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McClymont E, Atkinson A, Albert A, Av-Gay G, Andrade J, Barrett J, Bogler T, Boucoiran I, Castillo E, D'Souza R, El-Chaâr D, Fadel S, Fell DB, Korchinski I, Kuret V, Ogilvie G, Poliquin V, Sadarangani M, Scott H, Snelgrove JW, Tunde-Byass M, Money D. Reactogenicity, pregnancy outcomes, and SARS-CoV-2 infection following COVID-19 vaccination during pregnancy in Canada: A national prospective cohort study. Vaccine 2023; 41:7183-7191. [PMID: 37865598 DOI: 10.1016/j.vaccine.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
OBJECTIVE To describe self-reported reactogenicity, pregnancy outcomes, and SARS-CoV-2 infection following COVID-19 vaccination during pregnancy. DESIGN National, prospective cohort study. SETTING Participants across Canada were enrolled from July 2021 until June 2022. POPULATION Individuals pregnant during the COVID-19 pandemic, regardless of vaccination status, were included. METHODS The Canadian COVID-19 Vaccine Registry for Pregnant and Lactating Individuals (COVERED) was advertised through traditional and social media. Surveys were administered at baseline, following each vaccine dose if vaccinated, pregnancy conclusion, and every two months for 14 months. Changes to pregnancy or vaccination status, SARS-CoV-2 infections, or significant health events were recorded. MAIN OUTCOME MEASURES Reactogenicity (local and systemic adverse events, and serious adverse events) within 1 week post-vaccination, pregnancy and neonatal outcomes, and subsequent SARS-CoV-2 infection. RESULTS Among 2868 participants who received 1-2 doses of a COVID-19 vaccine during pregnancy, adverse events described included: headache (19.5-33.9%), nausea (4.8-13.8%), fever (2.7-10.2%), and myalgia (33.4-42.2%). Reactogenicity was highest after the 2nd dose of vaccine in pregnancy. Compared to 1660 unvaccinated participants, there were no statistically significant differences in adverse pregnancy or infant outcomes, aside from an increased risk of NICU admission ≥ 24 h among the unvaccinated group. During follow-up, there was a higher rate of participant-reported SARS-CoV-2 infection in the unvaccinated compared to the vaccinated group (18[47.4%] vs. 786[27.3%]). CONCLUSIONS Participant-reported reactogenicity was similar to reports from non-pregnant adults. There was no increase in adverse pregnancy and birth outcomes among vaccinated vs. unvaccinated participants and lower rates of SARS-CoV-2 infection were reported in vaccinated participants. TWEETABLE ABSTRACT No significant increase in adverse pregnancy or infant outcomes among vaccinated versus unvaccinated pregnant women in Canada.
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Affiliation(s)
- E McClymont
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, Canada
| | - A Atkinson
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, Canada
| | - A Albert
- Women's Health Research Institute, Vancouver, Canada
| | - G Av-Gay
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, Canada
| | - J Andrade
- Women's Health Research Institute, Vancouver, Canada
| | - J Barrett
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
| | - T Bogler
- Department of Family & Community Medicine, University of Toronto, Toronto, Canada
| | - I Boucoiran
- Department of Obstetrics & Gynecology and School of Public Health, Université de Montréal, Montreal, Canada
| | - E Castillo
- Department of Obstetrics & Gynecology, University of Calgary, Calgary, Canada
| | - R D'Souza
- Department of Obstetrics & Gynecology, University of Toronto, Toronto, Canada
| | - D El-Chaâr
- Department of Obstetrics & Gynecology, University of Ottawa, Ottawa, Canada
| | - S Fadel
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - D B Fell
- School of Epidemiology & Public Health, University of Ottawa, Ottawa, Canada
| | - I Korchinski
- Women's Health Research Institute, Vancouver, Canada
| | - V Kuret
- Department of Obstetrics & Gynecology, University of Calgary, Calgary, Canada
| | - G Ogilvie
- School of Population & Public Health, University of British Columbia, Vancouver, Canada
| | - V Poliquin
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - M Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
| | - H Scott
- Department of Obstetrics & Gynecology, Dalhousie University, Halifax, Canada
| | - J W Snelgrove
- Department of Obstetrics & Gynecology, University of Toronto, Toronto, Canada
| | - M Tunde-Byass
- Department of Obstetrics & Gynecology, University of Toronto, Toronto, Canada
| | - D Money
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, Canada; Women's Health Research Institute, Vancouver, Canada.
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De Sanctis B, Money D, Pedersen MW, Durbin R. A theoretical analysis of taxonomic binning accuracy. Mol Ecol Resour 2022; 22:2208-2219. [PMID: 35285150 DOI: 10.1111/1755-0998.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.
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Affiliation(s)
- Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
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3
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Grace MK, Akçakaya HR, Bennett EL, Brooks TM, Heath A, Hedges S, Hilton-Taylor C, Hoffmann M, Hochkirch A, Jenkins R, Keith DA, Long B, Mallon DP, Meijaard E, Milner-Gulland EJ, Rodriguez JP, Stephenson PJ, Stuart SN, Young RP, Acebes P, Alfaro-Shigueto J, Alvarez-Clare S, Andriantsimanarilafy RR, Arbetman M, Azat C, Bacchetta G, Badola R, Barcelos LMD, Barreiros JP, Basak S, Berger DJ, Bhattacharyya S, Bino G, Borges PAV, Boughton RK, Brockmann HJ, Buckley HL, Burfield IJ, Burton J, Camacho-Badani T, Cano-Alonso LS, Carmichael RH, Carrero C, Carroll JP, Catsadorakis G, Chapple DG, Chapron G, Chowdhury GW, Claassens L, Cogoni D, Constantine R, Craig CA, Cunningham AA, Dahal N, Daltry JC, Das GC, Dasgupta N, Davey A, Davies K, Develey P, Elangovan V, Fairclough D, Febbraro MD, Fenu G, Fernandes FM, Fernandez EP, Finucci B, Földesi R, Foley CM, Ford M, Forstner MRJ, García N, Garcia-Sandoval R, Gardner PC, Garibay-Orijel R, Gatan-Balbas M, Gauto I, Ghazi MGU, Godfrey SS, Gollock M, González BA, Grant TD, Gray T, Gregory AJ, van Grunsven RHA, Gryzenhout M, Guernsey NC, Gupta G, Hagen C, Hagen CA, Hall MB, Hallerman E, Hare K, Hart T, Hartdegen R, Harvey-Brown Y, Hatfield R, Hawke T, Hermes C, Hitchmough R, Hoffmann PM, Howarth C, Hudson MA, Hussain SA, Huveneers C, Jacques H, Jorgensen D, Katdare S, Katsis LKD, Kaul R, Kaunda-Arara B, Keith-Diagne L, Kraus DT, de Lima TM, Lindeman K, Linsky J, Louis E, Loy A, Lughadha EN, Mangel JC, Marinari PE, Martin GM, Martinelli G, McGowan PJK, McInnes A, Teles Barbosa Mendes E, Millard MJ, Mirande C, Money D, Monks JM, Morales CL, Mumu NN, Negrao R, Nguyen AH, Niloy MNH, Norbury GL, Nordmeyer C, Norris D, O'Brien M, Oda GA, Orsenigo S, Outerbridge ME, Pasachnik S, Pérez-Jiménez JC, Pike C, Pilkington F, Plumb G, Portela RDCQ, Prohaska A, Quintana MG, Rakotondrasoa EF, Ranglack DH, Rankou H, Rawat AP, Reardon JT, Rheingantz ML, Richter SC, Rivers MC, Rogers LR, da Rosa P, Rose P, Royer E, Ryan C, de Mitcheson YJS, Salmon L, Salvador CH, Samways MJ, Sanjuan T, Souza Dos Santos A, Sasaki H, Schutz E, Scott HA, Scott RM, Serena F, Sharma SP, Shuey JA, Silva CJP, Simaika JP, Smith DR, Spaet JLY, Sultana S, Talukdar BK, Tatayah V, Thomas P, Tringali A, Trinh-Dinh H, Tuboi C, Usmani AA, Vasco-Palacios AM, Vié JC, Virens J, Walker A, Wallace B, Waller LJ, Wang H, Wearn OR, van Weerd M, Weigmann S, Willcox D, Woinarski J, Yong JWH, Young S. Testing a global standard for quantifying species recovery and assessing conservation impact. Conserv Biol 2021; 35:1833-1849. [PMID: 34289517 DOI: 10.1111/cobi.13756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/29/2021] [Accepted: 04/10/2021] [Indexed: 06/13/2023]
Abstract
Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard.
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Affiliation(s)
- Molly K Grace
- Department of Zoology, University of Oxford, Oxford, UK
- IUCN Species Survival Commission, Caracas, Venezuela
| | - H Resit Akçakaya
- IUCN Species Survival Commission, Caracas, Venezuela
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | | | - Thomas M Brooks
- International Union for Conservation of Nature (IUCN), Gland, Switzerland
- World Agroforestry Center (ICRAF), University of the Philippines, Los Baños, Philippines
- Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Simon Hedges
- Wildlife Conservation Society, Bronx, New York, USA
- IUCN SSC Asian Elephant Specialist Group, Noida, India
- IUCN SSC Asian Wild Cattle Specialist Group, Chester, UK
| | | | - Michael Hoffmann
- IUCN Species Survival Commission, Caracas, Venezuela
- Conservation Programmes, Zoological Society of London, London, UK
| | - Axel Hochkirch
- Department of Biogeography, Trier University, Trier, Germany
| | | | - David A Keith
- IUCN Species Survival Commission, Caracas, Venezuela
- Centre for Ecosystem Sciences, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- NSW Office of Environment and Heritage, Hurstville, New South Wales, Australia
| | | | - David P Mallon
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, UK
- IUCN SSC Antelope Specialist Group, Manchester, UK
| | - Erik Meijaard
- IUCN SSC Wild Pig Specialist Group and Centre of Excellence for Environmental Decisions, University of Queensland, Brisbane, Queensland, Australia
| | | | - Jon Paul Rodriguez
- IUCN Species Survival Commission, Caracas, Venezuela
- Instituto Venezolano de Investigaciones Científicas, and Provita, Caracas, Venezuela
| | - P J Stephenson
- IUCN SSC Species Monitoring Specialist Group, Gingins, Switzerland
- Laboratory for Conservation Biology, Department of Ecology & Evolution, UNIL - University of Lausanne, Lausanne, Switzerland
| | - Simon N Stuart
- IUCN Species Survival Commission, Caracas, Venezuela
- Synchronicity Earth, London, UK
| | | | - Pablo Acebes
- Centro de Investigación en Biodiversidad y Cambio Global, Departamento de Ecología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | | | - Marina Arbetman
- Grupo Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue, CONICET, Bariloche, Argentina
| | - Claudio Azat
- Sustainability Research Centre & PhD Programme in Conservation Medicine, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Gianluigi Bacchetta
- Centre for Conservation of Biodiversity, University of Cagliari, Cagliari, Italy
| | | | - Luís M D Barcelos
- Azorean Biodiversity Group, Centre for Ecology, Evolution, and Environmental Changes, Faculty of Agricultural and Environmental Sciences, University of the Azores, Angra do Heroísmo, Portugal
| | - Joao Pedro Barreiros
- Universidade dos Açores, Faculdade de Ciências Agrárias e do Ambiente, Rua Capitão João d'Ávila, Angra do Heroísmo, Portugal
| | | | - Danielle J Berger
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sabuj Bhattacharyya
- Centre for Ecological Sciences, Indian Institute of Sciences, Bangalore, India
| | - Gilad Bino
- University of New South Wales, Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Randwick, New South Wales, Australia
| | - Paulo A V Borges
- Departamento de Ciências e Engenharia do Ambiente Universidade dos Açores, Azores, Portugal
| | - Raoul K Boughton
- Range Cattle Research and Education Center, University of Florida, Gainesville, Florida, USA
| | - H Jane Brockmann
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | | | - James Burton
- IUCN SSC Asian Wild Cattle Specialist Group, Cedar House, Chester, UK
| | | | | | | | | | - John P Carroll
- University of Nebraska, School of Natural Resources, Lincoln, Nebraska, USA
| | | | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Guillaume Chapron
- Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | | | | | - Donatella Cogoni
- Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy
| | - Rochelle Constantine
- School of Biological Sciences & Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Christie Anne Craig
- Endangered Wildlife Trust, Office 8 & 9, Centre for Biodiversity Conservation, Cape Town, South Africa
| | | | - Nishma Dahal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | | | | | | | | | | | | | | | - David Fairclough
- Department of Primary Industries and Regional Development, Department of Fisheries, Hillarys, Western Australia, Australia
| | | | - Giuseppe Fenu
- Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy
| | | | | | - Brittany Finucci
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Rita Földesi
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Catherine M Foley
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawai'i, USA
| | - Matthew Ford
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | | | - Ricardo Garcia-Sandoval
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, Mexico
| | - Penny C Gardner
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Malaysia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autonoma de Mexico, Tercer Circuito s/n, Ciudad Universitaria, Ciudad de México, México
| | | | - Irene Gauto
- Asociación Etnobotánica Paraguaya, Lambaré, Paraguay
| | | | | | | | - Benito A González
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Tandora D Grant
- San Diego Zoo Institute for Conservation Research, San Diego, California, USA
| | | | - Andrew J Gregory
- Bowling Green State University, School of Earth Environment and Society, Bowling Green, Ohio, USA
| | | | - Marieka Gryzenhout
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Noelle C Guernsey
- World Wildlife Fund Inc., Northern Great Plains Program, Bozeman, Montana, USA
| | - Garima Gupta
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
| | | | - Christian A Hagen
- Department of Fisheries & Wildlife, Oregon State University, Corvallis, Oregon, USA
| | - Madison B Hall
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Eric Hallerman
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kelly Hare
- Urban Wildlife Trust, Wellington/Hamilton, New Zealand
| | - Tom Hart
- Department of Zoology, Oxford University, Oxford, UK
| | | | | | - Richard Hatfield
- The Xerces Society for Invertebrate Conservation, Portland, Oregon, USA
| | - Tahneal Hawke
- University of New South Wales, Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Randwick, New South Wales, Australia
| | | | - Rod Hitchmough
- Department of Conservation-Te Papa Atawhai, Wellington, New Zealand
| | | | | | | | | | - Charlie Huveneers
- Southern Shark Ecology Group, Flinders University, Adelaide, South Australia, Australia
| | | | - Dennis Jorgensen
- World Wildlife Fund Inc., Northern Great Plains Program, Bozeman, Montana, USA
| | | | - Lydia K D Katsis
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon, UK
| | | | - Boaz Kaunda-Arara
- Department of Fisheries and Aquatic Sciences, University of Eldoret, Eldoret, Kenya
| | | | - Daniel T Kraus
- University of Waterloo, School of Environment, Resources and Sustainability, Waterloo, Ontario, Canada
| | | | - Ken Lindeman
- Florida Institute of Technology, Program in Sustainability Studies, Melbourne, Florida, USA
| | - Jean Linsky
- Botanic Gardens Conservation International, Richmond, UK
| | - Edward Louis
- Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | - Anna Loy
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | | | - Jeffrey C Mangel
- Carrera de Biologia Marina, Universidad Cientifica del Sur, Lima, Peru
| | - Paul E Marinari
- Smithsonian Conservation Biology Institute, Front Royal, Virginia, USA
| | - Gabriel M Martin
- Centro de Investigación Esquel de Montaña y Estepa Patagónica, CONICET, Buenos Aires, Argentina
| | - Gustavo Martinelli
- National Center for Flora Conservation (CNCFlora), Rio de Janeiro, Brazil
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
| | - Alistair McInnes
- Seabird Conservation Programme, BirdLife South Africa, Foreshore, South Africa
| | | | | | | | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Carolina Laura Morales
- Grupo Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue, CONICET, Bariloche, Argentina
| | | | | | - Anh Ha Nguyen
- Fauna & Flora International - Vietnam Programme, Hanoi, Vietnam
| | | | | | | | - Darren Norris
- School of Environmental Sciences, Federal University of Amapá, Macapá, Brazil
| | - Mark O'Brien
- BirdLife International Pacific Regional Office, Suva, Fiji
| | - Gabriela Akemi Oda
- Federal Rural University of Rio de Janeiro - UFRRJ, Department of Environmental Sciences, Forestry Institute, Seropédica, Rio de Janeiro, Brazil
| | - Simone Orsenigo
- Dipartimento di Scienze della Terra e dell'Ambiente, Università di Pavia; Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy
| | | | | | | | | | | | - Glenn Plumb
- US National Park Service, Livingston, Montana, USA
| | | | - Ana Prohaska
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Manuel G Quintana
- Division of Invertebrates, Argentine Museum of Natural Sciences, Buenos Aires, Argentina
| | | | | | - Hassan Rankou
- IUCN SSC Orchid Specialist Group, Royal Botanic Gardens, Richmond, Surrey, UK
| | | | - James Thomas Reardon
- Department of Conservation, New Zealand, Fiordland District Office, Te Anau, New Zealand
| | - Marcelo Lopes Rheingantz
- Universidade Federal do Rio de Janeiro, Laboratório de Ecologia e Conservação de Populações, Centro de Ciências da Saúde - Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Stephen C Richter
- Division of Natural Areas and Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky, USA
| | - Malin C Rivers
- Botanic Gardens Conservation International, Richmond, UK
| | | | - Patrícia da Rosa
- National Center for Flora Conservation (CNCFlora), Rio de Janeiro, Brazil
| | | | | | - Catherine Ryan
- Auckland University of Technology, School of Science, Auckland City, New Zealand
| | | | - Lily Salmon
- Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, UK
| | | | - Michael J Samways
- Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Amanda Souza Dos Santos
- Universidade Federal do Rio de Janeiro, Health Science Centre, Biology Institute, Plant Ecology Laboratory, Rio de Janeiro, Brazil
| | | | - Emmanuel Schutz
- D'ABOVILLE Foundation and Demo Farm Inc, Makati, Philippines
| | | | | | - Fabrizio Serena
- Institute for Biological Resources and Marine Biotechnology, National Research Council-(CNR -IRBIM), Mazara del Vallo, Italy
| | | | - John A Shuey
- The Nature Conservancy, Indianapolis, Indiana, USA
| | - Carlos Julio Polo Silva
- Facultad de Ciencias Naturales e Ingeniería, Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia
| | - John P Simaika
- Department of Water Resources and Ecosystems, IHE Delft Institute for Water Education, Delft, The Netherlands
| | - David R Smith
- U.S. Geological Survey, Kearneysville, West Virginia, USA
| | - Julia L Y Spaet
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | | | | | - Aída M Vasco-Palacios
- Grupo de Microbiología Ambiental - BioMicro, Escuela de Microbiología, Universidad de Antioquia, UdeA, Medellín, Colombia
- Fundación Biodiversa Colombia, FBC, Bogotá, Colombia
| | | | - Jo Virens
- University of Otago, Dunedin, New Zealand
| | - Alan Walker
- Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, Suffolk, UK
| | | | - Lauren J Waller
- Southern African Foundation for the Conservation of Coastal Birds, Cape Town, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Belville, South Africa
| | | | - Oliver R Wearn
- Fauna & Flora International - Vietnam Programme, Hanoi, Vietnam
| | - Merlijn van Weerd
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
| | - Simon Weigmann
- Elasmo-Lab, Elasmobranch Research Laboratory, Hamburg, Germany
- Center of Natural History, University of Hamburg, Hamburg, Germany
| | - Daniel Willcox
- Save Vietnam's Wildlife, Cuc Phuong National Park, Ninh Bình Province, Vietnam
| | - John Woinarski
- Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Jean W H Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Stuart Young
- IUCN SSC Asian Wild Cattle Specialist Group, Cedar House, Chester, UK
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4
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Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A, Rouillard A, Lammers Y, Alberti A, Denoeud F, Money D, Ruter AH, McColl H, Larsen NK, Cherezova AA, Edwards ME, Fedorov GB, Haile J, Orlando L, Vinner L, Korneliussen TS, Beilman DW, Bjørk AA, Cao J, Dockter C, Esdale J, Gusarova G, Kjeldsen KK, Mangerud J, Rasic JT, Skadhauge B, Svendsen JI, Tikhonov A, Wincker P, Xing Y, Zhang Y, Froese DG, Rahbek C, Bravo DN, Holden PB, Edwards NR, Durbin R, Meltzer DJ, Kjær KH, Möller P, Willerslev E. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 2021; 600:86-92. [PMID: 34671161 PMCID: PMC8636272 DOI: 10.1038/s41586-021-04016-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
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Affiliation(s)
- Yucheng Wang
- Department of Zoology, University of Cambridge, Cambridge, UK
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Hannah Lois Owens
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nicolaj Krog Larsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anna A Cherezova
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Mary E Edwards
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Grigory B Fedorov
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - James Haile
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Sand Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- National Research University, Higher School of Economics, Moscow, Russia
| | - David W Beilman
- Department of Geography and Environment, University of Hawaii, Honolulu, HI, USA
| | - Anders A Bjørk
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Jialu Cao
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Julie Esdale
- Center for Environmental Management of Military Lands, Colorado State University, Fort Collins, CO, USA
| | - Galina Gusarova
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
- Faculty of Biology, St Petersburg State University, St Petersburg, Russia
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Jan Mangerud
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Jeffrey T Rasic
- US National Park Service, Gates of the Arctic National Park and Preserve, Fairbanks, AK, USA
| | | | - John Inge Svendsen
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Alexei Tikhonov
- Zoological Institute, , Russian Academy of Sciences, St Petersburg, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Yingchun Xing
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yubin Zhang
- College of Plant Science, Jilin University, Changchun, China
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Nogues Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Philip B Holden
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Neil R Edwards
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Per Möller
- Department of Geology, Quaternary Sciences, Lund University, Lund, Sweden
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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McClymont E, Fell D, Albert A, Alton G, Barrett J, El-Chaar D, Harrold J, Krajden M, Lipsky N, Maan E, Malinowski A, Othman M, Raeside A, Ray J, Roberts A, Ryan G, Sadarangani M, Sauve L, van Schalkwyk J, Shah P, Snelgrove J, Sprague A, Ting J, Walker M, Whittle W, Williams C, Yudin M, Zipursky J, Abenhaim H, Boucoiran I, Castillo E, Crane J, Elwood C, Joynt C, Kotaska A, Martel J, Murphy-Kaulbeck L, Poliquin V, Ryan S, Saunders S, Scott H, Money D. Canadian surveillance of COVID-19 in pregnancy: Epidemiology and maternal and infant outcomes. Am J Obstet Gynecol 2020. [PMCID: PMC7683302 DOI: 10.1016/j.ajog.2020.08.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Money D, Wilson D, Jenko J, Whalen A, Thorn S, Gorjanc G, Hickey JM. Extending long-range phasing and haplotype library imputation algorithms to large and heterogeneous datasets. Genet Sel Evol 2020; 52:38. [PMID: 32640985 PMCID: PMC7346379 DOI: 10.1186/s12711-020-00558-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Background We describe the latest improvements to the long-range phasing (LRP) and haplotype library imputation (HLI) algorithms for successful phasing of both datasets with one million individuals and datasets genotyped using different sets of single nucleotide polymorphisms (SNPs). Previous publicly available implementations of the LRP algorithm implemented in AlphaPhase could not phase large datasets due to the computational cost of defining surrogate parents by exhaustive all-against-all searches. Furthermore, the AlphaPhase implementations of LRP and HLI were not designed to deal with large amounts of missing data that are inherent when using multiple SNP arrays. Methods We developed methods that avoid the need for all-against-all searches by performing LRP on subsets of individuals and then concatenating the results. We also extended LRP and HLI algorithms to enable the use of different sets of markers, including missing values, when determining surrogate parents and identifying haplotypes. We implemented and tested these extensions in an updated version of AlphaPhase, and compared its performance to the software package Eagle2. Results A simulated dataset with one million individuals genotyped with the same 6711 SNPs for a single chromosome took less than a day to phase, compared to more than seven days for Eagle2. The percentage of correctly phased alleles at heterozygous loci was 90.2 and 99.9% for AlphaPhase and Eagle2, respectively. A larger dataset with one million individuals genotyped with 49,579 SNPs for a single chromosome took AlphaPhase 23 days to phase, with 89.9% of alleles at heterozygous loci phased correctly. The phasing accuracy was generally lower for datasets with different sets of markers than with one set of markers. For a simulated dataset with three sets of markers, 1.5% of alleles at heterozygous positions were phased incorrectly, compared to 0.4% with one set of markers. Conclusions The improved LRP and HLI algorithms enable AlphaPhase to quickly and accurately phase very large and heterogeneous datasets. AlphaPhase is an order of magnitude faster than the other tested packages, although Eagle2 showed a higher level of phasing accuracy. The speed gain will make phasing achievable for very large genomic datasets in livestock, enabling more powerful breeding and genetics research and application.
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Affiliation(s)
- Daniel Money
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - David Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Steve Thorn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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McClymont E, Johnston A, Albert A, Coutlée F, Lee M, Walmsley S, Lipsky N, Money D. A natural immune boosting effect among HPV-vaccinated women living with HIV. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2019.10.030] [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: 11/28/2022]
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8
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Elwood C, Albert A, McClymont E, Wagner E, Mahal D, Devakandan K, Quiqley BL, Pakzad Z, Yudin MH, Hill JE, Money D. Different and diverse anaerobic microbiota were seen in women living with HIV with unsuppressed HIV viral load and in women with recurrent bacterial vaginosis: a cohort study. BJOG 2019; 127:250-259. [PMID: 31498547 DOI: 10.1111/1471-0528.15930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To compare the vaginal microbiota of women living with HIV (WLWH) with the vaginal microbiota of women with recurrent bacterial vaginosis (BV) and healthy women without HIV to determine if there are differences in the vaginal microbiome, what factors influence these differences, and to characterise HIV clinical parameters including viral load and CD4 count in relation to the vaginal microbiome. DESIGN Observational cohort study. SETTING Canada. POPULATION Women aged 18-49 years who were premenopausal and not pregnant were recruited into three cohorts: healthy women, WLWH and women with recurrent BV. METHODS Demographic and clinical data were collected via interviews and medical chart reviews. Vaginal swabs were collected for Gram-stain assessment and microbiome profiling using the cpn60 barcode sequence. MAIN OUTCOME MEASURES To compare overall community composition differences, we used compositional data analysis methods, hierarchical clustering and Kruskal-Wallis tests where appropriate. RESULTS Clinical markers such as odour and abnormal discharge, but not irritation, were associated with higher microbial diversity. WLWH with unsuppressed HIV viral loads were more likely than other groups to have non-Gardnerella-dominated microbiomes. HIV was associated with higher vaginal microbial diversity and this was related to HIV viral load, with unsuppressed women demonstrating significantly higher relative abundance of Megasphaera genomosp. 1, Atopobium vaginae and Clostridiales sp. (all P < 0.05) compared with all other groups. CONCLUSIONS In WLWH, unsuppressed HIV viral loads were associated with a distinct dysbiotic profile consisting of very low levels of Lactobacillus and high levels of anaerobes. TWEETABLE ABSTRACT Vaginal microbiomes in WLWH with viral load >50 copies/ml have distinct dysbiotic profiles with high levels of anaerobes.
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Affiliation(s)
- C Elwood
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - Ayk Albert
- Women's Health Research Institute, Vancouver, BC, Canada
| | - E McClymont
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - E Wagner
- Women's Health Research Institute, Vancouver, BC, Canada
| | - D Mahal
- Women's Health Research Institute, Vancouver, BC, Canada
| | - K Devakandan
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - B L Quiqley
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Z Pakzad
- Women's Health Research Institute, Vancouver, BC, Canada
| | - M H Yudin
- Department of Obstetrics and Gynaecology, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - J E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - D Money
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
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Money D, Lee T, O'Brien C, Brophy J, Bitnun A, Kakkar F, Boucoiran I, Alimenti A, Vaudry W, Singer J, Sauve LJ. Congenital anomalies following antenatal exposure to dolutegravir: a Canadian surveillance study. BJOG 2019; 126:1338-1345. [PMID: 31188522 DOI: 10.1111/1471-0528.15838] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2019] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Dolutegravir is recommended worldwide as a first-line antiretroviral therapy (ART) for individuals living with HIV. A recent study reported increased rates of neural tube defects in infants of dolutegravir-treated women. This study examined rates of congenital anomalies in infants born to women living with HIV (WLWH) in Canada. DESIGN The Canadian Perinatal HIV Surveillance Programme captures surveillance data on pregnant WLWH and their babies and was analysed to examine the incidence of congenital anomalies. SETTING Paediatric HIV clinics. POPULATION Live-born infants born in Canada to WLWH between 2007 and 2017. METHODS Data on mother-infant pairs, including maternal ART use at conception and during pregnancy, are collected by participating sites. MAIN OUTCOME MEASURES Congenital anomalies. RESULTS Of the 2423 WLWH, 85 (3.5%, 95% CI 2.85-4.36%) had non-chromosomal congenital anomalies. There was no evidence of a significant difference in rates of congenital anomalies between women who were on ART in their first trimester (3.9%, CI 1.7-7.6%) or later in the pregnancy (3.9%, 95% CI 2.6-5.6%). Four of the 80 (5.0%, 95% CI 1.4-12.3%) neonates born to WLWH on dolutegravir during the first trimester had congenital anomalies, none were neural tube defects (95% CI 0.00-3.10%). CONCLUSION Despite recent evidence raising a safety concern, this analysis found no signal for increased congenital anomalies. TWEETABLE ABSTRACT Five percent of the infants of Canadian women living with HIV on dolutegravir at conception had congenital anomalies; none had neural tube defects.
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Affiliation(s)
- D Money
- Women's Hospital and Health Centre of British Columbia, University of British Columbia, Vancouver, BC, Canada
| | - T Lee
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada
| | - C O'Brien
- BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - J Brophy
- Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - A Bitnun
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - F Kakkar
- CHU Ste-Justine, Université de Montréal, Montréal, QC, Canada
| | - I Boucoiran
- Stollery Children's Hospital, University of Alberta, Edmonton, AB, Canada
| | - A Alimenti
- Women's Hospital and Health Centre of British Columbia, University of British Columbia, Vancouver, BC, Canada
| | - W Vaudry
- Stollery Children's Hospital, University of Alberta, Edmonton, AB, Canada
| | - J Singer
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada
| | - L J Sauve
- Women's Hospital and Health Centre of British Columbia, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
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McClymont E, Lee M, Blitz S, Raboud J, Coutlée F, Walmsley S, Lipsky N, Money D. The efficacy of the quadrivalent human papillomavirus vaccine in HIV-positive girls and women. Am J Obstet Gynecol 2017. [DOI: 10.1016/j.ajog.2017.08.066] [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: 10/18/2022]
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Pakzad Z, Wagner E, Chaworth-Musters T, Berg K, Albert A, van Schalkwyk J, Maan E, Azampanah A, McClymont E, Alimenti A, Forbes J, Money D. Do protease inhibitor-containing combination antiretroviral therapy regimens increase risk of spontaneous preterm birth in pregnant HIV-Positive women? Am J Obstet Gynecol 2017. [DOI: 10.1016/j.ajog.2017.08.087] [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: 11/17/2022]
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12
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Van Ommen C, Marquez V, Lowe C, Yoshida E, Money D, van Schalkwyk J. Assessing maternity care providers’ knowledge of the management of hepatitis B in pregnancy. Am J Obstet Gynecol 2017. [DOI: 10.1016/j.ajog.2017.08.064] [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: 11/26/2022]
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13
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Money D, Migicovsky Z, Gardner K, Myles S. LinkImputeR: user-guided genotype calling and imputation for non-model organisms. BMC Genomics 2017; 18:523. [PMID: 28693460 PMCID: PMC5504746 DOI: 10.1186/s12864-017-3873-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/20/2017] [Indexed: 11/24/2022] Open
Abstract
Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Results Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. Conclusions By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from NGS technologies. It enables the user to quickly and easily examine the effects of varying thresholds and filters on the number and quality of the resulting genotype calls. In this manner, users can decide on thresholds that are most suitable for their purposes. We show that LinkImputeR can significantly augment the value and utility of NGS data sets, especially in non-model organisms with poor genomic resources. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3873-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada.
| | - Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Kyle Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
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Antolín R, Nettelblad C, Gorjanc G, Money D, Hickey JM. A hybrid method for the imputation of genomic data in livestock populations. Genet Sel Evol 2017; 49:30. [PMID: 28253858 PMCID: PMC5439152 DOI: 10.1186/s12711-017-0300-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 09/05/2016] [Accepted: 02/13/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND This paper describes a combined heuristic and hidden Markov model (HMM) method to accurately impute missing genotypes in livestock datasets. Genomic selection in breeding programs requires high-density genotyping of many individuals, making algorithms that economically generate this information crucial. There are two common classes of imputation methods, heuristic methods and probabilistic methods, the latter being largely based on hidden Markov models. Heuristic methods are robust, but fail to impute markers in regions where the thresholds of heuristic rules are not met, or the pedigree is inconsistent. Hidden Markov models are probabilistic methods which typically do not require specific family structures or pedigree information, making them very flexible, but they are computationally expensive and, in some cases, less accurate. RESULTS We implemented a new hybrid imputation method that combined heuristic and HMM methods, AlphaImpute and MaCH, and compared the computation time and imputation accuracy of the three methods. AlphaImpute was the fastest, followed by the hybrid method and then the HMM. The computation time of the hybrid method and the HMM increased linearly with the number of iterations used in the hidden Markov model, however, the computation time of the hybrid method increased almost linearly and that of the HMM quadratically with the number of template haplotypes. The hybrid method was the most accurate imputation method for low-density panels when pedigree information was missing, especially if minor allele frequency was also low. The accuracy of the hybrid method and the HMM increased with the number of template haplotypes. The imputation accuracy of all three methods increased with the marker density of the low-density panels. Excluding the pedigree information reduced imputation accuracy for the hybrid method and AlphaImpute. Finally, the imputation accuracy of the three methods decreased with decreasing minor allele frequency. CONCLUSIONS The hybrid heuristic and probabilistic imputation method is able to impute all markers for all individuals in a population, as the HMM. The hybrid method is usually more accurate and never significantly less accurate than a purely heuristic method or a purely probabilistic method and is faster than a standard probabilistic method.
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Affiliation(s)
- Roberto Antolín
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Research Centre, Midlothian, EH25 9RG Scotland, UK
| | - Carl Nettelblad
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2, Box 337, 751 05 Uppsala, Sweden
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Research Centre, Midlothian, EH25 9RG Scotland, UK
| | - Daniel Money
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Research Centre, Midlothian, EH25 9RG Scotland, UK
| | - John M. Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Research Centre, Midlothian, EH25 9RG Scotland, UK
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15
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Boucoiran I, McClymont E, Varin J, van Schalkwyk J, Boucher M, Money D. 36: Causes of preterm delivery among HIV-positive women in canada and association with antiretroviral exposure. Am J Obstet Gynecol 2016. [DOI: 10.1016/j.ajog.2016.09.063] [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: 10/20/2022]
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16
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Migicovsky Z, Gardner KM, Money D, Sawler J, Bloom JS, Moffett P, Chao CT, Schwaninger H, Fazio G, Zhong GY, Myles S. Genome to Phenome Mapping in Apple Using Historical Data. Plant Genome 2016; 9. [PMID: 27898813 DOI: 10.3835/plantgenome2015.11.0113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Apple ( X Borkh.) is one of the world's most valuable fruit crops. Its large size and long juvenile phase make it a particularly promising candidate for marker-assisted selection (MAS). However, advances in MAS in apple have been limited by a lack of phenotype and genotype data from sufficiently large samples. To establish genotype-phenotype relationships and advance MAS in apple, we extracted over 24,000 phenotype scores from the USDA-Germplasm Resources Information Network (GRIN) database and linked them with over 8000 single nucleotide polymorphisms (SNPs) from 689 apple accessions from the USDA apple germplasm collection clonally preserved in Geneva, NY. We find significant genetic differentiation between Old World and New World cultivars and demonstrate that the genetic structure of the domesticated apple also reflects the time required for ripening. A genome-wide association study (GWAS) of 36 phenotypes confirms the association between fruit color and the MYB1 locus, and we also report a novel association between the transcription factor, NAC18.1, and harvest date and fruit firmness. We demonstrate that harvest time and fruit size can be predicted with relatively high accuracies ( > 0.46) using genomic prediction. Rapid decay of linkage disequilibrium (LD) in apples means millions of SNPs may be required for well-powered GWAS. However, rapid LD decay also promises to enable extremely high resolution mapping of causal variants, which holds great potential for advancing MAS.
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17
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Migicovsky Z, Sawler J, Money D, Eibach R, Miller AJ, Luby JJ, Jamieson AR, Velasco D, von Kintzel S, Warner J, Wührer W, Brown PJ, Myles S. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics 2016; 17:478. [PMID: 27357509 PMCID: PMC4928267 DOI: 10.1186/s12864-016-2834-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/13/2016] [Indexed: 11/24/2022] Open
Abstract
Background Grapes are one of the world’s most valuable crops and most are made into wine. Grapes belong to the genus Vitis, which includes over 60 inter-fertile species. The most common grape cultivars derive their entire ancestry from the species Vitis vinifera, but wild relatives have also been exploited to create hybrid cultivars, often with increased disease resistance. Results We evaluate the genetic ancestry of some of the most widely grown commercial hybrids from North America and Europe. Using genotyping-by-sequencing (GBS), we generated 2482 SNPs and 56 indels from 7 wild Vitis, 7 V. vinifera, and 64 hybrid cultivars. We used a principal component analysis (PCA) based ancestry estimation procedure and verified its accuracy with both empirical and simulated data. V. vinifera ancestry ranged from 11 % to 76 % across hybrids studied. Approximately one third (22/64) of the hybrids have ancestry estimates consistent with F1 hybridization: they derive half of their ancestry from wild Vitis and half from V. vinifera. Conclusions Our results suggest that hybrid grape breeding is in its infancy. The distribution of V. vinifera ancestry across hybrids also suggests that backcrosses to wild Vitis species have been more frequent than backcrosses to V. vinifera during hybrid grape breeding. This pattern is unusual in crop breeding, as it is most common to repeatedly backcross to elite, or domesticated, germplasm. We anticipate our method can be extended to facilitate marker-assisted selection in order to introgress beneficial wild Vitis traits, while allowing for offspring with the highest V. vinifera content to be selected at the seedling stage. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2834-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.,Anandia Labs, 2259 Lower Mall, Vancouver, BC, Canada
| | - Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Rudolph Eibach
- JKI Institute for Grapevine Breeding, Geilweilerhof, Germany
| | - Allison J Miller
- Department of Biology, Saint Louis University, Saint Louis, MO, USA
| | - James J Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - Andrew R Jamieson
- Agriculture & Agri-Food Canada, Atlantic Food & Horticulture Research Centre, Kentville, NS, Canada
| | | | | | - John Warner
- Warner Vineyards, 391 Thorpe Rd, RR#2, Centreville, NS, Canada
| | - Walter Wührer
- Wührer Vineyards, 187 Highway 221, RR#1, Kingston, NS, Canada
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
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18
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Van Schalkwyk J, Wong F, Prestley N, Dhillon S, Albert A, Collet J, Thomas E, Dewar K, Hippman C, Shaw D, Giesbrecht E, Money D. 2: Improving post-discharge surveillance of surgical site infection following cesarean section. Am J Obstet Gynecol 2015. [DOI: 10.1016/j.ajog.2015.09.035] [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: 10/22/2022]
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19
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Mitchell S, Moses E, Pedersen H, Sekikubo M, Mwesigwa D, Singer J, Biryabarema C, Byamugisha J, Money D, Ogilvie G. O18.5 Examining hpv prevalence and uptake of cervical cancer screening among hiv positive and negative women participating in a pilot rct in uganda comparing self-collection based hpv testing to via. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.180] [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: 11/04/2022]
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20
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Salters KA, Cescon A, Zhang W, Ogilvie G, Murray MCM, Coldman A, Hamm J, Chiu CG, Montaner JSG, Wiseman SM, Money D, Pick N, Hogg RS. Cancer incidence among HIV-positive women in British Columbia, Canada: Heightened risk of virus-related malignancies. HIV Med 2015; 17:188-95. [PMID: 26268461 DOI: 10.1111/hiv.12290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVES We used population-based data to identify incident cancer cases and correlates of cancer among women living with HIV/AIDS in British Columbia (BC), Canada between 1994 and 2008. METHODS Data were obtained from a retrospective population-based cohort created from linkage of two province-wide databases: (1) the database of the BC Cancer Agency, a province-wide population-based cancer registry, and (2) a database managed by the BC Centre for Excellence in HIV/AIDS, which contains data on all persons treated with antiretroviral therapy in BC. This analysis included women (≥ 19 years old) living with HIV in BC, Canada. Incident cancer diagnoses that occurred after highly active antiretroviral therapy (HAART) initiation were included. We obtained a general population comparison of cancer incidence among women from the BC Cancer Agency. Bivariate analysis (Pearson χ(2) , Fisher's exact or Wilcoxon rank-sum test) compared women with and without incident cancer across relevant clinical and sociodemographic variables. Standardized incidence ratios (SIRs) were calculated for selected cancers compared with the general population sample. RESULTS We identified 2211 women with 12 529 person-years (PY) of follow-up who were at risk of developing cancer after HAART initiation. A total of 77 incident cancers (615/100 000 PY) were identified between 1994 and 2008. HIV-positive women with cancer, in comparison to the general population sample, were more likely to be diagnosed with invasive cervical cancer, Hodgkin's lymphoma, non-Hodgkin's lymphoma and Kaposi's sarcoma and less likely to be diagnosed with cancers of the digestive system. CONCLUSIONS This study observed elevated rates of cancer among HIV-positive women compared to a general population sample. HIV-positive women may have an increased risk for cancers of viral-related pathogenesis.
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Affiliation(s)
- K A Salters
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - A Cescon
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Northern Ontario School of Medicine, Sudbury, Canada
| | - W Zhang
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - G Ogilvie
- Faculty of Medicine, University of British Columbia, Vancouver, Canada.,BC Centre for Disease Control, Vancouver, Canada
| | - M C M Murray
- Faculty of Medicine, University of British Columbia, Vancouver, Canada.,BC Women's Hospital and Health Centre, Vancouver, Canada.,Women's Health Research Institute, Vancouver, Canada
| | | | - J Hamm
- BC Cancer Agency, Vancouver, Canada
| | - C G Chiu
- Department of Surgery, St Paul's Hospital & University of British Columbia, Vancouver, Canada
| | - J S G Montaner
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - S M Wiseman
- Department of Surgery, St Paul's Hospital & University of British Columbia, Vancouver, Canada
| | - D Money
- Faculty of Medicine, University of British Columbia, Vancouver, Canada.,BC Women's Hospital and Health Centre, Vancouver, Canada.,Women's Health Research Institute, Vancouver, Canada
| | - N Pick
- Faculty of Medicine, University of British Columbia, Vancouver, Canada.,BC Women's Hospital and Health Centre, Vancouver, Canada.,Women's Health Research Institute, Vancouver, Canada
| | - R S Hogg
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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21
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Money D, Whelan S. GeLL: a generalized likelihood library for phylogenetic models. Bioinformatics 2015; 31:2391-3. [PMID: 25725494 DOI: 10.1093/bioinformatics/btv126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/23/2015] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Phylogenetic models are an important tool in molecular evolution allowing us to study the pattern and rate of sequence change. The recent influx of new sequence data in the biosciences means that to address evolutionary questions, we need a means for rapid and easy model development and implementation. Here we present GeLL, a Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation. AVAILABILITY AND IMPLEMENTATION http://phylo.bio.ku.edu/GeLL under a GPL v3 license.
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Affiliation(s)
- Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, B2N 5E3 Canada, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA and
| | - Simon Whelan
- Department of Evolutionary Biology, Uppsala University, Uppsala, 75236, Sweden
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22
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Abstract
Perennial crops represent important fresh and processed food sources worldwide, but advancements in breeding perennials are often impeded due to their very nature. The perennial crops we rely on most for food take several years to reach production maturity and require large spaces to grow, which make breeding new cultivars costly compared with most annual crops. Because breeding perennials is inefficient and expensive, they are often grown in monocultures consisting of small numbers of elite cultivars that are vegetatively propagated for decades or even centuries. This practice puts many perennial crops at risk for calamity since they remain stationary in the face of evolving pest and disease pressures. Although there is tremendous genetic diversity available to them, perennial crop breeders often struggle to generate commercially successful cultivars in a timely and cost-effective manner because of the high costs of breeding. Moreover, consumers often expect the same cultivars to be available indefinitely, and there is often little or no incentive for growers and retailers to take the risk of adopting new cultivars. While genomics studies linking DNA variants to commercially important traits have been performed in diverse perennial crops, the translation of these studies into accelerated breeding of improved cultivars has been limited. Here we explain the "perennial problem" in detail and demonstrate how modern genomics tools can significantly improve the cost effectiveness of breeding perennial crops and thereby prevent crucial food sources from succumbing to the perils of perpetual propagation.
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Affiliation(s)
- Kendra A McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Kyle M Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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Abstract
The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.
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Affiliation(s)
- Ryan M. Ames
- Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Daniel Money
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Simon C. Lovell
- Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
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24
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Gilbert M, Alvarez M, Krajden M, Buxton JA, Lester R, Money D, Kuo M, Ogilvie G. P3.197 Uptake and Case Detection of Prenatal Screening of Maternal Syphilis, HIV and Hepatitis C, in British Columbia, Canada, 2007–2011. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0654] [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: 11/03/2022]
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25
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Moses E, Blitz S, Raboud J, Singer J, Loutfy M, Smaill F, Walmsley S, Money D. P3.209 Low Rates of STI Co Infection Observed in HIV Positive Women Participating in an HPV Vaccine Study In Canada. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0666] [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: 11/03/2022]
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26
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Abstract
Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.
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Affiliation(s)
- Daniel Money
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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27
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Abstract
MOTIVATION Recent large-scale studies of individuals within a population have demonstrated that there is widespread variation in copy number in many gene families. In addition, there is increasing evidence that the variation in gene copy number can give rise to substantial phenotypic effects. In some cases, these variations have been shown to be adaptive. These observations show that a full understanding of the evolution of biological function requires an understanding of gene gain and gene loss. Accurate, robust evolutionary models of gain and loss events are, therefore, required. RESULTS We have developed weighted parsimony and maximum likelihood methods for inferring gain and loss events. To test these methods, we have used Markov models of gain and loss to simulate data with known properties. We examine three models: a simple birth-death model, a single rate model and a birth-death innovation model with parameters estimated from Drosophila genome data. We find that for all simulations maximum likelihood-based methods are very accurate for reconstructing the number of duplication events on the phylogenetic tree, and that maximum likelihood and weighted parsimony have similar accuracy for reconstructing the ancestral state. Our implementations are robust to different model parameters and provide accurate inferences of ancestral states and the number of gain and loss events. For ancestral reconstruction, we recommend weighted parsimony because it has similar accuracy to maximum likelihood, but is much faster. For inferring the number of individual gene loss or gain events, maximum likelihood is noticeably more accurate, albeit at greater computational cost. AVAILABILITY www.bioinf.manchester.ac.uk/dupliphy CONTACT simon.lovell@manchester.ac.uk; simon.whelan@manchester.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ryan M Ames
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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28
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Abstract
Phylogenetic tree-search is a major aspect of many evolutionary studies. Several tree rearrangement algorithms are available for tree-search, but it is hard to draw general conclusions about their relative performance because many effects are data set specific and can be highly dependent on individual implementations (e.g., RAxML or phyml). Using only the structure of the rearrangements proposed by the Nearest Neighbor Interchange (NNI) algorithm, we show tree-search can prematurely terminate if it encounters multifurcating trees. We validate the relevance of this result by demonstrating that in real data the majority of possible bifurcating trees potentially encountered during tree-search are actually multifurcations, which suggests NNI would be expected to perform poorly. We also show that the star-decomposition algorithm is a special case of two other popular tree-search algorithms, subtree pruning and regrafting (SPR) and tree bisection and reconnection (TBR), which means that these two algorithms can efficiently escape when they encounter multifurcations. We caution against the use of the NNI algorithm and for most applications we recommend the use of more robust tree-search algorithms, such as SPR and TBR.
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Dube E, Duval B, Gilca V, McNeil S, Dobson S, Money D, Gemmill I, Sauvageau C, Lavoie F, Ouakki M. Canadian Paediatricians’ Knowledge, Attitudes and Beliefs Regarding Hpv Vaccination. Paediatr Child Health 2009. [DOI: 10.1093/pch/14.suppl_a.39ab] [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: 11/13/2022] Open
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30
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Delisle MF, Valimohamed F, Money D, Douglas MJ. Central nervous system complications of von Hippel-Lindau disease and pregnancy; perinatal considerations: case report and literature review. J Matern Fetal Med 2000; 9:242-7. [PMID: 11048837 DOI: 10.1002/1520-6661(200007/08)9:4<242::aid-mfm11>3.0.co;2-5] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A 30-year-old woman with von Hippel-Lindau disease presented at 30 weeks' gestation with a symptomatic cerebellar hemangioblastoma. She underwent a craniotomy for complete removal of the tumor. The postoperative period and the remaining of the pregnancy were uneventful. She delivered under epidural anesthesia after induction for postterm.
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Affiliation(s)
- M F Delisle
- Maternal-Fetal Medicine, BC Women's Hospital and Health Centre, Vancouver BC, Canada.
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31
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Money D. A comparison of three approaches to delivering a speech and language therapy service to people with learning disabilities. Eur J Disord Commun 1997; 32:449-466. [PMID: 9519119 DOI: 10.3109/13682829709082259] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This research aimed to compare three different approaches to delivering a speech and language therapy service to people with learning disabilities, in order to make recommendations for future service delivery. The three approaches all involved working with key communication partners in the environment. They were: (i) working directly on a one-to-one basis with the person and partner; (ii) working indirectly by providing teaching for partners; and (iii) a combination of these two approaches. A teaching course called 'Talkabout' was used. Talkabout aims for staff to reach a recognised level of knowledge and competence in communication skills, thus facilitating the communication skills of their service users. The results indicated that whilst communication changed in all three approaches, overall changes were greater in the combination approach. Only the combination approach demonstrated statistically significant differences following intervention, in terms of staff initiations, service user responses, and their use of additional modalities.
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Affiliation(s)
- D Money
- Central Nottinghamshire Healthcare (NHS) Trust, UK
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