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Mitchell J, Milite S, Bartram J, Walker S, Volkova N, Yavorska O, Zarowiecki M, Chalker J, Thomas R, Vago L, Sosinsky A, Caravagna G. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun 2024; 15:323. [PMID: 38238294 PMCID: PMC10796348 DOI: 10.1038/s41467-023-44158-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
The unexpected contamination of normal samples with tumour cells reduces variant detection sensitivity, compromising downstream analyses in canonical tumour-normal analyses. Leveraging whole-genome sequencing data available at Genomics England, we develop a tool for normal sample contamination assessment, which we validate in silico and against minimal residual disease testing. From a systematic review of [Formula: see text] patients with haematological malignancies and sarcomas, we find contamination across a range of cancer clinical indications and DNA sources, with highest prevalence in saliva samples from acute myeloid leukaemia patients, and sorted CD3+ T-cells from myeloproliferative neoplasms. Further exploration reveals 108 hotspot mutations in genes associated with haematological cancers at risk of being subtracted by standard variant calling pipelines. Our work highlights the importance of contamination assessment for accurate somatic variants detection in research and clinical settings, especially with large-scale sequencing projects being utilised to deliver accurate data from which to make clinical decisions for patient care.
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Affiliation(s)
| | - Salvatore Milite
- Computational Biology Research Centre, Human Technopole, Milan, Italy
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | | | | | | | | | - Jane Chalker
- Specialist Integrated Haematological Malignancy Diagnostic Service - Acquired Genomics, Great Ormond Street Hospital for Children, London, UK
| | - Rebecca Thomas
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Luca Vago
- Research Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS Hospital San Raffaele, Milan, Italy
| | | | - Giulio Caravagna
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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Al-Sabbagh M, Hawasli A, Almehmadi N, Omami G, Miller CS. Hemorrhagic enlargement of the mandibular gingiva. J Am Dent Assoc 2023; 154:74-78. [PMID: 34836620 DOI: 10.1016/j.adaj.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 01/11/2023]
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3
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Owaidhah NA, Khawaji ZY, Alahmadi MA, Badawi AS, Mogharbel GH, Makhdoom ON. Epidemiological Trends and Clinical Characteristics of Childhood Leukemia in Saudi Arabia: A Review. Cureus 2022; 14:e28178. [PMID: 36148187 PMCID: PMC9482806 DOI: 10.7759/cureus.28178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
Leukemia is the most prevalent type of cancer among children in Saudi Arabia. It has variable clinical presentations and accounts for a large scale of mortality and morbidity. Acute lymphoblastic leukemia (ALL) constituted the majority of pediatric leukemic cases with male gender predisposition. The most common first presentation that patients come with are manifestations of anemia, thrombocytopenia, and fever. Bone pain, fatigue, weight loss, organomegaly, and pale skin are among the commonest manifestations of pediatric leukemia. Childhood ALL and acute myeloid leukemia (AML) clinical manifestations seem to be very similar, even though there’re some considerable differences in how common the clinical characteristics are. Chromosomal abnormalities are taken into consideration to determine survival and treatment. PubMed and Google Scholar were searched for the childhood leukemia population in Saudi Arabia. Our review article aims at providing comprehensible and updated statistical data on the different types of leukemia and their clinical presentations in Saudi Arabia.
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Hu X, Yin J, He R, Chao R, Zhu S. Circ_KCNQ5 participates in the progression of childhood acute myeloid leukemia by enhancing the expression of RAB10 via binding to miR-622. Hematology 2022; 27:431-440. [PMID: 35413218 DOI: 10.1080/16078454.2022.2056983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND : Acute myeloid leukemia (AML) is regarded as a haematological malignancy and seriously threatens the public's health. Circular RNA (circRNA) is gradually confirmed to be involved in the development of AML. The purpose of this study was to disclose the role of circRNA Potassium Voltage-Gated Channel Subfamily Q Member 5 (circ_KCNQ5) in AML. METHODS : Quantitative real-time PCR (qPCR) and western blot were used for expression analysis. Colony formation assay, EdU assay and MTT assay were performed to determine cell proliferation. Flow cytometry assay was conducted to determine cell apoptosis. The predicted binding relationship between miR-622 and circ_KCNQ5 or RAS oncogene family member 10 (RAB10) was verified by dual-luciferase reporter assay. RESULTS : The expression of circ_KCNQ5 was increased in bone marrow samples of childhood AML patients and AML cell lines. The knockdown of circ_KCNQ5 largely suppressed AML cell proliferation and promoted cell apoptosis. Circ_KCNQ5 directly bound to miR-622 and inhibited miR-622 expression. The cotransfection of miR-622 inhibitor reversed the effects of circ_KCNQ5 knockdown and thus recovered cell proliferation and depleted cell apoptosis. RAB10 was a target of miR-622, and circ_KCNQ5 bound to miR-622 to increase the expression of RAB10. MiR-622 restoration inhibited AML cell proliferation and induced cell apoptosis, while RAB10 overexpression abolished these effects. CONCLUSION : Circ_KCNQ5 high expression was associated with childhood AML malignant development, and circ_KCNQ5 participated in AML progression by regulating the miR-622/RAB10 pathway.
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Affiliation(s)
- Xiaoyan Hu
- Department of Pediatric Hematology, Gansu Provincial Maternity and Child-care Hospital, Lanzhou City, People's Republic of China
| | - Jiaojiao Yin
- Department of Clinical Laboratory, Gansu Provincial Maternity and Child-care Hospital, Lanzhou City, People's Republic of China
| | - Rui He
- Department of Clinical Laboratory, Gansu Provincial Maternity and Child-care Hospital, Lanzhou City, People's Republic of China
| | - Rong Chao
- Department of Pediatric Hematology, Gansu Provincial Maternity and Child-care Hospital, Lanzhou City, People's Republic of China
| | - Shengdong Zhu
- Department of Pediatric Hematology, Gansu Provincial Maternity and Child-care Hospital, Lanzhou City, People's Republic of China
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Abstract
Non-plaque induced diffuse gingival overgrowth represents a broad class of conditions caused by several etiological factors. The aim of this review is to highlight the most recent updates and classifications of all the existent gingival overgrowths. In addition, we highlighted the diagnostic pathway that should be employed in patients affected by gingival overgrowth. Gingival overgrowth can be related to syndromic diseases including a wide spectrum of genetic and chromosomal alterations. However, thanks to scientific sharing and the availability of genetic panels it is possible to obtain an accurate phenotypic identification of well-known syndromes and also to identify new ones. This narrative review shows that through rigid, strict diagnostic protocols, the work of the clinician is greatly facilitated, despite the wide variety of pathologies considered. In conclusion, the exchange of specialists’ competencies and the multidisciplinary management of these patients, are crucial to reach diagnosis and the correct clinical-therapeutic management.
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Portnoy PS, Lee SY, McMullen A, Qu V. Amlodipine-Induced Gingival Overgrowth: A Health Justice Issue. J Nurse Pract 2022. [DOI: 10.1016/j.nurpra.2021.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Liu Y, Zeng X, Ding Y, Xu Y, Duan D. Hyaline fibromatosis syndrome: a case presenting with gingival enlargement as the only clinical manifestation and a report of two new mutations in the ANTXR2 gene. BMC Oral Health 2021; 21:508. [PMID: 34627224 PMCID: PMC8501544 DOI: 10.1186/s12903-021-01840-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hyaline fibromatosis syndrome (HFS) is a rare autosomal recessive disorder caused by mutations in the gene for anthrax toxin receptor-2 (ANTXR2). The clinical features of HFS include skin thickening with nodules, papules and plaques, gingival enlargement, joint stiffness and contractures, and systemic manifestations. Notably, in all patients with HFS reported in the literature, gingival enlargement has never occurred alone. CASE PRESENTATION A case of a child with gingival enlargement as the only clinical manifestation, who was later diagnosed with HFS, is described. In this case, the absence of skin and joint lesions and other characteristic clinical presentations gave rise to a diagnostic problem. This uncommon condition was clinically indistinguishable from other diseases or conditions that presented with diffuse gingival enlargement. A definitive diagnosis of HFS was reached through genetic analysis. Trio whole exome sequencing revealed compound heterozygous mutations of ANTXR2 in this patient and two new mutations were reported. CONCLUSIONS The findings of this case serve as an important reminder to clinicians. When dental practitioners encounter gingival manifestations of HFS without accompanied skin or joint involvement, there is a need to pay attention to the differential diagnosis and increase awareness of HFS.
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Affiliation(s)
- Yiying Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontology, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Renmin South Road, Chengdu, 610041, China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontology, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Renmin South Road, Chengdu, 610041, China
| | - Yi Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontology, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Renmin South Road, Chengdu, 610041, China
| | - Dingyu Duan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontology, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Renmin South Road, Chengdu, 610041, China.
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Cammarata-Scalisi F, Girardi K, Strocchio L, Merli P, Bernardin AG, Galeotti A, Magliarditi F, Inserra A, Callea M. Oral Manifestations and Complications in Childhood Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12061634. [PMID: 32575613 PMCID: PMC7352340 DOI: 10.3390/cancers12061634] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of diseases, whose classification is based on lineage-commitment and genetics. Although rare in childhood, it is the most common type of acute leukemia in adults, accounting for 80% of all cases in this age group. The prognosis of this disease remains poor (especially in childhood, as compared to acute lymphoblastic leukemia); however, overall survival has significantly improved over the past 30 years. The health of the oral cavity is a remarkable reflection of the systemic status of an individual. Identification of the signs and symptoms of oral lesions can act as a warning sign of hidden and serious systemic involvement. Moreover, they may be the presenting feature of acute leukemia and provide important diagnostic indicators. Primary oral alterations are identified in up to 90% of cases of acute myeloid leukemia and consist of petechiae, spontaneous bleeding, mucosal ulceration, gingival enlargement with or without necrosis, infections, hemorrhagic bullae on the tongue, and cracked lips. Poor oral hygiene is a well-known risk factor for local and systemic infectious complications. Oro-dental complications due to AML treatment can affect the teeth, oral mucosa, soft and bone tissue, and contribute to opportunistic infections, dental decay, and enamel discoloration. The treatment of acute myeloid leukemia is still associated with high mortality and morbidity. The management is multimodal, involving aggressive multidrug chemotherapy and, in most cases, allogenic bone marrow transplantation. Periodontal and dental treatment for patients with leukemia should always be planned and concerted with hematologists.
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Affiliation(s)
- Francisco Cammarata-Scalisi
- Pediatrics Service, Regional Hospital of Antofagasta, Antofagasta 12440, Chile
- Correspondence: (F.C.-S.); (M.C.)
| | - Katia Girardi
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (K.G.); (L.S.); (P.M.)
| | - Luisa Strocchio
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (K.G.); (L.S.); (P.M.)
| | - Pietro Merli
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (K.G.); (L.S.); (P.M.)
| | | | - Angela Galeotti
- Unit of Dentistry, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (A.G.B.); (A.G.); (F.M.)
| | - Fabio Magliarditi
- Unit of Dentistry, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (A.G.B.); (A.G.); (F.M.)
| | | | - Michele Callea
- Unit of Dentistry, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (A.G.B.); (A.G.); (F.M.)
- Correspondence: (F.C.-S.); (M.C.)
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9
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Barbe AG, Röhrig G, Hieggelke L, Noack MJ, Derman SHM. Interdisciplinary assessment and management of a patient with a fibrous gingival enlargement of unknown origin: A case report. Clin Case Rep 2020; 8:159-165. [PMID: 31998508 PMCID: PMC6982473 DOI: 10.1002/ccr3.2605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/21/2022] Open
Abstract
A gingival enlargement of unclear cause could only be diagnosed after interdisciplinary cooperation as plasma cell gingivitis of unknown origin. Interdisciplinary approaches remain crucial when diagnosing rare gum diseases.
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Affiliation(s)
- Anna Greta Barbe
- Department of Operative Dentistry and PeriodontologyCenter of Dental MedicineUniversity of CologneKölnGermany
| | - Gabriele Röhrig
- Geriatric Diagnostic CenterMVZ Medicum Köln OstCologneGermany
| | - Lena Hieggelke
- Institute of PathologyUniversity Hospital CologneCologneGermany
| | - Michael Johannes Noack
- Department of Operative Dentistry and PeriodontologyCenter of Dental MedicineUniversity of CologneKölnGermany
| | - Sonja Henny Maria Derman
- Department of Operative Dentistry and PeriodontologyCenter of Dental MedicineUniversity of CologneKölnGermany
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