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Ip BBK, Wong ATC, Law JHY, Au CH, Ma SY, Chim JCS, Liang RHS, Leung AYH, Wan TSK, Ma ESK. Application of droplet digital PCR in minimal residual disease monitoring of rare fusion transcripts and mutations in haematological malignancies. Sci Rep 2024; 14:6400. [PMID: 38493200 PMCID: PMC10944481 DOI: 10.1038/s41598-024-57016-y] [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: 12/13/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Leukaemia of various subtypes are driven by distinct chromosomal rearrangement or genetic abnormalities. The leukaemogenic fusion transcripts or genetic mutations serve as molecular markers for minimal residual disease (MRD) monitoring. The current study evaluated the applicability of several droplet digital PCR assays for the detection of these targets at RNA and DNA levels (atypical BCR::ABL1 e19a2, e23a2ins52, e13a2ins74, rare types of CBFB::MYH11 (G and I), PCM1::JAK2, KMT2A::ELL2, PICALM::MLLT10 fusion transcripts and CEBPA frame-shift and insertion/duplication mutations) with high sensitivity. The analytical performances were assessed by the limit of blanks, limit of detection, limit of quantification and linear regression. Our data demonstrated serial MRD monitoring for patients at molecular level could become "digitalized", which was deemed important to guide clinicians in treatment decision for better patient care.
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Affiliation(s)
- Beca B K Ip
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Anthony T C Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Janet Hei Yin Law
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Shing Yan Ma
- Specialist in Haematology & Haematological Oncology, Causeway Bay, Hong Kong
| | - James C S Chim
- Department of Medicine and Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Raymond H S Liang
- Department of Medicine and Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Anskar Y H Leung
- Department of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Thomas S K Wan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong.
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Rajaby R, Liu DX, Au CH, Cheung YT, Lau AYT, Yang QY, Sung WK. INSurVeyor: improving insertion calling from short read sequencing data. Nat Commun 2023; 14:3243. [PMID: 37277343 DOI: 10.1038/s41467-023-38870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Insertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, a fast, sensitive and precise method that detects insertions from next-generation sequencing paired-end data. Using publicly available benchmark datasets (both human and non-human), we show that INSurVeyor is not only more sensitive than any individual caller we tested, but also more sensitive than all of them combined. Furthermore, for most types of insertions, INSurVeyor is almost as sensitive as long reads callers. Second, we provide state-of-the-art catalogues of insertions for 1047 Arabidopsis Thaliana genomes from the 1001 Genomes Project and 3202 human genomes from the 1000 Genomes Project, both generated with INSurVeyor. We show that they are more complete and precise than existing resources, and important insertions are missed by existing methods.
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Affiliation(s)
- Ramesh Rajaby
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
- A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Dong-Xu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun Hang Au
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Yuen-Ting Cheung
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Amy Yuet Ting Lau
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wing-Kin Sung
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China.
- A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore.
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China.
- Laboratory of Computational Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore.
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Dong P, Cai Z, Li B, Zhu Y, Chan AKY, Chiang MWL, Au CH, Sung WK, Cheung TT, Lo CM, Man K, Lee NP. HFE promotes mitotic cell division through recruitment of cytokinetic abscission machinery in hepatocellular carcinoma. Oncogene 2022; 41:4185-4199. [PMID: 35882980 DOI: 10.1038/s41388-022-02419-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022]
Abstract
HFE (Hemochromatosis) is a conventional iron level regulator and its loss of function due to gene mutations increases the risk of cancers including hepatocellular carcinoma (HCC). Likewise, studies focusing on HFE overexpression in cancers are all limited to linking up these events as a consequence of iron level deregulation. No study has explored any iron unrelated role of HFE in cancers. Here, we first reported HFE as an oncogene in HCC and its undescribed function on promoting abscission in cytokinesis during mitotic cell division, independent of its iron-regulating ability. Clinical analyses revealed HFE upregulation in tumors linking to large tumor size and poor prognosis. Functionally and mechanistically, HFE promoted cytokinetic abscission via facilitating ESCRT abscission machinery recruitment to the abscission site through signaling a novel HFE/ALK3/Smads/LIF/Hippo/YAP/YY1/KIF13A axis. Pharmacological blockage of HFE signaling axis impeded tumor phenotypes in vitro and in vivo. Our data on HFE-driven HCC unveiled a new mechanism utilized by cancer cells to propel rapid cell division. This study also laid the groundwork for tumor intolerable therapeutics development given the high cytokinetic dependency of cancer cells and their vulnerability to cytokinetic blockage.
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Affiliation(s)
- Pingping Dong
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong.,Department of Radiation Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziqing Cai
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Bingfeng Li
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yueqin Zhu
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Alice K Y Chan
- Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong.,Po Leung Kuk Tong Nai Kan Junior Secondary College, Hong Kong, Hong Kong
| | - Michael W L Chiang
- Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong
| | - Chun Hang Au
- Hong Kong Genome Institute, Hong Kong, Hong Kong
| | - Wing Kin Sung
- Hong Kong Genome Institute, Hong Kong, Hong Kong.,School of Computing, National University of Singapore, Singapore, Singapore.,Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Tan To Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chung Mau Lo
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Kwan Man
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong.
| | - Nikki P Lee
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Hong Kong, Hong Kong.
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4
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Kwong A, Ho CYS, Shin VY, Au CH, Chan TL, Ma ESK. How does re-classification of variants of unknown significance (VUS) impact the management of patients at risk for hereditary breast cancer? BMC Med Genomics 2022; 15:122. [PMID: 35641994 PMCID: PMC9158111 DOI: 10.1186/s12920-022-01270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background The popularity of multigene testing increases the probability of identifying variants of uncertain significance (VUS). While accurate variant interpretation enables clinicians to be better informed of the genetic risk of their patients, currently, there is a lack of consensus management guidelines for clinicians on VUS. Methods Among the BRCA1 and BRCA2 mutations screening in 3,544 subjects, 236 unique variants (BRCA1: 86; BRCA2: 150) identified in 459 patients were being reviewed. These variants consist of 231 VUS and 5 likely benign variants at the initial classification. Results The variants in 31.8% (146/459) patients were reclassified during the review, which involved 26 unique variants (11.0%). Also, 31 probands (6.8%) and their family members were offered high-risk surveillance and related management after these variants were reclassified to pathogenic or likely pathogenic. At the same time, 69 probands (15%) had their VUS downgraded to cancer risk equivalent to the general population level. Conclusion A review of archival variants from BRCA1 and BRCA2 genetic testing changed the management for 31.8% of the families due to increased or reduced risk. We encourage regular updates of variant databases, reference to normal population and collaboration between research laboratories on functional studies to define the clinical significances of VUS better. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01270-4.
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Affiliation(s)
- Ava Kwong
- Chief of Breast Surgery Division, Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Pokfulam, Hong Kong SAR. .,Department of Surgery, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR. .,Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.
| | - Cecilia Yuen Sze Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Vivian Yvonne Shin
- Chief of Breast Surgery Division, Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Pokfulam, Hong Kong SAR
| | - Chun Hang Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
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5
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Kwong A, Ho CYS, Shin VY, Au CH, Luk WP, Fung LH, Chan TL, Chan KKL, Ngan HYS, Ma ESK. Germline mutations in Chinese ovarian cancer with or without breast cancer. Mol Genet Genomic Med 2022; 10:e1940. [PMID: 35608067 PMCID: PMC9266594 DOI: 10.1002/mgg3.1940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/08/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ovarian and breast cancers are known to have significant genetic components. Considering the differences in the mutation spectrum across ethnicity, it is important to identify hereditary breast and ovarian cancer (HBOC) genes mutation in Chinese for clinical management. METHODS Two cohorts of 451 patients with ovarian cancer only (OV) and 93 patients with both breast and ovarian (BROV) cancers were initially screened for BRCA1, BRCA2, TP53, and PTEN. 109 OV and 43 BROV patients with extensive clinical risk and were being tested negative, were then further characterized by 30-gene panel analysis. RESULTS Pathogenic BRCA1/2 variants were identified in 45 OV patients and 33 BROV patients, giving a prevalence of 10% and 35.5%, respectively. After the extended screening, mutations in other HBOC genes were identified in an additional 12.8% (14/109) of the OV cohort and 14% (6/43) in the BROV cohort. The most commonly mutated genes in the OV cohort were MSH2 (4.6%) while in the BROV cohort were MSH2 (4.7%) and PALB2 (4.7%). With this extended multigene testing strategy, pathogenic mutations were detected in 12.8% of OV patients (BRCAs: 10%; additional genes: 12.8%) and 40.9% (BRCAs: 35.5%; additional genes: 14%) of BROV patients. CONCLUSION Extended characterization of the contributions of HBOC genes to OV and BROV patients has significant impacts on further management in patients and their families, expanding the screening net for more asymptomatic individuals.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Pofulam, Hong Kong SAR.,Department of Surgery, University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Surgery, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR.,Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR
| | - Cecilia Yuen Sze Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Chun Hang Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Wing Pan Luk
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Ling Hiu Fung
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Karen Kar Loen Chan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Hextan Yuen Sheung Ngan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pofulam, Hong Kong SAR
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
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Kwong A, Au CH, Shin VY, Ho DN, Wong EYL, Ho CYS, Chung Y, Chan TL, Ma ESK. Rapid Breakpoint Mapping of a Novel Germline PALB2 Duplication by PCR-Free Long-Read Sequencing for Interpretation of Its Pathogenicity. JCO Precis Oncol 2022; 5:1044-1047. [PMID: 34994627 DOI: 10.1200/po.20.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China.,Department of Surgery and Cancer Genetics Centre, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Elaine Y L Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Cecilia Y S Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yvonne Chung
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
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7
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Kwong A, Shin VY, Ho CYS, Khalid A, Au CH, Chan KKL, Ngan HYS, Chan TL, Ma ESK. Germline PALB2 Mutation in High-Risk Chinese Breast and/or Ovarian Cancer Patients. Cancers (Basel) 2021; 13:4195. [PMID: 34439348 PMCID: PMC8394494 DOI: 10.3390/cancers13164195] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
The prevalence of the PALB2 mutation in breast cancer varies across different ethnic groups; hence, it is of intense interest to evaluate the cancer risk and clinical association of the PALB2 mutation in Chinese breast and/or ovarian cancer patients. We performed sequencing with a 6-gene test panel (BRCA1, BRCA2, TP53, PTEN, PALB2, and CDH1) to identify the prevalence of the PALB2 germline mutation among 2631 patients with breast and/or ovarian cancer. In this cohort, 39 mutations were identified with 24 types of mutation variants, where the majority of the mutations were frame-shift mutations and resulted in early termination. We also identified seven novel PALB2 mutations. Most of the PALB2 mutation carriers had breast cancer (36, 92.3%) and were more likely to have family history of breast cancer (19, 48.7%). The majority of the breast tumors were invasive ductal carcinoma (NOS type) (34, 81.0%) and hormonal positive (ER: 32, 84.2%; PR: 23, 60.5%). Pathogenic mutations of PALB2 were found in 39 probands with a mutation frequency of 1.6% and 1% in breast cancer and ovarian cancer patients, respectively. PALB2 mutation carriers were more likely have hormonal positive tumors and were likely to have familial aggregation of breast cancer.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, China; (V.Y.S.); (A.K.)
- University of Hong Kong-Shenzhen Hospital, Hong Kong, China
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, China
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China; (T.-L.C.); (E.S.K.M.)
| | - Vivian Y. Shin
- Department of Surgery, The University of Hong Kong, Hong Kong, China; (V.Y.S.); (A.K.)
- University of Hong Kong-Shenzhen Hospital, Hong Kong, China
| | - Cecilia Y. S. Ho
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China; (C.Y.S.H.); (C.H.A.)
| | - Aleena Khalid
- Department of Surgery, The University of Hong Kong, Hong Kong, China; (V.Y.S.); (A.K.)
- University of Hong Kong-Shenzhen Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China; (C.Y.S.H.); (C.H.A.)
| | - Karen K. L. Chan
- Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, China; (K.K.L.C.); (H.Y.S.N.)
| | - Hextan Y. S. Ngan
- Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, China; (K.K.L.C.); (H.Y.S.N.)
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China; (T.-L.C.); (E.S.K.M.)
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China; (C.Y.S.H.); (C.H.A.)
| | - Edmond S. K. Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China; (T.-L.C.); (E.S.K.M.)
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China; (C.Y.S.H.); (C.H.A.)
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Abstract
BACKGROUND Repetitive transcranial magnetic stimulation (rTMS) is effective in treating unipolar depression. However, the efficacy of rTMS in bipolar disorder (BD) is unclear. This meta-analysis aimed to examine the efficacy and tolerability of rTMS for both depressive and manic phases in BD. METHODS MEDLINE, EMBASE, PsycINFO, CENTRAL databases were searched for controlled trials on treatment of BD with rTMS. Primary outcomes included changes in depression or mania scores, response and remission rates. Secondary outcomes included quality of life and functioning assessment. We used random-effects model, Hedge's g, risk differences (RDs) and the number needed to treat (NNT). RESULTS Eleven randomized sham-controlled studies were included, with a total of 345 patients with BD (bipolar depression = 257, mania = 86, mixed affective = 2). Trials of rTMS in bipolar depression (N = 8) demonstrated small but significant improvement in depression scores [standardized mean difference = 0.302, p < 0.05], compared to control group. Furthermore, rTMS brought a higher remission rate than sham-controls [RD = 0.104 ± 0.044, p < 0.05, NNT = 10; and a trend of greater response rate [RD = 0.074 ± 0.039, p = 0.06]. Results were inconclusive for effect of rTMS in mania. In both depressive and manic groups, no serious adverse events were reported. Risk of treatment-emergent mania appeared low. LIMITATIONS There was limited number of eligible primary studies, with variable randomization procedures. CONCLUSION rTMS appears safe and effective in treating bipolar depression. More stringent RCTs are necessary for concrete conclusion about efficacy in mania.
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Affiliation(s)
- Maggie M K Tee
- Department of Psychiatry, Kwai Chung Hospital, 3-15 Kwai Chung Hospital Road, Hong Kong, China.
| | - C H Au
- Department of Psychiatry, Queen Mary Hospital, Hong Kong, China
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Chan WS, Au CH, Lam HY, Wang CLN, Ho DNY, Lam YM, Chu DKW, Poon LLM, Chan TL, Zee JST, Ma ESK, Tang BSF. Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Virol J 2020; 17:183. [PMID: 33225958 PMCID: PMC7681180 DOI: 10.1186/s12985-020-01454-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/11/2020] [Indexed: 01/12/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has been a catastrophic burden to global healthcare systems. The fast spread of the etiologic agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need to identify unknown coronaviruses rapidly for prompt clinical and public health decision making. Moreover, owing to the high mutation rate of RNA viruses, periodic surveillance on emerging variants of key virus components is essential for evaluating the efficacy of antiviral drugs, diagnostic assays and vaccines. These 2 knowledge gaps formed the basis of this study. In the first place, we evaluated the feasibility of characterizing coronaviruses directly from respiratory specimens. We amplified partial RdRP gene, a stable genetic marker of coronaviruses, from a collection of 57 clinical specimens positive for SARS-CoV-2 or other human coronaviruses, and sequenced the amplicons with Nanopore Flongle and MinION, the fastest and the most scalable massively-parallel sequencing platforms to-date. Partial RdRP sequences were successfully amplified and sequenced from 82.46% (47/57) of specimens, ranging from 75 to 100% by virus type, with consensus accuracy of 100% compared with Sanger sequences available (n = 40). In the second part, we further compared 19 SARS-CoV-2 RdRP sequences collected from the first to third waves of COVID-19 outbreak in Hong Kong with 22,173 genomes from GISAID EpiCoV™ database. No single nucleotide variants (SNVs) were found in our sequences, and 125 SNVs were observed from global data, with 56.8% being low-frequency (n = 1-47) missense mutations affecting the rear part of RNA polymerase. Among the 9 SNVs found on 4 conserved domains, the frequency of 15438G > T was highest (n = 34) and was predominantly found in Europe. Our data provided a glimpse into the sequence diversity of a primary antiviral drug and diagnostic target. Further studies are warranted to investigate the significance of these mutations.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Ho Yin Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Candy Ling Na Wang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Dona Ngar-Yin Ho
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yuk Man Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Daniel Ka Wing Chu
- School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | | | - Edmond Shiu Kwan Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China.
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10
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Kwong A, Shin VY, Ho CYS, Au CH, Slavin TP, Weitzel JN, Chan TL, Ma ESK. Mutation screening of germline TP53 mutations in high-risk Chinese breast cancer patients. BMC Cancer 2020; 20:1053. [PMID: 33138793 PMCID: PMC7607817 DOI: 10.1186/s12885-020-07476-y] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/30/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Germline TP53 mutations are associated with Li-Fraumeni syndrome, a severe and rare hereditary cancer syndrome. Despite the rarity of germline TP53 mutations, the clinical implication for mutation carriers and their families is significant. The risk management of TP53 germline mutation carriers is more stringent than BRCA carriers, and radiotherapy should be avoided when possible. METHODS TP53 gene mutation screening was performed in 2538 Chinese breast cancer patients who tested negative for BRCA mutations. RESULTS Twenty TP53 mutations were identified with high next-generation sequencing concerning for germline mutations in Chinese breast cancer families. The majorities of the TP53 carriers had early-onset, hormone receptor-positive breast cancer, and had strong family history of cancer. Among all, 11 patients carried a germline mutation and 6 of which were likely de novo germline mutations. In addition, 1 case was suspected to be induced by chemotherapy or radiation, as this patient had no significant family history of cancer and aberrant clonal expansion can commonly include TP53 mutations. Furthermore, we have identified one mosaic LFS case. Two novel mutations (c.524_547dup and c.529_546del) were identified in patients with early-onset. CONCLUSIONS In view of the high lifetime risk of malignancy, identification of patients with germline TP53 mutations are important for clinicians to aid in accurate risk assessment and offer surveillance for patients and their families.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Hong Kong SAR, China.
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China.
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China.
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Hong Kong SAR, China
| | - Cecilia Y S Ho
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Chun Hang Au
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Thomas P Slavin
- Department of Medical Oncology & Therapeutics Research, Division of Clinical Cancer Genetics, City of Hope, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jeffrey N Weitzel
- Department of Medical Oncology & Therapeutics Research, Division of Clinical Cancer Genetics, City of Hope, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
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11
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Chan WS, Au CH, Chung Y, Leung HCM, Ho DN, Wong EYL, Lam TW, Chan TL, Ma ESK, Tang BSF. Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis. BMC Res Notes 2020; 13:444. [PMID: 32948225 PMCID: PMC7501614 DOI: 10.1186/s13104-020-05287-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/11/2020] [Indexed: 01/30/2023] Open
Abstract
Objective We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden. Results At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Yvonne Chung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Henry Chi Ming Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.,L3 Bioinformatics Limited, Hong Kong, China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Tak Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.,L3 Bioinformatics Limited, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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12
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Mak KY, Au CH, Chan TL, Ma ESK, Chow EYD, Lin SY, Choi WWL. Next-generation sequencing panel for diagnosis and management of chronic neutrophilic leukaemia: a case report. Hong Kong Med J 2020; 25:248-250. [PMID: 31182673 DOI: 10.12809/hkmj176959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- K Y Mak
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - C H Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - T L Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - E S K Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - E Y D Chow
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - S Y Lin
- Department of Medicine and Geriatrics, United Christian Hospital, Kwun Tong, Hong Kong
| | - W W L Choi
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
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13
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Chan WS, Chan TL, Au CH, Leung CP, To MY, Ng MK, Leung SM, Chan MKM, Ma ESK, Tang BSF. An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping. Diagn Pathol 2020; 15:45. [PMID: 32375813 PMCID: PMC7203875 DOI: 10.1186/s13000-020-00964-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022] Open
Abstract
Background Human papillomavirus (HPV) testing has been employed by several European countries to augment cytology-based cervical screening programs. A number of research groups have demonstrated potential utility of next-generation sequencing (NGS) for HPV genotyping, with comparable performance and broader detection spectrum than current gold standards. Nevertheless, most of these NGS platforms may not be the best choice for medium sample throughput and laboratories with less resources and space. In light of this, we developed a Nanopore sequencing assay for HPV genotyping and compared its performance with cobas HPV Test and Roche Linear Array HPV Genotyping Test (LA). Methods Two hundred and one cervicovaginal swabs were routinely tested for Papanicolaou smear, cobas HPV Test and LA. Residual DNA was used for Nanopore protocol after routine testing. Briefly, HPV L1 region was amplified using PGMY and MGP primers, and PCR-positive specimens were sequenced on MinION flow cells (R9.4.1). Data generated in first 2 h were aligned with reference sequences from Papillomavirus Episteme database for genotyping. Results Nanopore detected 96 HPV-positive (47.76%) and 95 HPV-negative (47.26%) specimens, with 10 lacking β-globin band and not further analyzed (4.98%). Substantial agreement was achieved with cobas HPV Test and LA (κ: 0.83–0.93). In particular, Nanopore appeared to be more sensitive than cobas HPV Test for HPV 52 (n = 7). For LA, Nanopore revealed higher concordance for high-risk (κ: 0.93) than non-high risk types (κ: 0.83), and with similar high-risk positivity in each cytology grading. Nanopore also provided better resolution for HPV 52 in 3 specimens co-infected with HPV 33 or 58, and for HPV 87 which was identified as HPV 84 by LA. Interestingly, Nanopore identified 5 additional HPV types, with an unexpected high incidence of HPV 90 (n = 12) which was reported in North America and Belgium but not in Hong Kong. Conclusions We developed a Nanopore workflow for HPV genotyping which was economical (about USD 50.77 per patient specimen for 24-plex runs), and with comparable or better performance than 2 reference methods in the market. Future prospective study with larger sample size is warranted to further evaluate test performance and streamline the protocol.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chin Pang Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Yan To
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - May Kwok Mei Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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14
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Chan WS, Au CH, Leung SM, Ho DN, Wong EYL, To MY, Ng MK, Chan TL, Ma ESK, Tang BSF. Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection. Diagn Pathol 2020; 15:41. [PMID: 32340617 PMCID: PMC7184685 DOI: 10.1186/s13000-020-00960-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Background Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements. In this study, we explored the use of Nanopore sequencing as a supplementary tool to alleviate this diagnostic bottleneck. Methods We developed a targeted Nanopore method based on amplification of bacterial 16S rRNA gene and fungal internal transcribed spacer region. The performance was compared with routine infectious disease workups on 43 respiratory specimens. Results Nanopore successfully identified majority of microbes (47/54, 87.04%) and 7 possible pathogens not detected by routine workups, which were attributable to the content of microbiological investigations (n = 5) and negative culture (n = 2). The average sequencing time for first target reads was 7 min (1–43 min) plus 5 h of pre-sequencing preparation. Conclusions The Nanopore method described here was rapid, economical and hypothesis-free, which might provide valuable hints to further microbiological follow-up for opportunistic pathogens missed or not detectable by conventional tests.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | | | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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15
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Au CH, Ho DN, Ip BBK, Wan TSK, Ng MHL, Chiu EKW, Chan TL, Ma ESK. Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing. Cancer Genet 2019; 239:22-25. [PMID: 31473470 DOI: 10.1016/j.cancergen.2019.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/03/2019] [Revised: 07/21/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and clinically practical tool, but it depends on expression of RNA transcript from the underlying DNA translocation. Here, we show the clinical utility of nanopore long-read sequencing in rapidly detecting DNA translocation with exact breakpoints. In a newly diagnosed patient with AML, conventional karyotyping showed translocation t(10;12)(q22;p13) but RNA NGS detected NUP98-NSD1 fusion transcripts from a known cryptic translocation t(5;11)(q35;p15). Rapid PCR-free nanopore whole-genome sequencing yielded a 26,194 bp sequencing read and revealed the t(10;12) breakpoint to be DUSP13 and GRIN2B in head-to-head configuration. This translocation was then classified as a passenger structural variant. The sequencing also yielded a 20,709 bp sequencing read and revealed the t(5;11) breakpoint of the driver NUP98-NSD1 fusion. The identified DNA breakpoints also served as markers for molecular monitoring, in addition to fusion transcript expression by digital PCR and sequence mutations by NGS. We illustrate that third-generation nanopore sequencing is a simple and low-cost workflow for DNA translocation detection.
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Affiliation(s)
- Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong.
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong.
| | - Beca B K Ip
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong.
| | - Thomas S K Wan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong.
| | - Margaret H L Ng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong.
| | - Edmond K W Chiu
- Honorary Consultant in Hematology and Hematological Oncology, Hong Kong Sanatorium and Hospital, Hong Kong.
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong.
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong.
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16
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Kwong A, Shin V, Au CH, Ho C, Slavin T, Weitzel J, Chan TL, Ma E. Abstract P5-09-12: Germline mutation in TP53 gene in a cohort of 2,561 Chinese high-risk breast cancer patients using multigene panel testing. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-09-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Li-Fraumeni syndrome (LFS) is a rare autosomal genetic disorder with germline TP53 mutations. Patients with TP53 mutations have a higher risk of developing breast cancer than those harboring BRCA mutations. Although limited studies have shown that TP53 mutation carriers are less responsive to low dose radiation and more susceptible to induce new malignancies from radiotherapy. Moreover screening strategies allows early detection of a spectrum of cancers related to TP53 mutations. From work of BRCA mutations where over 40% novel mutations were detected in Chinese cohort, it is important to evaluate the frequency of TP53 mutation in Chinese to better understand the spectrum to guide appropriate clinical management of these high risk individuals.
Methods: TP53 gene mutation screening was performed on 2,561 high-risk breast cancer patients using multigene panel testing. The patients were accrued by Hong Kong Hereditary and High Risk Breast Cancer Program from March 2007 to May 2018. All detected pathogenic mutations were further validated by bi-directional DNA sequencing and analyzed by our in-house developed bioinformatics pipeline.
Results: Sixteen distinct pathogenic or likely pathogenic variants were identified, and 3 of them were de novo TP53 mutations (18.75%). The mean age of patients who harbored TP53 mutation was 30.44 years (range 18-44), and 50% of the tumors were bilateral breast cancer. Of sixteen different pathogenic mutations, majority of them were missense mutation (87.5%), and 2 were nonsense mutation (12.5%). Four of the sixteen TP53 mutation carriers had family history of breast cancer, while others had a family history of lung cancer (43.75%).
Conclusion: This study revealed that seven patients were found to habor TP53 mutation even when they did not meet the criteria of LFS of LFS-like phenotype, implicated the importance of using multigene panel test for probands and their relatives to offer a comprehensive surveillance programe for TP53 carriers.
Citation Format: Kwong A, Shin V, Au CH, Ho C, Slavin T, Weitzel J, Chan TL, Ma E. Germline mutation in TP53 gene in a cohort of 2,561 Chinese high-risk breast cancer patients using multigene panel testing [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-12.
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Affiliation(s)
- A Kwong
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - V Shin
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - CH Au
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - C Ho
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - T Slavin
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - J Weitzel
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - TL Chan
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
| | - E Ma
- The University of Hong Kong, Pokfulam, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong; Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; City of Hope, Duarte, CA
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Kwong A, Shin V, Au CH, Ho C, Chan TL, Ma E. Multigene panel testing for hereditary breast and ovarian cancers: An analysis of 1303 BRCA-negative Chinese patients. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e13625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ava Kwong
- The University of Hong Kong, Hong Kong, Hong Kong
| | - Vivian Shin
- The University of Hong Kong, Pokfulam, Hong Kong
| | - Chun Hang Au
- Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Cecilia Ho
- Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | | | - Edmond Ma
- Hong Kong Sanatorium & Hospital, Happy Valley, HK
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Ma ESK, Wan TSK, Au CH, Ho DN, Ma SY, Ng MHL, Chan TL. Next-generation sequencing and molecular cytogenetic characterization of ETV6-LYN fusion due to chromosomes 1, 8 and 12 rearrangement in acute myeloid leukemia. Cancer Genet 2017; 218-219:15-19. [PMID: 29153093 DOI: 10.1016/j.cancergen.2017.09.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
In a newly diagnosed patient with acute myeloid leukemia (AML) and complex cytogenetics and negative for gene mutations associated with myeloid neoplasms, RNA sequencing by next-generation sequencing (NGS) through a large cancer-related gene panel showed ETV6-LYN leukemic fusion transcript. Breakpoint analysis of the NGS reads showed fusion of exon 5 of the ETV6 gene to exon 8 of the LYN gene. Metaphase fluorescence in situ hybridization (FISH) inferred a four-break rearrangement of three chromosomes, namely 1, 8 and 12. First, there was a balanced translocation t(1;12)(p13;p13.2) in which the ETV6 was split between der(1) and der(12). Second, an inverted insertion of 8q12.1~q24.21 into 1p13 occurred, thus bringing ETV6 and LYN into juxtaposition in the correct 5' to 3' orientation to produce an in-frame chimeric fusion gene on der(1). Notwithstanding two previous reports of ETV6-LYN fusion in myeloproliferative neoplasms (MPN), we report the first case of this fusion in AML and hence broaden its disease association. We also illustrate the clinical utility of NGS based detection of gene fusion in the setting of complex karyotype or cryptic aberration, since this method does not require a priori knowledge of the translocation partner and exact breakpoints to guide the application of appropriate primers or probes.
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MESH Headings
- Adult
- Chromosome Aberrations
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 8/genetics
- Gene Rearrangement
- High-Throughput Nucleotide Sequencing/methods
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Male
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogene Proteins c-ets/genetics
- Repressor Proteins/genetics
- src-Family Kinases/genetics
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong.
| | - Thomas S K Wan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical & Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong
| | - Shing Yan Ma
- Specialist in Hematology & Hematological Oncology in private practice, Hong Kong
| | - Margaret H L Ng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical & Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong
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19
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Au CH, Leung AYH, Kwong A, Chan TL, Ma ESK. INDELseek: detection of complex insertions and deletions from next-generation sequencing data. BMC Genomics 2017; 18:16. [PMID: 28056804 PMCID: PMC5217656 DOI: 10.1186/s12864-016-3449-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022] Open
Abstract
Background Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. Results INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of “pileup” of each reference position across multiple alignments. In benchmarking against the reference material NA12878 genome (n = 160 derived from high-confidence variant calls), GATK, SAMtools and INDELseek showed complex indel detection sensitivities of 0%, 0% and 100%, respectively. INDELseek also detected all known germline (BRCA1 and BRCA2) and somatic (CALR and JAK2) complex indels in human clinical samples (n = 8). Further experiments validated all 10 detected KIT complex indels in a discovery cohort of clinical samples. In silico semi-simulation showed sensitivities of 93.7–96.2% based on 8671 unique complex indels in >5000 genes from dbSNP and COSMIC. We also demonstrated the importance of complex indel detection in accurately annotating BRCA1, BRCA2 and TP53 mutations with gained or rescued protein-truncating effects. Conclusions INDELseek is an accurate and versatile tool for complex indel detection in NGS data. It complements other variant callers in NGS-based genomics studies targeting a wide spectrum of genetic variations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3449-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Anskar Y H Leung
- Department of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Ava Kwong
- Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Surgery and Cancer Genetics Center, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR.,Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR.
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20
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Lam WY, Cheung MK, Fung WY, Law PT, Kam KM, Au CH, Nong WY, Hwang D, Chan RC, Kwan HS, Tsui SK. Metagenomics of tuberculosis infection in Hong Kong. Hong Kong Med J 2016; 22 Suppl 7:15-17. [PMID: 29941686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Affiliation(s)
- W Y Lam
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - M K Cheung
- School of Life Sciences, The Chinese University of Hong Kong
| | - W Yw Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - P Tw Law
- School of Life Sciences, The Chinese University of Hong Kong
| | - K M Kam
- Centre for Health Protection, Department of Health
| | - C H Au
- School of Life Sciences, The Chinese University of Hong Kong
| | - W Y Nong
- School of Life Sciences, The Chinese University of Hong Kong
| | - D Hwang
- Department of Laboratory Medicine and Pathology, University of Toronto, Canada
| | - R Cy Chan
- Department of Microbiology, The Chinese University of Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese University of Hong Kong
| | - S Kw Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong
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Cher CY, Leung GMK, Au CH, Chan TL, Ma ESK, Sim JPY, Gill H, Lie AKW, Liang R, Wong KF, Siu LLP, Tsui CSP, So CC, Wong HWW, Yip SF, Lee HKK, Liu HSY, Lau JSM, Luk TH, Lau CK, Lin SY, Kwong YL, Leung AYH. Next-generation sequencing with a myeloid gene panel in core-binding factor AML showed KIT activation loop and TET2 mutations predictive of outcome. Blood Cancer J 2016; 6:e442. [PMID: 27391574 PMCID: PMC5030377 DOI: 10.1038/bcj.2016.51] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 12/21/2022] Open
Abstract
Clinical outcome and mutations of 96 core-binding factor acute myeloid leukemia (AML) patients 18–60 years old were examined. Complete remission (CR) after induction was 94.6%. There was no significant difference in CR, leukemia-free-survival (LFS) and overall survival (OS) between t(8;21) (N=67) and inv(16) patients (N=29). Univariate analysis showed hematopoietic stem cell transplantation at CR1 as the only clinical parameter associated with superior LFS. Next-generation sequencing based on a myeloid gene panel was performed in 72 patients. Mutations in genes involved in cell signaling were associated with inferior LFS and OS, whereas those in genes involved in DNA methylation were associated with inferior LFS. KIT activation loop (AL) mutations occurred in 25 patients, and were associated with inferior LFS (P=0.003) and OS (P=0.001). TET2 mutations occurred in 8 patients, and were associated with significantly shorter LFS (P=0.015) but not OS. Patients negative for KIT-AL and TET2 mutations (N=41) had significantly better LFS (P<0.001) and OS (P=0.012) than those positive for both or either mutation. Multivariate analysis showed that KIT-AL and TET2 mutations were associated with inferior LFS, whereas age ⩾40 years and marrow blast ⩾70% were associated with inferior OS. These observations provide new insights that may guide better treatment for this AML subtype.
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Affiliation(s)
- C Y Cher
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - G M K Leung
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - C H Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - T L Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - E S K Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - J P Y Sim
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - H Gill
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - A K W Lie
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - R Liang
- Department of Medicine, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - K F Wong
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - L L P Siu
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - C S P Tsui
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - C C So
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - H W W Wong
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - S F Yip
- Department of Medicine, Tuen Mun Hospital, Hong Kong, China
| | - H K K Lee
- Department of Medicine, Princess Margaret Hospital, Hong Kong, China
| | - H S Y Liu
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | - J S M Lau
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - T H Luk
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - C K Lau
- Department of Medicine, Tseung Kwan O Hospital, Hong Kong, China
| | - S Y Lin
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China
| | - Y L Kwong
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - A Y H Leung
- Division of Haematology, Department of Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
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22
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Kwong A, Shin VY, Au CH, Law FB, Ho DN, Ip BK, Wong AT, Lau SS, To RM, Choy G, Ford JM, Ma ES, Chan TL. Abstract P2-09-20: Evaluation on the mutation screening by next-generation sequencing in hereditary breast and ovarian cancer: Implementation of recurrent mutation panel. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p2-09-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Hereditary disposition accounts for 10-15% in breast cancers and 20-25% in ovarian cancers, in which 5-10% of women have genomic alteration in breast cancer predisposition genes, BRCA1 and BRCA2, while the rest are likely due to less penetrant genes. In specific ethnicities such as Ashkenazi Jewish, three founder mutations have been identified which covers 95 % of all the BRCA mutations identified in this race. These genes are screened prior to the gold standard Sanger Sequencing in order to reduce cost. Sanger Sequencing, however, still has the limitation on the necessity of laborious processing and results interpretation. Moreover, it limits the number of genes that can be analyzed in one setting. With the use of next-generation sequencing (NGS), identification of hereditary breast and ovarian cancer (HBOC) syndrome associated genes, other than BRCA, can be sequenced at the same time but yet a faster turnover time. This allows more timely targeted risk-reducing strategies and interventions to be implemented for mutation positive carriers and their family members.
Methods: In this study cohort, 948 high-risk breast/ovarian patients who met the HBOC selection criteria were recruited for mutation screening by our NGS pipeline. With the inclusion of 90 Sanger-validated known mutation cases, the performance of the NGS pipeline were proven to be comparable to Sanger sequencing. PTEN and TP53, other than BRCA1 and BRCA2, a 4 gene sequencing panel were included in the mutation screening for high-risk patients.
Results: The prevalence of BRCA1/BRCA2 germline mutations was 7.28% in our Chinese cohort and 47.8% of the mutation were recurrent mutations. Based on this finding, we further adopted a new workflow by screening the recurrent mutations including founder mutations from Chinese cohort prior to NGS for those who tested negative. In a testing cohort of 343 cases, the recurrent mutation pick-up rate was 3.5%, this implicated a more cost-effective method for mutation screening in the clinical setting. Moreover, the frequencies of PTEN and TP53 were 0.21% and 0.53% respectively in our population with breast and ovarian cases.
Conclusion: Taken together, our data demonstrated a strategic upfront screening for recurrent mutations in Chinese population which is highly applicable in most of the diagnostic laboratories. Multi-gene sequencing using the NGS technology will be the upcoming strategies for mutation screening for HBOC patients.
Citation Format: Kwong A, Shin VY, Au CH, Law FB, Ho DN, Ip BK, Wong AT, Lau SS, To RM, Choy G, Ford JM, Ma ES, Chan TL. Evaluation on the mutation screening by next-generation sequencing in hereditary breast and ovarian cancer: Implementation of recurrent mutation panel. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-20.
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Affiliation(s)
- A Kwong
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - VY Shin
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - CH Au
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - FB Law
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - DN Ho
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - BK Ip
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - AT Wong
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - SS Lau
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - RM To
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - G Choy
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - JM Ford
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - ES Ma
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
| | - TL Chan
- The University of Hong Kong, Hong Kong; Hong Kong Sanatorium & Hospital, Hong Kong; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong; Stanford University School of Medicine
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Au CH, Wa A, Ho DN, Chan TL, Ma ESK. Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms. Diagn Pathol 2016; 11:11. [PMID: 26796102 PMCID: PMC4722624 DOI: 10.1186/s13000-016-0456-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/14/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic techniques in recent years have allowed the identification of many mutated genes important in the pathogenesis of acute myeloid leukemia (AML). Together with cytogenetic aberrations, these gene mutations are powerful prognostic markers in AML and can be used to guide patient management, for example selection of optimal post-remission therapy. The mutated genes also hold promise as therapeutic targets themselves. We evaluated the applicability of a gene panel for the detection of AML mutations in a diagnostic molecular pathology laboratory. METHODS Fifty patient samples comprising 46 AML and 4 other myeloid neoplasms were accrued for the study. They consisted of 19 males and 31 females at a median age of 60 years (range: 18-88 years). A total of 54 genes (full coding exons of 15 genes and exonic hotspots of 39 genes) were targeted by 568 amplicons that ranged from 225 to 275 bp. The combined coverage was 141 kb in sequence length. Amplicon libraries were prepared by TruSight myeloid sequencing panel (Illumina, CA) and paired-end sequencing runs were performed on a MiSeq (Illumina) genome sequencer. Sequences obtained were analyzed by in-house bioinformatics pipeline, namely BWA-MEM, Samtools, GATK, Pindel, Ensembl Variant Effect Predictor and a novel algorithm ITDseek. RESULTS The mean count of sequencing reads obtained per sample was 3.81 million and the mean sequencing depth was over 3000X. Seventy-seven mutations in 24 genes were detected in 37 of 50 samples (74 %). On average, 2 mutations (range 1-5) were detected per positive sample. TP53 gene mutations were found in 3 out of 4 patients with complex and unfavorable cytogenetics. Comparing NGS results with that of conventional molecular testing showed a concordance rate of 95.5 %. After further resolution and application of a novel bioinformatics algorithm ITDseek to aid the detection of FLT3 internal tandem duplication (ITD), the concordance rate was revised to 98.2 %. CONCLUSIONS Gene panel testing by NGS approach was applicable for sensitive and accurate detection of actionable AML gene mutations in the clinical laboratory to individualize patient management. A novel algorithm ITDseek was presented that improved the detection of FLT3-ITD of varying length, position and at low allelic burden.
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Affiliation(s)
- Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Anna Wa
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
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Ou M, Ma R, Cheung J, Lo K, Yee P, Luo T, Chan TL, Au CH, Kwong A, Luo R, Lam TW. database.bio: a web application for interpreting human variations. Bioinformatics 2015; 31:4035-7. [PMID: 26315902 DOI: 10.1093/bioinformatics/btv500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 08/18/2015] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Rapid advances of next-generation sequencing technology have led to the integration of genetic information with clinical care. Genetic basis of diseases and response to drugs provide new ways of disease diagnosis and safer drug usage. This integration reveals the urgent need for effective and accurate tools to analyze genetic variants. Due to the number and diversity of sources for annotation, automating variant analysis is a challenging task. Here, we present database.bio, a web application that combines variant annotation, prioritization and visualization so as to support insight into the individual genetic characteristics. It enhances annotation speed by preprocessing data on a supercomputer, and reduces database space via a unified database representation with compressed fields. AVAILABILITY AND IMPLEMENTATION Freely available at https://database.bio.
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Affiliation(s)
- Min Ou
- HKU-BGI Bioinformatics Algorithms Research Laboratory and Department of Computer Science, University of Hong Kong
| | | | | | | | | | - Tewei Luo
- HKU-BGI Bioinformatics Algorithms Research Laboratory and Department of Computer Science, University of Hong Kong
| | - T L Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium and Hospital
| | - Ava Kwong
- Department of Surgery, University of Hong Kong and Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong and
| | - Ruibang Luo
- HKU-BGI Bioinformatics Algorithms Research Laboratory and Department of Computer Science, University of Hong Kong, L3 Bioinformatics Limited, United Electronics Co., Ltd., Beijing, China
| | - Tak-Wah Lam
- HKU-BGI Bioinformatics Algorithms Research Laboratory and Department of Computer Science, University of Hong Kong, L3 Bioinformatics Limited
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25
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Kwong A, Chen J, Shin VY, Ho JCW, Law FBF, Au CH, Chan TL, Ma ESK, Ford JM. The importance of analysis of long-range rearrangement of BRCA1 and BRCA2 in genetic diagnosis of familial breast cancer. Cancer Genet 2015; 208:448-54. [PMID: 26271414 DOI: 10.1016/j.cancergen.2015.05.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/30/2022]
Abstract
Germline BRCA gene mutations are reportedly associated with hereditary breast and ovarian cancers. Identification of BRCA mutations greatly improves the preventive strategies and management of breast cancer. Sanger sequencing has been the gold standard in identifying these mutations. However, 4-28% of inherited BRCA mutations may be due to large genomic rearrangements (LGRs), which could be missed by using Sanger sequencing alone. Our aim is to evaluate the pick-up rate of LGRs in our cohort. A total of 1,236 clinically high-risk patients with breast and/or ovarian cancers were recruited through The Hong Kong Hereditary Breast Cancer Family Registry from 2007 to 2014. Full gene sequencing (either Sanger or next generation sequencing) and multiplex ligation-dependent probe amplification (MLPA) were performed. We identified 120 deleterious BRCA mutations: 57 (4.61%) were in BRCA1 and 63 (5.10%) were in BRCA2. LGRs accounted for 6.67% (8 of 120) of all BRCA mutations, whereas 8.77 % (5 of 57) were BRCA1 mutations and 4.76% (3 of 63) were BRCA2 mutations. Through this integrated approach, both small nucleotide variations and LGRs could be detected. We suggest that MLPA should be incorporated into the standard practice for genetic testing to avoid false-negative results, which would greatly affect the management of these high-risk families.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China; Department of Oncology, Stanford University School of Medicine, Stanford, California, USA; Department of Surgery, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China.
| | - Jiawei Chen
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - John C W Ho
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China; Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Fian B F Law
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China; Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Chun Hang Au
- Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China; Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China; Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - James M Ford
- Department of Oncology, Stanford University School of Medicine, Stanford, California, USA
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Kan CW, Au CH. Effect of biopolishing and UV absorber treatment on the UV protection properties of cotton knitted fabrics. Carbohydr Polym 2014; 101:451-6. [PMID: 24299797 DOI: 10.1016/j.carbpol.2013.09.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/16/2013] [Accepted: 09/14/2013] [Indexed: 11/29/2022]
Affiliation(s)
- C W Kan
- Institute of Textiles and Clothing, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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27
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Kwong A, Au CH, Law FB, Ho DN, Ip BK, Wong AT, Shin VY, Chan TL, Ma ES. Abstract P2-07-03: High-throughput germline mutation screening for hereditary breast cancer in southern Chinese patients by massively parallel DNA sequencing. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p2-07-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Breast cancer is the most common malignancy and 3rd leading cause of deaths among the female population in Hong Kong. Since the establishment of The Hong Kong Hereditary Breast Cancer Family Registry in 2007, 1344 patients with breast and/or ovarian cancer who met the selection criteria were recruited for genetic testing in Hong Kong. Since 2011 we started to employ next-generation DNA sequencing (NGS) to expedite the analysis workflow and expand the panel of genes for sequencing.
Aim: To evaluate the workflow of NGS in mutation screening of BRCA1, BRCA2, TP53 and PTEN genes, and compared with the sequence data obtained by Sanger sequencing.
Methods: We sequenced BRCA1, BRCA2, TP53 and PTEN genes in peripheral blood samples of 410 patients, 53 positive controls and 107 healthy local individuals using 454 GS Junior System. Generation of barcoded amplicon libraries was streamlined by microfluidic PCR using Fluidigm Access Array System. Sequencing data were analyzed by an in-house developed fully automatic bioinformatics pipeline, which mainly consists of GS Amplicon Variant Analyzer, SAMtools and Ensembl Variant Effect Predictor. All putative mutations identified were validated by Sanger sequencing. Furthermore, the frequency of BRCA1, BRCA2 and PTEN missense variants of unknown significance (VUS) identified in the cohort were compared among 107 healthy local individuals and 1000 Genomes project samples. The VUS were also subjected to a panel of in silico prediction methods including PolyPhen and SIFT.
Results: Among 410 patients, there were 7 in BRCA1, 6 in BRCA2 and 1 in TP53 mutations found, including 1 novel recurrent BRCA2 (c.7007G>T) and 1 novel founder BRCA2 (c.5164_5165delAG) mutations. Based on multiple criteria, 12 in BRCA1, 12 in BRCA2 and 1 in PTEN VUS could be prioritized for further investigation. The bioinformatics pipeline was extensively evaluated with Sanger-validated controls. The evaluation determined minimum sequencing coverage needed in this sequencing platform for accurate analysis. The pipeline accuracy was demonstrated by successful detecting mutations from 53 positive controls, including single nucleotide variants, insertions and deletions in different sequence context.
Conclusion: BRCA1, BRCA2, TP53 and PTEN mutation screening of 410 patients were expedited by high-throughput DNA sequencing. This method could detect 14 positive cases, including recurrent mutations, in a shorter period of time when compared with Sanger full gene sequencing. High-risk patients who are negative for the gene panel may need further investigation other than screening for BRCA1/2. The in-house developed bioinformatics pipeline was validated to detect various types of mutations and potentially become a conventional platform for genetic screening.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-07-03.
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Affiliation(s)
- A Kwong
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - CH Au
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - FB Law
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - DN Ho
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - BK Ip
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - AT Wong
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - VY Shin
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - TL Chan
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
| | - ES Ma
- The University of Hong Kong; Hong Kong Sanatorium & Hospital; Hong Kong Hereditary Breast Cancer Family Registry
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Au CH, Wong MC, Bao D, Zhang M, Song C, Song W, Law PTW, Kües U, Kwan HS. The genetic structure of the A mating-type locus of Lentinula edodes. Gene 2013; 535:184-90. [PMID: 24295887 DOI: 10.1016/j.gene.2013.11.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [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: 06/20/2013] [Revised: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 11/29/2022]
Abstract
The Shiitake mushroom, Lentinula edodes (Berk.) Pegler is a tetrapolar basidiomycete with two unlinked mating-type loci, commonly called the A and B loci. Identifying the mating-types in shiitake is important for enhancing the breeding and cultivation of this economically-important edible mushroom. Here, we identified the A mating-type locus from the first draft genome sequence of L. edodes and characterized multiple alleles from different monokaryotic strains. Two intron-length polymorphism markers were developed to facilitate rapid molecular determination of A mating-type. L. edodes sequences were compared with those of known tetrapolar and bipolar basidiomycete species. The A mating-type genes are conserved at the homeodomain region across the order Agaricales. However, we observed unique genomic organization of the locus in L. edodes which exhibits atypical gene order and multiple repetitive elements around its A locus. To our knowledge, this is the first known exception among Homobasidiomycetes, in which the mitochondrial intermediate peptidase (mip) gene is not closely linked to A locus.
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Affiliation(s)
- Chun Hang Au
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man Chun Wong
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Dapeng Bao
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenhua Song
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Patrick Tik Wan Law
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ursula Kües
- Division of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Hoi Shan Kwan
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Au CH, Cheung MK, Wong MC, Chu AKK, Law PTW, Kwan HS. Rapid genotyping by low-coverage resequencing to construct genetic linkage maps of fungi: a case study in Lentinula edodes. BMC Res Notes 2013; 6:307. [PMID: 23915543 PMCID: PMC3750829 DOI: 10.1186/1756-0500-6-307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/01/2013] [Indexed: 01/25/2023] Open
Abstract
Background Genetic linkage maps are important tools in breeding programmes and quantitative trait analyses. Traditional molecular markers used for genotyping are limited in throughput and efficiency. The advent of next-generation sequencing technologies has facilitated progeny genotyping and genetic linkage map construction in the major grains. However, the applicability of the approach remains untested in the fungal system. Findings Shiitake mushroom, Lentinula edodes, is a basidiomycetous fungus that represents one of the most popular cultivated edible mushrooms. Here, we developed a rapid genotyping method based on low-coverage (~0.5 to 1.5-fold) whole-genome resequencing. We used the approach to genotype 20 single-spore isolates derived from L. edodes strain L54 and constructed the first high-density sequence-based genetic linkage map of L. edodes. The accuracy of the proposed genotyping method was verified experimentally with results from mating compatibility tests and PCR-single-strand conformation polymorphism on a few known genes. The linkage map spanned a total genetic distance of 637.1 cM and contained 13 linkage groups. Two hundred sequence-based markers were placed on the map, with an average marker spacing of 3.4 cM. The accuracy of the map was confirmed by comparing with previous maps the locations of known genes such as matA and matB. Conclusions We used the shiitake mushroom as an example to provide a proof-of-principle that low-coverage resequencing could allow rapid genotyping of basidiospore-derived progenies, which could in turn facilitate the construction of high-density genetic linkage maps of basidiomycetous fungi for quantitative trait analyses and improvement of genome assembly.
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Affiliation(s)
- Chun Hang Au
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS. 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics 2013; 14:195. [PMID: 23514374 PMCID: PMC3606632 DOI: 10.1186/1471-2164-14-195] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/08/2013] [Indexed: 12/02/2022] Open
Abstract
Background The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life cycle of many basidiomycete fungi. Understanding the molecular mechanisms underlying this process has long been a goal of research on basidiomycetes. Large scale assessment of the expressed transcriptomes of these developmental stages will facilitate the generation of a more comprehensive picture of the mushroom fruiting process. In this study, we coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. Results We evaluated the expression of >3,000 genes in the two respective growth stages and discovered that almost one-third of these genes were preferentially expressed in either stage. This identified a significant turnover of the transcriptome during the course of fruiting body development. Additionally, we annotated more than 79,000 transcription start sites (TSSs) based on the transcriptomes of the mycelium and stage 1 primoridum stages. Patterns of enrichment based on gene annotations from the GO and KEGG databases indicated that various structural and functional protein families were uniquely employed in either stage and that during primordial growth, cellular metabolism is highly up-regulated. Various signaling pathways such as the cAMP-PKA, MAPK and TOR pathways were also identified as up-regulated, consistent with the model that sensing of nutrient levels and the environment are important in this developmental transition. More than 100 up-regulated genes were also found to be unique to mushroom forming basidiomycetes, highlighting the novelty of fruiting body development in the fungal kingdom. Conclusions We implicated a wealth of new candidate genes important to early stages of mushroom fruiting development, though their precise molecular functions and biological roles are not yet fully known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.
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Affiliation(s)
- Chi Keung Cheng
- Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong
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Cheung MK, Lam WY, Fung WYW, Law PTW, Au CH, Nong W, Kam KM, Kwan HS, Tsui SKW. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing. PLoS One 2013; 8:e54574. [PMID: 23365674 PMCID: PMC3554703 DOI: 10.1371/journal.pone.0054574] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/12/2012] [Indexed: 01/31/2023] Open
Abstract
Background Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease. Methodology/Principal Findings Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples. Conclusions/Significance The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai Yip Lam
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wendy Yin Wan Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Patrick Tik Wan Law
- Core Facilities Genome Sequencing Laboratory, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Hang Au
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kai Man Kam
- Tuberculosis Reference Laboratory, Department of Health, Hong Kong SAR, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail: (HSK); (SKWT)
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail: (HSK); (SKWT)
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Jiang J, Li J, Kwan HS, Au CH, Wan Law PT, Li L, Kam KM, Lun Ling JM, Leung FC. A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. BMC Res Notes 2012; 5:80. [PMID: 22289569 PMCID: PMC3296665 DOI: 10.1186/1756-0500-5-80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/31/2012] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. FINDINGS Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. CONCLUSIONS A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.
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Affiliation(s)
- Jingwei Jiang
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China.
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Yip PY, Wong KS, Li L, Huang QL, Kwan HS, Au CH, Wong MC, Qin J, Kwok ISW, Nong WY, Chum WWY. Genome sequence and genetic linkage analysis of Shiitake mushroom Lentinula edodes. ACTA ACUST UNITED AC 2012. [DOI: 10.1038/npre.2012.6855.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractLentinula edodes (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of L. edodes allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of L. edodes monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups of L. edodes genome sequence compared across genomes of several fungi including mushrooms identified gene families unique to mushroom-forming fungi. We used a mapping population of haploid basidiospores of dikaryon L54 for genetic linkage analysis. High-quality variations such as single nucleotide polymorphisms, insertions, and deletions of the mapping population formed a high-density genetic linkage map. We compared the linkage map to the L. edodes L54A genome sequence and located selected quantitative trait loci. The Shiitake community will benefit from these resources for genetic studies and breeding.
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Chum WWY, Kwan HS, Au CH, Kwok ISW, Fung YW. Cataloging and profiling genes expressed in Lentinula edodes fruiting body by massive cDNA pyrosequencing and LongSAGE. Fungal Genet Biol 2011; 48:359-69. [PMID: 21281728 DOI: 10.1016/j.fgb.2011.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 12/29/2010] [Accepted: 01/23/2011] [Indexed: 11/25/2022]
Abstract
This study investigated the molecular mechanism of the fruiting body development and sporulation in the cap of the Shiitake mushroom, Lentinula edodes. Although there has been much research into L. edodes, there remain significant gaps in our knowledge of how the species reproduces. In order to provide molecular resources and to understand the molecular mechanism of the fruiting body development in basidiomycete comprehensively, we searched for the genes which are important for fruiting body development and sporulation in the cap of mature fruiting body of L. edodes by using the whole-genome approach. Massive cDNA pyrosequencing was used to generate >7000 sequence contigs from mature fruiting bodies. We used Gene Ontology to categorize the contigs to form the catalog of genes expressed at the stage of the mature fruiting body. We also assigned the contigs into the KEGG pathways. The catalog of expressed genes indicates that the mature fruiting bodies (1) sense the external environment, (2) transmit signals to express genes through regulatory systems, (3) produce many proteins, (4) degrade unwanted proteins, (5) perform extensive biosynthesis, (6) generate energy, (7) regulate the internal environment, (8) transport molecules, (9) carry out cell division, and (10) differentiate and develop. After establishing the catalog of expressed genes in L. edodes, we used the LongSAGE approach to analyze the expression levels of genes found in mature fruiting bodies before (FB) and after (FBS) spores appeared. Gene-expression patterns according to GO categories were similar in these two stages. We have also successfully identified genes differentially expressed in FB and FBS. Fold-changes in expression levels of selected genes based on LongSAGE tag counts were similar to those obtained by real-time RT-PCR. The consistency between real-time RT-PCR and LongSAGE results indicates reliability of the LongSAGE results. Overall, this study provides valuable information on the fruiting processes of L. edodes through a combination of massive cDNA pyrosequencing and LongSAGE sequencing, and the knowledge thereby obtained may provide insight into the improvement of the yield of commercially grown Shiitake mushrooms.
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Affiliation(s)
- W W Y Chum
- Division of Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK. Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J 2010; 4:1053-9. [PMID: 20336159 DOI: 10.1038/ismej.2010.26] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Information on genetic diversity of picoeukaryotes (<2-3 microm) comes mainly from traditional gene cloning and sequencing, but this method suffers from cloning biases and limited throughput. In this study, we explored the feasibility of using the cloning-independent and massively parallel 454 pyrosequencing technology to study the composition and genetic diversity of picoeukaryotes in the coastal waters of the subtropical western Pacific using the hypervariable V4 region of the 18S rRNA gene. Picoeukaryote assemblages between two sites with different hydrography and trophic status were also compared. The approach gave a high coverage of the community at genetic difference > or =5% but still underestimated the total diversity at a genetic difference < or =2%. Diversity of picoeukaryotes was higher in an oligomesotrophic bay than in a eutrophic bay. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups comprising approximately 27, 19, 11 and 11%, respectively, of the picoeukaryotes. Water samples collected from the two bays contained different high-level taxonomic groups and phylotype operational taxonomic units of picoeukaryotes. Our study represents one of the first and most comprehensive examinations of marine picoeukaryotic diversity using the 454 sequencing-by-synthesis technology.
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Affiliation(s)
- Man Kit Cheung
- Department of Biology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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