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Jin S, Sun Z, Fang X, Chen H, Yang W, Wang S, Fan J. A chorea-acanthocytosis patient with novel mutations in the VPS13A gene without acanthocyte. Neurol Sci 2024; 45:2057-2061. [PMID: 37985634 DOI: 10.1007/s10072-023-07174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Chorea-acanthocytosis (ChAc) is a rare clinical genetic disorder of the nervous system, which is characterized by choreiform movement disorder, cognitive decline, and psychiatric disorders. ChAc is mostly diagnosed based on its typical clinical manifestations and the increased number of acanthocytes in peripheral blood smears. Here, we report a patient, who has the characteristic clinical manifestations of ChAc with limb choreiform movements, involuntary lip and tongue bites, seizures, and emotional instability. However, her blood smear was negative for acanthocytes with scanning electron microscopy. We later identified two novel pathogenic mutations in the patient's vacuolar protein sorting homolog 13 A (VPS13A) on chromosome 9q21 by targeted gene sequencing, and she was definitively diagnosed with "ChAc." After treatment with carbamazepine, haloperidol, the patient's symptoms gradually improved. We consider that an acanthocyte negative blood smear cannot rule out ChAC diagnosis, and genetic testing is the "gold standard" for the diagnosis. Through a review of previous research, it is rare for a patient to have a clear diagnosis of ChAc by genetic testing, but whose blood smear is negative for acanthocytes with electron microscopy. In addition, in this report, we discovered two novel pathogenic mutations, which have not been reported previously, and extended the genetic characteristics of ChAc.
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Affiliation(s)
- Shan Jin
- The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Shushan District, No.117, Meishan Road, Hefei, 230000, Anhui, China
| | - Zhengzhe Sun
- Anhui University of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Xiang Fang
- The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Shushan District, No.117, Meishan Road, Hefei, 230000, Anhui, China.
| | - Huaizhen Chen
- The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Shushan District, No.117, Meishan Road, Hefei, 230000, Anhui, China
| | - Wenming Yang
- The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Shushan District, No.117, Meishan Road, Hefei, 230000, Anhui, China
- Key Laboratory of Xin'an Medicine Ministry of Education, Hefei, Anhui, China
| | - Shan Wang
- Anhui University of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Jinwei Fan
- Anhui University of Traditional Chinese Medicine, Hefei, Anhui, China
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Al-Tamemi S, Al-Zadjali S, Bruwer Z, Naseem SUR, Al-Siyabi N, ALRawahi M, Alkharusi K, Al-Thihli K, Al-Murshedi F, AlSayegh A, Al-Maawali A, Dennison D. Genetic Causes, Clinical Features, and Survival of Underlying Inborn Errors of Immunity in Omani Patients: a Single-Center Study. J Clin Immunol 2023; 43:452-465. [PMID: 36324046 DOI: 10.1007/s10875-022-01394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE Early identification of inborn errors of immunity (IEIs) is crucial due to the significant risk of morbidity and mortality. This study aimed to describe the genetic causes, clinical features, and survival rate of IEIs in Omani patients. METHODS A prospective study of all Omani patients evaluated for immunodeficiency was conducted over a 17-year period. Clinical features and diagnostic immunological findings were recorded. Targeted gene testing was performed in cases of obvious immunodeficiency. For cases with less conclusive phenotypes, a gene panel was performed, followed by whole-exome sequencing if necessary. RESULTS A total of 185 patients were diagnosed with IEIs during the study period; of these, 60.5% were male. Mean ages at symptom onset and diagnosis were 30.0 and 50.5 months, respectively. Consanguinity and a family history of IEIs were present in 86.9% and 50.8%, respectively. Most patients presented with lower respiratory infections (65.9%), followed by growth and development manifestations (43.2%). Phagocytic defects were the most common cause of IEIs (31.9%), followed by combined immunodeficiency (21.1%). Overall, 109 of 132 patients (82.6%) who underwent genetic testing received a genetic diagnosis, while testing was inconclusive for the remaining 23 patients (17.4%). Among patients with established diagnoses, 37 genes and 44 variants were identified. Autosomal recessive inheritance was present in 81.7% of patients with gene defects. Several variants were novel. Intravenous immunoglobulin therapy was administered to 39.4% of patients and 21.6% received hematopoietic stem cell transplantation. The overall survival rate was 75.1%. CONCLUSION This study highlights the genetic causes of IEIs in Omani patients. This information may help in the early identification and management of the disease, thereby improving survival and quality of life.
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Affiliation(s)
- Salem Al-Tamemi
- Clinical Immunology & Allergy Unit, Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman.
| | - Shoaib Al-Zadjali
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Zandre Bruwer
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Shafiq-Ur-Rehman Naseem
- Clinical Immunology & Allergy Unit, Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nabila Al-Siyabi
- Clinical Immunology & Allergy Unit, Directorate of Nursing, Sultan Qaboos University Hospital, Muscat, Oman
| | - Mohammed ALRawahi
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalsa Alkharusi
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Fathiya Al-Murshedi
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer AlSayegh
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - David Dennison
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
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Han B, Kim S, Koh J, Bae JM, Yun H, Jeon YK. An unusual case of microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) diffuse large B-cell lymphoma revealed by targeted gene sequencing. J Pathol Transl Med 2021; 56:92-96. [PMID: 34775735 PMCID: PMC8934995 DOI: 10.4132/jptm.2021.10.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022] Open
Abstract
Microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) status has been approved as a tissue-agnostic biomarker for immune checkpoint inhibitor therapy in patients with solid tumors. We report the case of an MSI-H/dMMR diffuse large B-cell lymphoma (DLBCL) identified by targeted gene sequencing (TGS). A 90-year-old female who presented with vaginal bleeding and a large mass in the upper vagina was diagnosed with germinal center-B-cell-like DLBCL, which recurred at the uterine cervix at 9 months after chemotherapy. Based on TGS of 121 lymphoma-related genes and the LymphGen algorithm, the tumor was classified genetically as DLBCL of EZB subtype. Mutations in multiple genes, including frequent frameshift mutations, were detected by TGS and further suggested MSI. The MSI-H/dMMR and loss of MLH1 and PMS2 expression were determined in MSI-fragment analysis, MSI real-time polymerase chain reaction, and immunohistochemical tests. This case demonstrates the potential diagnostic and therapeutic utility of lymphoma panel sequencing for DLBCL with MSI-H/dMMR.
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Affiliation(s)
- Bogyeong Han
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sehui Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea
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Beyzaei Z, Ezgu F, Geramizadeh B, Alborzi A, Shojazadeh A. Novel mutations in the PHKB gene in an iranian girl with severe liver involvement and glycogen storage disease type IX: a case report and review of literature. BMC Pediatr 2021; 21:175. [PMID: 33858366 PMCID: PMC8050929 DOI: 10.1186/s12887-021-02648-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycogen storage disease (GSD) type IXb is one of the rare variants of GSDs. It is a genetically heterogeneous metabolic disorder due to deficient hepatic phosphorylase kinase activity. Diagnosis of GSD can be difficult because of overlapping manifestations. Mutation analysis of the genes related to each type of GSD is supposed to be problem-solving, however, the presence of novel mutations can be confusing. In this case report, we will describe our experience with a young girl with the diagnosis of GSD and two novel mutations related to GSD type IXb. CASE PRESENTATION A 3-year- old girl presented with short stature, hepatomegaly, and liver cirrhosis. No specific diagnosis was made based on laboratory data, so liver biopsy and targeted-gene sequencing (TGS) were performed to find out the specific molecular basis of her disease. It was confirmed that the patient carries two novel variants in the PHKB gene. The variant in the PHKB gene was classified as pathogenic. CONCLUSIONS This is the first reported case of a dual molecular mutation of glycogen storage disease type IXb in the same patient. Two novel variants in PHKB were identified and one of them was a pathogenic split-site mutation. In conclusion, for the first time, identification of the novel variants in this patient expands the molecular and the phenotype basis of dual variants in GSD-IXb.
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Affiliation(s)
- Zahra Beyzaei
- Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatih Ezgu
- Department of Pediatric Metabolism and Genetic, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Bita Geramizadeh
- Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran. .,, Shiraz, Iran.
| | - Alireza Alborzi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Shojazadeh
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
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Beyzaei Z, Ezgu F, Geramizadeh B, Alborzi A, Shojazadeh A. Novel PRKAG2 variant presenting as liver cirrhosis: report of a family with 2 cases and review of literature. BMC Med Genomics 2021; 14:33. [PMID: 33509202 PMCID: PMC7845137 DOI: 10.1186/s12920-021-00879-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/19/2021] [Indexed: 11/30/2022] Open
Abstract
Background Mutations in the PRKAG2 gene encoding the 5′ Adenosine Monophosphate-Activated Protein Kinase (AMPK), specifically in its γ2 regulatory subunit, lead to Glycogen storage disease of heart, fetal congenital disorder (PRKAG2 syndrome). These mutations are rare, and their functional roles have not been fully elucidated. PRKAG2 syndrome is autosomal dominant disorder inherited with full penetrance. It is characterized by the accumulation of glycogen in the heart tissue, which is clinically manifested as hypertrophic cardiomyopathy. There is little knowledge about the characteristics of this disease. This study reports a genetic defect in an Iranian family with liver problems using targeted-gene sequencing. Case presentation A 4-year-old girl presented with short stature, hepatomegaly, and liver cirrhosis. As there was no specific diagnosis made based on the laboratory data and liver biopsy results, targeted-gene sequencing (TGS) was performed to detect the molecular basis of the disease. It was confirmed that this patient carried a novel heterozygous variant in the PRKAG2 gene. The echocardiography was a normal. Conclusion A novel heterozygous variant c.592A > T (p.Met198Leu) expands the mutational spectrum of the PRKAG2 gene in this family. Also, liver damage in patients with PRKAG2 syndrome has never been reported, which deserves further discussion.
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Affiliation(s)
- Zahra Beyzaei
- Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatih Ezgu
- Department of Pediatric Metabolism and Genetic, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Bita Geramizadeh
- Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Pathology, Shiraz University of Medical Sciences, Khalili St., Research Tower, Seventh Floor, Shiraz Transplant Research Center (STRC), Shiraz, Iran.
| | - Alireza Alborzi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Shojazadeh
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
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Lee KC, Koh J, Chung DH, Jeon YK. A case of concomitant EGFR/ALK alteration against a mutated EGFR background in early-stage lung adenocarcinoma. J Pathol Transl Med 2021; 55:139-144. [PMID: 33472332 PMCID: PMC7987517 DOI: 10.4132/jptm.2020.12.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
Rare cases of lung adenocarcinoma (LUAD) with concomitant epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) translocation have been reported. However, their clonal and evolutional relationship remains unclear. We report a case of early-stage EGFR-mutated LUAD with a focal concomitant EGFR/ALK alteration. A 63-year-old male underwent lobectomy to remove a 1.9-cm-sized lung nodule, which was diagnosed with EGFR-mutated LUAD. ALK immunohistochemistry (IHC) showed focal positivity within the part of the tumor characterized by lepidic pattern, also confirmed by fluorescence in-situ hybridization (FISH). Targeted next-generation sequencing was performed separately on the ALK IHC/FISH-positive and -negative areas. EGFR L833V/L858R mutations were detected in both areas, whereas EML4 (echinoderm microtubule-associated protein-like 4)-ALK translocations was confirmed only in the ALK IHC/FISH-positive area, suggesting the divergence of an EGFR/ALK co-altered subclone from the original EGFR-mutant clone. Our study suggests that concurrent alterations of EGFR and ALK can arise via divergent tumor evolution, even in the relatively early phases of tumorigenesis.
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Affiliation(s)
- Ki-Chang Lee
- Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea
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Chang YS, Tu SJ, Chen YC, Liu TY, Lee YT, Yen JC, Fang HY, Chang JG. Mutation profile of non-small cell lung cancer revealed by next generation sequencing. Respir Res 2021; 22:3. [PMID: 33407425 PMCID: PMC7789556 DOI: 10.1186/s12931-020-01608-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Precision therapy for lung cancer requires comprehensive genomic analyses. Specific effects of targeted therapies have been reported in Asia populations, including Taiwanese, but genomic studies have rarely been performed in these populations. METHOD We enrolled 72 patients with non-small cell lung cancer, of whom 61 had adenocarcinoma, 10 had squamous cell carcinoma, and 1 had combined adenocarcinoma and squamous cell carcinoma. Whole-exome or targeted gene sequencing was performed. To identify trunk mutations, we performed whole-exome sequencing in two tumor regions in four patients. RESULTS Nineteen known driver mutations in EGFR, PIK3CA, KRAS, CTNNB1, and MET were identified in 34 of the 72 tumors evaluated (47.22%). A comparison with the Cancer Genome Atlas dataset showed that EGFR was mutated at a much higher frequency in our cohort than in Caucasians, whereas KRAS and TP53 mutations were found in only 5.56% and 25% of our Taiwanese patients, respectively. We also identified new mutations in ARID1A, ARID2, CDK12, CHEK2, GNAS, H3F3A, KDM6A, KMT2C, NOTCH1, RB1, RBM10, RUNX1, SETD2, SF3B1, SMARCA4, THRAP3, TP53, and ZMYM2. Moreover, all ClinVar pathogenic variants were trunk mutations present in two regions of a tumor. RNA sequencing revealed that the trunk or branch genes were expressed at similar levels among different tumor regions. CONCLUSIONS We identified novel variants potentially associated with lung cancer tumorigenesis. The specific mutation pattern in Taiwanese patients with non-small cell lung cancer may influence targeted therapies.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Siang-Jyun Tu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Chia Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ya-Ting Lee
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
| | - Ju-Chen Yen
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
| | - Hsin-Yuan Fang
- Department of Thoracic Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan. .,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. .,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan. .,School of Medicine, China Medical University, Taichung, Taiwan. .,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.
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Beyzaei Z, Geramizadeh B, Karimzadeh S. Diagnosis of hepatic glycogen storage disease patients with overlapping clinical symptoms by massively parallel sequencing: a systematic review of literature. Orphanet J Rare Dis 2020; 15:286. [PMID: 33054851 PMCID: PMC7557034 DOI: 10.1186/s13023-020-01573-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Glycogen storage diseases (GSDs) with liver involvement are complex disorders with similar manifestations. Currently, the main diagnostic methods such as tissue diagnosis, either histopathology or enzyme assay, are invasive. Meanwhile, GSDs are diseases with significant genetic heterogeneity, and gene-sequencing methods can be more useful. This systematic review aims to review the literature to assess the value of massively parallel sequencing in the diagnosis of GSDs on patients with previously undiagnosed hepatic involvement. Methods Relevant studies identified in the MEDLINE/PubMed, EMBASE, Cochrane Library, Scopus, and Web of Science Core Collection databases up to July 2019 with no time and language restrictions. Publications were included in the review if they analyzed GSDs with hepatic involvement (GSD I, GSD III, GSD IV, GSD VI, GSD IX), using targeted gene sequencing (TGS) or exome sequencing (ES). Results Eleven studies were included in this systematic review. ES demonstrated a 93% diagnostic yield. These methods correctly distinguished all types of pathogenic variants. The diagnostic yield of the TGS method was around 79.7%. Conclusions According to our results, TGS analysis can be considered as the first-line diagnostic method with valuable results and ES can be used to diagnose complex cases of GSD with liver involvement. Overall, these molecular methods are considered as accurate diagnostic tools, which expedite correct diagnosis and treatment with significant cost-effectiveness by reducing unnecessary and inaccurate tests. PROSPERO registration CRD42020139931. Registered 8 January 2020.
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Affiliation(s)
- Zahra Beyzaei
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bita Geramizadeh
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Pathology, Shiraz University of Medical Sciences, Zand St., Shiraz, Iran.
| | - Sara Karimzadeh
- Shiraz Medical School Library, Shiraz University of Medical Sciences, Shiraz, Iran
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Zhang J, Meng L, Jiang W, Zhang H, Zhou A, Zeng N. Identification of clinical molecular targets for childhood Burkitt lymphoma. Transl Oncol 2020; 13:100855. [PMID: 32947237 PMCID: PMC7502376 DOI: 10.1016/j.tranon.2020.100855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Burkitt lymphoma (BL) is a malignant tumor in children. Although BL is generally curable, early relapse and refractoriness may occur. Some molecular indicators have been recently suggested for BL diagnosis, but large heterogeneity still exists. This study aimed at providing clinical molecular targets and methods that may help improve diagnosis and treatment of childhood BL. Only children patients were included in the study, and targeted gene sequencing was conducted to identify tumor specific mutations. The mRNA and protein level expression of potential target genes were measured by real-time PCR and immunohistochemistry. The relationship between BL specific gene mutation and differential expression with clinical features was analyzed. The results showed that i) detailed analysis of c-MYC/BCL2/BCL6 gene loci alteration and gene expression would help in accurate diagnosis and treatment determination of childhood BL; ii) loss-of-function mutations in SOCS1 or CIITA gene might be used as malignant markers for BL diagnosis and prognosis; iii) specific mutations of CD79A, MYD88, KLF2, DNMT3A and NFKBIE genes often concurrently existed in BL and showed association with benign clinical outcomes; iv) the high expression of MYC, TCF3 and loss-of-function ID3 genes in tumor may be potential therapeutic targets and could be used for treatment monitoring; and v) four MYC-translocation negative cases were re-defined as high-grade B-cell lymphoma-not otherwise specified (HGBL-NOS) but showed similar clinical outcomes and molecular features to other BL cases in the study, suggesting more studies needed to explore the molecular mechanisms and clinical significance of this provisional tumor entity. Detailed analysis of c-MYC/BCL2/BCL6 gene alteration and expression may help in accurate diagnosis and treatment; The MYC-translocation negative cases (HGBL-NOS) showed similar clinical outcomes and molecular features to other cases; Loss-of-function mutations of SOCS1 or CIITA gene could be used as malignant markers for diagnosis and prognosis; Concurrent mutations in CD79A, MYD88, KLF2, DNMT3A and NFKBIE genes associated with benign clinical outcomes; High expression of MYC, TCF3 and loss-of-function ID3 gene in tumor may be potential therapeutic targets.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Leijun Meng
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai 200040, China
| | - Weiyun Jiang
- Yu Kang Biotechnology Co., Ltd, Jiaxing 314100, Zhejiang, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai 200040, China
| | - Aiwu Zhou
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Naiyan Zeng
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Xiao Y, Xiang C, Yang D, Zhao B, Li Y, Yin H. Targeted-gene sequencing of an undifferentiated gallbladder carcinoma: a case report. Diagn Pathol 2020; 15:66. [PMID: 32487254 DOI: 10.1186/s13000-020-00981-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022] Open
Abstract
Background Undifferentiated carcinomas of the gallbladder are extremely rare. Most undifferentiated carcinomas are accompanied by adjacent foci of other conventional carcinomas, and a transition zone is shared between them. However, genetic alterations of undifferentiated gallbladder carcinoma and the similarities or differences between the undifferentiated carcinoma and the foci conventional carcinoma are unknown. Case presentation Herein, we report a case of undifferentiated gallbladder carcinoma with osteoclast-like giant cells with invasion into the liver, duodenum, and stomach in a 56-year-old man. The tumor was microscopically formed from the tubular adenocarcinoma (< 5% of the entire tumor), the undifferentiated carcinoma, and a transition zone between them. Four somatic mutations (TP53, TERT, ARID2, and CDH1), three amplifications (CCND1, FGF19, and MET), and a tumor mutation burden (TMB) of 3.45 muts/Mb were detected in the undifferentiated component using targeted gene sequencing, whereas 102 somatic mutations (including TP53, TERT, ARID2, and CDH1), one amplification (CCND1), and a higher TMB of 87.07 muts/Mb were detected in the tubular component. This patient died of tumor recurrence 2 months after the surgery. Conclusions The undifferentiated gallbladder carcinoma had its unique molecular alterations. The similarities in the genetic alterations of the undifferentiated carcinoma and adenocarcinoma provide evidence of a common origin at the genetic level. The occurrence of an undifferentiated carcinoma may be due to heterogeneity-associated branched evolution from the tubular adenocarcinoma.
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Dallali H, Pezzilli S, Hechmi M, Sallem OK, Elouej S, Jmel H, Ben Halima Y, Chargui M, Gharbi M, Mercuri L, Alberico F, Mazza T, Bahlous A, Ben Ahmed M, Jamoussi H, Abid A, Trischitta V, Abdelhak S, Prudente S, Kefi R. Genetic characterization of suspected MODY patients in Tunisia by targeted next-generation sequencing. Acta Diabetol 2019; 56:515-523. [PMID: 30656436 DOI: 10.1007/s00592-018-01283-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 12/25/2018] [Indexed: 01/05/2023]
Abstract
AIMS Maturity Onset Diabetes of the Young (MODY) is a monogenic form of diabetes with autosomal dominant inheritance pattern. The diagnosis of MODY and its subtypes is based on genetic testing. Our aim was investigating MODY by means of next-generation sequencing in the Tunisian population. METHODS We performed a targeted sequencing of 27 genes known to cause monogenic diabetes in 11 phenotypically suspected Tunisian patients. We retained genetic variants passing filters of frequency in public databases as well as their probable effects on protein structures and functions evaluated by bioinformatics prediction tools. RESULTS Five heterozygous variants were found in four patients. They include two mutations in HNF1A and GCK that are the causative genes of the two most prevalent MODY subtypes described in the literature. Other possible mutations, including novel frameshift and splice-site variants were identified in ABCC8 gene. CONCLUSIONS Our study is the first to investigate the clinical application of targeted next-generation sequencing for the diagnosis of MODY in Africa. The combination of this approach with a filtering/prioritization strategy made a step towards the identification of MODY mutations in the Tunisian population.
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Affiliation(s)
- Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
| | - Serena Pezzilli
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
| | | | - Sahar Elouej
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- Faculty of Medicine La Timone, INSERM, GMGF, Aix Marseille University, 27 bd Jean Moulin, 13385, Marseille, France
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- Faculty of Sciences of Bizerte, University of Carthage, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- University of Tunis El Manar, El Manar I, 2092, Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
| | - Mariem Gharbi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
| | - Luana Mercuri
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Federica Alberico
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Afaf Bahlous
- Central Laboratory of Medical Biology, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
| | - Melika Ben Ahmed
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- Research Unit on Obesity, National Institute of Nutrition and Food Technology, 11 rue Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- Research Unit on Obesity, National Institute of Nutrition and Food Technology, 11 rue Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Vincenzo Trischitta
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia
- University of Tunis El Manar, El Manar I, 2092, Tunis, Tunisia
| | - Sabrina Prudente
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, 1002, Tunis, Tunisia.
- University of Tunis El Manar, El Manar I, 2092, Tunis, Tunisia.
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Fielding D, Dalley AJ, Bashirzadeh F, Singh M, Nandakumar L, McCart Reed AE, Black D, Kazakoff S, Pearson JV, Nones K, Waddell N, Lakhani SR, Simpson PT. Diff-Quik Cytology Smears from Endobronchial Ultrasound Transbronchial Needle Aspiration Lymph Node Specimens as a Source of DNA for Next-Generation Sequencing Instead of Cell Blocks. Respiration 2019; 97:525-539. [PMID: 30731462 DOI: 10.1159/000495661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/21/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) in lung cancer specimens from endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) is usually performed on formalin-fixed paraffin-embedded cell block material. OBJECTIVES Since DNA can be damaged by this process, we investigated the potential of using DNA extracted from Diff-Quik cytology smears made for rapid on-site evaluation during EBUS-TBNA. METHODS In a prospective study, 67 patients undergoing diagnostic EBUS-TBNA were ana-lysed. We compared cell blocks and smears for DNA yields and sequencing (TruSeq Amplicon Cancer Panel) outcomes. Smears were also evaluated for tumour cell fraction and overall cellularity (cell count). RESULTS Primary lung cancer was diagnosed in 64 patients and metastatic malignancy in 3 patients. The DNA yield from smears was significantly higher than that obtained from matched cell blocks (mean 1,740 vs. 434 ng; p = 0.001). For 33 cases with matched smears and cell blocks the mutation profiles were similar. Smears with abundant malignant cells (using a cut-off of > 25% tumour cell fraction and > 1,000 cells) accurately predicted high (> 50 ng) DNA yield and therefore success in triaging samples to sequencing. In terms of tissue workflow, using only smears as source DNA for sequencing was an improvement in the use of only cell blocks (54/67 [80.6%] vs. 41/67 [61.2%]); however, the use of cell blocks when smears were not available or did not yield sufficient DNA further improved the success rate to 62/67 (92.5%) cases. CONCLUSION We recommend smears in laboratory workflows as the primary source of DNA for NGS following an EBUS procedure.
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Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia, .,Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia,
| | - Andrew J Dalley
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Mahendra Singh
- Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Debra Black
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sunil R Lakhani
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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13
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Zhao X, McCutcheon JN, Kallakury B, Chahine JJ, Pratt D, Raffeld M, Chen Y, Wang C, Giaccone G. Combined Small Cell Carcinoma of the Lung: Is It a Single Entity? J Thorac Oncol 2018; 13:237-45. [PMID: 29101056 DOI: 10.1016/j.jtho.2017.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND SCLC accounts for 15% and 20% of all lung cancers, with combined SCLC (CSCLC) comprising 2% to 5%. Little is known about the clinical characteristics and molecular changes associated with the various histologic components. METHODS A total of 205 SCLC cases were resected between 2005 and 2015. Clinical and pathologic features were analyzed. All CSCLC cases were confirmed by histologic examination and immunohistochemistry. The individual components were microdissected using a novel automated dissection system, and DNA was extracted and subjected to targeted exome sequencing. RESULTS A total of 10 cases of CSCLC were identified out of 170 cases with adequate histologic material; squamous cell carcinoma comprised the second component in half of these (n = 5). There were no significant differences between CSCLC and pure SCLC with respect to clinical features. The median follow-up time was 36 months. The median survival times of patients with pure SCLC and CSCLC were 58 months and 26 months, respectively (p = 0.030). The different components of three cases of CSCLC were deemed adequate for microdissection and sequencing. Approximately 75% of the identified somatic mutations were present in both components. There were also 15 gene mutations or six amplifications unique to only one of the components. CONCLUSIONS We identified no significant clinical or pathologic differences between pure SCLC and CSCLC; CSCLC was associated with decreased overall survival compared with pure SCLC. The histologic components of CSCLC had high genetic concordance but also showed divergent genotypes. These findings may suggest a common precursor with subsequent acquisition of oncogenic changes in CSCLC.
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Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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15
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Abstract
BACKGROUND Targeted gene sequencing (TGS) and whole exome sequencing (WES) are being used in clinical testing in laboratories. We compared the performances of TGS and WES using the same DNA samples. METHODS DNA was extracted from 10 endometrial tumor tissue specimens. Sequencing were performed with an Illumina HiSeq 2000. We randomly selected variants to confirm through Sanger sequencing or mutant-enriched PCR with Sanger sequencing. RESULTS We found that the variants identified in both TGS and WES were true positives (47/47), regardless of the sequencing depth. Most variants found in TGS only were true positives (34/40), and most of the variants found by WES only were false positives (8/18). From these results, we suggest that the sequencing depth may not play important role in the accuracy of NGS-based methods. After analysis, we found that WES had a sensitivity of 72.70%, specificity of 96.27%, precision of 99.44%, and accuracy of 75.03%. CONCLUSIONS The results of NGS-based methods must currently be validated, especially for important reported variants regardless of the methods used, and for the use of WES in cancers a higher false negative rate must be considered. More sensitive methods should be used to confirm the NGS results in uneven cancer tissues.
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16
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Li B, Gale RP, Xu Z, Qin T, Song Z, Zhang P, Bai J, Zhang L, Zhang Y, Liu J, Huang G, Xiao Z. Non-driver mutations in myeloproliferative neoplasm-associated myelofibrosis. J Hematol Oncol 2017; 10:99. [PMID: 28464892 PMCID: PMC5414291 DOI: 10.1186/s13045-017-0472-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/26/2017] [Indexed: 11/30/2022] Open
Abstract
We studied non-driver mutations in 62 subjects with myeloproliferative neoplasm (MPN)-associated myelofibrosis upon diagnosis, including 45 subjects with primary myelofibrosis (PMF) and 17 with post-polycythemia vera or post-essential thrombocythemia myelofibrosis (post-PV/ET MF). Fifty-eight subjects had ≥1 non-driver mutation upon diagnosis. Mutations in mRNA splicing genes, especially in U2AF1, were significantly more frequent in PMF than in post-PV/ET MF (33 vs. 6%; P = 0.015). There were also striking differences in clonal architecture. These data indicate different genomic spectrums between PMF and post-PV/ET MF.
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Affiliation(s)
- Bing Li
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020 China
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Robert Peter Gale
- Haematology Research Centre, Division of Experimental Medicine, Department of Medicine, Imperial College London, London, UK
| | - Zefeng Xu
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020 China
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Tiejun Qin
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020 China
| | - Zhen Song
- Medical Service Division, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Peihong Zhang
- Department of Pathology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jie Bai
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yue Zhang
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020 China
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jinqin Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Gang Huang
- Divisions of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Zhijian Xiao
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020 China
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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17
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Ayers KL, Bouty A, Robevska G, van den Bergen JA, Juniarto AZ, Listyasari NA, Sinclair AH, Faradz SMH. Variants in congenital hypogonadotrophic hypogonadism genes identified in an Indonesian cohort of 46,XY under-virilised boys. Hum Genomics 2017; 11:1. [PMID: 28209183 PMCID: PMC5314676 DOI: 10.1186/s40246-017-0098-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Congenital hypogonadotrophic hypogonadism (CHH) and Kallmann syndrome (KS) are caused by disruption to the hypothalamic-pituitary-gonadal (H-P-G) axis. In particular, reduced production, secretion or action of gonadotrophin-releasing hormone (GnRH) is often responsible. Various genes, many of which play a role in the development and function of the GnRH neurons, have been implicated in these disorders. Clinically, CHH and KS are heterogeneous; however, in 46,XY patients, they can be characterised by under-virilisation phenotypes such as cryptorchidism and micropenis or delayed puberty. In rare cases, hypospadias may also be present. Results Here, we describe genetic mutational analysis of CHH genes in Indonesian 46,XY disorder of sex development patients with under-virilisation. We present 11 male patients with varying degrees of under-virilisation who have rare variants in known CHH genes. Interestingly, many of these patients had hypospadias. Conclusions We postulate that variants in CHH genes, in particular PROKR2, PROK2, WDR11 and FGFR1 with CHD7, may contribute to under-virilisation phenotypes including hypospadias in Indonesia.
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Affiliation(s)
- Katie L Ayers
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Aurore Bouty
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.,The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Gorjana Robevska
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | | | - Achmad Zulfa Juniarto
- Division of Human Genetics, Centre for Biomedical Research, Faculty of Medicine, Diponegoro University (FMDU), JL. Prof. H. Soedarto, SH, Tembalang, Semarang, 50275, Central Java, Indonesia
| | - Nurin Aisyiyah Listyasari
- Division of Human Genetics, Centre for Biomedical Research, Faculty of Medicine, Diponegoro University (FMDU), JL. Prof. H. Soedarto, SH, Tembalang, Semarang, 50275, Central Java, Indonesia
| | - Andrew H Sinclair
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sultana M H Faradz
- Division of Human Genetics, Centre for Biomedical Research, Faculty of Medicine, Diponegoro University (FMDU), JL. Prof. H. Soedarto, SH, Tembalang, Semarang, 50275, Central Java, Indonesia.
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18
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Ock CY, Son B, Keam B, Lee SY, Moon J, Kwak H, Kim S, Kim TM, Jeon YK, Kwon SK, Hah JH, Lee SH, Kwon TK, Kim DW, Wu HG, Sung MW, Heo DS. Identification of genomic mutations associated with clinical outcomes of induction chemotherapy in patients with head and neck squamous cell carcinoma. J Cancer Res Clin Oncol 2016; 142:873-83. [PMID: 26677030 DOI: 10.1007/s00432-015-2083-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022]
Abstract
PURPOSE We performed deep sequencing of target genes in head and neck squamous cell carcinoma (HNSCC) tumors to identify somatic mutations that are associated with induction chemotherapy (IC) response. METHODS Patients who were diagnosed with HNSCC were retrospectively identified. Patients who were treated with IC were divided into two groups: good responders and poor responders by tumor response and progression-free survival. Targeted gene sequencing for 2404 somatic mutations of 44 genes was performed on HNSCC tissues. Mutations with total coverage of <500 were excluded, and the cutoff for altered allele frequency was >10 %. RESULTS Of the 71 patients, 45 were treated upfront with IC. Mean total coverage was 1941 per locus, and 42.2 % of tumors had TP53 mutations. Thirty-three mutations in TP53, NOTCH3, FGFR2, FGFR3, ATM, EGFR, MET, PTEN, FBXW7, SYNE1, and SUFU were frequently altered in poor responders. Among the patients who were treated with IC, those with unfavorable genomic profiles had significantly poorer overall survival than those without unfavorable genomic profiles (hazard ratio 6.45, 95 % confidence interval 2.07-20.10, P < 0.001). CONCLUSIONS Comprehensive analysis of mutation frequencies identified unfavorable genomic profiles, and the patients without unfavorable genomic profiles can obtain clinical benefits from IC in patients with HNSCC.
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Chen Z, Wang JL, Tang BS, Sun ZF, Shi YT, Shen L, Lei LF, Wei XM, Xiao JJ, Hu ZM, Pan Q, Xia K, Zhang QY, Dai MZ, Liu Y, Ashizawa T, Jiang H. Using next-generation sequencing as a genetic diagnostic tool in rare autosomal recessive neurologic Mendelian disorders. Neurobiol Aging 2013; 34:2442.e11-7. [PMID: 23726790 DOI: 10.1016/j.neurobiolaging.2013.04.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 04/18/2013] [Accepted: 04/27/2013] [Indexed: 01/20/2023]
Abstract
Next-generation sequencing was used to investigate 9 rare Chinese pedigrees with rare autosomal recessive neurologic Mendelian disorders. Five probands with ataxia-telangectasia and 1 proband with chorea-acanthocytosis were analyzed by targeted gene sequencing. Whole-exome sequencing was used to investigate 3 affected individuals with Joubert syndrome, nemaline myopathy, or spastic ataxia Charlevoix-Saguenay type. A list of known and novel candidate variants was identified for each causative gene. All variants were genetically verified by Sanger sequencing or quantitative polymerase chain reaction with the strategy of disease segregation in related pedigrees and healthy controls. The advantages of using next-generation sequencing to diagnose rare autosomal recessive neurologic Mendelian disorders characterized by genetic and phenotypic heterogeneity are demonstrated. A genetic diagnostic strategy combining the use of targeted gene sequencing and whole-exome sequencing with the aid of next-generation sequencing platforms has shown great promise for improving the diagnosis of neurologic Mendelian disorders.
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Affiliation(s)
- Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
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