraja Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Saurabh Gupta
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Vinayak Palve
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Linu Varghese
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Swetansu Pattnaik
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Prach Jain
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Costerwell Khyriem
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Arun Hariharan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Kunal Dhas
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Jayalakshmi Nair
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Manisha Pareek
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Venkatesh Prasad
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Gangotri Siddappa
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India
| | - Amritha Suresh
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India
| | - Vikram Kekatpure
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Bangalore, 560 099, India
| | - Moni Kuriakose
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India; Head and Neck Oncology, Mazumdar Shaw Medical Centre, Bangalore, 560 099, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India; Strand Life Sciences, Bangalore, 560 024, India
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37
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Dumur CI. Available resources and challenges for the clinical annotation of somatic variations. Cancer Cytopathol 2014; 122:730-6. [PMID: 25111663 PMCID: PMC4231254 DOI: 10.1002/cncy.21471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a number of such resources that have been designed to catalog and mine a plethora of germline variants or mutations. However, when analyzing tumor specimens in clinical settings, one may need to use different or ancillary resources that are specific for somatic variants or actionable mutations that may have clinical or treatment implications. The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology. In addition, the current need for collating various annotation sources into one-stop solutions to facilitate faster query execution and better integration into existing laboratory information systems are discussed.
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Affiliation(s)
- Catherine I Dumur
- Department of Pathology, Virginia Commonwealth UniversityRichmond, Virginia
- Corresponding author: Catherine I. Dumur, PhD, Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA 23298; Fax: (804) 827-4738;
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