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Kimura H, Paranal RM, Nanda N, Wood LD, Eshleman JR, Hruban RH, Goggins MG, Klein AP, Roberts NJ. Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance. eLife 2022; 11:71137. [PMID: 35001868 PMCID: PMC8824478 DOI: 10.7554/elife.71137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/06/2022] [Indexed: 12/25/2022] Open
Abstract
Pathogenic germline CDKN2A variants are associated with an increased risk of pancreatic ductal adenocarcinoma (PDAC). CDKN2A variants of uncertain significance (VUSs) are reported in up to 4.3% of patients with PDAC and result in significant uncertainty for patients and their family members as an unknown fraction are functionally deleterious, and therefore, likely pathogenic. Functional characterization of CDKN2A VUSs is needed to reclassify variants and inform clinical management. Twenty-nine germline CDKN2A VUSs previously reported in patients with PDAC or in ClinVar were evaluated using a validated in vitro cell proliferation assay. Twelve of the 29 CDKN2A VUSs were functionally deleterious (11 VUSs) or potentially functionally deleterious (1 VUS) and were reclassified as likely pathogenic variants. Thus, over 40% of CDKN2A VUSs identified in patients with PDAC are functionally deleterious and likely pathogenic. When incorporating VUSs found to be functionally deleterious, and reclassified as likely pathogenic, the prevalence of pathogenic/likely pathogenic CDKN2A in patients with PDAC reported in the published literature is increased to up to 4.1% of patients, depending on family history. Therefore, CDKN2A VUSs may play a significant, unappreciated role in risk of pancreatic cancer. These findings have significant implications for the counselling and care of patients and their relatives.
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Affiliation(s)
- Hirokazu Kimura
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States
| | - Raymond M Paranal
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Human Genetics Predoctoral Training Program, the McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Neha Nanda
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States
| | - Laura D Wood
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - James R Eshleman
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Ralph H Hruban
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Michael G Goggins
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Alison P Klein
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | | | - Nicholas J Roberts
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
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Kavuncuoglu A, Durmaz CD, Gokoz O, Uner A, Kosemehmetoglu K. Undifferentiated Melanoma Resembling Undifferentiated Round Cell Sarcoma: The Diagnostic Power of Molecular Melanoma Signature. Int J Surg Pathol 2021; 30:346-349. [PMID: 34617795 DOI: 10.1177/10668969211052238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Melanomas presenting in primary or metastatic sites with a poorly differentiated histology comprise dedifferentiated (DM) and undifferentiated melanomas (UM), the latter consisting purely of undifferentiated cells and totally lacking immunophenotypic features of melanoma. These entities have a wide morphological spectrum including round cell sarcoma-like features which pose a significant diagnostic challenge. Here we present a case of UM with morphological and immunohistochemical features resembling undifferentiated round cell sarcoma, whose diagnosis could only be established after proper integration of clinical and molecular data. This diagnostically challenging case, fulfilling the previously proposed diagnostic criteria by Agaimy et al, expands the clinicopathological spectrum of DM/UM, highlights the essence of molecular signature, and further emphasizes the importance of patient's history in any morphological setting.
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Affiliation(s)
| | - Ceren Damla Durmaz
- Department of Medical Genetics, 37515Hacettepe University, Ankara, Turkey
| | - Ozay Gokoz
- Department of Pathology, 37515Hacettepe University, Ankara, Turkey
| | - Aysegul Uner
- Department of Pathology, 37515Hacettepe University, Ankara, Turkey
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3
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Jolissaint JS, Soares KC, Seier KP, Kundra R, Gönen M, Shin PJ, Boerner T, Sigel C, Madupuri R, Vakiani E, Cercek A, Harding JJ, Kemeny NE, Connell LC, Balachandran VP, D'Angelica MI, Drebin JA, Kingham TP, Wei AC, Jarnagin WR. Intrahepatic Cholangiocarcinoma with Lymph Node Metastasis: Treatment-Related Outcomes and the Role of Tumor Genomics in Patient Selection. Clin Cancer Res 2021; 27:4101-4108. [PMID: 33963001 DOI: 10.1158/1078-0432.ccr-21-0412] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE Lymph node metastasis (LNM) drastically reduces survival after resection of intrahepatic cholangiocarcinoma (IHC). Optimal treatment is ill defined, and it is unclear whether tumor mutational profiling can support treatment decisions. EXPERIMENTAL DESIGN Patients with liver-limited IHC with or without LNM treated with resection (N = 237), hepatic arterial infusion chemotherapy (HAIC; N = 196), or systemic chemotherapy alone (SYS; N = 140) at our institution between 2000 and 2018 were included. Genomic sequencing was analyzed to determine whether genetic alterations could stratify outcomes for patients with LNM. RESULTS For node-negative patients, resection was associated with the longest median overall survival [OS, 59.9 months; 95% confidence interval (CI), 47.2-74.31], followed by HAIC (24.9 months; 95% CI, 20.3-29.6), and SYS (13.7 months; 95% CI, 8.9-15.9; P < 0.001). There was no difference in survival for node-positive patients treated with resection (median OS, 19.7 months; 95% CI, 12.1-27.2) or HAIC (18.1 months; 95% CI, 14.1-26.6; P = 0.560); however, survival in both groups was greater than SYS (11.2 months; 95% CI, 14.1-26.6; P = 0.024). Node-positive patients with at least one high-risk genetic alteration (TP53 mutation, KRAS mutation, CDKN2A/B deletion) had worse survival compared to wild-type patients (median OS, 12.1 months; 95% CI, 5.7-21.5; P = 0.002), regardless of treatment. Conversely, there was no difference in survival for node-positive patients with IDH1/2 mutations compared to wild-type patients. CONCLUSIONS There was no difference in OS for patients with node-positive IHC treated by resection versus HAIC, and both treatments had better survival than SYS alone. The presence of high-risk genetic alterations provides valuable prognostic information that may help guide treatment.
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Affiliation(s)
- Joshua S Jolissaint
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kevin C Soares
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth P Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul J Shin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas Boerner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carlie Sigel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy E Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Louise C Connell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod P Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey A Drebin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - T Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alice C Wei
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
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Tovar-Parra JD, Gutiérrez-Castañeda LD, Gil-Quiñones SR, Nova JA, Pulido L. CDKN2A Polymorphism in Melanoma Patients in Colombian Population: A Case-Control Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7458917. [PMID: 33102592 PMCID: PMC7576359 DOI: 10.1155/2020/7458917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/06/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Melanoma is the most aggressive type of skin cancer, with poor prognosis in advanced stages. The incidence and mortality rates have increased in recent years. Single nucleotide polymorphisms p.R24P, p.M53I, p.G101W, p.V126D, and p.A148T in the CDKN2A (HGNC ID: 1787) gene have been associated with the development of melanoma in different populations; however, this association has not been studied in Colombia. METHODS Cutaneous melanoma patients and healthy controls (85 cases and 166 controls) were included in this study. These subjects were screened through HRM-qPCR assay and detected variants in exon 1 and 2 of CDKN2A gene and confirmed with Sanger sequencing. Chi-square test was used to compare allele and genotype distributions between cases and controls. Odds ratio (OR) with 95% confidence interval (CI) was calculated to determine the association between polymorphisms and haplotypes with melanoma susceptibility. Statistical and haplotype analyses were performed using Stata® and R-Studio®. RESULTS Fifty-four percent of women were identified both in cases and controls. The frequencies of melanoma subtypes were 36,47% lentigo maligna, 24,71% acral lentiginous, 23,53% superficial extension, and 15,29% nodular. Variants in the CDKN2A gene were 11.76% in cases and 8.43% in controls. The most frequent was p.A148T in 5.88% of cases and in 4.82% of controls. GGTTG haplotype showed statistically significant differences between cases and controls (p value = 0.04). CONCLUSION CDKN2A polymorphisms p.G101W, p.R24P, p.M53I, and A148T are not associated with melanoma susceptibility in the Colombian population; further studies regarding genetic interaction and additive effects between more variants are required.
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Affiliation(s)
- Jose D. Tovar-Parra
- Hospital Universitario-Centro Dermatológico Federico Lleras Acosta, E.S.E., DC, Bogotá, Colombia 111511, Colombia
| | - Luz D. Gutiérrez-Castañeda
- Hospital Universitario-Centro Dermatológico Federico Lleras Acosta, E.S.E., DC, Bogotá, Colombia 111511, Colombia
| | - Sebastián R. Gil-Quiñones
- Hospital Universitario-Centro Dermatológico Federico Lleras Acosta, E.S.E., DC, Bogotá, Colombia 111511, Colombia
| | - Jhon A. Nova
- Hospital Universitario-Centro Dermatológico Federico Lleras Acosta, E.S.E., DC, Bogotá, Colombia 111511, Colombia
| | - Leonardo Pulido
- Hospital Universitario-Centro Dermatológico Federico Lleras Acosta, E.S.E., DC, Bogotá, Colombia 111511, Colombia
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5
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Feng YC, Liu XY, Teng L, Ji Q, Wu Y, Li JM, Gao W, Zhang YY, La T, Tabatabaee H, Yan XG, Jamaluddin MFB, Zhang D, Guo ST, Scott RJ, Liu T, Thorne RF, Zhang XD, Jin L. c-Myc inactivation of p53 through the pan-cancer lncRNA MILIP drives cancer pathogenesis. Nat Commun 2020; 11:4980. [PMID: 33020477 PMCID: PMC7536215 DOI: 10.1038/s41467-020-18735-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
The functions of the proto-oncoprotein c-Myc and the tumor suppressor p53 in controlling cell survival and proliferation are inextricably linked as “Yin and Yang” partners in normal cells to maintain tissue homeostasis: c-Myc induces the expression of ARF tumor suppressor (p14ARF in human and p19ARF in mouse) that binds to and inhibits mouse double minute 2 homolog (MDM2) leading to p53 activation, whereas p53 suppresses c-Myc through a combination of mechanisms involving transcriptional inactivation and microRNA-mediated repression. Nonetheless, the regulatory interactions between c-Myc and p53 are not retained by cancer cells as is evident from the often-imbalanced expression of c-Myc over wildtype p53. Although p53 repression in cancer cells is frequently associated with the loss of ARF, we disclose here an alternate mechanism whereby c-Myc inactivates p53 through the actions of the c-Myc-Inducible Long noncoding RNA Inactivating P53 (MILIP). MILIP functions to promote p53 polyubiquitination and turnover by reducing p53 SUMOylation through suppressing tripartite-motif family-like 2 (TRIML2). MILIP upregulation is observed amongst diverse cancer types and is shown to support cell survival, division and tumourigenicity. Thus our results uncover an inhibitory axis targeting p53 through a pan-cancer expressed RNA accomplice that links c-Myc to suppression of p53. c-Myc and p53 operate in a negative feedback manner to maintain cellular homeostasis. Here, the authors report a long noncoding RNA, MILIP as a downstream target of c-Myc and that MILIP represses p53 to support tumorigenicity.
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Affiliation(s)
- Yu Chen Feng
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Xiao Ying Liu
- Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Liu Teng
- Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Qiang Ji
- Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Yongyan Wu
- Department of Otolaryngology, Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, the first affiliated hospital, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jin Ming Li
- Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Wei Gao
- Department of Otolaryngology, Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, the first affiliated hospital, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yuan Yuan Zhang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Ting La
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Hessam Tabatabaee
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Xu Guang Yan
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - M Fairuz B Jamaluddin
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Didi Zhang
- Department of Orthopaedics, John Hunter Hospital, Hunter New England Health, Newcastle, 2305, NSW, Australia
| | - Su Tang Guo
- Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Taiyuan, 030013, Shanxi, China
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, 2750, NSW, Australia
| | - Rick F Thorne
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia.,Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Xu Dong Zhang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, 2308, NSW, Australia. .,Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China.
| | - Lei Jin
- Translational Research Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450053, Henan, China. .,School of Medicine and Public Health, The University of Newcastle, Newcastle, 2308, NSW, Australia.
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Holland EA, Lo S, Kelly B, Schmid H, Cust AE, Palmer JM, Drummond M, Hayward NK, Pritchard AL, Mann GJ. FRAMe: Familial Risk Assessment of Melanoma-a risk prediction tool to guide CDKN2A germline mutation testing in Australian familial melanoma. Fam Cancer 2020; 20:231-239. [PMID: 32989607 DOI: 10.1007/s10689-020-00209-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/19/2020] [Indexed: 11/30/2022]
Abstract
Germline mutations in CDKN2A greatly increase risk of developing cutaneous melanoma. We have constructed a risk prediction model, Familial Risk Assessment of Melanoma (FRAMe), for estimating the likelihood of carrying a heritable CDKN2A mutation among Australian families, where the prevalence of these mutations is low. Using logistic regression, we analysed characteristics of 299 Australian families recruited through the Sydney site of GenoMEL (international melanoma genetics consortium) with at least three cases of cutaneous melanoma (in situ and invasive) among first-degree blood relatives, for predictors of the presence of a pathogenic CDKN2A mutation. The final multivariable prediction model was externally validated in an independent cohort of 61 melanoma kindreds recruited through GenoMEL Queensland. Family variables independently associated with the presence of a CDKN2A mutation in a multivariable model were number of individuals diagnosed with melanoma under 40 years of age, number of individuals diagnosed with more than one primary melanoma, and number of individuals blood related to a melanoma case in the first degree diagnosed with any cancer excluding melanoma and non-melanoma skin cancer. The number of individuals diagnosed with pancreatic cancer was not independently associated with mutation status. The risk prediction model had an area under the receiver operating characteristic curve (AUC) of 0.851 (95% CI 0.793, 0.909) in the training dataset, and 0.745 (95%CI 0.612, 0.877) in the validation dataset. This model is the first to be developed and validated using only Australian data, which is important given the higher rate of melanoma in the population. This model will help to effectively identify families suitable for genetic counselling and testing in areas of high ambient ultraviolet radiation. A user-friendly electronic nomogram is available at www.melanomarisk.org.au .
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Affiliation(s)
- Elizabeth A Holland
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, 2145, Australia.
| | - Serigne Lo
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2065, Australia
| | - Blake Kelly
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, 2145, Australia
| | - Helen Schmid
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, 2145, Australia
| | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2065, Australia.,Cancer Epidemiology and Prevention Research, Sydney School of Public Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jane M Palmer
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4005, Australia
| | - Martin Drummond
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2065, Australia.,Cancer Epidemiology and Prevention Research, Sydney School of Public Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Nicholas K Hayward
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4005, Australia
| | - Antonia L Pritchard
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4005, Australia.,Genetics and Immunology, An L`ochran, University of the Highlands and Islands, Inverness, UK
| | - Graham J Mann
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, 2145, Australia.,Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2065, Australia.,The John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, ACT, 2601, Australia
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7
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Curated multiple sequence alignment for the Adenomatous Polyposis Coli (APC) gene and accuracy of in silico pathogenicity predictions. PLoS One 2020; 15:e0233673. [PMID: 32750050 PMCID: PMC7402488 DOI: 10.1371/journal.pone.0233673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
Computational algorithms are often used to assess pathogenicity of Variants of Uncertain Significance (VUS) that are found in disease-associated genes. Most computational methods include analysis of protein multiple sequence alignments (PMSA), assessing interspecies variation. Careful validation of PMSA-based methods has been done for relatively few genes, partially because creation of curated PMSAs is labor-intensive. We assessed how PMSA-based computational tools predict the effects of the missense changes in the APC gene, in which pathogenic variants cause Familial Adenomatous Polyposis. Most Pathogenic or Likely Pathogenic APC variants are protein-truncating changes. However, public databases now contain thousands of variants reported as missense. We created a curated APC PMSA that contained >3 substitutions/site, which is large enough for statistically robust in silico analysis. The creation of the PMSA was not easily automated, requiring significant querying and computational analysis of protein and genome sequences. Of 1924 missense APC variants in the NCBI ClinVar database, 1800 (93.5%) are reported as VUS. All but two missense variants listed as P/LP occur at canonical splice or Exonic Splice Enhancer sites. Pathogenicity predictions by five computational tools (Align-GVGD, SIFT, PolyPhen2, MAPP, REVEL) differed widely in their predictions of Pathogenic/Likely Pathogenic (range 17.5–75.0%) and Benign/Likely Benign (range 25.0–82.5%) for APC missense variants in ClinVar. When applied to 21 missense variants reported in ClinVar and securely classified as Benign, the five methods ranged in accuracy from 76.2–100%. Computational PMSA-based methods can be an excellent classifier for variants of some hereditary cancer genes. However, there may be characteristics of the APC gene and protein that confound the results of in silico algorithms. A systematic study of these features could greatly improve the automation of alignment-based techniques and the use of predictive algorithms in hereditary cancer genes.
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9
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Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med 2019; 12:3. [PMID: 31892348 PMCID: PMC6938631 DOI: 10.1186/s13073-019-0690-2] [Citation(s) in RCA: 294] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria for different types of evidence. This includes the strong evidence codes PS3 and BS3 for "well-established" functional assays demonstrating a variant has abnormal or normal gene/protein function, respectively. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes are a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation. METHODS The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated the odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development. RESULTS The SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are as follows: (1) define the disease mechanism, (2) evaluate the applicability of general classes of assays used in the field, (3) evaluate the validity of specific instances of assays, and (4) apply evidence to individual variant interpretation. We found that a minimum of 11 total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis. CONCLUSIONS The recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.
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Affiliation(s)
- Sarah E Brnich
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Ahmad N Abou Tayoun
- Genomics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Dona M Kanavy
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Shannon M McNulty
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Matt W Wright
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA.
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10
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Gironi LC, Colombo E, Pasini B, Giorgione R, Farinelli P, Zottarelli F, Esposto E, Zavattaro E, Allara E, Ogliara P, Betti M, Dianzani I, Savoia P. Melanoma-prone families: new evidence of distinctive clinical and histological features of melanomas in CDKN2A mutation carriers. Arch Dermatol Res 2018; 310:769-784. [PMID: 30218143 DOI: 10.1007/s00403-018-1866-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/30/2018] [Accepted: 09/08/2018] [Indexed: 11/26/2022]
Abstract
Germline mutations on the CDKN2A gene, the most important known genetic factors associated with cutaneous melanomas (CMs), predispose carriers to multiple primary CMs (MPMs) with higher frequency and younger onset compared to non-carriers. Most of the largest published studies concerning clinical and histological characteristics of CMs with CDKN2A mutation carriers did not specify if the described CMs are first or subsequent to the first, and they used sporadic CMs from non-genotyped patients as controls. We conducted a single-centre observational study to compare clinical and histological CM features of 32 unrelated carriers (MUT) of 5 germline CDKN2A mutations (one of which was never previously described) compared to 100 genotyped wild-type (WT) patients. We stratified the data based on time of diagnosis, anatomical site and histological subtype of CMs, demonstrating several significant unreported differences between the two groups. MUT developed a higher number of dysplastic nevi and MPMs. We proved for the first time that anatomical distribution of CMs in MUT was independent of gender, unlike WTs. MUTs developed in situ and superficial spreading melanomas (SSMs) more frequently, with significantly higher number of SSMs on the head/neck. In MUTs, Breslow thickness was significantly lower for all invasive CMs. When CMs were stratified on the basis of the time of occurrence, statistical significance was maintained only for SSMs subsequent to the first. In WTs, Clark level was significantly higher, and ulceration was more prevalent than in MUTs. Significant differences in ulceration were observed only in SSMs. In nodular CMs, we did not find differences in terms of Breslow thickness or ulceration between WTs and MUTs. In situ CMs developed 10 years earlier in MUTs with respect to WTs, whereas no significant differences were observed in invasive CMs. In contrast to those reported previously by other authors, we did not find a difference in skin phototype.
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Affiliation(s)
- Laura Cristina Gironi
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy.
| | - Enrico Colombo
- Department of Translational Medicine, A. Avogadro University of Eastern Piedmont, Novara, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Roberto Giorgione
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Pamela Farinelli
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Francesca Zottarelli
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Elia Esposto
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Elisa Zavattaro
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Elias Allara
- NIHR Blood and Transplant Research Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paola Ogliara
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Marta Betti
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Irma Dianzani
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
| | - Paola Savoia
- Department of Health Sciences, A. Avogadro University of Eastern Piedmont, Corso Mazzini 18, 28100, Novara, Italy
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11
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Jouenne F, Chauvot de Beauchene I, Bollaert E, Avril MF, Caron O, Ingster O, Lecesne A, Benusiglio P, Terrier P, Caumette V, Pissaloux D, de la Fouchardière A, Cabaret O, N'Diaye B, Velghe A, Bougeard G, Mann GJ, Koscielny S, Barrett JH, Harland M, Newton-Bishop J, Gruis N, Van Doorn R, Gauthier-Villars M, Pierron G, Stoppa-Lyonnet D, Coupier I, Guimbaud R, Delnatte C, Scoazec JY, Eggermont AM, Feunteun J, Tchertanov L, Demoulin JB, Frebourg T, Bressac-de Paillerets B. Germline CDKN2A/P16INK4A mutations contribute to genetic determinism of sarcoma. J Med Genet 2017; 54:607-612. [PMID: 28592523 DOI: 10.1136/jmedgenet-2016-104402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Sarcomas are rare mesenchymal malignancies whose pathogenesis is poorly understood; both environmental and genetic risk factors could contribute to their aetiology. METHODS AND RESULTS We performed whole-exome sequencing (WES) in a familial aggregation of three individuals affected with soft-tissue sarcoma (STS) without TP53 mutation (Li-Fraumeni-like, LFL) and found a shared pathogenic mutation in CDKN2A tumour suppressor gene. We searched for individuals with sarcoma among 474 melanoma-prone families with a CDKN2A-/+ genotype and for CDKN2A mutations in 190 TP53-negative LFL families where the index case was a sarcoma. Including the initial family, eight independent sarcoma cases carried a germline mutation in the CDKN2A/p16INK4A gene. In five out of seven formalin-fixed paraffin-embedded sarcomas, heterozygosity was lost at germline CDKN2A mutations sites demonstrating complete loss of function. As sarcomas are rare in CDKN2A/p16INK4A carriers, we searched in constitutional WES of nine carriers for potential modifying rare variants and identified three in platelet-derived growth factor receptor (PDGFRA) gene. Molecular modelling showed that two never-described variants could impact the PDGFRA extracellular domain structure. CONCLUSION Germline mutations in CDKN2A/P16INK4A, a gene known to predispose to hereditary melanoma, pancreatic cancer and tobacco-related cancers, account also for a subset of hereditary sarcoma. In addition, we identified PDGFRA as a candidate modifier gene.
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Affiliation(s)
- Fanélie Jouenne
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM, U1186, Université Paris-Saclay, Villejuif, France
| | | | - Emeline Bollaert
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Marie-Françoise Avril
- Department of Dermatology, Assistance Publique-Hopitaux de Paris, Hopital Cochin Tarnier, Paris, France
- Faculté de Médecine, Paris 5 Descartes, Paris, France
| | - Olivier Caron
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Axel Lecesne
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Patrick Benusiglio
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Philippe Terrier
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Vincent Caumette
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Daniel Pissaloux
- Department of Pathology, Centre Leon Bérard, Lyon, Rhône-Alpes, France
| | | | - Odile Cabaret
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Birama N'Diaye
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Amélie Velghe
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Gaelle Bougeard
- Faculty of Medicine, INSERM U1079, Normandy University, Rouen, France
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and personalized Medicine, Rouen, Haute-Normandie, France
| | - Graham J Mann
- Centre for Cancer Research, Weastmead Institute for Medical Research and Melanoma Institute, Sydney, New South Wales, Australia
| | - Serge Koscielny
- Service de Biostatistiques et d'Epidemiologie, Gustave Roussy, Villejuif, France
- INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Jennifer H Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco Van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Gaelle Pierron
- Institut Curie Hospital Group, Service de Génétique, Paris, France
| | | | - Isabelle Coupier
- Hopital Arnaud de Villeneuve, Service de Génétique Médicale et Oncogénétique, CHU de Montpellier, Montpellier, France
- CRCM Val d'Aurellle, INSERM U896, Montpellier, France
| | | | - Capucine Delnatte
- Unité d'Oncogénétique, Centre René Gauducheau, Nantes Saint Herblain, France
| | - Jean-Yves Scoazec
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Alexander M Eggermont
- INSERM U1015 and Faculté de médecine, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean Feunteun
- CNRS UMR8200, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Luba Tchertanov
- Centre de Mathématiques et de leurs applications, Ecole Normale Supérieure de Cachan, Université Paris-Saclay, Cachan, France
| | | | - Thierry Frebourg
- Faculty of Medicine, INSERM U1079, Normandy University, Rouen, France
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and personalized Medicine, Rouen, Haute-Normandie, France
| | - Brigitte Bressac-de Paillerets
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM, U1186, Université Paris-Saclay, Villejuif, France
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12
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Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat 2017; 38:1042-1050. [PMID: 28440912 PMCID: PMC5561474 DOI: 10.1002/humu.23235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 12/31/2022]
Abstract
Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of 10 variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene. Twenty-two pathogenicity predictors were assessed with a variety of accuracy measures for reliability in a medical context. Different assessment measures were combined in an overall ranking to provide more robust results. The R scripts used for assessment are publicly available from a GitHub repository for future use in similar assessment exercises. Despite a limited test-set size, our findings show a variety of results, with some methods performing significantly better. Methods combining different strategies frequently outperform simpler approaches. The best predictor, Yang&Zhou lab, uses a machine learning method combining an empirical energy function measuring protein stability with an evolutionary conservation term. The p16INK4a challenge highlights how subtle structural effects can neutralize otherwise deleterious variants.
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Affiliation(s)
- Marco Carraro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Manuel Giollo
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
- Department of Genetics, Rutgers University, Piscataway, New Jersey
- Technical University of Munich Institute for Advanced Study (TUM-IAS), Garching/Munich, Germany
| | - Emidio Capriotti
- BioFolD Unit, Department of Biological, Geological, and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Biological, Geological, and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Roland Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Pietro Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - Carlo Ferrari
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Julian Gough
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Panagiotis Katsonis
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Olivier Lichtarge
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Pier Luigi Martelli
- BioFolD Unit, Department of Biological, Geological, and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Abhishek Niroula
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Susanna Repo
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Mauno Vihinen
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Qiong Wei
- Biocomputing Group, Department of Biological, Geological, and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Qifang Xu
- Biocomputing Group, Department of Biological, Geological, and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, Queensland, Australia
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | - Jan Zaucha
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Huiying Zhao
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, Queensland, Australia
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- CNR Institute of Neuroscience, Padova, Italy
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13
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Mangas C, Potrony M, Mainetti C, Bianchi E, Carrozza Merlani P, Mancarella Eberhardt A, Maspoli-Postizzi E, Marazza G, Marcollo-Pini A, Pelloni F, Sessa C, Simona B, Puig-Butillé JA, Badenas C, Puig S. Genetic susceptibility to cutaneous melanoma in southern Switzerland: role of CDKN2A, MC1R and MITF. Br J Dermatol 2016; 175:1030-1037. [PMID: 27473757 DOI: 10.1111/bjd.14897] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Nearly 10% of all cases of cutaneous melanoma (CM) occur in patients with a personal or family history of the disease. OBJECTIVES To obtain information about genetic predisposition to CM in Ticino, the southern region of Switzerland, a zone with moderate-to-high CM incidence. METHODS We identified germline mutations in highly CM-associated genes (CDKN2A and CDK4) and low/medium-penetrance variants (MC1R and MITF) in patients with multiple primary CMs or individuals with one or more CM and a positive family history for CM or pancreatic cancer among first- or second-degree relatives. Healthy blood donors (n = 146) were included as a control group. RESULTS From July 2010 to July 2012, 57 patients (41 pedigrees) were included. Twenty-six were melanoma-prone families (with at least two cases) and 15 had multiple CMs. Pancreatic cancer was found in six families. The CDKN2A mutation p.V126D was identified in seven patients (four families) with a founder effect, whereas CDKN2A A148T was detected in seven cases (five families) and seven healthy donors (odds ratio 2·76, 95% confidence interval 0·83-9·20). At least one MC1R melanoma-associated polymorphism was detected in 32 patients (78%) and 97 healthy donors (66%), with more than one polymorphism in 12 patients (29%) and 25 healthy donors (17%). The MITF variant p.E318K was identified in four patients from three additional pedigrees (7%) and one healthy control (0·7%). CONCLUSIONS Inclusion criteria for the Ticino population for genetic assessment should follow the rule of two (two affected individuals in a family or a patient with multiple CMs), as we detected a CDKN2A mutation in almost 10% of our pedigrees (four of 41), MITF p.E318K in 7% (three of 41) and a higher number of MC1R variants than in the control population.
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Affiliation(s)
- C Mangas
- Dermatologia Ente Ospedaliero Cantonale (EOC), Ospedale Regionale Bellinzona e Valli, Bellinzona, Switzerland. ,
| | - M Potrony
- Melanoma Unit, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - C Mainetti
- Dermatologia Ente Ospedaliero Cantonale (EOC), Ospedale Regionale Bellinzona e Valli, Bellinzona, Switzerland
| | - E Bianchi
- Private Dermatology Practice, Lugano, Switzerland
| | | | | | | | - G Marazza
- Dermatologia Ente Ospedaliero Cantonale (EOC), Ospedale Regionale Bellinzona e Valli, Bellinzona, Switzerland
| | | | - F Pelloni
- Private Dermatology Practice, Lugano, Switzerland
| | - C Sessa
- Istituto Oncologico della Svizzera Italiana (IOSI), Ospedale Regionale Bellinzona e Valli, Bellinzona, Switzerland
| | - B Simona
- Private Dermatology Practice, Locarno, Switzerland
| | - J A Puig-Butillé
- Melanoma Unit, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic of Barcelona, Spain
| | - C Badenas
- Melanoma Unit, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic of Barcelona, Spain
| | - S Puig
- Melanoma Unit, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
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14
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Johnston SB, Raines RT. PTENpred: A Designer Protein Impact Predictor for PTEN-related Disorders. J Comput Biol 2016; 23:969-975. [PMID: 27310656 DOI: 10.1089/cmb.2016.0058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Connecting a genotype with a phenotype can provide immediate advantages in the context of modern medicine. Especially useful would be an algorithm for predicting the impact of nonsynonymous single-nucleotide polymorphisms in the gene for PTEN, a protein that is implicated in most human cancers and connected to germline disorders that include autism. We have developed a protein impact predictor, PTENpred, that integrates data from multiple analyses using a support vector machine algorithm. PTENpred can predict phenotypes related to a human PTEN mutation with high accuracy. The output of PTENpred is designed for use by biologists, clinicians, and laymen, and features an interactive display of the three-dimensional structure of PTEN. Using knowledge about the structure of proteins, in general, and the PTEN protein, in particular, enables the prediction of consequences from damage to the human PTEN gene. This algorithm, which can be accessed online, could facilitate the implementation of effective therapeutic regimens for cancer and other diseases.
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Affiliation(s)
- Sean B Johnston
- 1 Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin
| | - Ronald T Raines
- 1 Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin.,2 Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
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15
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Burgstaller-Muehlbacher S, Marko M, Müller C, Wendt J, Pehamberger H, Okamoto I. Novel CDKN2A mutations in Austrian melanoma patients. Melanoma Res 2015; 25:412-20. [PMID: 26225579 DOI: 10.1097/cmr.0000000000000179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CDKN2A is the most prominent familial melanoma gene, with mutations occurring in up to 40% of the families. Numerous mutations in the gene are known, several of them representing regional founder mutations. We sought to determine, for the first time, germline mutations in CDKN2A in Austria to identify novel mutations. In total, 700 individuals (136 patients with a positive family history and 164 with at least two primary melanomas as the high-risk groups; 200 with single primary melanomas; and 200 healthy individuals as the control groups) were Sanger sequenced for CDKN2A exon 1α, 1β, and 2. The 136 patients with affected relatives were also sequenced for CDK4 exon 2. We found the disease-associated mutations p.R24P (8×), p.N71T (1×), p.G101W (1×), and p.V126D (1×) in the group with affected relatives and p.R24P (2×) in the group with several primary melanomas. Furthermore, we discovered four mutations of unknown significance, two of which were novel: p.A34V and c.151-4 G>C, respectively. Computational effect prediction suggested p.A34V as conferring a high risk for melanoma, whereas c.151-4 G>C, although being predicted as a splice site mutation by MutationTaster, could not functionally be confirmed to alter splicing. Moreover, computational effect prediction confirmed accumulation of high-penetrance mutations in high-risk groups, whereas mutations of unknown significance were distributed across all groups. p.R24P is the most common high-risk mutation in Austria. In addition, we discovered two new mutations in Austrian melanoma patients, p.A34V and c.151-4 G>C, respectively.
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16
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17
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Minervini G, Quaglia F, Tosatto SCE. Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health. Biochimie 2015; 116:114-24. [PMID: 26187473 DOI: 10.1016/j.biochi.2015.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/12/2015] [Indexed: 12/18/2022]
Abstract
PHDs (proline hydroxylases) are a small protein family found in all organisms, considered the central regulator of the molecular hypoxia response due to PHDs being completely inactivated under low oxygen concentration. At physiological oxygen concentration, PHDs drive the degradation of the HIF-1α (hypoxia-inducible factor 1-α), which is responsible for upregulating the expression of genes involved in the cellular response to hypoxia. Hypoxia is a common feature of most tumors, in particular during metastasis development. Indeed, cancer reacts by activating pathways promoting new blood vessel formation and activating strategies aimed to improve survival. In this scenario, the PHD family regulates the activation of HIF-1α and cell-cycle regulation. Several PHD mutations were found in cancer patients, underlining their importance for human health. Here, we propose a Bayesian model able to predict the pathological effect of human PHD mutations and their correlation with cancer outcome. The model was developed through an integrative in silico approach, where data collected from the literature has been coupled with sequence evolution and structural analysis. The model was used to assess 135 human PHD variants. Finally, bioinformatics characterization was used to demonstrate how few amino acid changes are able to explain the functional specialization of PHD family members and their physiological role in human health.
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Affiliation(s)
- Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121, Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121, Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121, Padova, Italy.
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18
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Microsatellite instability use in mismatch repair gene sequence variant classification. Genes (Basel) 2015; 6:150-62. [PMID: 25831438 PMCID: PMC4488658 DOI: 10.3390/genes6020150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/04/2015] [Accepted: 03/23/2015] [Indexed: 01/05/2023] Open
Abstract
Inherited mutations in the DNA mismatch repair genes (MMR) can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI) is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants) are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review.
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Harland M, Cust AE, Badenas C, Chang YM, Holland EA, Aguilera P, Aitken JF, Armstrong BK, Barrett JH, Carrera C, Chan M, Gascoyne J, Giles GG, Agha-Hamilton C, Hopper JL, Jenkins MA, Kanetsky PA, Kefford RF, Kolm I, Lowery J, Malvehy J, Ogbah Z, Puig-Butille JA, Orihuela-Segalés J, Randerson-Moor JA, Schmid H, Taylor CF, Whitaker L, Bishop DT, Mann GJ, Newton-Bishop JA, Puig S. Prevalence and predictors of germline CDKN2A mutations for melanoma cases from Australia, Spain and the United Kingdom. Hered Cancer Clin Pract 2014; 12:20. [PMID: 25780468 PMCID: PMC4361137 DOI: 10.1186/1897-4287-12-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 11/06/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mutations in the CDKN2A and CDK4 genes predispose to melanoma. From three case-control studies of cutaneous melanoma, we estimated the prevalence and predictors of these mutations for people from regions with widely differing latitudes and melanoma incidence. METHODS Population-based cases and controls from the United Kingdom (1586 cases, 499 controls) and Australia (596 early-onset cases, 476 controls), and a hospital-based series from Spain (747 cases, 109 controls), were screened for variants in all exons of CDKN2A and the p16INK4A binding domain of CDK4. RESULTS The prevalence of mutations for people with melanoma was similar across regions: 2.3%, 2.5% and 2.0% for Australia, Spain and the United Kingdom respectively. The strongest predictors of carrying a mutation were having multiple primaries (odds ratio (OR) = 5.4, 95% confidence interval (CI: 2.5, 11.6) for 2 primaries and OR = 32.4 (95% CI: 14.7, 71.2) for 3 or more compared with 1 primary only); and family history (OR = 3.8; 95% CI:1.89, 7.5) for 1 affected first- or second-degree relative and OR = 23.2 (95% CI: 11.3, 47.6) for 2 or more compared with no affected relatives). Only 1.1% of melanoma cases with neither a family history nor multiple primaries had mutations. CONCLUSIONS There is a low probability (<2%) of detecting a germline CDKN2A mutation in people with melanoma except for those with a strong family history of melanoma (≥2 affected relatives, 25%), three or more primary melanomas (29%), or more than one primary melanoma who also have other affected relatives (27%).
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Affiliation(s)
- Mark Harland
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Anne E Cust
- />Cancer Epidemiology and Services Research (CESR), Sydney School of Public Health, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Celia Badenas
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Yu-Mei Chang
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Elizabeth A Holland
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - Paula Aguilera
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Joanne F Aitken
- />Viertel Centre for Research in Cancer Control, The Cancer Council Queensland, Spring Hill, Brisbane, Australia
| | - Bruce K Armstrong
- />Cancer Epidemiology and Services Research (CESR), Sydney School of Public Health, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Jennifer H Barrett
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Cristina Carrera
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - May Chan
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Joanne Gascoyne
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Graham G Giles
- />Centre for Epidemiology & Biostatistics, School of Population Health, University of Melbourne, Melbourne, Australia
- />Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Chantelle Agha-Hamilton
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - John L Hopper
- />Centre for Epidemiology & Biostatistics, School of Population Health, University of Melbourne, Melbourne, Australia
| | - Mark A Jenkins
- />Centre for Epidemiology & Biostatistics, School of Population Health, University of Melbourne, Melbourne, Australia
| | - Peter A Kanetsky
- />Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL USA
| | - Richard F Kefford
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - Isabel Kolm
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - Johanna Lowery
- />Genomics Facility, Leeds Cancer Research UK Centre, University of Leeds, Leeds, UK
| | - Josep Malvehy
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Zighereda Ogbah
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Joan-Anton Puig-Butille
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | | | - Juliette A Randerson-Moor
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Helen Schmid
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - Claire F Taylor
- />Genomics Facility, Leeds Cancer Research UK Centre, University of Leeds, Leeds, UK
| | - Linda Whitaker
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - D Timothy Bishop
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Graham J Mann
- />Westmead Institute for Cancer Research and Melanoma Institute, Australia, University of Sydney at Westmead Millennium Institute, Sydney, Australia
| | - Julia A Newton-Bishop
- />Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | - Susana Puig
- />Dermatology Department and Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- />Centro Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
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Scaini MC, Minervini G, Elefanti L, Ghiorzo P, Pastorino L, Tognazzo S, Agata S, Quaggio M, Zullato D, Bianchi-Scarrà G, Montagna M, D'Andrea E, Menin C, Tosatto SCE. CDKN2A unclassified variants in familial malignant melanoma: combining functional and computational approaches for their assessment. Hum Mutat 2014; 35:828-40. [PMID: 24659262 DOI: 10.1002/humu.22550] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 03/03/2014] [Indexed: 01/03/2023]
Abstract
CDKN2A codes for two oncosuppressors by alternative splicing of two first exons: p16INK4a and p14ARF. Germline mutations are found in about 40% of melanoma-prone families, and most of them are missense mutations mainly affecting p16INK4a. A growing number of p16INK4a variants of uncertain significance (VUS) are being identified but, unless their pathogenic role can be demonstrated, they cannot be used for identification of carriers at risk. Predicting the effect of these VUS by either a "standard" in silico approach, or functional tests alone, is rather difficult. Here, we report a protocol for the assessment of any p16INK4a VUS, which combines experimental and computational tools in an integrated approach. We analyzed p16INK4a VUS from melanoma patients as well as variants derived through permutation of conserved p16INK4a amino acids. Variants were expressed in a p16INK4a-null cell line (U2-OS) and tested for their ability to block proliferation. In parallel, these VUS underwent in silico prediction analysis and molecular dynamics simulations. Evaluation of in silico and functional data disclosed a high agreement for 15/16 missense mutations, suggesting that this approach could represent a pilot study for the definition of a protocol applicable to VUS in general, involved in other diseases, as well.
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Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
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Kurian AW, Hare EE, Mills MA, Kingham KE, McPherson L, Whittemore AS, McGuire V, Ladabaum U, Kobayashi Y, Lincoln SE, Cargill M, Ford JM. Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment. J Clin Oncol 2014; 32:2001-9. [PMID: 24733792 PMCID: PMC4067941 DOI: 10.1200/jco.2013.53.6607] [Citation(s) in RCA: 377] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Multiple-gene sequencing is entering practice, but its clinical value is unknown. We evaluated the performance of a customized germline-DNA sequencing panel for cancer-risk assessment in a representative clinical sample. METHODS Patients referred for clinical BRCA1/2 testing from 2002 to 2012 were invited to donate a research blood sample. Samples were frozen at -80° C, and DNA was extracted from them after 1 to 10 years. The entire coding region, exon-intron boundaries, and all known pathogenic variants in other regions were sequenced for 42 genes that had cancer risk associations. Potentially actionable results were disclosed to participants. RESULTS In total, 198 women participated in the study: 174 had breast cancer and 57 carried germline BRCA1/2 mutations. BRCA1/2 analysis was fully concordant with prior testing. Sixteen pathogenic variants were identified in ATM, BLM, CDH1, CDKN2A, MUTYH, MLH1, NBN, PRSS1, and SLX4 among 141 women without BRCA1/2 mutations. Fourteen participants carried 15 pathogenic variants, warranting a possible change in care; they were invited for targeted screening recommendations, enabling early detection and removal of a tubular adenoma by colonoscopy. Participants carried an average of 2.1 variants of uncertain significance among 42 genes. CONCLUSION Among women testing negative for BRCA1/2 mutations, multiple-gene sequencing identified 16 potentially pathogenic mutations in other genes (11.4%; 95% CI, 7.0% to 17.7%), of which 15 (10.6%; 95% CI, 6.5% to 16.9%) prompted consideration of a change in care, enabling early detection of a precancerous colon polyp. Additional studies are required to quantify the penetrance of identified mutations and determine clinical utility. However, these results suggest that multiple-gene sequencing may benefit appropriately selected patients.
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Affiliation(s)
- Allison W Kurian
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Emily E Hare
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Meredith A Mills
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Kerry E Kingham
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Lisa McPherson
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Alice S Whittemore
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Valerie McGuire
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Uri Ladabaum
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Yuya Kobayashi
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Stephen E Lincoln
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - Michele Cargill
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA
| | - James M Ford
- Allison W. Kurian, Meredith A. Mills, Kerry E. Kingham, Lisa McPherson, Alice S. Whittemore, Valerie McGuire, Uri Ladabaum, James M. Ford, Stanford University School of Medicine, Stanford; Emily E. Hare, Yuya Kobayashi, Stephen E. Lincoln, Michele Cargill, InVitae, San Francisco, CA.
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Jenkins NC, Jung J, Liu T, Wilde M, Holmen SL, Grossman D. Familial melanoma-associated mutations in p16 uncouple its tumor-suppressor functions. J Invest Dermatol 2012. [PMID: 23190892 PMCID: PMC3594444 DOI: 10.1038/jid.2012.401] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Familial melanoma is associated with point mutations in the cyclin-dependent kinase (CDK) inhibitor p16INK4A (p16). We recently reported that p16 regulates intracellular oxidative stress in a cell cycle-independent manner. Here, we constructed 12 different familial melanoma-associated point mutants spanning the p16 coding region and analyzed their capacity to regulate cell-cycle phase and suppress reactive oxygen species (ROS). Compared to wild-type p16 which fully restored both functions in p16-deficient fibroblasts, various p16 mutants differed in their capacity to normalize ROS and cell cycle profiles. While some mutations did not impair either function, others impaired both. Interestingly, several impaired cell-cycle (R24Q, R99P, V126D) or oxidative function (A36P, A57V, P114S) selectively, indicating that these two functions of p16 can be uncoupled. Similar activities were confirmed with selected mutants in human melanoma cells. Many mutations impairing both cell-cycle and oxidative functions, or only cell cycle function, localize to the third ankyrin repeat of the p16 molecule. Alternatively, most mutations impairing oxidative but not cell-cycle function, or those not impairing either function, lie outside this region. These results demonstrate that particular familial melanoma-associated mutations in p16 can selectively compromise these two independent tumor-suppressor functions, which may be mediated by distinct regions of the protein.
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Affiliation(s)
- Noah C Jenkins
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT, USA
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Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RMW, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat 2012; 34:255-65. [PMID: 22949387 DOI: 10.1002/humu.22214] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/26/2012] [Indexed: 11/11/2022]
Abstract
Classification of rare missense substitutions observed during genetic testing for patient management is a considerable problem in clinical genetics. The Bayesian integrated evaluation of unclassified variants is a solution originally developed for BRCA1/2. Here, we take a step toward an analogous system for the mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) that confer colon cancer susceptibility in Lynch syndrome by calibrating in silico tools to estimate prior probabilities of pathogenicity for MMR gene missense substitutions. A qualitative five-class classification system was developed and applied to 143 MMR missense variants. This identified 74 missense substitutions suitable for calibration. These substitutions were scored using six different in silico tools (Align-Grantham Variation Grantham Deviation, multivariate analysis of protein polymorphisms [MAPP], MutPred, PolyPhen-2.1, Sorting Intolerant From Tolerant, and Xvar), using curated MMR multiple sequence alignments where possible. The output from each tool was calibrated by regression against the classifications of the 74 missense substitutions; these calibrated outputs are interpretable as prior probabilities of pathogenicity. MAPP was the most accurate tool and MAPP + PolyPhen-2.1 provided the best-combined model (R(2) = 0.62 and area under receiver operating characteristic = 0.93). The MAPP + PolyPhen-2.1 output is sufficiently predictive to feed as a continuous variable into the quantitative Bayesian integrated evaluation for clinical classification of MMR gene missense substitutions.
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Affiliation(s)
- Bryony A Thompson
- Queensland Institute of Medical Research, Herston, Brisbane, Australia
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