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Law JHY, Chan WS, Chan TL, Ma ESK, Tang BSF. Evaluation of a Commercial Point-of-Care RT-LAMP Assay for Rapid Detection of SARS-CoV-2. Biomedicines 2023; 11:2344. [PMID: 37760785 PMCID: PMC10525214 DOI: 10.3390/biomedicines11092344] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
The goal of this study was to evaluate the performance of a commercial reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay (Detect COVID-19 Test) in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A total of 202 human respiratory and viral culture specimens were tested retrospectively. The performance of the Detect COVID-19 Test was comparable to that of commercial real-time polymerase chain reaction assays (sensitivity: 93.42%; specificity: 100%), and better than that of the rapid antigen test (sensitivity: 48.00%; specificity: 100%) for specimens with threshold cycle (Ct) values of less than 30. The Beta, Delta, and Omicron variants of concern were successfully detected. With their simplicity of use and good assay sensitivity, point-of-care RT-LAMP assays may be a viable option for SARS-CoV-2 testing at home, or in regions without sophisticated laboratory facilities.
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Affiliation(s)
| | | | | | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China; (J.H.Y.L.); (W.S.C.); (T.L.C.); (E.S.K.M.)
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2
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Kwong A, Ho CYS, Shin VY, Ng ATL, Chan TL, Ma ESK. Molecular characteristics of Asian male BRCA-related cancers. Breast Cancer Res Treat 2023; 198:391-400. [PMID: 36637704 DOI: 10.1007/s10549-022-06651-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/13/2022] [Indexed: 01/14/2023]
Abstract
PURPOSE Germline mutations of BRCA1 or BRCA2 predispose men to develop various cancers, including breast cancers and prostate cancers. Male breast cancer (MBC) is a rare disease while prostate cancer (PRC) is uncommon in young men at the age of less than 40. The prevalence of BRCA genes in Asian male patients has to be elevated. METHODS Germline mutations screening was performed in 98 high-risk Chinese MBC and PRC patients. RESULT We have identified 16 pathogenic BRCA2 mutation carriers, 12 were MBC patients, 2 were PRC patients and 2 were patients with both MBC and PRC. The mutation percentages were 18.8%, 6.7% and 50% for MBC, PRC and both MBC and PRC patients, respectively. BRCA2 gene mutations confer a significantly higher risk of breast/prostate cancers in men than those with BRCA1 mutations. BRCA mutated MBC patients had a younger age of diagnosis and strong family histories of breast cancers while BRCA mutated PRC patients had strong family histories of ovarian cancers. CONCLUSION Male BRCA carriers with breast cancers or prostate cancers showed distinct clinical and molecular characteristics, a male-specific genetic screening model would be useful to identify male cancer patients who have a high risk of BRCA mutation.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, China.
- Department of Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China.
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, China.
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China.
| | - Cecilia Yuen Sze Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Ada Tsui Lin Ng
- Division of Urology, Department of Surgery, Queen Mary Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
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Chan WS, Law JHY, Ho MKS, Chan TL, Ma ESK, Tang BSF. Genomic characteristics and viral load dynamics of a SARS-CoV-2 Omicron BA.2.2 variant from a hospitalized patient treated with molnupiravir. Infect Genet Evol 2022; 105:105376. [PMID: 36220486 PMCID: PMC9547395 DOI: 10.1016/j.meegid.2022.105376] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022]
Abstract
We sequenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from nasal and throat swabs of a hospitalized patient during the fifth wave of coronavirus disease 2019 (COVID-19) pandemic in Hong Kong. Genomic characteristics and viral load dynamics of an Omicron BA.2.2 variant before and after molnupiravir treatment were presented.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Janet Hei Yin Law
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Matthew Kam Shing Ho
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Edmond Shiu Kwan Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China.
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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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Chiu RYT, Kojima N, Mosley GL, Cheng KK, Pereira DY, Brobeck M, Chan TL, Zee JST, Kittur H, Chung CYT, Tsang E, Maran K, Yung RWH, Leung ACP, Siu RHP, Ng JPL, Choi TH, Fung MW, Chan WS, Lam HY, Lee KH, Parkin S, Chao FC, Ho SKN, Marshak DR, Ma ESK, Klausner JD. Evaluation of the INDICAID COVID-19 Rapid Antigen Test in Symptomatic Populations and Asymptomatic Community Testing. Microbiol Spectr 2021; 9:e0034221. [PMID: 34346748 PMCID: PMC8552729 DOI: 10.1128/spectrum.00342-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/24/2021] [Indexed: 12/03/2022] Open
Abstract
As the COVID-19 pandemic progresses, there is an increasing need for rapid, accessible assays for SARS-CoV-2 detection. We present a clinical evaluation and real-world implementation of the INDICAID COVID-19 rapid antigen test (INDICAID rapid test). A multisite clinical evaluation of the INDICAID rapid test using prospectively collected nasal (bilateral anterior) swab samples from symptomatic subjects was performed. The INDICAID rapid test demonstrated a positive percent agreement (PPA) and negative percent agreement (NPA) of 85.3% (95% confidence interval [95% CI], 75.6% to 91.6%) and 94.9% (95% CI, 91.6% to 96.9%), respectively, compared to laboratory-based reverse transcriptase PCR (RT-PCR) using nasal specimens. The INDICAID rapid test was then implemented at COVID-19 outbreak screening centers in Hong Kong as part of a testing algorithm (termed "dual-track") to screen asymptomatic individuals for prioritization for confirmatory RT-PCR testing. In one approach, preliminary positive INDICAID rapid test results triggered expedited processing for laboratory-based RT-PCR, reducing the average time to confirmatory result from 10.85 h to 7.0 h. In a second approach, preliminary positive results triggered subsequent testing with an onsite rapid RT-PCR, reducing the average time to confirmatory result to 0.84 h. In 22,994 asymptomatic patients, the INDICAID rapid test demonstrated a PPA of 84.2% (95% CI, 69.6% to 92.6%) and an NPA of 99.9% (95% CI, 99.9% to 100%) compared to laboratory-based RT-PCR using combined nasal/oropharyngeal specimens. The INDICAID rapid test has excellent performance compared to laboratory-based RT-PCR testing and, when used in tandem with RT-PCR, reduces the time to confirmatory positive result. IMPORTANCE Laboratory-based RT-PCR, the current gold standard for COVID-19 testing, can require a turnaround time of 24 to 48 h from sample collection to result. The delayed time to result limits the effectiveness of centralized RT-PCR testing to reduce transmission and stem potential outbreaks. To address this, we conducted a thorough evaluation of the INDICAID COVID-19 rapid antigen test, a 20-minute rapid antigen test, in both symptomatic and asymptomatic populations. The INDICAID rapid test demonstrated high sensitivity and specificity with RT-PCR as the comparator method. A dual-track testing algorithm was also evaluated utilizing the INDICAID rapid test to screen for preliminary positive patients, whose samples were then prioritized for RT-PCR testing. The dual-track method demonstrated significant improvements in expediting the reporting of positive RT-PCR test results compared to standard RT-PCR testing without prioritization, offering an improved strategy for community testing and controlling SARS-CoV-2 outbreaks.
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Affiliation(s)
- Ricky Y. T. Chiu
- Phase Scientific International Ltd., Garden Grove, California, USA
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Noah Kojima
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Garrett L. Mosley
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Kwok Kin Cheng
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - David Y. Pereira
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Matthew Brobeck
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Jonpaul Sze-Tsing Zee
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Harsha Kittur
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | | | - Eric Tsang
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Kajal Maran
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Raymond Wai-Hung Yung
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Alex Chin-Pang Leung
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Ryan Ho-Ping Siu
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | | | - Tsz Hei Choi
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Mei Wai Fung
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Ho Yin Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Koon Hung Lee
- Department of Hospital Administration, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Sean Parkin
- CityHealth Urgent Care, Alameda, California, USA
| | - Felix C. Chao
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Stephen Ka-Nung Ho
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Daniel R. Marshak
- Phase Scientific International Ltd., Garden Grove, California, USA
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Edmond Shiu-Kwan Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Jeffrey D. Klausner
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
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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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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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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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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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10
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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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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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12
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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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13
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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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14
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Rebbeck TR, Friebel TM, Friedman E, Hamann U, Huo D, Kwong A, Olah E, Olopade OI, Solano AR, Teo SH, Thomassen M, Weitzel JN, Chan TL, Couch FJ, Goldgar DE, Kruse TA, Palmero EI, Park SK, Torres D, van Rensburg EJ, McGuffog L, Parsons MT, Leslie G, Aalfs CM, Abugattas J, Adlard J, Agata S, Aittomäki K, Andrews L, Andrulis IL, Arason A, Arnold N, Arun BK, Asseryanis E, Auerbach L, Azzollini J, Balmaña J, Barile M, Barkardottir RB, Barrowdale D, Benitez J, Berger A, Berger R, Blanco AM, Blazer KR, Blok MJ, Bonadona V, Bonanni B, Bradbury AR, Brewer C, Buecher B, Buys SS, Caldes T, Caliebe A, Caligo MA, Campbell I, Caputo S, Chiquette J, Chung WK, Claes KB, Collée JM, Cook J, Davidson R, de la Hoya M, De Leeneer K, de Pauw A, Delnatte C, Diez O, Ding YC, Ditsch N, Domchek SM, Dorfling CM, Velazquez C, Dworniczak B, Eason J, Easton DF, Eeles R, Ehrencrona H, Ejlertsen B, Engel C, Engert S, Evans DG, Faivre L, Feliubadaló L, Ferrer SF, Foretova L, Fowler J, Frost D, Galvão HCR, Ganz PA, Garber J, Gauthier-Villars M, Gehrig A, Gerdes AM, Gesta P, Giannini G, Giraud S, Glendon G, Godwin AK, Greene MH, Gronwald J, Gutierrez-Barrera A, Hahnen E, Hauke J, Henderson A, Hentschel J, Hogervorst FB, Honisch E, Imyanitov EN, Isaacs C, Izatt L, Izquierdo A, Jakubowska A, James P, Janavicius R, Jensen UB, John EM, Joseph V, Kaczmarek K, Karlan BY, Kast K, Kim SW, Konstantopoulou I, Korach J, Laitman Y, Lasa A, Lasset C, Lázaro C, Lee A, Lee MH, Lester J, Lesueur F, Liljegren A, Lindor NM, Longy M, Loud JT, Lu KH, Lubinski J, Machackova E, Manoukian S, Mari V, Martínez-Bouzas C, Matrai Z, Mebirouk N, Meijers-Heijboer HE, Meindl A, Mensenkamp AR, Mickys U, Miller A, Montagna M, Moysich KB, Mulligan AM, Musinsky J, Neuhausen SL, Nevanlinna H, Ngeow J, Nguyen HP, Niederacher D, Nielsen HR, Nielsen FC, Nussbaum RL, Offit K, Öfverholm A, Ong KR, Osorio A, Papi L, Papp J, Pasini B, Pedersen IS, Peixoto A, Peruga N, Peterlongo P, Pohl E, Pradhan N, Prajzendanc K, Prieur F, Pujol P, Radice P, Ramus SJ, Rantala J, Rashid MU, Rhiem K, Robson M, Rodriguez GC, Rogers MT, Rudaitis V, Schmidt AY, Schmutzler RK, Senter L, Shah PD, Sharma P, Side LE, Simard J, Singer CF, Skytte AB, Slavin TP, Snape K, Sobol H, Southey M, Steele L, Steinemann D, Sukiennicki G, Sutter C, Szabo CI, Tan YY, Teixeira MR, Terry MB, Teulé A, Thomas A, Thull DL, Tischkowitz M, Tognazzo S, Toland AE, Topka S, Trainer AH, Tung N, van Asperen CJ, van der Hout AH, van der Kolk LE, van der Luijt RB, Van Heetvelde M, Varesco L, Varon-Mateeva R, Vega A, Villarreal-Garza C, von Wachenfeldt A, Walker L, Wang-Gohrke S, Wappenschmidt B, Weber BHF, Yannoukakos D, Yoon SY, Zanzottera C, Zidan J, Zorn KK, Hutten Selkirk CG, Hulick PJ, Chenevix-Trench G, Spurdle AB, Antoniou AC, Nathanson KL. Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations. Hum Mutat 2018; 39:593-620. [PMID: 29446198 PMCID: PMC5903938 DOI: 10.1002/humu.23406] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 01/19/2023]
Abstract
The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) has assembled data on 18,435 families with BRCA1 mutations and 11,351 families with BRCA2 mutations ascertained from 69 centers in 49 countries on six continents. This study comprehensively describes the characteristics of the 1,650 unique BRCA1 and 1,731 unique BRCA2 deleterious (disease-associated) mutations identified in the CIMBA database. We observed substantial variation in mutation type and frequency by geographical region and race/ethnicity. In addition to known founder mutations, mutations of relatively high frequency were identified in specific racial/ethnic or geographic groups that may reflect founder mutations and which could be used in targeted (panel) first pass genotyping for specific populations. Knowledge of the population-specific mutational spectrum in BRCA1 and BRCA2 could inform efficient strategies for genetic testing and may justify a more broad-based oncogenetic testing in some populations.
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Affiliation(s)
- Timothy R. Rebbeck
- Harvard TH Chan School of Public Health and Dana Farber Cancer Institute, 1101 Dana Building, 450 Brookline Ave, Boston, MA 02215, USA
| | - Tara M. Friebel
- Harvard TH Chan School of Public Health and Dana Farber Cancer Institute, 1101 Dana Building, 450 Brookline Ave, Boston, MA 02215, USA
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan 52621, and the Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Dezheng Huo
- 5841 South Maryland Avenue, MC 2115 Chicago, IL, USA
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Angela R. Solano
- INBIOMED, Faculty of Medicine, University of Buenos Aires/CONICET and CEMIC, Department of Clinical Chemistry, Medical Direction, Buenos Aires, Paraguay 2155, C1121ABG, Argentina
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 1 Jalan SS12/1A, Subang Jaya, 47500, Malaysia
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Sonder Boulevard 29, Odense C, Denmark
| | - Jeffrey N. Weitzel
- Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, California 91010 USA
| | - TL Chan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, Minnesota, USA
| | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, 30 North 1900 East, SOM 4B454, Salt Lake City, UT 84132, USA
| | - Torben A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Sonder Boulevard 29, Odense C, Denmark
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Sue Kyung Park
- 1) Department of Preventive Medicine, Seoul National University College of Medicine; 2) Department of Biomedical Science, Seoul National University Graduate School; 3) Cancer Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, Korea
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Carrera 7, Bogota, 11001000, Colombia
| | - Elizabeth J. van Rensburg
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, Private Bag X323, Arcadia 0007, South Africa
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Michael T. Parsons
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston Road, Brisbane, QLD 4006, Australia
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Cora M. Aalfs
- Department of Clinical Genetics, Academic Medical Center, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands
| | - Julio Abugattas
- City of Hope Clinical Cancer Genomics Community Research Network, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Via Gattamelata 64, Padua, Italy
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, P.O. BOX 160 (Meilahdentie 2), 00029 HUS, Finland
| | - Lesley Andrews
- Hereditary Cancer Clinic, Prince of Wales Hospital, High Street, Randwick, NSW 2031 Australia
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario
| | - Adalgeir Arason
- Department of Pathology, hus 9, Landspitali-LSH v/Hringbraut, 101 Reykjavik, Iceland
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Banu K. Arun
- Department of Breast Medical Oncology and Clinical Cancer Genetics Program, University Of Texas MD Anderson Cancer Center, 1515 Pressler Street, CBP 5, Houston, TX, USA
| | - Ella Asseryanis
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Leo Auerbach
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Instituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Judith Balmaña
- Department of Medical Oncology. University Hospital, Vall d'Hebron, Barcelona, Spain
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), via Ripamonti 435, 20141 Milan, Italy
| | - Rosa B. Barkardottir
- Laboratory of Cell Biology, Department of Pathology, hus 9, Landspitali-LSH v/Hringbraut, 101 Reykjavik, Iceland and BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Javier Benitez
- Human Genetics Group and Genotyping Unit (CEGEN), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Andreas Berger
- Dept of OB/GYN, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Raanan Berger
- The Institute of Oncology, Chaim Sheba Medical Center, Ramat Gan 52621, Israel
| | - Amie M. Blanco
- UCSF Cancer Genetics and Prevention Program, San Francisco, CA 94143-1714
| | - Kathleen R. Blazer
- Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, California 91010 USA
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Valérie Bonadona
- Unité de Prévention et d’Epidémiologie Génétique, Centre Léon Bérard, 28 rue Laënnec, Lyon, France
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), via Ripamonti 435, 20141 Milan, Italy
| | - Angela R. Bradbury
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, UK
| | - Bruno Buecher
- Service de Génétique, Institut Curie, 26, rue d’Ulm, Paris Cedex 05, France
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, CIBERONC. Martin Lagos s/n, Madrid, Spain
| | - Almuth Caliebe
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Maria A. Caligo
- Section of Genetic Oncology, Dept. of Laboratory Medicine, University and University Hospital of Pisa, Pisa, Italy
| | - Ian Campbell
- Research Division, Peter MacCallum Cancer Centre, 305 Gratten Street, Melbourne, VIC 3000, Australia
| | - Sandrine Caputo
- Service de Génétique, Institut Curie, 26, rue d’Ulm, Paris Cedex 05, France
| | - Jocelyne Chiquette
- CRCHU de Quebec-oncologie, Centre des maladies du sein Deschênes-Fabia, Hôpital du Saint-Sacrement,1050, chemin Sainte-Foy, Québec Canada
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, 1150 St. Nicholas Avenue, Columbia University, New York, NY, 10032 USA
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Gent, Belgium
| | - J. Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, UK
| | - Rosemarie Davidson
- Department of Clinical Genetics, South Glasgow University Hospitals, Glasgow, UK
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, CIBERONC. Martin Lagos s/n, Madrid, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Gent, Belgium
| | - Antoine de Pauw
- Service de Génétique, Institut Curie, 26, rue d’Ulm, Paris Cedex 05, France
| | - Capucine Delnatte
- Unité d'oncogénétique, ICO-Centre René Gauducheau, Boulevard Jacques Monod, 44805 Nantes Saint Herblain Cedex, France
| | - Orland Diez
- Oncogenetics Group, Vall d’Hebron Institute of Oncology (VHIO), Clinical and Molecular Genetics Area, Vall d’Hebron University Hospital, Passeig Vall d'Hebron 119-129, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA USA
| | - Nina Ditsch
- Department of Gynaecology and Obstetrics, Ludwig-Maximilian University Munich, Germany
| | - Susan M. Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Cecilia M. Dorfling
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, Private Bag X323, Arcadia 0007, South Africa
| | - Carolina Velazquez
- Cáncer Hereditario, Instituto de Biología y Genética Molecular, IBGM, Universidad de Valladolid, Centro Superior de Investigaciones Científicas, UVA-CSIC. Valladolid, Spain
| | - Bernd Dworniczak
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Jacqueline Eason
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Hans Ehrencrona
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - EMBRACE
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Germany
| | - Stefanie Engert
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Germany
| | - D. Gareth Evans
- Genomic Medicine, Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Laurence Faivre
- Centre de Lutte Contre le Cancer Georges François Leclerc, 1 rue Professeur Marion, BP 77 980, Dijon Cedex, France and Genomic and Immunotherapy Medical Institute, Dijon University Hospital, Dijon, France
| | - Lidia Feliubadaló
- Molecular Diagnostic Unit, Hereditary Cancer Program, ICO-IDIBELL (Catalan Institute of Oncology-Bellvitge Biomedical Research Institute), CIBERONC, Gran Via de l'Hospitalet, 199-203. 08908 L'Hospitalet. Barcelona, Spain
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, BP 1125 Chambéry, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno, 65653, Czech Republic
| | - Jeffrey Fowler
- Ohio State University /Columbus Cancer Council, Columbus, OH 43221, USA
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | | | - Patricia A. Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, 650 Charles Young Drive South, Room A2-125 HS, Los Angeles, CA 90095-6900, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | | | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University Würzburg, Germany
| | - GEMO Study Collaborators
- Institut Curie, Department of Tumour Biology, Paris, France; Institut Curie, INSERM U830, Paris, France
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet 4062, Blegdamsvej 9, København Ø, Denmark
| | - Paul Gesta
- Service Régional Oncogénétique Poitou-Charentes, Centre Hospitalier, 79021 Niort
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, and Istituto Pasteur - Fondazione Cenci-Bolognetti, viale Regina Elena 291, 00161 Rome, Italy
| | - Sophie Giraud
- Bâtiment Cheney D, Centre Léon Bérard, 28 rue Laënnec, Lyon, France
| | - Gord Glendon
- Ontario Cancer Genetics Network: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, 3901 Rainbow Boulevard,4019 Wahl Hall East, MS 3040, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mark H. Greene
- Clinical Genetics Branch, DCEG, NCI, NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Angelica Gutierrez-Barrera
- Department of Breast Medical Oncology and Clinical Cancer Genetics Program, University Of Texas MD Anderson Cancer Center, 1515 Pressler Street, CBP 5, Houston, TX, USA
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Coordinating center: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Henderson
- Institute of Genetic Medicine, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Julia Hentschel
- Institute of Human Genetics, University Leipzig, 04107 Leipzig, Germany
| | - Frans B.L. Hogervorst
- Family Cancer Clinic, Netherlands Cancer Institute, P.O. Box 90203, 1006 BE Amsterdam, The Netherlands
| | - Ellen Honisch
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Germany
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, 3800 Reservoir Road NW, Washington, DC, USA
| | - Louise Izatt
- Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Angel Izquierdo
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d'Investigació Biomèdica de Girona), Catalan Institute of Oncology, CIBERONC, Av. França s/n. 1707 Girona, Spain
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Paul James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, 305 Gratten Street, Melbourne, VIC 3000, Australia
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hereditary Cancer Competence Center Hematology, Oncology and Transfusion Medicine Center Room P519 Santariskiu st. 2, LT-08661 Vilnius, Lithuania
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, Aarhus N, Denmark
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA 94538, USA and Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijai Joseph
- Clinical Genetics Research Laboratory, Dept. of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Katarzyna Kaczmarek
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Karin Kast
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - KConFab Investigators
- Research Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia and The Sir Peter MacCallum Department of Oncology University of Melbourne, Parkville, Australia
| | - Sung-Won Kim
- Department of Surgery, Daerim St. Mary's Hospital, 657 Siheung-daero, Yeongdeungpo-gu, Seoul, Korea
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES (Institute of Nuclear and Radiological Sciences and Technology), National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou & Neapoleos str., Aghia Paraskevi Attikis, Athens, Greece
| | - Jacob Korach
- The Gyneco-Oncology Department, Chaim Sheba Medical Center, Ramat Gan 52621, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan 52621, and the Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Adriana Lasa
- Servicio de Genética-CIBERER U705, Hospital de la Santa Creu i Sant Pau, Barcelona
| | - Christine Lasset
- Unité de Prévention et d’Epidémiologie Génétique, Centre Léon Bérard, 28 rue Laënnec, Lyon, France
| | - Conxi Lázaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, ICO-IDIBELL (Catalan Institute of Oncology-Bellvitge Biomedical Research Institute), CIBERONC, Gran Via de l'Hospitalet, 199-203. 08908 L'Hospitalet. Barcelona, Spain
| | - Annette Lee
- The Feinstein Institute for Medical Research 350 Community Drive Manhasset NY
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University and Seoul Hospital, 59 Daesagwan-Ro, Yongsan-Gu, Seoul, Korea
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Institut Curie, PSL Research University, Mines ParisTech, Inserm U900, 26 rue d'Ulm, F-75005 Paris, France
| | - Annelie Liljegren
- Department of Oncology Radiumhemmet and Institution of Oncology and Patology, Karolinska University Hospital and Karolinska Institutet
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, 13400 E. Scottsdale Blvd., Scottsdale, AZ, USA
| | - Michel Longy
- Oncogénétique, Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux, France
| | - Jennifer T. Loud
- Clinical Genetics Branch, DCEG, NCI, NIH, 9609 Medical Center Drive, Room 6E-536, Bethesda, MD, USA
| | - Karen H. Lu
- Department of Gynecological Oncology and Clinical Cancer Genetics Program, University Of Texas MD Anderson Cancer Center, 1515 Pressler Street, CPB 6, Houston, TX, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno, 65653, Czech Republic
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Instituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Véronique Mari
- Centre Antoine Lacassagne, 33 Avenue de Valombrose, Nice, France
| | - Cristina Martínez-Bouzas
- Laboratorio de Genética Molecular, Servicio de Genética, Hospital Universitario Cruces, BioCruces Health Research Institute, Spain
| | - Zoltan Matrai
- Department of Surgery, National Institute of Oncology, Budapest, Hungary
| | - Noura Mebirouk
- Institut Curie, PSL Research University, Mines ParisTech, Inserm U900, 26 rue d'Ulm, F-75005 Paris, France
| | - Hanne E.J. Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, P.O. Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Germany
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ugnius Mickys
- Vilnius university Santariskiu hospital, National Center of Pathology, Baublio st. 5, Vilnius, Lithuania
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Elm St & Carlton St, Buffalo, NY 14263, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Via Gattamelata 64, Padua, Italy
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jacob Musinsky
- Clinical Genetics Research Laboratory, Dept. of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Biomedicum Helsinki, P.O. BOX 700 (Haartmaninkatu 8), 00029 HUS, Finland
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610
| | - Huu Phuc Nguyen
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Germany
| | - Dieter Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Germany
| | - Henriette Roed Nielsen
- Department of Clinical Genetics, Odense University Hospital, Sonder Boulevard 29, Odense C, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Denmark
| | | | - Kenneth Offit
- Clinical Genetics Research Laboratory, Dept. of Medicine, Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Anna Öfverholm
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kai-ren Ong
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, UK
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Via Santena 19, 10126 Turin, Italy
| | - Inge Sokilde Pedersen
- Section of Molecular Diagnostics, Department of Biochemistry, Aalborg University Hospital, Reberbansgade 15, Aalborg, Denmark
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal, and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Nina Peruga
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, via Adamello 16, 20139 Milan, Italy
| | - Esther Pohl
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Nisha Pradhan
- Clinical Genetics Research Laboratory, Dept. of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Fabienne Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire, Hôpital Nord, CHU Saint Etienne, St Etienne cedex 2, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, 34295 Montpellier Cedex 5, France
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), c/o Amaedeolab, via GA Amadeo 42, 20133 Milan, Italy
| | - Susan J. Ramus
- School of Women's and Children's Health, UNSW Sydney, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Australia
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital L5:03, Stockholm S-171 76, Sweden
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC) 7A, Block R3, Johar Town, Lahore, Punjab 54000, Pakistan
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Mark Robson
- Clinical Genetics Services, Dept. of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gustavo C. Rodriguez
- Division of Gynecologic Oncology, North Shore University Health System, Clinical Professor, University of Chicago, 2650 Ridge Avenue, Suite 1507 Walgreens, Evanston, IL 60201, USA
| | - Mark T. Rogers
- All Wales Medical Genetics Services, University Hospital of Wales, Cardiff, UK
| | - Vilius Rudaitis
- Vilnius University Hospital Santariskiu Clinics, Centre of Woman's Health and pathology, Department of Gynecology, Santariskiu st. 2, Vilnius, Lithuania
| | - Ane Y. Schmidt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Denmark
| | - Rita Katharina Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Payal D. Shah
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Priyanka Sharma
- Department of Hematology and Oncology, University of Kansas Medical Center, Suite 210, 2330 Shawnee Mission Parkway, Westwood, KS, USA
| | - Lucy E. Side
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec City (Quebec), Canada
| | - Christian F. Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, Aarhus N, Denmark
| | - Thomas P. Slavin
- Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, California 91010 USA
| | - Katie Snape
- Medical Genetics Unit, St George's, University of London, UK
| | - Hagay Sobol
- Département Oncologie Génétique, Prévention et Dépistage, Institut Paoli-Calmettes, 232 boulevard Sainte-Margueritte, Marseille, France
| | - Melissa Southey
- Département Oncologie Génétique, Prévention et Dépistage, Institut Paoli-Calmettes, 232 boulevard Sainte-Margueritte, Marseille, France
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA USA
| | - Doris Steinemann
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | - Christian Sutter
- Department of Human Genetics, University Hospital Heidelberg, Germany
| | - Csilla I. Szabo
- National Human Genome Research Institute, National Institutes of Health Building 50, Room 5312, 50 South Drive, MSC 004, Bethesda, MD, USA
| | - Yen Y. Tan
- Dept of OB/GYN, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal, and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, CIBERONC, Gran Via de l'Hospitalet, 199-203. 08908 L'Hospitalet, Barcelona, Spain
| | - Abigail Thomas
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, Minnesota, USA
| | - Darcy L. Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Quebec, Canada
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Via Gattamelata 64, Padua, Italy
| | - Amanda Ewart Toland
- Division of Human Genetics, Departments of Internal Medicine and Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, 460 W. 12 Avenue, Columbus, OH, USA
| | - Sabine Topka
- Clinical Genetics Research Laboratory, Dept. of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, Australia
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue Boston, Massachusetts 02215, USA
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | | | | | - Rob B. van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | | | - Liliana Varesco
- Unit of Hereditary Cancer, Department of Epidemiology, Prevention and Special Functions, IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, largo Rosanna Benzi 10, 16132 Genoa, Italy
| | | | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, calle Choupana s/n, Edificio de Consultas, Planta menos dos Santiago de Compostal, A Coruña, Spain
| | - Cynthia Villarreal-Garza
- Departamento de Investigacion y de Tumores Mamarios del Instituto Nacional de Cancerologia, Mexico City; and Centro de Cancer de Mama del Hospital Zambrano Hellion, Tecnologico de Monterrey, San Pedro Garza Garcia, Nuevo Leon
| | | | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Germany
| | - Barbara Wappenschmidt
- Department of Genetics and Pathology, Pomeranian Medical University, Unii Lubelskiej 1, Szczecin, Poland
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES (Institute of Nuclear and Radiological Sciences and Technology), National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou & Neapoleos str., Aghia Paraskevi Attikis, Athens, Greece
| | - Sook-Yee Yoon
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 1 Jalan SS12/1A, Subang Jaya, 47500, Malaysia
| | - Cristina Zanzottera
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Instituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Jamal Zidan
- Institute of Oncology, Rivka Ziv Medical Center, 13000 Zefat, Israel
| | - Kristin K. Zorn
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christina G. Hutten Selkirk
- Center for Medical Genetics, NorthShore University HealthSystem,1000 Central St, Suite 620, Evanston, IL, USA
| | - Peter J. Hulick
- Medical Director, Center for Medical Genetics, North Shore University Health System, Clinical Assistant Professor of Medicine, University of Chicago Pritzker School of Medicine, 1000 Central Street, Suite 620, Evanston, IL 60201, USA
| | - Georgia Chenevix-Trench
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston Road, Brisbane, QLD 4006, Australia
| | - Amanda B. Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston Road, Brisbane, QLD 4006, Australia
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Katherine L. Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
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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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16
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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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Ma ESK, Wang CLN, Wong ATC, Choy G, Chan TL. Target fluorescence in-situ hybridization (Target FISH) for plasma cell enrichment in myeloma. Mol Cytogenet 2016; 9:63. [PMID: 27532015 PMCID: PMC4986355 DOI: 10.1186/s13039-016-0263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytogenetic abnormalities are important prognostic markers in plasma cell myeloma (PCM) and detection is routinely performed by interphase fluorescence in-situ hybridization (FISH) with a panel of probes after enrichment of the plasma cells in the bone marrow specimen. Cell sorting by immunomagnetic beads and concurrent labeling of the cytoplasmic immunoglobulin are the usual enrichment methods. We present an alternative method of plasma cell enrichment termed Target FISH, which is an automated system that combines the images of May-Grünwald- Giemsa (MGG) staining and FISH study on the same plasma cell for analysis. RESULTS Our experience of Target FISH on 40 PCM patients was described. Briefly, plasma cells were MGG stained, image captured, de-stained, FISH probe hybridized and finally relocated for simultaneous analysis of morphology and FISH signal pattern. The FISH probe panel was TP53/CEP17, t(4;14) IGH/FGFR3, t(14;16) IGH/MAF and CKS1B(1q21)/CDKN2C(P18). Gain of 1q21 was the most common abnormality detected in 18 patients (45 %), to be followed by t(4;14) IGH/FGFR3 detected in 11 patients (27.5 %). Of note, 10 patients showed coexistence of both t(4;14) and 1q21 gain. Two patients showed del(17p)/TP53, one in association with t(4;14) and 1q gain while the other was stand alone. None of this patient cohort showed t(14;16) IGH/MAF. Using the critical binomial function, the normal cutoff FISH positive value for del(17p)/TP53 was 3.4 %, t(4;14) IGH/FGFR3 was 6.8 %, t(14;16) IGH/MAF was 5.6 % and +1q21 was 5.7 %. CONCLUSIONS The equipment cost notwithstanding, when compared with cell sorting, the total reagent cost was around 10 % lower in Target FISH. The total processing time was longer for Target FISH but manual fluorescence microscopy was no longer necessary. The main advantage of Target FISH was the complete certainty that the cytogenetic abnormality was detected in the cells of interest, and hence a more stringent analytical cutoff value might be considered. Optimization of the cell collection and slide preparation process upfront was required to accrue adequate target cells on each slide for analysis. Our experience suggested that Target FISH was applicable as a routine method of plasma cell enrichment in clinical diagnostic laboratories.
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Affiliation(s)
- Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Clinical Pathology Laboratory, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong
| | - Candy L N Wang
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Clinical Pathology Laboratory, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong
| | - Anthony T C Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Clinical Pathology Laboratory, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong
| | - Gigi Choy
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Clinical Pathology Laboratory, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, Hong Kong
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Clinical Pathology Laboratory, 1/F Li Shu Fan Block, 2 Village Road, Happy Valley, 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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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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Yan HHN, Lau JKY, Chan ASY, Tsui WY, Chan TL, Leung SY. Abstract 179: Regulation of stromal miR-125b on normal colonic epithelial cell renewal and its putative role in tumorigenesis. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-179] [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
MicroRNAs (miRNAs) are small non-coding RNAs which exert their effects by post-transcriptionally silencing target mRNAs. Deregulation of miRNA expression is a frequent event in tumorigenesis. MiR-125b is a highly conserved miRNA among various species and is composed of three homologs: hsa-miR-125a, hsa-miR-125b-1 and hsa-miR-125-2. The tumorigenic roles of miR-125b have been studied in various cancers including prostate, colon, glioma etc, and studies have demonstrated that it can act as a tumor suppressor or an oncogene depending on the cellular context. It was characterized as an oncogene in prostate cancer and glioma through down-regulation of pro-apoptotic regulators BAK1 and Bcl-2 modifying factor (BMF), respectively. In colon cancer, a recent clinico-pathological study showed that high expression of miR-125b was associated with tumor invasion and poor prognosis. However, the localization of miR125b in normal colon and tumors is currently unknown. Therefore, we aimed to address the precise expression and the functional role of miR-125b in normal colon, which may provide insight on its potential oncogenic effects during carcinogenesis.
We performed gene expression analysis of miR-125b in normal colon tissues from 16 pairs of colon top versus basal crypts and 4 pairs of crypts versus stroma by real-time RT-PCR. Colon top and basal crypts were microdissected from frozen sections, whereas pure normal crypts and stromal fractions were isolated from freshly resected human colon specimens. We found that miR-125b was significantly enriched in the basal crypts (p<0.001) and the stromal compartment (p = 0.027). Functionally, knockdown of miR-125b by a specific miRCURY antisense oligonucleotide was able to dose dependently inhibit the growth of a normal colon myofibroblast cell line, CCD18, and significantly increase the mRNA level of several key Hedgehog signaling components, including PTCH (p<0.001), SMO (p<0.001), GLI1 (p<0.001) and its downstream target BMP4 (p = 0.017). Finally, we observed a drastic decrease in both the number and size of normal colon organoids when they were co-cultured with myofibroblasts transfected with miR-125b antisense oligonucleotide, as compared with negative control. Our results suggest that expression of miR-125b in the colonic stromal basal crypt compartment functions to inhibit Hedgehog signaling, leading to paracrine enhancement of colon crypt proliferation and stem cell renewal. Thus, given the well-known importance of hedgehog signaling in colon cancer, our findings suggest that dysregulated miR-125b
expression may contribute to carcinogenesis through disruption of this pathway.
Note: This abstract was not presented at the meeting.
Citation Format: Helen H N Yan, Jackie K Y Lau, Annie S Y Chan, Wai Yin Tsui, Tsun Leung Chan, Suet Yi Leung. Regulation of stromal miR-125b on normal colonic epithelial cell renewal and its putative role in tumorigenesis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 179. doi:10.1158/1538-7445.AM2015-179
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jackie K Y Lau
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Annie S Y Chan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wai Yin Tsui
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tsun Leung Chan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
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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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Whiley PJ, de la Hoya M, Thomassen M, Becker A, Brandão R, Pedersen IS, Montagna M, Menéndez M, Quiles F, Gutiérrez-Enríquez S, De Leeneer K, Tenés A, Montalban G, Tserpelis D, Yoshimatsu T, Tirapo C, Raponi M, Caldes T, Blanco A, Santamariña M, Guidugli L, de Garibay GR, Wong M, Tancredi M, Fachal L, Ding YC, Kruse T, Lattimore V, Kwong A, Chan TL, Colombo M, De Vecchi G, Caligo M, Baralle D, Lázaro C, Couch F, Radice P, Southey MC, Neuhausen S, Houdayer C, Fackenthal J, Hansen TVO, Vega A, Diez O, Blok R, Claes K, Wappenschmidt B, Walker L, Spurdle AB, Brown MA. Comparison of mRNA splicing assay protocols across multiple laboratories: recommendations for best practice in standardized clinical testing. Clin Chem 2013; 60:341-52. [PMID: 24212087 DOI: 10.1373/clinchem.2013.210658] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting. METHODS We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2) gene variants known to alter splicing (BRCA1: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and BRCA2: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design. RESULTS PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with BRCA1, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., BRCA2 c.8632+1G>A Δ19,20 and BRCA1 c.135-1G>T Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., BRCA2 c.426-12_8delGTTTT ins18bp). CONCLUSIONS We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.
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Affiliation(s)
- Phillip J Whiley
- Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
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Leung TW, Yip SF, Lam CW, Chan TL, Lam WWM, Siu DYW, Fan YH, Chan NPH, Liu HSY, Chan LC, Wong KS. Genetic predisposition of white matter infarction with protein S deficiency and R355C mutation. Neurology 2011; 75:2185-9. [PMID: 21172841 DOI: 10.1212/wnl.0b013e3182020379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The association between protein S deficiency (PSD) and ischemic stroke is controversial and warrants further investigation. METHODS We conducted a genotype and MRI correlation study in a Chinese family in which hereditary PSD cosegregated with premature ischemic strokes. Six out of 11 family members inherited PSD type III in an autosomal dominant manner. RESULTS Among all PSD members, a novel missense mutation 1063C→T in exon 10 of protein S alpha (PROS1) was identified, which encoded a substitution of arginine to cysteine at position 355 (R355C) in the first globular domain of laminin A of protein S. Wild-type PROS1 sequences were retained in non-PSD members. MRI detected deep white matter infarctions predominantly distributed in the borderzone regions. The infarct topography was homogeneous in all adult mutant carriers. By contrast, cerebral infarction was absent in nonmutant carriers. Extensive investigation in the family did not reveal any confounding stroke risk. Haplotype analysis with high-density single nucleotide polymorphism markers revealed a 6.1-Mb minimally rearranged region (rs12494685 to rs1598240) in 3q11.2, lod = 3.0. Among the 7 annotated genes in this region, PROS1 is known to be associated with thrombotic disorders. MRI screening in an additional 10 PSD families without R355C showed no cerebral infarction. CONCLUSIONS PROS1 R355C mutation cosegregated with PSD type III and premature white matter infarctions in the index family. The findings substantiate an association between PSD and stroke. Study of the mechanism underlying this association may improve our understanding of premature cryptogenic white matter infarction.
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Affiliation(s)
- T W Leung
- Division of Neurology, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Li C, Yuen ST, Anthony, Chan KW, Tsui WWY, Chan ASY, Leung SY, Chan TL. Abstract 4909: The role of CpG island methylator phenotype 2 (CIMP2) in early onset colorectal cancer patients. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4909] [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
CpG Island Methylator Phenotype (CIMP), characterized by methylation at various promoter sites, has been reported as a subgroup in colorectal cancer. CIMP1 is often associated with microsatellite instability (MSI) as well as BRAF mutation while CIMP negative enriched with P53 mutant. Besides, a CIMP2 classification has also been established and indicated to be associated with KRAS mutation. Most of these experiments related to CIMP were carried out on tumor samples from late onset patients with a mean or median age of at least 60. Thus it was of interest to observe any deviation of such pattern among early onset colorectal cancer population. Bisulfite conversion of the extracted DNA from 73 tumor samples with MSS status were examined via pyrosequence for their methylation status among loci MINT1, MINT2 and MINT27, the most frequently methylated sites reported in CIMP 2 phenomenon. These samples were free from MLH1 methylation and BRAF mutation to exclude conditions of CIMP1. The age group ranged from 29 to 68 years old with a mean age of 50.7 years old. Sequencing of its genomic DNA for KRas mutation was also screened as per se to previous studies. It was found that CIMP2 appeared more frequently in patients over the age of 50 (p=0.04) when compared with patients below 50 years old. Furthermore, methylation of the CIMP 2 loci examined (MINT1, MINT2 and MINT27) were most likely accompanied with the mutation of KRas in patients over 50 years old (p=0.05) while there was no observed correlation of CIMP 2 loci and KRas mutation in patient samples under 50 years of age. Since the CIMP2 phenotype is not seen in early-onset CRC samples, our data suggests that an alternative pathway, but not CIMP, may be responsible for the tumorigenesis of early-onset MSS CRC. Moreover, current studies proposed chromosomal instability may be a distinct mechanism in the pathogenesis of CRC, thus investigation would be carried on this aspect.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4909.
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Affiliation(s)
- Carmen Li
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Siu Tsan Yuen
- 2Hereditary Gastrointestinal Cancer Registry, Department of Pathology, St. Paul's Hospital, Hong Kong
| | | | - Kin Wang Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Wendy Wai Yin Tsui
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Annie Suk Yee Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Suet Yi Leung
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Tsun Leung Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
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Zhang ZH, Cheung CS, Chan TL, Yao CD. Experimental investigation on regulated and unregulated emissions of a diesel/methanol compound combustion engine with and without diesel oxidation catalyst. Sci Total Environ 2010; 408:865-872. [PMID: 19919875 DOI: 10.1016/j.scitotenv.2009.10.060] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 10/09/2009] [Accepted: 10/20/2009] [Indexed: 05/28/2023]
Abstract
The use of methanol in combination with diesel fuel is an effective measure to reduce particulate matter (PM) and nitrogen oxides (NOx) emissions from in-use diesel vehicles. In this study, a diesel/methanol compound combustion (DMCC) scheme was proposed and a 4-cylinder naturally-aspirated direct-injection diesel engine modified to operate on the proposed combustion scheme. The effect of DMCC and diesel oxidation catalyst (DOC) on the regulated emissions of total hydrocarbons (THC), carbon monoxide (CO), NOx and PM was investigated based on the Japanese 13 Mode test cycle. Certain unregulated emissions, including methane, ethyne, ethene, 1,3-butadiene, BTX (benzene, toluene, xylene), unburned methanol and formaldehyde were also evaluated based on the same test cycle. In addition, the soluble organic fraction (SOF) in the particulate and the particulate number concentration and size distribution were investigated at certain selected modes of operation. The results show that the DMCC scheme can effectively reduce NOx, particulate mass and number concentrations, ethyne, ethene and 1,3-butadiene emissions but significantly increase the emissions of THC, CO, NO(2), BTX, unburned methanol, formaldehyde, and the proportion of SOF in the particles. After the DOC, the emission of THC, CO, NO(2), as well as the unregulated gaseous emissions, can be significantly reduced when the exhaust gas temperature is sufficiently high while the particulate mass concentration is further reduced due to oxidation of the SOF.
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Affiliation(s)
- Z H Zhang
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, PR China
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Zhang ZH, Cheung CS, Chan TL, Yao CD. Emission reduction from diesel engine using fumigation methanol and diesel oxidation catalyst. Sci Total Environ 2009; 407:4497-4505. [PMID: 19446309 DOI: 10.1016/j.scitotenv.2009.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/17/2009] [Accepted: 04/21/2009] [Indexed: 05/27/2023]
Abstract
This study is aimed to investigate the combined application of fumigation methanol and a diesel oxidation catalyst for reducing emissions of an in-use diesel engine. Experiments were performed on a 4-cylinder naturally-aspirated direct-injection diesel engine operating at a constant speed of 1800 rev/min for five engine loads. The experimental results show that at low engine loads, the brake thermal efficiency decreases with increase in fumigation methanol; but at high loads, it slightly increases with increase in fumigation methanol. The fumigation method results in a significant increase in hydrocarbon (HC), carbon monoxide (CO), and nitrogen dioxide (NO(2)) emissions, but decrease in nitrogen oxides (NO(x)), smoke opacity and the particulate mass concentration. For the submicron particles, the total number of particles decreases. In all cases, there is little change in geometrical mean diameter of the particles. After catalytic conversion, the HC, CO, NO(2), particulate mass and particulate number concentrations were significantly reduced at medium to high engine loads; while the geometrical mean diameter of the particles becomes larger. Thus, the combined use of fumigation methanol and diesel oxidation catalyst leads to a reduction of HC, CO, NO(x), particulate mass and particulate number concentrations at medium to high engine loads.
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Affiliation(s)
- Z H Zhang
- Department of Mechanical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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Li VSW, Yuen ST, Chan TL, Yan HHN, Law WL, Yeung BHY, Chan ASY, Tsui WY, So S, Chen X, Leung SY. Frequent inactivation of axon guidance molecule RGMA in human colon cancer through genetic and epigenetic mechanisms. Gastroenterology 2009; 137:176-87. [PMID: 19303019 DOI: 10.1053/j.gastro.2009.03.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 03/07/2009] [Accepted: 03/10/2009] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Repulsive guidance molecule member A (RGMA) is a glycosylphosphatidylinositol-anchored glycoprotein and axon guidance molecule that signals through its receptor, neogenin (NEO1), a homologue of the deleted-in-colorectal cancer (DCC) gene. RGMA also functions as a bone morphogenetic protein (BMP) coreceptor. We studied the potential roles of RGMA and NEO1 in colorectal cancer (CRC) pathogenesis. METHODS We analyzed expression of RGMA and NEO1, as well as their epigenetic and genetic changes, in a large series of CRC samples, normal colon tissues, adenomas, and cell lines. These studies were accompanied by in vitro functional assay. RESULTS RGMA and NEO1 expression were significantly down-regulated in most CRCs, adenomas, and cell lines. RGMA was frequently silenced by promoter methylation in CRCs (86.7%), adenomas (90.9%), and CRC cell lines (92.3%) but not in normal colon tissues; allelic imbalance of RGMA and NEO1 was observed in 40% and 49% of CRCs, respectively. In CRC samples, reduced RGMA levels were significantly associated with mismatch repair deficiency or mutations in KRAS or BRAF. Exposure to 5-aza-2'-deoxycytidine restored RGMA expression in CRC cell lines. Transfection of RGMA into CRC cells suppressed cell proliferation, migration, and invasion and also increased apoptosis in response to DNA-damaging agent. CONCLUSIONS The frequent genetic and epigenetic inactivation of RGMA in CRCs and adenomas along with its in vitro function collectively support its role as a tumor suppressor in colon cells. These findings add to the expanding list of axon guidance molecules with disrupted function during colon carcinogenesis and create new opportunities for early detection and drug development.
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Affiliation(s)
- Vivian S W Li
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
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Ligtenberg MJL, Kuiper RP, Chan TL, Goossens M, Hebeda KM, Voorendt M, Lee TYH, Bodmer D, Hoenselaar E, Hendriks-Cornelissen SJB, Tsui WY, Kong CK, Brunner HG, van Kessel AG, Yuen ST, van Krieken JHJM, Leung SY, Hoogerbrugge N. Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3' exons of TACSTD1. Nat Genet 2008; 41:112-7. [PMID: 19098912 DOI: 10.1038/ng.283] [Citation(s) in RCA: 532] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/07/2008] [Indexed: 12/17/2022]
Abstract
Lynch syndrome patients are susceptible to colorectal and endometrial cancers owing to inactivating germline mutations in mismatch repair genes, including MSH2 (ref. 1). Here we describe patients from Dutch and Chinese families with MSH2-deficient tumors carrying heterozygous germline deletions of the last exons of TACSTD1, a gene directly upstream of MSH2 encoding Ep-CAM. Due to these deletions, transcription of TACSTD1 extends into MSH2. The MSH2 promoter in cis with the deletion is methylated in Ep-CAM positive but not in Ep-CAM negative normal tissues, thus revealing a correlation between activity of the mutated TACSTD1 allele and epigenetic inactivation of the corresponding MSH2 allele. Gene silencing by transcriptional read-through of a neighboring gene in either sense, as demonstrated here, or antisense direction, could represent a general mutational mechanism. Depending on the expression pattern of the neighboring gene that lacks its normal polyadenylation signal, this may cause either generalized or mosaic patterns of epigenetic inactivation.
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Affiliation(s)
- Marjolijn J L Ligtenberg
- Department of Human Genetics 849, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Suehiro Y, Wong CW, Chirieac LR, Kondo Y, Shen L, Webb CR, Chan YW, Chan ASY, Chan TL, Wu TT, Rashid A, Hamanaka Y, Hinoda Y, Shannon RL, Wang X, Morris J, Issa JPJ, Yuen ST, Leung SY, Hamilton SR. Epigenetic-genetic interactions in the APC/WNT, RAS/RAF, and P53 pathways in colorectal carcinoma. Clin Cancer Res 2008; 14:2560-9. [PMID: 18451217 DOI: 10.1158/1078-0432.ccr-07-1802] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Early events in colorectal tumorigenesis include mutation of the adenomatous polyposis coli (APC) gene and epigenetic hypermethylation with transcriptional silencing of the O(6)-methylguanine DNA methyltransferase (MGMT), human mut L homologue 1 (hMLH1), and P16/CDKN2A genes. Epigenetic alterations affect genetic events: Loss of MGMT via hypermethylation reportedly predisposes to guanine-to-adenine or cytosine-to-thymine (G:C-->A:T) transition mutations in KRAS and P53, and silencing of hMLH1 leads to high levels of microsatellite instability (MSI-H)/mutator phenotype, suggesting that epigenetic-genetic subtypes exist. EXPERIMENTAL DESIGN We evaluated the relationships of aberrant methylation of APC, MGMT, hMLH1, P16, N33, and five MINTs to mutations in APC, KRAS, BRAF, and P53 in 208 colorectal carcinomas. RESULTS We found that APC hypermethylation was age related (P = 0.04), in contrast to the other genes, and did not cluster with CpG island methylator phenotype (CIMP) markers. Hypermethylation of APC concurrently with either MGMT or hMLH1 was strongly associated with occurrence of G-to-A transitions in APC [odds ratio (OR), 26.8; P < 0.0002 from multivariable logic regression model], but C-to-T transitions had no associations. There was no relationship of hypermethylation of any gene, including MGMT, with G-to-A or C-to-T transitions in KRAS or P53, although APC hypermethylation was associated with P53 mutation (P < 0.0002). CIMP with MSI-H due to hMLH1 hypermethylation, or CIMP with loss of MGMT expression in non-MSI-H tumors, was associated with BRAF mutation (OR, 4.5; P < 0.0002). CIMP was also associated with BRAF V600E T-to-A transversion (OR, 48.5; P < 0.0002). CONCLUSIONS Our findings suggest that the heterogeneous epigenetic dysregulation of promoter methylation in various genes is interrelated with the occurrence of mutations, as manifested in epigenetic-genetic subgroups of tumors.
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Affiliation(s)
- Yutaka Suehiro
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TL, Kwong DLW, Au GKH, Liu CG, Calin GA, Croce CM, Harris CC. MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 2008; 299:425-36. [PMID: 18230780 PMCID: PMC2614237 DOI: 10.1001/jama.299.4.425] [Citation(s) in RCA: 1171] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT MicroRNAs have potential as diagnostic biomarkers and therapeutic targets in cancer. No study has evaluated the association between microRNA expression patterns and colon cancer prognosis or therapeutic outcome. OBJECTIVE To identify microRNA expression patterns associated with colon adenocarcinomas, prognosis, or therapeutic outcome. DESIGN, SETTING, AND PATIENTS MicroRNA microarray expression profiling of tumors and paired nontumorous tissues was performed on a US test cohort of 84 patients with incident colon adenocarcinoma, recruited between 1993 and 2002. We evaluated associations with tumor status, TNM staging, survival prognosis, and response to adjuvant chemotherapy. Associations were validated in a second, independent Chinese cohort of 113 patients recruited between 1991 and 2000, using quantitative reverse transcription polymerase chain reaction assays. The final date of follow-up was December 31, 2005, for the Maryland cohort and August 16, 2004, for the Hong Kong cohort. MAIN OUTCOME MEASURES MicroRNAs that were differentially expressed in tumors and microRNA expression patterns associated with survival using cancer-specific death as the end point. RESULTS Thirty-seven microRNAs were differentially expressed in tumors from the test cohort. Selected for validation were miR-20a, miR-21, miR-106a, miR-181b, and miR-203, and all 5 were enriched in tumors from the validation cohort (P < .001). Higher miR-21 expression was present in adenomas (P = .006) and in tumors with more advanced TNM staging (P < .001). In situ hybridization demonstrated miR-21 to be expressed at high levels in colonic carcinoma cells. The 5-year cancer-specific survival rate was 57.5% for the Maryland cohort and was 49.5% for the Hong Kong cohort. High miR-21 expression was associated with poor survival in both the training (hazard ratio, 2.5; 95% confidence interval, 1.2-5.2) and validation cohorts (hazard ratio, 2.4; 95% confidence interval, 1.4-3.9), independent of clinical covariates, including TNM staging, and was associated with a poor therapeutic outcome. CONCLUSIONS Expression patterns of microRNAs are systematically altered in colon adenocarcinomas. High miR-21 expression is associated with poor survival and poor therapeutic outcome.
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Affiliation(s)
- Aaron J Schetter
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Cheng CH, Cheung CS, Chan TL, Lee SC, Yao CD. Experimental investigation on the performance, gaseous and particulate emissions of a methanol fumigated diesel engine. Sci Total Environ 2008; 389:115-124. [PMID: 17920660 DOI: 10.1016/j.scitotenv.2007.08.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 08/10/2007] [Accepted: 08/19/2007] [Indexed: 05/25/2023]
Abstract
Experiments were conducted on a 4-cylinder direct-injection diesel engine with fumigation methanol injected into the air intake of each cylinder. The fumigation methanol was injected to top up 10%, 20% and 30% of the power output under different engine operating conditions. The effects of fumigation methanol on engine performance, gaseous emissions and particulate emission were investigated. The experimental results show that there is a decrease in the brake thermal efficiency when fumigation methanol is applied, except at the highest load of 0.67 MPa. At low loads, the brake thermal efficiency decreases with increase in fumigation methanol; but at high loads, it increases with increase in fumigation methanol. The fumigation method results in a significant increase in hydrocarbon (HC), carbon monoxide (CO), and nitrogen dioxide (NO(2)) emissions. The concentration of nitrogen oxides (NOx) is significantly reduced except at close to full load condition. There is also a reduction in the smoke opacity and the particulate matter (PM) mass concentration. For the submicron particles, the total number of particles decreases at low and medium loads but increases at high loads. In all cases, there is a shift of the particles towards smaller geometrical mean diameter, especially at high loads. The increase in nano-sized particles and the increase in NO(2) emission could have serious impact on human health.
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Affiliation(s)
- C H Cheng
- Department of Mechanical Engineering, The Hong Kong Polytechnic University, Hong Kong.
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Kosinski C, Li VSW, Chan ASY, Zhang J, Ho C, Tsui WY, Chan TL, Mifflin RC, Powell DW, Yuen ST, Leung SY, Chen X. Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors. Proc Natl Acad Sci U S A 2007; 104:15418-23. [PMID: 17881565 PMCID: PMC2000506 DOI: 10.1073/pnas.0707210104] [Citation(s) in RCA: 439] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human colonic epithelial cell renewal, proliferation, and differentiation are stringently controlled by numerous regulatory pathways. To identify genetic programs of human colonic epithelial cell differentiation in vivo as well as candidate marker genes that define colonic epithelial stem/progenitor cells and the stem cell niche, we applied gene expression analysis of normal human colon tops and basal crypts by using expression microarrays with 30,000 genes. Nine hundred and sixty-nine cDNA clones were found to be differentially expressed between human colon crypts and tops. Pathway analysis revealed the differential expression of genes involved in cell cycle maintenance and apoptosis, as well as genes in bone morphogenetic protein (BMP), Notch, Wnt, EPH, and MYC signaling pathways. BMP antagonists gremlin 1, gremlin 2, and chordin-like 1 were found to be expressed by colon crypts. In situ hybridization and RT-PCR confirmed that these BMP antagonists are expressed by intestinal cryptal myofibroblasts and smooth muscle cells at the colon crypt. In vitro analysis demonstrated that gremlin 1 partially inhibits Caco-2 cell differentiation upon confluence and activates Wnt signaling in normal rat intestinal epithelial cells. Collectively, the expression data set provides a comprehensive picture of human colonic epithelial cell differentiation. Our study also suggests that BMP antagonists are candidate signaling components that make up the intestinal epithelial stem cell niche.
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Affiliation(s)
- Cynthia Kosinski
- *Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143
| | - Vivian S. W. Li
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S. Y. Chan
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Ji Zhang
- *Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143
- Department of Surgery, Beijing Cancer Hospital, Beijing 100036, China; and
| | - Coral Ho
- *Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143
| | - Wai Yin Tsui
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tsun Leung Chan
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Randy C. Mifflin
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-0144
| | - Don W. Powell
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-0144
| | - Siu Tsan Yuen
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
- To whom correspondence may be addressed. E-mail: or
| | - Xin Chen
- *Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143
- To whom correspondence may be addressed. E-mail: or
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Sheng JQ, Chan TL, Chan YW, Huang JS, Chen JG, Zhang MZ, Guo XL, Mu H, Chan AS, Li SR, Yuen ST, Leung SY. Microsatellite instability and novel mismatch repair gene mutations in northern Chinese population with hereditary non-polyposis colorectal cancer. ACTA ACUST UNITED AC 2007; 7:197-205. [PMID: 17054581 DOI: 10.1111/j.1443-9573.2006.00269.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Hereditary non-polyposis colorectal cancer (HNPCC) syndrome is the most common cause of hereditary colorectal cancer with an early age of onset. Microsatellite instability (MSI) and germline mutation in one of the DNA mismatch repair (MMR) genes are found in the majority of HNPCC families and provide an opportunity for genetic diagnosis and prophylactic screening. The MMR gene mutation spectrum may vary across different populations and be influenced by founder mutations that prevail in specific ethnic groups. China is a big and ancient nation with enormous genetic diversity, which is especially notable between the northern and southern Chinese populations. A MMR gene mutation database for the southern Chinese population based in Hong Kong has been previously established. This study compares the MMR gene mutation spectrum and the MSI of HNPCC between the northern and southern Chinese populations. METHODS Twenty-five HNPCC families from northern China were systematically analyzed. The MSI analysis was performed using five loci in the USA National Cancer Institute (NCI) panel (D2S123, D5S346, BAT-25, BAT-26 and BAT-40) by PCR from the tumor and normal tissue. MSH2, MSH6 and MLH1 were performed using immunohistochemical staining. Two founder mutations of MSH2 and MLH1 were examined by PCR base analyses using primers flanking the two deletion sites (c.1452_1455delAATG in MSH2 and 1.8 kb deletion involving exon 11 of MLH1). RESULTS Of the 25 families collected, 19 met Bethesda guideline (BG) 1 and six met BG3. Twenty-two (15.7%) were extra-colonic cancers with gastric cancer (in seven patients) being the most common cancer type. Of the 25 tumors analyzed, 21 (84%) were high level microsatellite instability (MSI-H) and four (16%) were microsatellite stable (MSS). Eighteen (86%) of the 21 MSI-H tumors showed loss of either the MLH1 or the MSH2 protein. Three MSI-H tumors and all four MSS tumors showed no loss of expression of the three MMR proteins. Out of the 21 patients with MSI-H tumors, 12 (57%) showed pathogenic germline mutations in either MLH1 (n = 8) or MSH2 (n = 4). Overall, three novel mutations (in patients H22, H17 and H29) have been identified. One of them, c.503_4insA, caused a frameshift mutation in the MLH1 gene. The other two were found in the MSH2 gene, including a frameshift (c.899_890insAT) and a splice junction (IVS7-1G-->A, SA of Exon 8) mutation. CONCLUSIONS The results suggest a distinctly different mutation spectrum of MMR genes between northern and southern Chinese populations and call for a systematic, nationwide study to facilitate the design of a MMR gene mutation detection strategy tailored for individual populations in China.
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Affiliation(s)
- Jian Qiu Sheng
- Hereditary non-polyposis colorectal cancer (HNPCC) group, Beijing Army General Hospital, Beijing, China
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Wang JS, Chan TL, Ning Z, Cheung CS, Huang Z. [Experimental study on ultrafine particle characteristics exhausted from various fuelled vehicles]. Huan Jing Ke Xue 2006; 27:2382-5. [PMID: 17304827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The fine particle size distribution characteristics obtained from a diesel taxi, a diesel light bus, a gasoline private car and a liquefied petroleum gas (LPG) fuelled taxi were carried out on a chassis dynamometer system. The measurements were performed at different driving modes, i.e. , with low and high idling and from 10 kmxh(-1) to 70 kmxh(-1), 4 cruise operations using the instrument SMPS for collecting particles of 0.015-0.7microm diameter in range. It was found that different fuelled vehicles and different driving modes characterize considerable differences in size number and mass concentration distributions. Diesel vehicles contribute much more nuclei and accumulation mode particles of 30 - 150 nm, while LPG and gasoline fuelled vehicles exhaust much more nuclei mode particles of 15-30 nm. Overall, diesel-fuelled vehicles exhaust much more particles number and mass than gasoline and LPG fuelled vehicles; In the present study, diesel vehicles exhaust the ranges of total SMPS particle number, mass concentration with (0.3-3.6) x 10(8) number x cm(-3), 0.03 - 0.6 microg cm(- 3) respectively, and gasoline and LPG fuelled vehicles exhaust 2.3 x 10(4) - 1.2 x 10(7) number x cm(-3), 8 x 10(-5)-0.1 microgxcm(-3); 8.2 x 10(3)8.8 x 10(6) number x cm(-3), 1.7 x 10(-5) -0.09 microg x cm(-3), respectively; For all types of vehicles, the particle number and mass concentrations are small at low-idle and low-speed-driving modes, and are large at high-idle and high-speed-driving modes. They generally increase with the vehicle speed increasing from 10 to 70 kmx h(-1).
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Affiliation(s)
- Jia-song Wang
- Research Center for Combustion and Environmental Technology, Shanghai Jiaotong University, Shanghai 200030, China.
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Chan TL, Yuen ST, Kong CK, Chan YW, Chan ASY, Ng WF, Tsui WY, Lo MWS, Tam WY, Li VSW, Leung SY. Heritable germline epimutation of MSH2 in a family with hereditary nonpolyposis colorectal cancer. Nat Genet 2006; 38:1178-83. [PMID: 16951683 DOI: 10.1038/ng1866] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 07/21/2006] [Indexed: 01/03/2023]
Abstract
Epimutations in the germline, such as methylation of the MLH1 gene, may contribute to hereditary cancer syndrome in human, but their transmission to offspring has never been documented. Here we report a family with inheritance, in three successive generations, of germline allele-specific and mosaic hypermethylation of the MSH2 gene, without evidence of DNA mismatch repair gene mutation. Three siblings carrying the germline methylation developed early-onset colorectal or endometrial cancers, all with microsatellite instability and MSH2 protein loss. Clonal bisulfite sequencing and pyrosequencing showed different methylation levels in different somatic tissues, with the highest level recorded in rectal mucosa and colon cancer tissue, and the lowest in blood leukocytes. This mosaic state of germline methylation with different tissue distribution could act as the first hit and provide a mechanism for genetic disease inheritance that may deviate from the mendelian pattern and be overlooked in conventional leukocyte-based genetic diagnosis strategy.
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Affiliation(s)
- Tsun Leung Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
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Edkins S, O’Meara S, Parker A, Stevens C, Reis M, Jones S, Greenman C, Davies H, Dalgliesh G, Forbes S, Hunter C, Smith R, Stephens P, Goldstraw P, Nicholson A, Chan TL, Velculescu VE, Yuen ST, Leung SY, Stratton MR, Futreal PA. Recurrent KRAS codon 146 mutations in human colorectal cancer. Cancer Biol Ther 2006; 5:928-32. [PMID: 16969076 PMCID: PMC2714972 DOI: 10.4161/cbt.5.8.3251] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An activating point mutation in codon 12 of the HRAS gene was the first somatic point mutation identified in a human cancer and established the role of somatic mutations as the common driver of oncogenesis. Since then, there have been over 11,000 mutations in the three RAS (HRAS, KRAS and NRAS) genes in codons 12, 13 and 61 reported in the literature. We report here the identification of recurrent somatic missense mutations at alanine 146, a highly conserved residue in the guanine nucleotide binding domain. In two independent series of colorectal cancers from Hong Kong and the United States we detected KRAS A146 mutations in 7/126 and 2/94 cases, respectively, giving a combined frequency of 4%. We also detected KRAS A146 mutations in 2/40 (5%) colorectal cell lines, including the NCI-60 colorectal cancer line HCC2998. Codon 146 mutations thus are likely to make an equal or greater contribution to colorectal cancer than codon 61 mutations (4.2% in our combined series, 1% in the literature). Lung adenocarcinomas and large cell carcinomas did not show codon 146 mutations. We did, however, identify a KRAS A146 mutation in the ML-2 acute myeloid leukemia cell line and an NRAS A146 mutation in the NALM-6 B-cell acute lymphoblastic leukemia line, suggesting that the contribution of codon 146 mutations is not entirely restricted to colorectal cancers or to KRAS.
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Affiliation(s)
- Sarah Edkins
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Sarah O’Meara
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Adrian Parker
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Claire Stevens
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Marcelo Reis
- Ludwig Center for Cancer Genetics and Therapeutics; Johns Hopkins University; Kimmel Cancer Center; Baltimore, Maryland, USA
| | - Siân Jones
- Ludwig Center for Cancer Genetics and Therapeutics; Johns Hopkins University; Kimmel Cancer Center; Baltimore, Maryland, USA
| | - Chris Greenman
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Helen Davies
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | | | - Simon Forbes
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Chris Hunter
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Raffaella Smith
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | - Philip Stephens
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
| | | | | | - Tsun Leung Chan
- Department of Pathology; The University of Hong Kong; Queen Mary Hospital; Hong Kong, China
| | - Victor E Velculescu
- Ludwig Center for Cancer Genetics and Therapeutics; Johns Hopkins University; Kimmel Cancer Center; Baltimore, Maryland, USA
| | - Siu Tsan Yuen
- Department of Pathology; The University of Hong Kong; Queen Mary Hospital; Hong Kong, China
| | - Suet Yi Leung
- Department of Pathology; The University of Hong Kong; Queen Mary Hospital; Hong Kong, China
| | - Michael R Stratton
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
- Institute for Cancer Research; Sutton, Surrey, UK
| | - P. Andrew Futreal
- Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton, UK
- Correspondence to: Andrew Futreal; Cancer Genome Project; Welcome Trust Sanger Institute; Hinxton CB10 1SA UK; Tel.:+44.0.1223.494857; Fax: +44.0. 1223.494809;
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Wong CW, Fan YS, Chan TL, Chan ASW, Ho LC, Ma TKF, Yuen ST, Leung SY. BRAF and NRAS mutations are uncommon in melanomas arising in diverse internal organs. J Clin Pathol 2005; 58:640-4. [PMID: 15917418 PMCID: PMC1770697 DOI: 10.1136/jcp.2004.022509] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2004] [Indexed: 01/22/2023]
Abstract
BACKGROUND Malignant melanoma arising from different body compartments may be associated with differing aetiological factors and clinical behaviour, and may manifest diverse molecular genetic profiles. Although many studies have focused on cutaneous melanoma, little is known of mucosal and other types of melanoma. In particular, malignant melanoma of soft parts is different from other melanomas in many respects, yet manifests a common melanocytic differentiation. Mutation of BRAF is now known to be common in cutaneous melanomas, and raises possible new therapeutic options of anti-RAF treatment for these patients. Few data are available for non-cutaneous melanomas. AIMS To study the incidence of BRAF and NRAS mutations in melanomas arising in diverse internal organs. METHODS Fifty one melanomas from various internal organs were investigated for BRAF and NRAS mutation by direct DNA sequencing. RESULTS BRAF and NRAS mutations were found in two and five mucosal melanomas arising from the aerodigestive and female genital tracts (n = 36). Their occurrence is mutually exclusive, giving a combined mutation incidence rate of 19.4% in mucosal melanomas. Both BRAF and NRAS mutations were absent in malignant melanoma of soft parts (n = 7). BRAF mutation was also absent in uveal melanoma (n = 6), but was seen in two of five cutaneous melanomas. The incidence of BRAF or combined BRAF/NRAS mutations in all non-cutaneous groups was significantly lower than published rates for cutaneous melanomas. CONCLUSION Each melanoma subtype may have a unique oncogenetic pathway of tumour development, and only a small fraction of non-cutaneous melanomas may benefit from anti-RAF treatment.
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Affiliation(s)
- C W Wong
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Hong Kong
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40
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Li VSW, Wong CW, Chan TL, Chan ASW, Zhao W, Chu KM, So S, Chen X, Yuen ST, Leung SY. Mutations of PIK3CA in gastric adenocarcinoma. BMC Cancer 2005; 5:29. [PMID: 15784156 PMCID: PMC1079799 DOI: 10.1186/1471-2407-5-29] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2004] [Accepted: 03/23/2005] [Indexed: 12/12/2022] Open
Abstract
Background Activation of the phosphatidylinositol 3-kinase (PI3K) through mutational inactivation of PTEN tumour suppressor gene is common in diverse cancer types, but rarely reported in gastric cancer. Recently, mutations in PIK3CA, which encodes the p110α catalytic subunit of PI3K, have been identified in various human cancers, including 3 of 12 gastric cancers. Eighty percent of these reported mutations clustered within 2 regions involving the helical and kinase domains. In vitro study on one of the "hot-spot" mutants has demonstrated it as an activating mutation. Methods Based on these data, we initiated PIK3CA mutation screening in 94 human gastric cancers by direct sequencing of the gene regions in which 80% of all the known PIK3CA mutations were found. We also examined PIK3CA expression level by extracting data from the previous large-scale gene expression profiling study. Using Significance Analysis of Microarrays (SAM), we further searched for genes that show correlating expression with PIK3CA. Results We have identified PIK3CA mutations in 4 cases (4.3%), all involving the previously reported hotspots. Among these 4 cases, 3 tumours demonstrated microsatellite instability and 2 tumours harboured concurrent KRAS mutation. Data extracted from microarray studies showed an increased expression of PIK3CA in gastric cancers when compared with the non-neoplastic gastric mucosae (p < 0.001). SAM further identified 2910 genes whose expression levels were positively associated with that of PIK3CA. Conclusion Our data suggested that activation of the PI3K signalling pathway in gastric cancer may be achieved through up-regulation or mutation of PIK3CA, in which the latter may be a consequence of mismatch repair deficiency.
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Affiliation(s)
- Vivian Sze Wing Li
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Chi Wai Wong
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Tsun Leung Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Agnes Sze Wah Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Wei Zhao
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Kent-Man Chu
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Samuel So
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xin Chen
- Department of Biopharmaceutical Sciences, University of California, San Francisco, USA
| | - Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Chan TL, Chan YW, Ho JWC, Chan C, Chan ASY, Chan E, Lam PWY, Tse CW, Lee KC, Lau CW, Gwi E, Leung SY, Yuen ST. MSH2 c.1452-1455delAATG is a founder mutation and an important cause of hereditary nonpolyposis colorectal cancer in the southern Chinese population. Am J Hum Genet 2004; 74:1035-42. [PMID: 15042510 PMCID: PMC1181966 DOI: 10.1086/383591] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 02/09/2004] [Indexed: 01/20/2023] Open
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) accounts for approximately 2% of all colorectal cancer (CRC) cases and is the most common hereditary CRC syndrome. We have previously reported a high incidence of microsatellite instability (MSI) and germline mismatch repair (MMR) gene mutations in young Hong Kong Chinese with CRC. Ongoing studies at the Hereditary Gastrointestinal Cancer Registry in Hong Kong have revealed a unique germline MSH2 c.1452-1455delAATG mutation that has not been reported in other ethnic groups. Detailed analysis showed that this specific MSH2 mutation constituted 21% of all germline MMR gene mutations and 36% of all MSH2 germline mutations identified. We designed a specific PCR-based diagnostic test on paraffin-embedded tissues and identified this germline mutation in 2 (1.5%) of 138 consecutive patients with early-onset CRC (<46 years of age at diagnosis). Haplotype analysis was performed using 11 microsatellite markers located between D2S391 and D2S123. All 10 families had the same disease haplotype, suggesting a founder effect. These 10 families all originated from the Chinese province of Guangdong, which historically included Hong Kong. It is the most populous of the Chinese provinces, with a population of >93 million. Further analysis suggested that this founder mutation may date back to between 22 and 103 generations ago. The identification of this MSH2 founder mutation has important implications for the design of mutation-detection strategies for the southern Chinese population. Since there were major emigrations from Hong Kong and Guangdong province during the 19th and 20th centuries, this finding is also significant for Chinese communities worldwide.
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Affiliation(s)
- Tsun Leung Chan
- Department of Pathology, The University of Hong Kong, Hong Kong
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Zhao W, Chan TL, Chu KM, Chan AS, Stratton MR, Yuen ST, Leung SY. Mutations of BRAF and KRAS in gastric cancer and their association with microsatellite instability. Int J Cancer 2003; 108:167-9. [PMID: 14618633 DOI: 10.1002/ijc.11553] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Chan ASW, Tsui WY, Chen X, Chu KM, Chan TL, Chan ASY, Li R, So S, Yuen ST, Leung SY. Downregulation of ID4 by promoter hypermethylation in gastric adenocarcinoma. Oncogene 2003; 22:6946-53. [PMID: 14534543 DOI: 10.1038/sj.onc.1206799] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Promoter hypermethylation has become apparent as a common mechanism of gene silencing in cancer. Based on our published microarray expression data, we noticed a prominent downregulation of ID4 in gastric adenocarcinoma. The dense 5' CpG island covering the previously mapped upstream promoter of ID4 has prompted us to relate its downregulation to promoter hypermethylation. ID proteins are distinct members in the helix-loop-helix family of transcriptional regulators, which modulate various key developmental processes. Emerging data have suggested the involvement of ID genes in tumorigenesis. In this study using bisulfite genomic sequencing, we have found hypermethylation of ID4 promoter in most gastric cancer cell lines and 30% of primary tumors. This correlated with decreased level of ID4 expression. Restoration of ID4 expression in various gastric cancer cell lines was achieved by treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine, which at times required the synergistic action of the histone deacetylase inhibitor trichostatin A, but not with trichostatin A alone. Re-expression was accompanied by the corresponding ID4 promoter demethylation. Furthermore, we have found significant association of ID4 promoter methylation with hMLH1 promoter methylation (P=0.008) and microsatellite instability (P=0.006). Overall, our results have shown that transcriptional silencing of ID4 is related to the aberrant methylation of its promoter in gastric cancer. The significant association of ID4 and hMLH1 promoter hypermethylation suggested that ID4 may also be among the genes being targeted in the CpG island methylator phenotype tumorigenic pathway.
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Affiliation(s)
- Agnes Sze Wah Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Abstract
AIM Knowledge of the spectrum and frequencies of pediatric emergencies presenting to an emergency department (ED) of individual developing countries is vital in optimizing the quality of care delivered locally. METHODS A prospective 6 wk review of all pediatric (< 18 y) attendees to an urban ED was done, with patient age, presenting complaints, diagnoses, time of arrival and disposition recorded. RESULTS Complete data were available on 1172 patients, with an age range of 4 d to 18 y (mean +/- SD 6.9 +/- 5.6 y); 43% were aged < or = 4 y. The main presenting complaints were injuries (26.9%), fever (24%) and breathing difficulties (16.6%). The most common diagnosis was minor trauma (24.2%), with soft-tissue injuries predominating (80.6%). The other diagnoses were asthma (12.6%), upper respiratory infections (12.1%), other infections (12.1%) and gastroenteritis (11.8%). Equal proportions of patients were seen throughout the day. 25% of patients were admitted. Young age (< 1 y); presence of past medical history, general practitioner referrals, diagnosis of bronchiolitis and pneumonia were significantly associated with risk of admission. CONCLUSION A wide spectrum of paediatric illnesses was seen in the ED, with an overrepresentation of young children. This supports the decision to have either a separate pediatric ED or paediatric residents on the staff. The training curricula should emphasize the management of pediatric trauma, infections and asthma. Alternatively, developing guidelines for the five most common presenting complaints would account for 82% of all attendees and could be directed towards all staff on the ED.
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Affiliation(s)
- A Y Goh
- Department of Pediatrics, University of Malaya Medical Centre, Kuala Lumpur, Malaysia.
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Yuen ST, Chan TL, Ho JWC, Chan ASY, Chung LP, Lam PWY, Tse CW, Wyllie AH, Leung SY. Germline, somatic and epigenetic events underlying mismatch repair deficiency in colorectal and HNPCC-related cancers. Oncogene 2002; 21:7585-92. [PMID: 12386821 DOI: 10.1038/sj.onc.1205968] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2002] [Revised: 08/08/2002] [Accepted: 08/08/2002] [Indexed: 11/08/2022]
Abstract
High-frequency microsatellite instability (MSI-H) results from deficiency in nucleotide mismatch repair. It contributes significantly to carcinogenesis in the human colorectal mucosa. Here we study 41 colorectal and three other HNPCC-related cancers with MSI-H to provide comprehensive information on the mechanisms of inactivation of the two major proteins involved, hMLH1 and hMSH2. Seventeen of the patients had family histories meeting the criteria for Bethesda grades 1, 2 or 3. Of these familial cases, 14 (83%) had early-onset disease, defined on the basis of diagnosis prior to the age of 50, but in three the disease was of late onset (>50 years). A second subset of 20 patients had early onset disease without family history. The remaining seven patients were selected to allow comparisons with sporadic, late-onset disease, the molecular basis of which has been extensively reported elsewhere. We stratified the tumours initially on the basis of hMLH1 or hMSH2 protein deficiency, detected by immunohistochemistry, and then by analysis of germline and somatic mutation, mRNA transcription, loss of heterozygosity (LOH) at the hMLH1 and hMSH2 loci, and methylation status in two regions of the hMLH1 promoter. The functional significance of several of these changes in the MSI-H tumours was confirmed by comparisons with 16 tumours with low-frequency microsatellite instability and 56 tumours with stable microsatellites. As anticipated, patients with family histories usually showed germline mutation of hMSH2 or hMLH1. In many cases the residual normal allele was silenced in their tumours by loss of heterozygosity (LOH). The small subset of late-onset, sporadic cases confirmed the preponderance in this group of biallelic hMLH1 promoter methylation. In the early-onset, apparently sporadic subset there were 11 tumours with hMLH1 deficiency, five with hMSH2 deficiency and four with no detectable abnormality in expression of either protein. These showed a complex mixture of lesions, including germline and somatic mutations, promoter methylation, LOH, suppression of wild-type RNA by as yet undiscovered mechanisms, or no detectable abnormality in any of these parameters. Evidence is presented to indicate that methylation in proximal region of the hMLH1 promoter is a more reliable correlate of transcriptional silencing in colorectal cancers than methylation in upstream region. These observations have significant implications for management of patients with MSI-H tumours.
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Affiliation(s)
- Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Chan JHM, Tsui EYK, Chau LF, Chow KY, Chan MSM, Yuen MK, Chan TL, Cheng WK, Wong KPC. Discrimination of an infected brain tumor from a cerebral abscess by combined MR perfusion and diffusion imaging. Comput Med Imaging Graph 2002; 26:19-23. [PMID: 11734370 DOI: 10.1016/s0895-6111(01)00023-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this study was to investigate the signal characteristics of the abscess wall and tumor wall on diffusion-weighted and perfusion-weighted images and thus to evaluate the feasibility of using combined MR diffusion and perfusion imaging to differentiate pyogenic cerebral abscess from infected brain tumor. The tumor wall of various types of cystic or necrotic brain tumor was significantly hyperintense relative to that of cerebral abscess wall on both diffusion-weighted images and regional cerebral blood volume maps. Sixteen patients who had cerebral masses with large cystic or necrotic cavities were imaged to generate diffusion-weighted images and regional cerebral blood volume maps using single-shot echoplanar imaging (EPI) pulse sequences. Apart from qualitative analysis, apparent diffusion coefficients (ADC) as well as regional cerebral blood volume (rCBV) ratios were calculated from the abscess wall and peripheral tumor wall and comparison was made by using Student's t-test. The tumor wall of various types of cystic or necrotic brain tumor had significantly lower ADCs relative to those of the abscess wall (P<0.005) and thus appeared relatively hyperintense on diffusion-weighted images. The mean rCBV ratio relative to normal white matter (2.90+/-0.62) of the peripheral tumor wall of various types of cystic or necrotic brain tumor were significantly larger than the mean rCBV ratio (0.45+/-0.11) of the pyogenic cerebral abscess wall (P<0.001) by Student's t-test. It is concluded that the combined MR diffusion and perfusion imaging might be capable of differentiating an infected brain tumor from a pyogenic cerebral abscess.
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Affiliation(s)
- J H M Chan
- Department of Diagnostic Radiology, Tuen Mun Hospital, Tsing Chung Koon Road, Tuen Mun, NT, Hong Kong.
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Lee WS, Chan TL, Koh MT, Ariffin WA, Lin HP. Acquired immunodeficiency syndrome presenting as childhood non-Hodgkin's lymphoma. Singapore Med J 2001; 42:530-3. [PMID: 11876380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Two children with non-Hodgkin's lymphoma (NHL) as the presenting illness of acquired immunodeficiency syndrome (AIDS) are described. There was a delay in diagnosing the underlying AIDS in both cases. In the first case, an 18-month-old boy with stage IV, high-grade,T-cell NHL, the diagnosis of underlying AIDS was suspected only when he developed recurrent and profound opportunistic infection during chemotherapy. The second case, an eight-month-old female infant presented initially with hepatosplenomegaly and thrombocytopenia of undetermined cause. She had progressive abdominal distension and swelling of her right eye one year later due to high grade B-cell NHL. She was later found to be sero-positive for HIV during pre-chemotherapy screening. As the prevalence of HIV infection continues to increase, HIV infection should be considered in the differential diagnoses of childhood hepatosplenomegaly and thrombocytopenia, and as a possible underlying cause of childhood cancer, especially NHL.
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Affiliation(s)
- W S Lee
- Department of Paediatrics, University of Malaya Medical Centre, Kuala Lumpur Malaysia.
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Chan TL, Martin PR, Clunas N, Grünert U. Bipolar cell diversity in the primate retina: morphologic and immunocytochemical analysis of a new world monkey, the marmoset Callithrix jacchus. J Comp Neurol 2001; 437:219-39. [PMID: 11494253 DOI: 10.1002/cne.1280] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this study was to identify the bipolar cell types in the retina of a New World monkey, the common marmoset, and compare them with those found in the Old World macaque monkey. Retinal whole-mounts, sections, or both, were stained by using DiI labeling and immunohistochemical methods. Semithin sections were analyzed by using quantitative methods. We show that the same morphologic types of bipolar cell as described for the Old World macaque monkey by Boycott and Wässle (Boycott and Wässle [1991] Eur. J. Neurosci. 3:1069-1088) are present in marmoset retina: two types of midget bipolar cells, six type of diffuse bipolar cells, a blue cone bipolar cell, and one type of rod bipolar cell. The pattern of staining with different immunohistochemical markers ("fingerprint") of each bipolar cell type in marmoset was also the same as described for macaque, with one exception: the flat midget bipolar cell (FMB) class is labeled by antibodies to recoverin in macaque but is labeled by antibodies to CD15 in marmoset. The labeled FMB cells in marmoset make contact with multiple cone photoreceptors throughout most of the extrafoveal retina. The spatial density of bipolar cells in marmoset is shown to be sufficient to support one-to-one connectivity of midget bipolar and ganglion cells in the fovea and to allow for parallel pathways to ganglion cells throughout the retina. Quantitative differences in the morphology and receptor connectivity between marmoset and macaque can be related to differences in cone and rod photoreceptor density between the species. We conclude that bipolar cell diversity is a preserved feature of the primate retina.
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Affiliation(s)
- T L Chan
- Department of Physiology F13, Institute for Biomedical Research, The University of Sydney, Sydney 2006, Australia
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Chan TL, Curtis LC, Leung SY, Farrington SM, Ho JW, Chan AS, Lam PW, Tse CW, Dunlop MG, Wyllie AH, Yuen ST. Early-onset colorectal cancer with stable microsatellite DNA and near-diploid chromosomes. Oncogene 2001; 20:4871-6. [PMID: 11521198 DOI: 10.1038/sj.onc.1204653] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2001] [Revised: 02/27/2001] [Accepted: 05/23/2001] [Indexed: 12/25/2022]
Abstract
Colorectal cancer has been described in terms of genetic instability selectively affecting either microsatellite sequences (MIN) or chromosome number and structure (CIN). A subgroup with apparently stable, near-diploid chromosomes and stable microsatellites (MACS) also exists. These distinctions are important, partly because of their value in highlighting different pathways of carcinogenesis, and partly because of their direct relevance to prognosis. Study of early-onset cancer has often proved a fruitful resource for the identification of the nature and function of cancer susceptibility genes. In a study of colorectal cancer with stable microsatellite DNA, we describe 22 early-onset tumours (mean age=33), compared with 16 late-onset tumours (mean age=68). Both groups contained carcinomas with the MACS phenotype, characterized by near diploid DNA content, as defined by flow cytometry, and minimal chromosome arm deletion or amplification (six or less events per genome), determined by comparative genomic hybridization (CGH). Minimal chromosome imbalance correlated strongly with diploid DNA content (P<0.001). The proportion of MACS cancers was significantly greater in early-onset as compared to late-onset tumours (64 vs 13%, P=0.005). Of the chromosome arm imbalances commonly observed in late-onset tumours, only 18q- was observed more than twice amongst the 14 early-onset MACS tumours. Seventy-nine per cent of these MACS tumours were located in the distal colon, and 69% were at advanced clinico-pathological stages (with lymph node or distant metastasis). A positive family history of colorectal or other cancers was elicited in seven patients in the MACS early-onset group, and one additional patient in this group had a metachronous ovarian cancer. The results suggest that MACS cancer may have a genetic basis different from either MIN or CIN, and further studies of these cancers may lead to discovery of new mechanisms of colorectal carcinogenesis and cancer susceptibility.
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Affiliation(s)
- T L Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Chan TL, Yuen ST, Ho JW, Chan AS, Kwan K, Chung LP, Lam PW, Tse CW, Leung SY. A novel germline 1.8-kb deletion of hMLH1 mimicking alternative splicing: a founder mutation in the Chinese population. Oncogene 2001; 20:2976-81. [PMID: 11420710 DOI: 10.1038/sj.onc.1204376] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2000] [Revised: 01/24/2001] [Accepted: 02/12/2001] [Indexed: 12/24/2022]
Abstract
We have previously reported that there is a high incidence of microsatellite instability (MSI) and germline mismatch repair gene mutation in colorectal cancer arising from young Hong Kong Chinese. Most of the germline mutations involve hMSH2, which is different from the mutation spectrum in the Western population. It is well known that alternative splicing is common in hMLH1, which complicates RNA based mutation detection methods. In contrast, large deletions in hMLH1, commonly observed in some ethnic groups, tend to escape detection by exon-by-exon direct DNA sequencing. Here we report the detection of a novel germline 1.8 kb deletion involving exon 11 of hMLH1 in a local hereditary non-polyposis colorectal cancer family. This mutation generates a mRNA transcript with deletion of exons 10-11, which is indistinguishable from one of the most common and predominant hMLH1 splice variants. A diagnostic test based on PCR of the breakpoint region led to the identification of an additional young colorectal cancer patient with this mutation. Haplotype analysis suggests that they may share a common ancestral mutation. Our results caution investigators in the interpretation of alternative splicing and have important implications for the design of hMLH1 mutation detection strategy in the Chinese population.
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Affiliation(s)
- T L Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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