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Beaubier N, Tell R, Lau D, Parsons JR, Bush S, Perera J, Sorrells S, Baker T, Chang A, Michuda J, Iguartua C, MacNeil S, Shah K, Ellis P, Yeatts K, Mahon B, Taxter T, Bontrager M, Khan A, Huether R, Lefkofsky E, White KP. Clinical validation of the tempus xT next-generation targeted oncology sequencing assay. Oncotarget 2019; 10:2384-2396. [PMID: 31040929 PMCID: PMC6481324 DOI: 10.18632/oncotarget.26797] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/03/2019] [Indexed: 12/13/2022] Open
Abstract
We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations and microsatellite instability in solid tumors and hematologic malignancies. This targeted oncology assay utilizes tumor-normal matched samples for highly accurate somatic alteration calling and whole transcriptome RNA sequencing for unbiased identification of gene fusion events. The assay was validated with a combination of clinical specimens and cell lines, and recorded a sensitivity of 99.1% for single nucleotide variants, 98.1% for indels, 99.9% for gene rearrangements, 98.4% for copy number variations, and 99.9% for microsatellite instability detection. This assay presents a wide array of data for clinical management and clinical trial enrollment while conserving limited tissue.
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Affiliation(s)
| | | | - Denise Lau
- Tempus Labs Inc., Chicago, IL 60654, USA
| | | | | | | | | | | | - Alan Chang
- Tempus Labs Inc., Chicago, IL 60654, USA
| | | | | | | | | | | | | | | | | | | | - Aly Khan
- Tempus Labs Inc., Chicago, IL 60654, USA
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2
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Beaubier N, Tell R, Huether R, Bontrager M, Bush S, Parsons J, Shah K, Baker T, Selkov G, Taxter T, Thomas A, Bettis S, Khan A, Lau D, Lee C, Barber M, Cieslik M, Frankenberger C, Franzen A, Weiner A, Palmer G, Lonigro R, Robinson D, Wu YM, Cao X, Lefkofsky E, Chinnaiyan A, White KP. Clinical validation of the Tempus xO assay. Oncotarget 2018; 9:25826-25832. [PMID: 29899824 PMCID: PMC5995233 DOI: 10.18632/oncotarget.25381] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/21/2018] [Indexed: 01/01/2023] Open
Abstract
We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.
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Affiliation(s)
| | - Robert Tell
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | | | | | - Kaanan Shah
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Baker
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gene Selkov
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Taxter
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | - Sam Bettis
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Aly Khan
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Denise Lau
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | - Marcin Cieslik
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Amy Franzen
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Ali Weiner
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gary Palmer
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Robert Lonigro
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dan Robinson
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yi-Mi Wu
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xuhong Cao
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Arul Chinnaiyan
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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3
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Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus. PLoS Genet 2016; 12:e1006155. [PMID: 27385107 PMCID: PMC4934787 DOI: 10.1371/journal.pgen.1006155] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [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: 11/05/2015] [Accepted: 06/08/2016] [Indexed: 12/05/2022] Open
Abstract
Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn K. Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Martin Bontrager
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Jean-Baptiste Leducq
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagonico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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4
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Baum DA, Ané C, Larget B, Solís-Lemus C, Ho LST, Boone P, Drummond CP, Bontrager M, Hunter SJ, Saucier W. Statistical evidence for common ancestry: Application to primates. Evolution 2016; 70:1354-63. [PMID: 27139421 DOI: 10.1111/evo.12934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 11/28/2022]
Abstract
Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA.
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Affiliation(s)
- David A Baum
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.
| | - Cécile Ané
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.,Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706
| | - Bret Larget
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.,Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706
| | - Claudia Solís-Lemus
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706
| | - Lam Si Tung Ho
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706
| | - Peggy Boone
- Department of Zoology, University of Wisconsin, 250 N. Mills St., Madison, Wisconsin, 53706
| | - Chloe P Drummond
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706
| | - Martin Bontrager
- 5Laboratory of Genetics, University of Wisconsin, 425 Henry Mall, Madison, Wisconsin, 53706
| | - Steven J Hunter
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706
| | - William Saucier
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706
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5
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Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun 2014; 5:4044. [PMID: 24887054 DOI: 10.1038/ncomms5044] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/02/2014] [Indexed: 12/16/2022] Open
Abstract
In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with human-driven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum.
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Affiliation(s)
- Pedro Almeida
- 1] Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal [2]
| | - Carla Gonçalves
- 1] Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal [2]
| | - Sara Teixeira
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, INIBIOMA (CONICET-UNComahue), 8400 Bariloche, Argentina
| | - Martin Bontrager
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Warren Albertin
- University Bordeaux, EA Œnologie 4577, ISVV, Villenave d'Ornon F-33882, France
| | - Pascal Durrens
- CNRS UMR 5800, University Bordeaux, INRIA project-team Magnome, Talence F33400, France
| | - David James Sherman
- CNRS UMR 5800, University Bordeaux, INRIA project-team Magnome, Talence F33400, France
| | - Philippe Marullo
- 1] University Bordeaux, EA Œnologie 4577, ISVV, Villenave d'Ornon F-33882, France [2] BIOLAFFORT, Bordeaux F-33072, France
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Paula Gonçalves
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Paulo Sampaio
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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