1
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Zhan SH, Alamouti SM, Daneshpajouh H, Kwok BS, Lee MH, Khattra J, Houck HJ, Rand KH. Target capture sequencing of SARS-CoV-2 genomes using the ONETest Coronaviruses Plus. Diagn Microbiol Infect Dis 2021; 101:115508. [PMID: 34391075 PMCID: PMC8299291 DOI: 10.1016/j.diagmicrobio.2021.115508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/06/2021] [Revised: 07/03/2021] [Accepted: 07/17/2021] [Indexed: 12/01/2022]
Abstract
We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence the SARS-CoV-2 genome and select loci of other respiratory viruses. We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a PCR assay. For 48 of the samples, we also applied the ARTIC protocol. Of the 70 ONETest libraries, 45 (64%) had a (near-)complete sequence (>29,000 bases and >90% covered by >9 reads). Of the 48 ARTIC libraries, 25 (52%) had a (near-)complete sequence. In 19 out of 25 (76%) samples in which both the ONETest and ARTIC yielded (near-)complete sequences, the lineages assigned were identical. As a target capture approach, the ONETest is less prone to loss of sequence coverage than amplicon approaches, and thus can provide complete genomic information more often to track and monitor SARS-CoV-2 variants.
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Affiliation(s)
- Shing H Zhan
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada.
| | | | | | - Brian S Kwok
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada
| | - Meng-Hsun Lee
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada
| | | | - Herbert J Houck
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Kenneth H Rand
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
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2
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Lac V, Verhoef L, Aguirre-Hernandez R, Nazeran TM, Tessier-Cloutier B, Praetorius T, Orr NL, Noga H, Lum A, Khattra J, Prentice LM, Co D, Köbel M, Mijatovic V, Lee AF, Pasternak J, Bleeker MC, Krämer B, Brucker SY, Kommoss F, Kommoss S, Horlings HM, Yong PJ, Huntsman DG, Anglesio MS. Iatrogenic endometriosis harbors somatic cancer-driver mutations. Hum Reprod 2019; 34:69-78. [PMID: 30428062 DOI: 10.1093/humrep/dey332] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Does incisional endometriosis (IE) harbor somatic cancer-driver mutations? SUMMARY ANSWER We found that approximately one-quarter of IE cases harbor somatic-cancer mutations, which commonly affect components of the MAPK/RAS or PI3K-Akt-mTor signaling pathways. WHAT IS KNOWN ALREADY Despite the classification of endometriosis as a benign gynecological disease, it shares key features with cancers such as resistance to apoptosis and stimulation of angiogenesis and is well-established as the precursor of clear cell and endometrioid ovarian carcinomas. Our group has recently shown that deep infiltrating endometriosis (DE), a form of endometriosis that rarely undergoes malignant transformation, harbors recurrent somatic mutations. STUDY DESIGN, SIZE, DURATION In a retrospective study comparing iatrogenically induced and endogenously occurring forms of endometriosis unlikely to progress to cancer, we examined endometriosis specimens from 40 women with IE and 36 women with DE. Specimens were collected between 2004 and 2017 from five hospital sites in either Canada, Germany or the Netherlands. IE and DE cohorts were age-matched and all women presented with histologically typical endometriosis without known history of malignancy. PARTICIPANTS/MATERIALS, SETTING, METHODS Archival tissue specimens containing endometriotic lesions were macrodissected and/or laser-capture microdissected to enrich endometriotic stroma and epithelium and a hypersensitive cancer hotspot sequencing panel was used to assess for presence of somatic mutations. Mutations were subsequently validated using droplet digital PCR. PTEN and ARID1A immunohistochemistry (IHC) were performed as surrogates for somatic events resulting in functional loss of respective proteins. MAIN RESULTS AND THE ROLE OF CHANCE Overall, we detected somatic cancer-driver events in 11 of 40 (27.5%) IE cases and 13 of 36 (36.1%) DE cases, including hotspot mutations in KRAS, ERBB2, PIK3CA and CTNNB1. Heterogeneous PTEN loss occurred at similar rates in IE and DE (7/40 vs 5/36, respectively), whereas ARID1A loss only occurred in a single case of DE. While rates of detectable somatic cancer-driver events between IE and DE are not statistically significant (P > 0.05), KRAS activating mutations were more prevalent in DE. LIMITATIONS, REASONS FOR CAUTION Detection of somatic cancer-driver events were limited to hotspots analyzed in our panel-based sequencing assay and loss of protein expression by IHC from archival tissue. Whole genome or exome sequencing, or epigenetic analysis may uncover additional somatic alterations. Moreover, because of the descriptive nature of this study, the functional roles of identified mutations within the context of endometriosis remain unclear and causality cannot be established. WIDER IMPLICATIONS OF THE FINDINGS The alterations we report may be important in driving the growth and survival of endometriosis in ectopic regions of the body. Given the frequency of mutation in surgically displaced endometrium (IE), examination of similar somatic events in eutopic endometrium, as well as clinically annotated cases of other forms of endometriosis, in particular endometriomas that are most commonly linked to malignancy, is warranted. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by a Canadian Cancer Society Impact Grant [701603, PI Huntsman], Canadian Institutes of Health Research Transitional Open Operating Grant [MOP-142273, PI Yong], the Canadian Institutes of Health Research Foundation Grant [FDN-154290, PI Huntsman], the Canadian Institutes of Health Research Project Grant [PJT-156084, PIs Yong and Anglesio], and the Janet D. Cottrelle Foundation through the BC Cancer Foundation [PI Huntsman]. D.G. Huntsman is a co-founder and shareholder of Contextual Genomics Inc., a for profit company that provides clinical reporting to assist in cancer patient treatment. R. Aguirre-Hernandez, J. Khattra and L.M. Prentice have a patent MOLECULAR QUALITY ASSURANCE METHODS FOR USE IN SEQUENCING pending and are current (or former) employees of Contextual Genomics Inc. The remaining authors have no competing interests to declare. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- V Lac
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada
| | - L Verhoef
- Department of Pathology of Antoni van Leeuwenhoek, Netherlands Cancer Institute, Plesmanlaan 121, CX Amsterdam, The Netherlands
| | - R Aguirre-Hernandez
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - T M Nazeran
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada
| | - B Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada
| | - T Praetorius
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - N L Orr
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - H Noga
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - A Lum
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada
| | - J Khattra
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - L M Prentice
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - D Co
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada
| | - M Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada
| | - V Mijatovic
- Academic Endometriosis Center VUmc, Department of Reproductive Medicine, VU University Medical Center, De Boelelaan 1117, HV Amsterdam, The Netherlands
| | - A F Lee
- Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Pasternak
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - M C Bleeker
- Academic Endometriosis Center VUmc, Department of Reproductive Medicine, VU University Medical Center, De Boelelaan 1117, HV Amsterdam, The Netherlands
| | - B Krämer
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - S Y Brucker
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - F Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Roentgenstrasse 2, Friedrichshafen, Germany
| | - S Kommoss
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - H M Horlings
- Department of Pathology of Antoni van Leeuwenhoek, Netherlands Cancer Institute, Plesmanlaan 121, CX Amsterdam, The Netherlands
| | - P J Yong
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - D G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada
| | - M S Anglesio
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada
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3
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Lac V, Nazeran TM, Tessier‐Cloutier B, Aguirre‐Hernandez R, Albert A, Lum A, Khattra J, Praetorius T, Mason M, Chiu D, Köbel M, Yong PJ, Gilks BC, Anglesio MS, Huntsman DG. Oncogenic mutations in histologically normal endometrium: the new normal? J Pathol 2019; 249:173-181. [DOI: 10.1002/path.5314] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Vivian Lac
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
| | - Tayyebeh M Nazeran
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
- Department of Anatomical PathologyVancouver General Hospital Vancouver, BC Canada
| | - Basile Tessier‐Cloutier
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver, BC Canada
| | | | - Arianne Albert
- Women's Health Research Institute, British Columbia Women's Hospital Vancouver, BC Canada
| | - Amy Lum
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
| | | | - Teresa Praetorius
- Department of Women's HealthTuebingen University Hospital Tuebingen Germany
| | - Madeline Mason
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
| | - Derek Chiu
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
| | - Martin Köbel
- Department of Pathology and Laboratory MedicineUniversity of Calgary Calgary Canada
| | - Paul J Yong
- Department of Obstetrics and GynaecologyUniversity of British Columbia Vancouver, BC Canada
- BC Women's Centre for Pelvic Pain and EndometriosisBC Women's Hospital and Health Centre, Women' Health Centre Vancouver, BC Canada
| | - Blake C Gilks
- Department of Anatomical PathologyVancouver General Hospital Vancouver, BC Canada
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver, BC Canada
| | - Michael S Anglesio
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver, BC Canada
- Department of Obstetrics and GynaecologyUniversity of British Columbia Vancouver, BC Canada
| | - David G Huntsman
- Department of Molecular OncologyBC Cancer Research Centre Vancouver, BC Canada
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver, BC Canada
- Contextual Genomics Inc. Vancouver, BC Canada
- Department of Obstetrics and GynaecologyUniversity of British Columbia Vancouver, BC Canada
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4
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Lac V, Praetorius TH, Verhoef L, Aguirre-Hernandez R, Nazeran TM, Tessier-Cloutier B, Orr N, Noga H, Khattra J, Koebel M, Horlings HM, Kommoss F, Brucker SY, Pasternak J, Yong PJ, Huntsman DG, Kommoss S, Anglesio MS, Krämer B. Iatrogenic endometriosis harbors somatic cancer-driver mutations. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- V Lac
- British Columbia Cancer Agency, Department of Molecular Oncology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
| | - TH Praetorius
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
| | - L Verhoef
- Netherlands Cancer Institute, Amsterdam, Niederlande
| | | | - TM Nazeran
- British Columbia Cancer Agency, Department of Molecular Oncology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
| | - B Tessier-Cloutier
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
- Vancouver General Hospital, Department of Anatomical Pathology, Vancouver, Kanada
| | - N Orr
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
| | - H Noga
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
- British Columbia Women's Hospital and Health Centre, BC Women's Centre for Pelvic Pain & Endometriosis, Vancouver, Kanada
| | - J Khattra
- Contextual Genomics, Vancouver, Kanada
| | - M Koebel
- University of Calgary, Department of Pathology and Laboratory Medicine, Calgary, Kanada
| | - HM Horlings
- Netherlands Cancer Institute, Amsterdam, Niederlande
| | - F Kommoss
- Medizin Campus Bodensee, Institut für Pathologie, Friedrichshafen, Deutschland
| | - SY Brucker
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - J Pasternak
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - PJ Yong
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
- British Columbia Women's Hospital and Health Centre, BC Women's Centre for Pelvic Pain & Endometriosis, Vancouver, Kanada
| | - DG Huntsman
- British Columbia Cancer Agency, Department of Molecular Oncology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
- Contextual Genomics, Vancouver, Kanada
| | - S Kommoss
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - MS Anglesio
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
| | - B Krämer
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
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5
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Praetorius TH, Lac V, Aguirre-Hernandez R, Mason MC, Tessier-Cloutier B, Nazeran TM, Khattra J, Koebel M, Grube M, Goth M, Staebler A, Pasternak J, Andress J, Brucker SY, Yong PJ, Krämer B, Anglesio MS, Kommoss S. Hypersensitive Cancer hotspot sequencing panel in patients with two or more subtypes of endometriosis. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- TH Praetorius
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
| | - V Lac
- British Columbia Cancer Agency, Department of Molecular Oncology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
| | | | - MC Mason
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
| | - B Tessier-Cloutier
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
- Vancouver General Hospital, Department of Anatomical Pathology, Vancouver, Kanada
| | - TM Nazeran
- British Columbia Cancer Agency, Department of Molecular Oncology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
| | - J Khattra
- Contextual Genomics, Vancouver, Kanada
| | - M Koebel
- University of Calgary, Department of Pathology and Laboratory Medicine, Calgary, Kanada
| | - M Grube
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - M Goth
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - A Staebler
- Universitätsklinikum Tübingen, Institut für Pathologie und Neuropathologie, Tübingen, Deutschland
| | - J Pasternak
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - J Andress
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - SY Brucker
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - PJ Yong
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
- British Columbia Women's Hospital and Health Centre, BC Women's Centre for Pelvic Pain & Endometriosis, Vancouver, Kanada
| | - B Krämer
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
| | - MS Anglesio
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, Kanada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Kanada
| | - S Kommoss
- Universitätsklinikum Tübingen, Department für Frauengesundheit, Tübingen, Deutschland
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6
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McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genet 2016. [PMID: 27182968 DOI: 10.1038/ng.3573.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multiple intraperitoneal sites. Through whole-genome and single-nucleus sequencing, we identified evolutionary features including mutation loss, convergence of the structural genome and temporal activation of mutational processes that patterned clonal progression. We then determined the precise clonal mixtures comprising each tumor sample. The majority of sites were clonally pure or composed of clones from a single phylogenetic clade. However, each patient contained at least one site composed of polyphyletic clones. Five patients exhibited monoclonal and unidirectional seeding from the ovary to intraperitoneal sites, and two patients demonstrated polyclonal spread and reseeding. Our findings indicate that at least two distinct modes of intraperitoneal spread operate in clonal dissemination and highlight the distribution of migratory potential over clonal populations comprising high-grade serous ovarian cancers.
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Affiliation(s)
- Andrew McPherson
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.,Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emma Laks
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Gavin Ha
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Adrian Wan
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Leah M Prentice
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jaswinder Khattra
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Maia A Smith
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cydney B Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah C Mullaly
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steve Kalloger
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Anthony Karnezis
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Karey Shumansky
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Celia Siu
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hector Li Chan
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Julie Ho
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Nataliya Melnyk
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Janine Senz
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Winnie Yang
- Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Alexandre Bouchard-Côté
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Blake Gilks
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
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7
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Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJL, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval J, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall AJ, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature 2015; 518:422-6. [PMID: 25470049 PMCID: PMC4864027 DOI: 10.1038/nature13952] [Citation(s) in RCA: 449] [Impact Index Per Article: 49.9] [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] [Received: 08/22/2013] [Accepted: 10/08/2014] [Indexed: 11/08/2022]
Abstract
Human cancers, including breast cancers, comprise clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution, underpinning important emergent features such as drug resistance and metastasis. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours. However, the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours have not been systematically examined at single-cell resolution. Here we show, using deep-genome and single-cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single-cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies using patient-derived breast cancer xenoengraftment.
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Affiliation(s)
- Peter Eirew
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Adi Steif
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jaswinder Khattra
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Gavin Ha
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Hossein Farahani
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer Agency, 600 W10th Avenue, Vancouver, BC, V5Z 4E6, Canada
| | - Stephen Chia
- Department of Medical Oncology, BC Cancer Agency, 600 W10th Avenue, Vancouver, BC, V5Z 4E6, Canada
| | - Colin Mar
- Department of Medical Oncology, BC Cancer Agency, 600 W10th Avenue, Vancouver, BC, V5Z 4E6, Canada
| | - Adrian Wan
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Emma Laks
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Karey Shumansky
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Andrew McPherson
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Cydney Nielsen
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Andrew J. L. Roth
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Calvin Lefebvre
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Camila de Souza
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Celia Siu
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Radhouane Aniba
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Arusha Oloumi
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Tomo Osako
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Alejandra Bruna
- Department of Oncology, University of Cambridge, Hills Road, Cambridge, CB2 2XZ, UK
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Jose Sandoval
- Department of Oncology, University of Cambridge, Hills Road, Cambridge, CB2 2XZ, UK
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Teresa Algara
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Wendy Greenwood
- Department of Oncology, University of Cambridge, Hills Road, Cambridge, CB2 2XZ, UK
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Kaston Leung
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Hongwei Cheng
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Dong Lin
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Andrew J. Mungall
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Yongjun Zhao
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Julie Lorette
- Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada
| | - Long Nguyen
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - David Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada
| | - Connie J. Eaves
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Carl Hansen
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Marco A. Marra
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Carlos Caldas
- Department of Oncology, University of Cambridge, Hills Road, Cambridge, CB2 2XZ, UK
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Sohrab P. Shah
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 1L3, Canada
- Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada
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8
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Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res 2014; 24:1881-93. [PMID: 25060187 PMCID: PMC4216928 DOI: 10.1101/gr.180281.114] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [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] [Indexed: 12/12/2022]
Abstract
The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN.
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Affiliation(s)
- Gavin Ha
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada;
| | - Andrew Roth
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - Jaswinder Khattra
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Julie Ho
- Centre for Translational and Applied Genomics, Vancouver, BC V5Z 4E6, Canada
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Leah M Prentice
- Centre for Translational and Applied Genomics, Vancouver, BC V5Z 4E6, Canada
| | - Nataliya Melnyk
- Centre for Translational and Applied Genomics, Vancouver, BC V5Z 4E6, Canada
| | - Andrew McPherson
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Emma Laks
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Justina Biele
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alan Le
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Karey Shumansky
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - C Blake Gilks
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
| | - David G Huntsman
- Centre for Translational and Applied Genomics, Vancouver, BC V5Z 4E6, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada;
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9
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Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Côté A, Shah SP. PyClone: statistical inference of clonal population structure in cancer. Nat Methods 2014; 11:396-8. [PMID: 24633410 PMCID: PMC4864026 DOI: 10.1038/nmeth.2883] [Citation(s) in RCA: 645] [Impact Index Per Article: 64.5] [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] [Received: 11/18/2013] [Accepted: 01/31/2014] [Indexed: 12/25/2022]
Abstract
We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates PyClone's accuracy.
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Affiliation(s)
- Andrew Roth
- Bioinformatics Graduate Program, University Of British Columbia, Vancouver, Canada
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Jaswinder Khattra
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Damian Yap
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Adrian Wan
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Emma Laks
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Justina Biele
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Gavin Ha
- Bioinformatics Graduate Program, University Of British Columbia, Vancouver, Canada
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Samuel Aparicio
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | | | - Sohrab P. Shah
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
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10
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Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM, Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet 2009; 5:e1000537. [PMID: 19557190 PMCID: PMC2694363 DOI: 10.1371/journal.pgen.1000537] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/26/2009] [Indexed: 01/15/2023] Open
Abstract
A crucial step in the development of muscle cells in all metazoan animals is the assembly and anchorage of the sarcomere, the essential repeat unit responsible for muscle contraction. In Caenorhabditis elegans, many of the critical proteins involved in this process have been uncovered through mutational screens focusing on uncoordinated movement and embryonic arrest phenotypes. We propose that additional sarcomeric proteins exist for which there is a less severe, or entirely different, mutant phenotype produced in their absence. We have used Serial Analysis of Gene Expression (SAGE) to generate a comprehensive profile of late embryonic muscle gene expression. We generated two replicate long SAGE libraries for sorted embryonic muscle cells, identifying 7,974 protein-coding genes. A refined list of 3,577 genes expressed in muscle cells was compiled from the overlap between our SAGE data and available microarray data. Using the genes in our refined list, we have performed two separate RNA interference (RNAi) screens to identify novel genes that play a role in sarcomere assembly and/or maintenance in either embryonic or adult muscle. To identify muscle defects in embryos, we screened specifically for the Pat embryonic arrest phenotype. To visualize muscle defects in adult animals, we fed dsRNA to worms producing a GFP-tagged myosin protein, thus allowing us to analyze their myofilament organization under gene knockdown conditions using fluorescence microscopy. By eliminating or severely reducing the expression of 3,300 genes using RNAi, we identified 122 genes necessary for proper myofilament organization, 108 of which are genes without a previously characterized role in muscle. Many of the genes affecting sarcomere integrity have human homologs for which little or nothing is known. Muscular diseases affect many people worldwide. While we have learned much about the sarcomere, the basic building block of muscle cells, there are still numerous questions that remain to be answered. We must learn more about proteins expressed in muscle and how they interact so that better treatments for myopathies can be developed. The nematode Caenorhabditis elegans is a valuable model organism for the study of muscle due to similarities between worm body wall muscle and vertebrate muscle, along with its semi-transparent cuticle that allows for visualization of muscle structures in live animals. We have used transcriptional profiling methods to identify the majority of genes that are expressed in the embryonic body wall muscle cells of C. elegans. To gain insight into possible functions performed by these genes and their corresponding proteins, we examined animals and muscle cells for abnormalities after the targeted inactivation of about 3,300 genes. We identified 122 genes necessary for proper myofilament organization, 108 of which had no previously characterized role in muscle. This approach proved to be a rapid and sensitive means to identify genes that affect muscle differentiation and sarcomere assembly.
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Affiliation(s)
- Barbara Meissner
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adam Warner
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kim Wong
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Nicholas Dube
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adam Lorch
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sheldon J. McKay
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jaswinder Khattra
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Teresa Rogalski
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aruna Somasiri
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Iasha Chaudhry
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca M. Fox
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David L. Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Robert A. Holt
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J. M. Jones
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Donald G. Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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11
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Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand KC, Leung G, Zayed A, Mehl E, Kalloger SE, Sun M, Giuliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao Y, Zeng T, Glover JNM, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Bowtell DDL, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra M, Huntsman DG. Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med 2009; 360:2719-29. [PMID: 19516027 DOI: 10.1056/nejmoa0902542] [Citation(s) in RCA: 515] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Granulosa-cell tumors (GCTs) are the most common type of malignant ovarian sex cord-stromal tumor (SCST). The pathogenesis of these tumors is unknown. Moreover, their histopathological diagnosis can be challenging, and there is no curative treatment beyond surgery. METHODS We analyzed four adult-type GCTs using whole-transcriptome paired-end RNA sequencing. We identified putative GCT-specific mutations that were present in at least three of these samples but were absent from the transcriptomes of 11 epithelial ovarian tumors, published human genomes, and databases of single-nucleotide polymorphisms. We confirmed these variants by direct sequencing of complementary DNA and genomic DNA. We then analyzed additional tumors and matched normal genomic DNA, using a combination of direct sequencing, analyses of restriction-fragment-length polymorphisms, and TaqMan assays. RESULTS All four index GCTs had a missense point mutation, 402C-->G (C134W), in FOXL2, a gene encoding a transcription factor known to be critical for granulosa-cell development. The FOXL2 mutation was present in 86 of 89 additional adult-type GCTs (97%), in 3 of 14 thecomas (21%), and in 1 of 10 juvenile-type GCTs (10%). The mutation was absent in 49 SCSTs of other types and in 329 unrelated ovarian or breast tumors. CONCLUSIONS Whole-transcriptome sequencing of four GCTs identified a single, recurrent somatic mutation (402C-->G) in FOXL2 that was present in almost all morphologically identified adult-type GCTs. Mutant FOXL2 is a potential driver in the pathogenesis of adult-type GCTs.
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Affiliation(s)
- Sohrab P Shah
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada
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12
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Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu AL, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol 2008; 8:R113. [PMID: 17570852 PMCID: PMC2394759 DOI: 10.1186/gb-2007-8-6-r113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 04/23/2007] [Accepted: 06/14/2007] [Indexed: 12/20/2022] Open
Abstract
To facilitate discovery of novel human embryonic stem cell (ESC) transcripts, we generated 2.5 million LongSAGE tags from 9 human ESC lines. Analysis of this data revealed that ESCs express proportionately more RNA binding proteins compared with terminally differentiated cells, and identified novel ESC transcripts, at least one of which may represent a marker of the pluripotent state.
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Affiliation(s)
- Martin Hirst
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Allen Delaney
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Sean A Rogers
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Angelique Schnerch
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Deryck R Persaud
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Michael D O'Connor
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Thomas Zeng
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Michelle Moksa
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Keith Fichter
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Diana Mah
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Anne Go
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Ryan D Morin
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Agnes Baross
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Yongjun Zhao
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Jaswinder Khattra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Anna-Liisa Prabhu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Pawan Pandoh
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Helen McDonald
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Jennifer Asano
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Noreen Dhalla
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Kevin Ma
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Stephanie Lee
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Adrian Ally
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Neil Chahal
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Stephanie Menzies
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Asim Siddiqui
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Robert Holt
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Steven Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Daniela S Gerhard
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James A Thomson
- Wisconsin National Primate Research Centre and Department of Anatomy, School of Medicine, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
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13
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Zhao Y, Raouf A, Kent D, Khattra J, Delaney A, Schnerch A, Asano J, McDonald H, Chan C, Jones S, Marra MA, Eaves CJ. A Modified Polymerase Chain Reaction-Long Serial Analysis of Gene Expression Protocol Identifies Novel Transcripts in Human CD34+Bone Marrow Cells. Stem Cells 2007; 25:1681-9. [PMID: 17412892 DOI: 10.1634/stemcells.2006-0794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 01/26/2023]
Abstract
Transcriptome profiling offers a powerful approach to investigating developmental processes. Long serial analysis of gene expression (LongSAGE) is particularly attractive for this purpose because of its inherent quantitative features and independence of both hybridization variables and prior knowledge of transcript identity. Here, we describe the validation and initial application of a modified protocol for amplifying cDNA preparations from <10 ng of RNA (<10(3) cells) to allow representative LongSAGE libraries to be constructed from rare stem cell-enriched populations. Quantitative real-time polymerase chain reaction (Q-RT-PCR) analyses and comparison of tag frequencies in replicate LongSAGE libraries produced from amplified and nonamplified cDNA preparations demonstrated preservation of the relative levels of different transcripts originally present at widely varying levels. This PCR-LongSAGE protocol was then used to obtain a 200,000-tag library from the CD34+ subset of normal adult human bone marrow cells. Analysis of this library revealed many anticipated transcripts, as well as transcripts not previously known to be present in CD34+ hematopoietic cells. The latter included numerous novel tags that mapped to unique and conserved sites in the human genome but not previously identified as transcribed elements in human cells. Q-RT-PCR was used to demonstrate that 10 of these novel tags were expressed in cDNA pools and present in extracts of other sources of normal human CD34+ hematopoietic cells. These findings illustrate the power of LongSAGE to identify new transcripts in stem cell-enriched populations and indicate the potential of this approach to be extended to other sources of rare cells. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Yun Zhao
- Terry Fox Laboratory, Vancouver, BC, Canada V5Z 1L3
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14
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Chen N, Mah A, Blacque OE, Chu J, Phgora K, Bakhoum MW, Hunt Newbury CR, Khattra J, Chan S, Go A, Efimenko E, Johnsen R, Phirke P, Swoboda P, Marra M, Moerman DG, Leroux MR, Baillie DL, Stein LD. Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol 2007; 7:R126. [PMID: 17187676 PMCID: PMC1794439 DOI: 10.1186/gb-2006-7-12-r126] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [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: 08/08/2006] [Revised: 10/20/2006] [Accepted: 12/22/2006] [Indexed: 01/05/2023] Open
Abstract
Comparative genomic analysis of three nematode species identifies 93 genes that encode putative components of the ciliated neurons in C. elegans and are subject to the same regulatory control. Background The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes. Results By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of different tissue types and of daf-19(+) and daf-19(-) animals. Finally, we demonstrate that the dye-filling defect of dyf-5(mn400) animals, which is indicative of compromised exposure of cilia to the environment, is caused by a nonsense mutation in the serine/threonine protein kinase gene M04C9.5. Conclusion Our comparative genomics-based predictions may be useful for identifying genes involved in human ciliopathies, including Bardet-Biedl Syndrome (BBS), since the C. elegans orthologs of known human BBS genes contain X-box motifs and are required for normal dye filling in C. elegans ciliated neurons.
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Affiliation(s)
- Nansheng Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Allan Mah
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Oliver E Blacque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
- School of Biomolecular and Biomedical Sciences, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jeffrey Chu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Kiran Phgora
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Mathieu W Bakhoum
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - C Rebecca Hunt Newbury
- Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jaswinder Khattra
- Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Susanna Chan
- Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Anne Go
- Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Evgeni Efimenko
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Robert Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Prasad Phirke
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Marco Marra
- British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia, Canada V5Z 4S6
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Lincoln D Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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15
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Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res 2006; 17:108-16. [PMID: 17135571 PMCID: PMC1716260 DOI: 10.1101/gr.5488207] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 01/06/2023]
Abstract
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million SAGE tags primarily from sub-microgram amounts of total RNA purified from samples acquired by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures to automatically assess DNA sequencing results were implemented to analyze the integrity of ditag structure, linker or cross-species ditag contamination, and yield of high-quality tags per sequence read. Our analysis of singleton tag errors resulted in a method for correcting such errors to statistically determine tag accuracy. From the libraries generated, we produced an essentially complete mapping of reliable 21-base-pair tags to the mouse reference genome sequence for a meta-library of approximately 5 million tags. Our analyses led us to reject the commonly held notion that duplicate ditags are artifacts. Rather than the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling.
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Affiliation(s)
- Jaswinder Khattra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Allen D. Delaney
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Asim Siddiqui
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Jennifer Asano
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Helen McDonald
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Noreen Dhalla
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Anna-liisa Prabhu
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kevin Ma
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Stephanie Lee
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Adrian Ally
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Angela Tam
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Danne Sa
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Sean Rogers
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - David Charest
- Genome British Columbia, Vancouver, British Columbia V5Z 1C6, Canada
| | - Jeff Stott
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Scott Zuyderduyn
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Richard Varhol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Connie Eaves
- Terry Fox Laboratory, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Steven Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Robert Holt
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin Hirst
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
- Corresponding author.E-mail ; fax (604) 877-6085
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16
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McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 2006; 302:627-45. [PMID: 17113066 DOI: 10.1016/j.ydbio.2006.10.024] [Citation(s) in RCA: 135] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/08/2006] [Accepted: 10/14/2006] [Indexed: 12/18/2022]
Abstract
A SAGE library was prepared from hand-dissected intestines from adult Caenorhabditis elegans, allowing the identification of >4000 intestinally-expressed genes; this gene inventory provides fundamental information for understanding intestine function, structure and development. Intestinally-expressed genes fall into two broad classes: widely-expressed "housekeeping" genes and genes that are either intestine-specific or significantly intestine-enriched. Within this latter class of genes, we identified a subset of highly-expressed highly-validated genes that are expressed either exclusively or primarily in the intestine. Over half of the encoded proteins are candidates for secretion into the intestinal lumen to hydrolyze the bacterial food (e.g. lysozymes, amoebapores, lipases and especially proteases). The promoters of this subset of intestine-specific/intestine-enriched genes were analyzed computationally, using both a word-counting method (RSAT oligo-analysis) and a method based on Gibbs sampling (MotifSampler). Both methods returned the same over-represented site, namely an extended GATA-related sequence of the general form AHTGATAARR, which agrees with experimentally determined cis-acting control sequences found in intestine genes over the past 20 years. All promoters in the subset contain such a site, compared to <5% for control promoters; moreover, our analysis suggests that the majority (perhaps all) of genes expressed exclusively or primarily in the worm intestine are likely to contain such a site in their promoters. There are three zinc-finger GATA-type factors that are candidates to bind this extended GATA site in the differentiating C. elegans intestine: ELT-2, ELT-4 and ELT-7. All evidence points to ELT-2 being the most important of the three. We show that worms in which both the elt-4 and the elt-7 genes have been deleted from the genome are essentially wildtype, demonstrating that ELT-2 provides all essential GATA-factor functions in the intestine. The SAGE analysis also identifies more than a hundred other transcription factors in the adult intestine but few show an RNAi-induced loss-of-function phenotype and none (other than ELT-2) show a phenotype primarily in the intestine. We thus propose a simple model in which the ELT-2 GATA factor directly participates in the transcription of all intestine-specific/intestine-enriched genes, from the early embryo through to the dying adult. Other intestinal transcription factors would thus modulate the action of ELT-2, depending on the worm's nutritional and physiological needs.
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Affiliation(s)
- James D McGhee
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1.
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17
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Uh M, Khattra J, Devlin RH. Transgene constructs in coho salmon (Oncorhynchus kisutch) are repeated in a head-to-tail fashion and can be integrated adjacent to horizontally-transmitted parasite DNA. Transgenic Res 2006; 15:711-27. [PMID: 16952013 DOI: 10.1007/s11248-006-9016-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [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: 05/14/2006] [Accepted: 05/19/2006] [Indexed: 11/24/2022]
Abstract
Currently, little information is available regarding the molecular organization of integrated transgenes in genetically-engineered fish. We performed a detailed structural analysis of an inserted transgene in one strain (M77) of transgenic coho salmon (Oncorhynchus kisutch) containing a salmon growth hormone gene construct (OnMTGH1). Microinjected DNA was found to have inserted into a single site in the coho salmon genome, and was organized with four complete internal copies and two partial terminal copies of the OnMTGH1 construct. All construct copies were organized in a direct-tandem (head-to-tail) repeat fashion in strain M77 and five additional strains (one also possessed a second recombinant junction fragment). For strain M77, the junctions between the transgene insert and the insertion point within the wild-type genome were cloned from strain-specific cosmid libraries and sequenced, revealing that the transgene insertion was accompanied by a deletion of 587 bp of wild-type DNA as well as a small insertion (19 bp) of unknown DNA upstream and a 14 bp direct- tandem duplication of sequence downstream. Upstream and downstream wild-type DNA sequence contained several repetitive sequence elements based on Southern blot analysis and homology to repetitive sequences in GenBank. In the downstream flank, a pseudogene sequence was also identified which has high homology to the CA membrane protein gene from Schistosoma japonicum, a parasite closely related to Sanguinicola sp. parasites which infect salmonids. Whether the presence of an inserted transgene and the presence of potentially horizontally-transmitted DNA are indicative of a genomic region with a predisposition for insertion of foreign DNA requires further study. The information derived from this transgene structure provides information useful for comparison to other transgenic organisms and for determination of the mechanism of transgene integration in lower vertebrates.
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Affiliation(s)
- Mitchell Uh
- Centre for Aquaculture and Environmental Research, Fisheries and Oceans Canada, West Vancouver, BC, Canada
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18
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Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BYL, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A 2005; 102:18485-90. [PMID: 16352711 PMCID: PMC1311911 DOI: 10.1073/pnas.0509455102] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [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: 11/18/2022] Open
Abstract
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.
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Affiliation(s)
- Asim S Siddiqui
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6
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19
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Blacque OE, Perens EA, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJM, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional genomics of the cilium, a sensory organelle. Curr Biol 2005; 15:935-41. [PMID: 15916950 DOI: 10.1016/j.cub.2005.04.059] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Revised: 04/13/2005] [Accepted: 04/18/2005] [Indexed: 11/30/2022]
Abstract
Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development. The biogenesis and maintenance of cilia depend on intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Biedl syndrome (BBS). To uncover new ciliary components, including IFT proteins, we compared C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the ciliogenic transcription factor, DAF-19. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and bbs genes. Furthermore, we demonstrate that the ciliary structural defect of C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function.
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Affiliation(s)
- Oliver E Blacque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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20
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Warren R, Hsiao WWL, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJM, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol 2004; 186:7783-95. [PMID: 15516593 PMCID: PMC524921 DOI: 10.1128/jb.186.22.7783-7795.2004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [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: 11/20/2022] Open
Abstract
Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.
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Baross A, Butterfield YSN, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA. Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res 2004; 14:2083-92. [PMID: 15489330 PMCID: PMC528924 DOI: 10.1101/gr.2473704] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [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: 11/24/2022]
Abstract
The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical research, including human. To date over 15,200 human cDNA clones containing full-length open reading frames (ORFs) have been identified via systematic expressed sequence tag (EST) analysis of a diverse set of cDNA libraries; however, further systematic EST analysis is no longer an efficient method for identifying new cDNAs. As part of our involvement in the MGC program, we have developed a scalable method for targeted recovery of cDNA clones to facilitate recovery of genes absent from the MGC collection. First, cDNA is synthesized from various RNAs, followed by polymerase chain reaction (PCR) amplification of transcripts in 96-well plates using gene-specific primer pairs flanking the ORFs. Amplicons are cloned into a sequencing vector, and full-length sequences are obtained. Sequences are processed and assembled using Phred and Phrap, and analyzed using Consed and a number of bioinformatics methods we have developed. Sequences are compared with the Reference Sequence (RefSeq) database, and validation of sequence discrepancies is attempted using other sequence databases including dbEST and dbSNP. Clones with identical sequence to RefSeq or containing only validated changes will become part of the MGC human gene collection. Clones containing novel splice variants or polymorphisms have also been identified. Our approach to clone recovery, applied at large scale, has the potential to recover many and possibly most of the genes absent from the MGC collection.
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Affiliation(s)
- Agnes Baross
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 4E6, Canada
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McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, Wong K, Zhao Z, Moerman DG. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol 2004; 68:159-69. [PMID: 15338614 DOI: 10.1101/sqb.2003.68.159] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- S J McKay
- Genome Sciences Centre, BC Cancer Agency, Vancouver, B.C., Canada, V6T 1Z4
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Khattra J, Chan S, Asano J, Pandoh P, Coughlin S, McDonald H, Girn N, Jones S, Marra M. P-127 Transcriptome profiling technologies at the British Columbia Cancer Agency. Lung Cancer 2003. [DOI: 10.1016/s0169-5002(03)92096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Marra MA, Jones SJM, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YSN, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The Genome sequence of the SARS-associated coronavirus. Science 2003; 300:1399-404. [PMID: 12730501 DOI: 10.1126/science.1085953] [Citation(s) in RCA: 1536] [Impact Index Per Article: 73.1] [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: 12/16/2022]
Abstract
We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.
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Affiliation(s)
- Marco A Marra
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada.
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25
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Kent ML, Andree KB, Bartholomew JL, El-Matbouli M, Desser SS, Devlin RH, Feist SW, Hedrick RP, Hoffmann RW, Khattra J, Hallett SL, Lester RJ, Longshaw M, Palenzeula O, Siddall ME, Xiao C. Recent advances in our knowledge of the Myxozoa. J Eukaryot Microbiol 2001; 48:395-413. [PMID: 11456316 DOI: 10.1111/j.1550-7408.2001.tb00173.x] [Citation(s) in RCA: 352] [Impact Index Per Article: 15.3] [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: 11/26/2022]
Abstract
In the last few years two factors have helped to significantly advance our understanding of the Myxozoa. First, the phenomenal increase in fin fish aquaculture in the 1990s has lead to the increased importance of these parasites; in turn this has lead to intensified research efforts, which have increased knowledge of the development, diagnosis. and pathogenesis of myxozoans. The hallmark discovery in the 1980s that the life cycle of Myxobolus cerebralis requires development of an actinosporean stage in the oligochaete. Tubifex tubifex, led to the elucidation of the life cycles of several other myxozoans. Also, the life cycle and taxonomy of the enigmatic PKX myxozoan has been resolved: it is the alternate stage of the unusual myxozoan, Tetracapsula bryosalmonae, from bryozoans. The 18S rDNA gene of many species has been sequenced, and here we add 22 new sequences to the data set. Phylogenetic analyses using all these sequences indicate that: 1) the Myxozoa are closely related to Cnidaria (also supported by morphological data); 2) marine taxa at the genus level branch separately from genera that usually infect freshwater fishes; 3) taxa cluster more by development and tissue location than by spore morphology; 4) the tetracapsulids branched off early in myxozoan evolution, perhaps reflected by their having bryozoan, rather than annelid hosts; 5) the morphology of actinosporeans offers little information for determining their myxosporean counterparts (assuming that they exist); and 6) the marine actinosporeans from Australia appear to form a clade within the platysporinid myxosporeans. Ribosomal DNA sequences have also enabled development of diagnostic tests for myxozoans. PCR and in situ hybridisation tests based on rDNA sequences have been developed for Myxobolus cerebralis, Ceratomyxa shasta, Kudoa spp., and Tetracapsula bryosalmonae (PKX). Lectin-based and antibody tests have also been developed for certain myxozoans, such as PKX and C. shasta. We also review important diseases caused by myxozoans, which are emerging or re-emerging. Epizootics of whirling disease in wild rainbow trout (Oncorhynchus mykiss) have recently been reported throughout the Rocky Mountain states of the USA. With a dramatic increase in aquaculture of fishes using marine netpens, several marine myxozoans have been recognized or elevated in status as pathological agents. Kudoa thyrsites infections have caused severe post-harvest myoliquefaction in pen-reared Atlantic salmon (Salmo salar), and Ceratomyxa spp., Sphaerospora spp., and Myxidium leei cause disease in pen-reared sea bass (Dicentrarchus labrax) and sea bream species (family Sparidae) in Mediterranean countries.
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Affiliation(s)
- M L Kent
- Department of Microbiology and Center for Salmon Disease Research, Oregon State University, Corvallis 97331-3804, USA.
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Kent ML, Khattra J, Hedrick RP, Devlin RH. Tetracapsula renicola n. sp. (Myxozoa : Saccosporidae); the PKX myxozoan--the cause of proliferative kidney disease of salmonid fishes. J Parasitol 2000; 86:103-11. [PMID: 10701572 DOI: 10.1645/0022-3395(2000)086[0103:trnsms]2.0.co;2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [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: 11/10/2022] Open
Abstract
Proliferative kidney disease (PKD) of salmonid fishes is caused by the extrasporogonic stage of an enigmatic myxozoan, referred to as PKX. Sporogenesis occurs in the renal tubules, resulting in monosporous pseudoplasmodia. The spores are ovoid with indistinguishable valves and measure 12 microm in length and 7 microm in width. Two spherical polar capsules (2 microm diameter) with 4 coils occur at the anterior end of the spore. Prominent capsulogenic cell nuclei posterior to the polar capsules are evident in histological sections stained with hematoxylin and eosin. Regardless of the true nature of the valves (indistinguishable or absent), this myxozoan is morphologically distinct from all other described members of the phylum Myxozoa. Comparisons of small subunit rDNA sequences of PKX with other myxozoans demonstrated that it branches from all other members of the myxosporeans from fish examined thus far, including representatives of the phenotypically most closely related genera, Sphaerospora and Parvicapsula. Recent reports, based on rDNA comparisons, indicate that the alternate stage of PKX occurs in bryozoans, and that PKX clusters in a clade with Tetracapsula bryozoides. Our analyses and those of others, along with phenotypic observations, indicate that salmonids are the primary myxosporean hosts for PKX, that the cryptic spores of PKX in salmonids are the fully formed myxospores as they occur in the fish host, and that PKX represents distinct species that we previously place in the genus Tetracapsula in the family Saccosporidae. The latter 2 taxa were described based on stages from bryozoans, and the myxosporean stage in fish of the type species, T. bryozoides, has not been identified (if it exists). Thus, more complete resolution of the life cycle of both PKX and T. bryozoides, as well as more genetic data, are required to determine the precise relationship of these organisms.
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Affiliation(s)
- M L Kent
- Center for Salmon Disease Research, Department of Microbiology, Corvallis, Oregon 97331-3804, USA
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Kent ML, Khattra J, Hedrick RP, Devlin RH. Tetracapsula renicola n. sp. (Myxozoa:Saccosporidae); The PKX Myxozoan: The Cause of Proliferative Kidney Disease of Salmonid Fishes. J Parasitol 2000. [DOI: 10.2307/3284917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kent ML, Docker M, Khattra J, Vossbrinck CR, Speare DJ, Devlin RH. A New Microsporidium sp. (Microsporidia) from the Musculature of the Mountain Whitefish Prosopium williamsoni from British Columbia: Morphology and Phylogeny. J Parasitol 1999. [DOI: 10.2307/3285676] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kent ML, Docker M, Khattra J, Vossbrinck CR, Speare DJ, Devlin RH. A new Microsporidium sp. (microsporidia) from the musculature of the mountain whitefish Prosopium williamsoni from British Columbia: morphology and phylogeny. J Parasitol 1999; 85:1114-9. [PMID: 10647045] [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: 02/15/2023] Open
Abstract
Few microsporidia have been reported from whitefish species (subfamily Coregoninae). For the most part, these microsporidia have been incompletely described. In a survey of parasites of mountain whitefish Prosopium williamsoni collected from Kootenay Lake, British Columbia, we encountered an unusual microsporidium infecting the endomysium of the skeletal musculature. Spores were uninucleate, ovoid to pyriform, and were 5.6 (5-7) microm x 3.2 (3-4) microm with 13-16 coils in the polar filament. We describe here this organism as a new species based on its site of development and its relationship among fish microsporidia based on small subunit ribosomal DNA sequence data, i.e., our analysis showed that it is not closely related to other microsporidia for which ribosomal DNA sequence is available thus far.
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Affiliation(s)
- M L Kent
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia
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Hervio DML, Khattra J, Devlin RH, Kent ML, Sakanari J, Yokoyama H. Taxonomy of Kudoa species (Myxosporea), using a small-subunit ribosomal DNA sequence. CAN J ZOOL 1997. [DOI: 10.1139/z97-846] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myxosporeans in the genus Kudoa infect the flesh of many marine fishes and often cause unsightly lesions and softening of the flesh texture. We are particularly interested in K. thyrsites because it is associated with soft flesh in the Atlantic salmon (Salmo solar), an important commercial species in Canada. Sequences of the small-subunit (SSU) rDNA (about 1600 base pairs) were obtained from K. miniauriculata, K. amanuensis, and K. poniformis. We aligned these sequences with one obtained from coho salmon (Oncorhynchus kisutch) and designed "Kudoa general" primers (KUD1f and KUD2r). These primers, in combination with other general primers, were then used to obtain the SSU rDNA sequence of K. thyrsites from two host species, Atlantic salmon and tubesnout (Aulorhynchus flavidus), from British Columbia, Canada. Sequence comparisons of these isolates indicated that Kudoa species cluster by geographic location rather than by morphology of spores. The three species from the eastern Pacific were approximately 97% identical, whereas K. amamiensis (from Japan) was about 91% identical with these species. Sequence comparisons of K. thyrsites from Atlantic salmon and tubesnout revealed a difference of only 0.07% between these isolates. Comparison of SSU rDNA sequences from the four Kudoa species and Henneguya salminicolo analyzed in this study with those from other available myxosporean genera (Myxidium and Myxoholus) showed that taxonomic divisions at the order and suborder levels were consistent with classical views of the taxonomy of the Myxosporea. Using specific regions of the SSU rDNA, we also developed a sensitive and specific polymerase chain reaction test for detection of K. thyrsites.
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