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4,246 results on '"Brock, A."'

1. Exploring the Role of Disciplinary Knowledge in Students' Covariational Reasoning during Graphical Interpretation

Author

Nigar Altindis, Kathleen A. Bowe, Brock Couch, Christopher F. Bauer, and Melissa L. Aikens

Abstract

This study investigates undergraduate STEM students' interpretation of quantities and quantitative relationships on graphical representations in biology (population growth) and chemistry (titration) contexts. Interviews (n = 15) were conducted to explore the interplay between students' covariational reasoning skills and their use of disciplinary knowledge to form mental images during graphical interpretation. Our findings suggest that disciplinary knowledge plays an important role in students' ability to interpret scientific graphs. Interviews revealed that using disciplinary knowledge to form mental images of represented quantities may enhance students' covariational reasoning abilities, while lacking it may hinder more sophisticated covariational reasoning. Detailed descriptions of four students representing contrasting cases are analyzed, showing how mental imagery supports richer graphic sense-making. In the cases examined here, students who have a deep understanding of the disciplinary concepts behind the graphs are better able to make accurate interpretations and predictions. These findings have implications for science education, as they suggest instructors should focus on helping students to develop a deep understanding of disciplinary knowledge in order to improve their ability to interpret scientific graphs.

Published
2024
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2. The Development and Validation of the Mutation Criterion Referenced Assessment (MuCRA)

Author

Chloe Wasendorf, Joshua W. Reid, Rebecca Seipelt-Thiemann, Z. T. Grimes, Brock Couch, Nick T. Peters, Julia Massimelli Sewall, Audrey L. McCombs, Patrick I. Armstrong, and Nancy Boury

Abstract

Most biology undergraduates learn about mutations in multiple classrooms throughout their college career. Understanding personalised genome test results, genome editing controversies, and the appearance of new variants of viruses or antibiotic resistant bacteria all require foundational knowledge about mutations. However, the abstract nature of molecular processes surrounding mutations makes them one of the more difficult topics for students to understand and apply. Instructors need valid assessment tools to document student understanding and tailor their instructional methods to address student knowledge gaps. We describe here the development and validation of the Mutations Criterion Referenced Assessment (MuCRA). This formative assessment was developed through an iterative process involving expert feedback and student responses to both open-ended and multiple-choice questions. The final MuCRA is composed of 10 multiple-choice questions aligned with three learning objectives. The item difficulty for each question was between 0.32-0.65, while the discrimination index ranged from 0.31-0.75 and the reliability (KR20) for the MuCRA was 0.69. The congruence analyses demonstrated distractors are capturing student misconceptions in 9/10 questions. These data indicate that the MuCRA can be used to reliably assess student learning and common misconceptions about mutations.

Published
2024
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3. An Assessment to Investigate Student Conceptions of Pedigree Analysis

Author

Grimes, Zachary T., Boury, Nancy M., Wasendorf, Chloe, McCombs, Audrey L., Reid, Joshua W., James, Olena, Couch, Brock, Armstrong, Patrick I., and Seipelt-Thiemann, Rebecca L.

Abstract

Genetics plays an increasing role in modern life as evidenced by the development of revolutionary techniques such as CRISPR-based genome editing and the rise of personalized genome services. However, genetics is difficult to learn; known issues include its abstract nature, different scales, and technical language. Pedigree analysis is a convergence of these concepts, requiring use of multiple symbolic scales and understanding the relationships and nature of alleles, genes, and chromosomes. To measure student understanding of these concepts, as well as support biology educational reform toward student-centered instruction, we developed a formative assessment to provide reliable and valid evidence of student understanding, learning, and misconceptions for pedigree analysis. Nine multiple choice items targeted to four learning objectives were developed in an iterative process with faculty and student input. We designed distractor answers to capture common student misconceptions and deployed a novel statistical technique to assess the congruence of distractor language with targeted misconceptions. Psychometric analysis showed the instrument provides valid and reliable data and has utility to measure normalized learning gains. Finally, we employed cross-tabulation and distractor progression to identify several stable misconceptions that can be targeted for instructional intervention.

Published
2022
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4. Working Model Hearts

Author

Brock, David

Abstract

Despite student interest, the heart is often a poorly understood topic in biology. To help students understand this vital organ's physiology, the author created this investigation activity involving the mammalian heart and its role in the circulatory system. Students design, build, and demonstrate working artificial "hearts" to exhibit what they know about the circulatory system. This article describes how to incorporate the model heart activity into the classroom, including material that can be taught using the working product. (Contains 3 figures and 4 resources.)

Published
2009
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7. Teaching Bioethics from an Interdisciplinary Perspective.

Author

Singleton, Rivers and Brock, D. Heyward

Abstract

Outlines an interdisciplinary workshop in bioethics for secondary teachers taught by a team consisting of a scientist, a philosopher, and a literary critic. Discusses definitions, topics, reading selections, problems, and value. (DC)

Published
1982

8. Identifying novel genes associated with response to nicotine in a zebrafish model of drug dependence

Author

Brock, Alistair James

Subjects
362.29, Medicine, Biology, Smoking, Tobacco addiction, Zebrafish
Abstract

Tobacco addiction is a leading preventable cause of death worldwide and places a heavy social and financial burden on society. There exists a substantial genetic variability in smoking behavior, the mechanisms of which are largely unknown. Despite significant advances in sequencing power, progress in the identification of genetic variants affecting smoking behavior based on human genome wide association studies has been slow. Thus this thesis investigates the utility of zebrafish as a model species in which to search for genetic variants affecting nicotine seeking. The work is based on the premise that as zebrafish are vertebrate with conserved neurochemical pathways and circuitry with humans, and the pathways involved in drug mediated reward and addiction are evolutionarily ancient, homologues of genes affecting zebrafish nicotine-seeking behavior will likely affect human smoking behavior. Thus results in zebrafish can be used to direct human genetic studies. The first result chapter addresses the hypothesis that zebrafish show conserved reward responses to common drugs of abuse. A conditioned place preference assay is used to assess zebrafish reward responses to stimulants, opioids, benzodiazepines and alcohol. The results indicate that, with the exception of benzodiazepines, reward responses are conserved, supporting the use of this model in a screen for genetic variants affecting nicotine preference. The second and third results chapters describe the findings of a pilot screen of ENU-mutagenized zebrafish provided by the Sanger Institute, Cambridge. I demonstrate that nicotine preference is heritable in fish as in Abstract 5 humans and identify 3 mutant lines that show increased or decreased nicotine place preference. Genotyping indicated that one of the families showing increased nicotine preference carries a predicted loss of function mutation in the slit3 gene. The involvement of this gene in nicotine preference was confirmed in a separate line. Further characterization of this line using qPCR showed slit3 mutants to have altered developmental expression of key nicotinic and dopaminergic genes. Having identified the slit3 gene as a locus affecting nicotine seeking in fish, I then tested the hypothesis that results in fish could be used to predict loci that affect human smoking behavior. Cohorts of patients were genotyped for 20 SNPs within the slit3 locus. Results of this analysis identified 1 novel SNP in the slit3 gene associated with smoking behavior in a cohort of individuals that were heavy smokers. This result was validated in cohorts of low and normal smoking prevalence. These data demonstrate the utility of behavioral assays in zebrafish to identify genes affecting human behavior and pave the way for the use of zebrafish to inform human studies exploring the genetic basis of drug seeking and behavioral disease.

Published
2015

9. Debating Sexual Selection and Mating Strategies

Author

McNamara, John M., Wedell, Nina, Hosken, David J., Birkhead, Tim R., Colegrave, Nick, Harvey, Paul H., Hatchwell, Ben, Hunt, John, Moore, Allen J., Parker, Geoff A., Pitnick, Scott, Pizzari, Tommaso, Radwan, Jacek, Ritchie, Mike, Sheldon, Ben C., Shuker, David M., Simmons, Leigh W., Stockley, Paula, Tregenza, Tom, Zuk, Marlene, Pizzari, Tommaso, Blows, Mark W., Brooks, Rob, Buchanan, Katherine L., Clutton-Brock, Tim H., Jennions, Michael D., Kokko, Hanna, Kotiaho, Janne S., Macias-García, Constantino, Partridge, Linda, Snook, Rhonda R., Buss, David M., Day, Troy, Houle, David, Rowe, Locke, Ghiselin, Michael T., Hurd, Peter L., Miller, Geoffrey, Stewart, Jeffrey, Roughgarden, Joan, Akçay, Erol, and Oishi, Meeko

Published
2006

11. Causes and Consequences of Color Polymorphism

Author

Brock, Kinsey

Subjects
Biology, Behavioral ecology, color morphs, Color polymorphism, Diversification, Lacertidae, Podarcis
Abstract

One hundred and fifty years after Darwin and “On the Origin of Species,” understanding how phenotypic variation is generated, maintained, and lost remains a central goal in evolutionary biology. Color polymorphic species are model systems for examining phenotypic variation in nature because discrete color variants are phenotypic markers of underlying genetic variation, or allele frequencies. Color polymorphism is the presence of multiple discrete, heritable color phenotypes within a single breeding population. Color morphs have evolved in thousands of species across the plant and animal kingdoms. Lizards have repeatedly evolved strikingly similar color polymorphisms in distantly related lineages, providing an opportunity to examine the effects of heritable phenotypic variation on micro- and macroevolutionary dynamics, intraspecific geographic variation, correlated traits, and associated evolutionary processes.Herein, I take an interdisciplinary approach to understand the causes and consequences of color polymorphism at multiple biological scales, from molecules to macroevolution. In Chapter 1, I studied hundreds of individuals within a single population of lizards (Aegean wall lizard, Podarcis erhardii) to characterize a previously undescribed color polymorphism and identify color morph-correlated traits important for lizard fitness. I found that P. erhardii has three pure color morphs (orange, yellow, and white), and that male morphs display significant differences in body size traits, bite force, and chemical signal profiles extracted from their femoral pore exudate, whereas female morphs do not differ in head and body size dimensions or their maximum bite force capacity. I expand on these differences in traits in Chapter 2, where I conducted behavioral experiments on male P. erhardii color morphs from the same population to elucidate morph differences in behavior. Laboratory experiments revealed that male color morphs differ in their ability to access a limited space resource, and exhibit different levels of aggressive, bold, and signaling behaviors depending on the color morph identity of their competitor. In Chapter 3, I sampled lizards and measured environmental variation from 46 island populations across the range of P. erhardii to reconstruct the evolutionary history of color polymorphism and identify morph-environmental associations. I found that color polymorphism is likely the ancestral state of P. erhardii, and that morph variation is likely due to morph loss, which occurs at a much faster rate than evolutionary gains of color polymorphism. I also found that morph diversity seems to be lost in an ordered fashion, and that the rare orange morph is associated with cooler, wetter habitats, which are disappearing with climate change. Finally, in Chapter 4, I demonstrate that color polymorphism is a driver of diversification in the lizard family Lacertidae. Taken together, my dissertation suggests that the causes of color polymorphism is variation in the environment, and the consequences are variation within species that lead to the generation of new species.

Published
2021

13. Dispersal-induced social stress prolongs gestation in wild meerkats

Author

Maag, Nino, Cozzi, Gabriele, Seager, David, Manser, Marta, Sickmüller, Anna, Hildebrandt, Thomas B, Clutton-Brock, Tim, Ozgul, Arpat, and University of Zurich

Subjects
10127 Institute of Evolutionary Biology and Environmental Studies, 570 Life sciences, biology, 590 Animals (Zoology), General Agricultural and Biological Sciences, Agricultural and Biological Sciences (miscellaneous)
Published
2023

14. Rapid Ossification Helps Explain Small Body Size in Urspelerpes brucei (Caudata: Plethodontidae).

Author

Brock, Tyler L., Crookston, Claire M., Beachy, Christopher K., and Camp, Carlos D.

Subjects
*LUNGLESS salamanders, *BODY size, *OSSIFICATION, *SKELETON, *SALAMANDERS, *BIOLOGY, *PTERYGOID muscles
Abstract

Urspelerpes brucei (Patch-nosed Salamander) is a miniaturized lungless salamander (family Plethodontidae) native to select headwater tributaries of the Tugaloo River along the border of Georgia and South Carolina. Due to the rarity and relatively recent discovery of this species, many aspects of its biology are unstudied. In particular, there has not yet been any description of its larval skeleton. We provide the first description of larval osteology for U. brucei, and we compared cleared and stained specimens of U. brucei close to the minimum size at metamorphosis to similarly sized specimens of Eurycea cirrigera (Southern Two-lined Salamander). Our results showed that the skull and long bones of U. brucei are more heavily ossified at smaller sizes than in E. cirrigera. In addition, U. brucei possesses more robust vomers and pterygoids, coronoids that are already incorporated into the dentary, and an ossified os thyroideum. These discrepancies in ossification suggest that the skeletons of U. brucei complete development at smaller sizes than E. cirrigera, a result likely tied to heterochronic accelerations of mineralization and sexual maturation in U. brucei. Taken together, these factors appear to help explain how U. brucei has developed and maintained its small body size. [ABSTRACT FROM AUTHOR]

Published
2023
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15. APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell–Mediated Antitumor Immune Responses

Author

Elizabeth A Mendes, Sarah C. Van Alsten, Jeremy Force, Brock McKinney, Ashley V. DiMarco, Kouros Owzar, Jichun Xie, Nina Marie G. Garcia, Melissa A. Troester, Xiaodi Qin, Brent A. Hanks, and James V. Alvarez

Subjects
APOBEC, Cancer Research, T-Lymphocytes, medicine.medical_treatment, T cell, Immunology, Mice, Nude, Breast Neoplasms, Biology, Article, Mice, Breast cancer, Immune system, Antigens, Neoplasm, Cell Line, Tumor, Tumor Microenvironment, medicine, Animals, Humans, APOBEC Deaminases, Mice, Inbred BALB C, Mammary tumor, Immunogenicity, Cancer, Immunotherapy, medicine.disease, Xenograft Model Antitumor Assays, Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, Mutagenesis, Mutation, Cancer research, Female
Abstract

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4+ T cell–mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti–CTLA-4 checkpoint inhibition and led to a complete response to combination anti–CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2+) breast cancers.

Published
2022
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16. Benefits of cooperation in captive Damaraland mole-rats

Author

Thomas M. Houslay, Markus Zöttl, Tim H. Clutton-Brock, Philippe Vullioud, Houslay, Thomas [0000-0001-5592-9034], Clutton-Brock, Timothy [0000-0001-8110-8969], and Apollo - University of Cambridge Repository

Subjects
0106 biological sciences, 0303 health sciences, cooperative breeding, Ecology (disciplines), Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, Eusociality, eusocial, Queen (playing card), 03 medical and health sciences, mole-rats, Cooperative breeding, Animal Science and Zoology, Cooperative behavior, cooperative behavior, reproductive and urinary physiology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Although the social mole-rats are commonly classified as eusocial breeders on the grounds that groups include a single breeding female (the “queen”) and a number of nonbreeding individuals (“helpers”) of both sexes, alloparental care is not highly developed in these species and there is no direct evidence that the presence or number of nonbreeders is associated with reductions in the workload of the “queen.” An alternative interpretation of mole-rat groups is that the social mole-rats are cooperative foragers rather than cooperative or eusocial breeders. Here, in captive colonies of Damaraland mole-rats (Fukomys damarensis), we provide the first evidence that increases in the number of nonbreeding subordinates in mole-rat groups are associated with reductions in the workload of “queens” and with increases in their fecundity.

Published
2020
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17. Mast cell activation disease and immunoglobulin deficiency in patients with hypermobile <scp>Ehlers‐Danlos</scp> syndrome/hypermobility spectrum disorder

Author

Walter Prendergast, Isabelle Brock, and Anne Maitland

Subjects
Joint Instability, Allergy, medicine.medical_specialty, Mast Cell Activation Syndrome, Primary Immunodeficiency Diseases, Inflammation, Mast cell activation syndrome, Disease, Mast Cell Activation Disorders, Gastroenterology, Hypogammaglobulinemia, Internal medicine, Genetics, medicine, Humans, Genetics (clinical), biology, business.industry, nutritional and metabolic diseases, medicine.disease, Mast cell, medicine.anatomical_structure, Ehlers–Danlos syndrome, biology.protein, Ehlers-Danlos Syndrome, Female, medicine.symptom, Antibody, business
Abstract

Mast cell activation disease (MCAD) includes single organ disease such as asthma, urticaria, and gastroenteritis, as well as multiorgan system involvement such as mast cell activation syndrome and anaphylaxis. Reports link MCAD with hypermobile Ehlers-Danlos syndrome (hEDS), hypermobility spectrum disorder (HSD), and with primary immune deficiencies such as complement and immunoglobulin deficiencies (Ig Def). This study assesses the concurrence of these syndromes. We undertook a cohort analysis of patients seen in a community-based Allergy/Immunology clinic from 2015 to 2019. We searched for diagnostic codes for Ig Def disorders, hypermobility syndrome, hypermobile/Ehlers-Danlos syndrome, and MCADs. Of 974 patients with suspected MCAD, 449 (46%) had a diagnosis of MCAD; 496 (51%) of cases had a combination of at least two of hEDS/HSD, MCAD, and Ig Def. Ig Def was present in 417 (43%) of patients; 188 (19.3%) had hEDS/HSD with an Ig Def with or without MCAD and accounted for 45% of all the cases with Ig Def. Of 974 cases, 101 (10%) had hEDS/HSD and MCAD; 207 (21%) had Ig Def and MCAD; 7 (0.7%) had Ig Def and hEDS/HSD; and 181 (19%) had a combination of all three syndromes. Most patients (74%) with these comorbidities were female. The presence of MCAD and Ig Def should be explored in patients with hEDS/HSD. Identifying underlying contributors to recurrent/chronic inflammation and tissue injury is needed to tailor and personalize therapies. This, in turn, can reduce tissue damage, iatrogenic intervention, and optimize health outcomes.

Published
2021
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18. Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens

Author

Benjamin Noyovitz, Stephen A. McMahon, Nick P G Gauthier, Andrew J. Bennet, Tracey M. Gloster, Kobra Khazaei, Brock W. Byers, Jason R. Nesbitt, Verena Oehler, Nicholas J. Thornton, Jamie Baker, Ali Nejatie, Margo M. Moore, Wesley F. Zandberg, and Elizabeth Steves

Subjects
Glycan, Protein Conformation, Neuraminidase, Sialidase, Biochemistry, Catalysis, Substrate Specificity, Aspergillus fumigatus, 03 medical and health sciences, chemistry.chemical_compound, Ascomycota, Catalytic Domain, Enzyme Stability, Glycoside hydrolase, Aspergillus terreus, skin and connective tissue diseases, Fluorescent Dyes, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, 030306 microbiology, Temperature, Glycoside, General Medicine, Hydrogen-Ion Concentration, bacterial infections and mycoses, biology.organism_classification, Culture Media, Sialic acid, Kinetics, Enzyme, chemistry, biology.protein, Molecular Medicine
Abstract

Sialidases catalyze the release of sialic acid from the terminus of glycan chains. We previously characterized the sialidase from the opportunistic fungal pathogen, Aspergillus fumigatus, and showed that it is a Kdnase. That is, this enzyme prefers 3-deoxy-d-glycero-d-galacto-non-2-ulosonates (Kdn glycosides) as the substrate compared to N-acetylneuraminides (Neu5Ac). Here, we report characterization and crystal structures of putative sialidases from two other ascomycete fungal pathogens, Aspergillus terreus (AtS) and Trichophyton rubrum (TrS). Unlike A. fumigatus Kdnase (AfS), hydrolysis with the Neu5Ac substrates was negligible for TrS and AtS; thus, TrS and AtS are selective Kdnases. The second-order rate constant for hydrolysis of aryl Kdn glycosides by AtS is similar to that by AfS but 30-fold higher by TrS. The structures of these glycoside hydrolase family 33 (GH33) enzymes in complex with a range of ligands for both AtS and TrS show subtle changes in ring conformation that mimic the Michaelis complex, transition state, and covalent intermediate formed during catalysis. In addition, they can aid identification of important residues for distinguishing between Kdn and Neu5Ac substrates. When A. fumigatus, A. terreus, and T. rubrum were grown in chemically defined media, Kdn was detected in mycelial extracts, but Neu5Ac was only observed in A. terreus or T. rubrum extracts. The C8 monosaccharide 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) was also identified in A. fumigatus and T. rubrum samples. A fluorescent Kdn probe was synthesized and revealed the localization of AfS in vesicles at the cell surface.

Published
2021
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19. Biomacromolecules in recent phosphate-shelled brachiopods: identification and characterization of chitin matrix

Author

Kingsley C. Duru, Yue Liang, Glenn A. Brock, Lars E. Holmer, Oluwatoosin B. A. Agbaje, Zhifei Zhang, and Simon C. George

Subjects
chemistry.chemical_classification, Materials science, biology, Mechanical Engineering, Geology, engineering.material, Matrix (biology), Anatina, Polysaccharide, Phosphate, biology.organism_classification, Characterization (materials science), chemistry.chemical_compound, Chitin, chemistry, Chemical engineering, Mechanics of Materials, engineering, Ultrastructure, Geologi, General Materials Science, Biopolymer
Abstract

Abstract Phosphate-shelled brachiopods differ in filter-feeding lifestyle, with Lingula anatina an active infaunal burrower, and Discinisca tenuis a shallow marine epibenthic animal. The shells of these animals are built of organophosphatic constituents, the organic fibres/sheets reinforced with calcium phosphate to provide a sophisticated ultrastructural robustness. This investigation examined the nature of the organic fibres in order to improve understanding of how living organisms produce hierarchically structured biomaterials. Unlike powdered samples commonly used in previous studies, organic fibres were isolated for the first time and the shell fractions were purified, in order to study the content and nature of the biopolymer fibres. Biochemical methods including Calcofluor staining revealed a chitin matrix. Ultrastructural analysis, thermal gravimetric analysis, and spectroscopic analyses show that the core polysaccharide framework is composed of layers of β-chitin sheets and/or fibrils that are coated with a fibrous organic matrix. There is more chitin matrix in the L. anatina shells (26.6 wt.%) compared to the D. tenuis shells (12.9 wt.%). Taken together, the data show that the chitin matrix contributes to increased skeletal strength, making L. anatina highly adapted for life as an active burrower. In comparison, D. tenuis contains less chitin and lives as attached epibenthos in a shallow marine environment. Graphical abstract First spectroscopic evidence of β-chitin sheets in recent organophosphatic brachiopods

Published
2021
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20. Genetic modeling of GNAO1 disorder delineates mechanisms of Gαo dysfunction

Author

Brock Grill, Kirill A. Martemyanov, Andrew C. Giles, Brian S. Muntean, Maria Dao, and Dandan Wang

Subjects
Genetics, Brain Diseases, Cas9, Transgene, General Medicine, GTP-Binding Protein alpha Subunits, Gi-Go, Biology, medicine.disease, GNAO1, Disease Models, Animal, Mice, Neurodevelopmental disorder, Genome editing, GTP-Binding Proteins, Neurodevelopmental Disorders, Mutation, medicine, Animals, CRISPR, Allele, Caenorhabditis elegans, Molecular Biology, Genetics (clinical), Loss function
Abstract

GNAO1 encephalopathy is a neurodevelopmental disorder with a spectrum of symptoms that include dystonic movements, seizures and developmental delay. While numerous GNAO1 mutations are associated with this disorder, the functional consequences of pathological variants are not completely understood. Here, we deployed the invertebrate C. elegans as a whole-animal behavioral model to study the functional effects of GNAO1 disorder-associated mutations. We tested several pathological GNAO1 mutations for effects on locomotor behaviors using a combination of CRISPR/Cas9 gene editing and transgenic overexpression in vivo. We report that all three mutations tested (G42R, G203R and R209C) result in strong loss of function defects when evaluated as homozygous CRISPR alleles. In addition, mutations produced dominant negative effects assessed using both heterozygous CRISPR alleles and transgenic overexpression. Experiments in mice confirmed dominant negative effects of GNAO1 G42R, which impaired numerous motor behaviors. Thus, GNAO1 pathological mutations result in conserved functional outcomes across animal models. Our study further establishes the molecular genetic basis of GNAO1 encephalopathy, and develops a CRISPR-based pipeline for functionally evaluating mutations associated with neurodevelopmental disorders.

Published
2021
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21. Role of non-coding RNAs in tumor progression and metastasis in pancreatic cancer

Author

Andrew A. Brock, Katherine Powell, Lorenzo F. Sempere, Thomas D. Schmittgen, and Jatin Rana

Subjects
Long non-coding RNAs (lncRNA), Cancer Research, Biology, Article, Metastasis, Phosphatidylinositol 3-Kinases, Pancreatic cancer, microRNA, Tumor Microenvironment, medicine, Humans, microRNA (miR, Circular non-coding RNA (circRNA), PI3K/AKT/mTOR pathway, Tumor microenvironment, Cancer, Extracellular vesicles, miRNA), medicine.disease, Gene Expression Regulation, Neoplastic, Pancreatic Neoplasms, MicroRNAs, Oncology, Tumor progression, Cancer cell, Cancer research, Carcinoma, Pancreatic Ductal
Abstract

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of cancer with an overall 5-year survival rate of less than 10%. The 1-year survival rate of patients with locally advanced or metastatic disease is abysmal. The aggressive nature of cancer cells, hypovascularization, extensive desmoplastic stroma, and immunosuppressive tumor microenvironment (TME) endows PDAC tumors with multiple mechanisms of drug resistance. With no obvious genetic mutation(s) driving tumor progression or metastatic transition, the challenges for understanding the biological mechanism(s) of these processes are paramount. A better understanding of the molecular and cellular mechanisms of these processes could lead to new diagnostic tools for patient management and new targets for therapeutic intervention. microRNAs (miRNAs) are an evolutionarily conserved gene class of short non-coding regulatory RNAs. miRNAs are an extensive regulatory layer that controls gene expression at the posttranscriptional level. This review focuses on preclinical models that functionally dissect miRNA activity in tumor progression or metastatic processes in PDAC. Collectively, these studies suggest an influence of miRNAs and RNA-RNA networks in the processes of epithelial to mesenchymal cell transition and cancer cell stemness. At a cell-type level, some miRNAs mainly influence cancer cell–intrinsic processes and pathways, whereas other miRNAs predominantly act in distinct cellular compartments of the TME to regulate fibroblast and immune cell functions and/or influence other cell types’ function via cell-to-cell communications by transfer of extracellular vesicles. At a molecular level, the influence of miRNA-mediated regulation often converges in core signaling pathways, including TGF-β, JAK/STAT, PI3K/AKT, and NF-κB.

Published
2021
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22. Odour-based social recognition in Damaraland mole-rats, Fukomys damarensis

Author

Amy E. Leedale, Tim H. Clutton-Brock, and Jack Thorley

Subjects
Fukomys damarensis, Digging, Mate choice, Obligate, Breeding pair, Zoology, Biological dispersal, Animal Science and Zoology, Olfaction, Biology, Ecology, Evolution, Behavior and Systematics, Social recognition
Abstract

The ability to discriminate between conspecifics functions in mate choice, kin-selected cooperation and territory defence. In mammals, olfaction plays a key role in such social interactions. Olfactory cues may be particularly important for subterranean mammals, for which visual and acoustic cues are less effective. Damaraland mole-rats live in groups comprising a breeding pair and their nonbreeding offspring. They are xenophobic, obligate outbreeders and independent dispersal represents the usual route to reproduction for both sexes. As yet, little is known about how dispersing individuals locate mates. Using a series of behavioural experiments, we reveal that mole-rats can discriminate between unfamiliar breeding groups and solitary, nonbreeders of the opposite sex by using odour cues. Our experiments showed that subjects spent more time investigating sand taken from other mole-rat groups than control sand, indicating an ability to recognize substrate-borne conspecific odours. Mole-rats also spent more time digging and sweeping in sand taken from the tunnels of unfamiliar, solitary animals of the opposite sex than sand taken from unfamiliar breeding groups and removed a higher volume of this sand during the experiments. Together, these results suggest an olfactory preference in both sexes for solitary, opposite-sex animals over breeding groups. Our results are supported by observations from the field that immigration into breeding groups is rare, with dispersing females typically establishing new groups, where they are subsequently joined by unfamiliar males. This study supports olfaction as a potential recognition cue which may facilitate adaptive dispersal.

Published
2021
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23. Griddient: a microfluidic array to generate reconfigurable gradients on-demand for spatial biology applications.

Author

Sanchez-de-Diego, Cristina, Virumbrales-Muñoz, María, Hermes, Brock, Juang, Terry D., Juang, Duane S., Riendeau, Jeremiah, Guzman, Emmanuel Contreras, Reed-McBain, Catherine A., Abizanda-Campo, Sara, Patel, Janmesh, Hess, Nicholas J., Skala, Melissa C., Beebe, David J., and Ayuso, Jose M.

Subjects
BIOLOGY, FLUORESCENCE microscopy, CANCER invasiveness, MICROSCOPY, TISSUES
Abstract

Biological tissues are highly organized structures where spatial-temporal gradients (e.g., nutrients, hypoxia, cytokines) modulate multiple physiological and pathological processes including inflammation, tissue regeneration, embryogenesis, and cancer progression. Current in vitro technologies struggle to capture the complexity of these transient microenvironmental gradients, do not provide dynamic control over the gradient profile, are complex and poorly suited for high throughput applications. Therefore, we have designed Griddent, a user-friendly platform with the capability of generating controllable and reversible gradients in a 3D microenvironment. Our platform consists of an array of 32 microfluidic chambers connected to a 384 well-array through a diffusion port at the bottom of each reservoir well. The diffusion ports are optimized to ensure gradient stability and facilitate manual micropipette loading. This platform is compatible with molecular and functional spatial biology as well as optical and fluorescence microscopy. In this work, we have used this platform to study cancer progression. Griddient is a user-friendly platform that enables generation of controllable and reversible biochemical gradients in a 3D microenvironment. [ABSTRACT FROM AUTHOR]

Published
2023
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24. Crystal structure of the Na+/H+ antiporter NhaA at active pH reveals the mechanistic basis for pH sensing

Author

Iven Winkelmann, Povilas Uzdavinys, Ian M. Kenney, Joseph Brock, Pascal F. Meier, Lina-Marie Wagner, Florian Gabriel, Sukkyeong Jung, Rei Matsuoka, Christoph von Ballmoos, Oliver Beckstein, and David Drew

Subjects
Multidisciplinary, 540 Chemistry, General Physics and Astronomy, 570 Life sciences, biology, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract

The strict exchange of protons for sodium ions across cell membranes by Na+/H+ exchangers is a fundamental mechanism for cell homeostasis. At active pH, Na+/H+ exchange can be modelled as competition between H+ and Na+ to an ion-binding site, harbouring either one or two aspartic-acid residues. Nevertheless, extensive analysis on the model Na+/H+ antiporter NhaA from Escherichia coli, has shown that residues on the cytoplasmic surface, termed the pH sensor, shifts the pH at which NhaA becomes active. It was unclear how to incorporate the pH senor model into an alternating-access mechanism based on the NhaA structure at inactive pH 4. Here, we report the crystal structure of NhaA at active pH 6.5, and to an improved resolution of 2.2 Å. We show that at pH 6.5, residues in the pH sensor rearrange to form new salt-bridge interactions involving key histidine residues that widen the inward-facing cavity. What we now refer to as a pH gate, triggers a conformational change that enables water and Na+ to access the ion-binding site, as supported by molecular dynamics (MD) simulations. Our work highlights a unique, channel-like switch prior to substrate translocation in a secondary-active transporter.

Published
2022
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26. No loss of orexin/hypocretin, melanin‐concentrating hormone or locus coeruleus noradrenergic neurons in a rat model of chronic sleep restriction

Author

Andrew Baldin, Kazue Semba, Samuel Deurveilher, Michael Antonchuk, and Brock St C Saumure

Subjects
Adrenergic Neurons, Male, medicine.medical_specialty, Lateral hypothalamus, Melanin-concentrating hormone, chemical and pharmacologic phenomena, Stereology, Biology, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, medicine, Animals, Effects of sleep deprivation on cognitive performance, Rats, Wistar, Axon, 030304 developmental biology, Sleep restriction, Melanins, Orexins, 0303 health sciences, Hypothalamic Hormones, General Neuroscience, Rats, Orexin, Pituitary Hormones, medicine.anatomical_structure, Endocrinology, nervous system, chemistry, Locus coeruleus, Locus Coeruleus, Sleep, 030217 neurology & neurosurgery
Abstract

Chronic sleep restriction (CSR) is common in modern society, adversely affecting cognitive performance and health. Yet how it impacts neurons regulating sleep remains unclear. Several studies using mice reported substantial losses of wake-active orexin/hypocretin and locus coeruleus (LC) noradrenergic neurons, but not rapid eye movement sleep-active melanin-concentrating hormone (MCH) neurons, following CSR. Here, we used immunohistochemistry and stereology to examine orexin, MCH and LC noradrenergic neurons in a rat model of CSR that uses programmed wheel rotation (3 h on/1 h off; '3/1' protocol). Adult male Wistar rats underwent one or four cycles of the 4-day 3/1 CSR protocol, with 2-day recovery between cycles in home cages. Time-matched control rats were housed in locked wheels/home cages. We found no significant differences in the numbers of orexin, MCH and LC noradrenergic neurons following either one- or four-cycle CSR protocol compared to respective controls. Similarly, the four-cycle CSR protocol had no effect on the densities of orexin axon terminals in the LC, noradrenergic dendrites in the LC and noradrenergic axon terminals in the frontal cortex. Body weights, however, decreased after one cycle of CSR and then increased with diminishing slope over the next three cycles. Thus, we found no evidence for loss of orexin or LC noradrenergic neurons following one and four cycles of the 4-day 3/1 CSR protocol in rats. Differences in CSR protocols and/or possible species differences in neuronal vulnerability to sleep loss may account for the discrepancy between the current results in rats and previous findings in mice.

Published
2021
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27. Microglia and its Genetics in Alzheimer's Disease

Author

Xinyan Liang, Zhen Zhao, Xinying Guo, Shupeng Dong, Mark Colt, Haijian Wu, Jianxiong Zeng, and Brock Pluimer

Subjects
Central Nervous System, Apolipoprotein E, Amyloid beta-Peptides, biology, Microglia, TREM2, Tau protein, Context (language use), Disease, medicine.disease, Article, medicine.anatomical_structure, Neurology, Alzheimer Disease, biology.protein, medicine, Humans, Dementia, Neurology (clinical), Neuroscience, Neuroinflammation, Genome-Wide Association Study
Abstract

Alzheimer’s Disease (AD) is the most prevalent form of dementia across the world. While its discovery and pathological manifestations are centered on protein aggregations of amyloid- beta (Aβ) and hyperphosphorylated tau protein, neuroinflammation has emerged in the last decade as a main component of the disease in terms of both pathogenesis and progression. As the main innate immune cell type in the central nervous system (CNS), microglia play a very important role in regulating neuroinflammation, which occurs commonly in neurodegenerative conditions, including AD. Under inflammatory response, microglia undergo morphological changes and status transition from homeostatic to activated forms. Different microglia subtypes displaying distinct genetic profiles have been identified in AD, and these signatures often link to AD risk genes identified from the genome-wide association studies (GWAS), such as APOE and TREM2. Furthermore, many AD risk genes are highly enriched in microglia and specifically influence the functions of microglia in pathogenesis, e.g. releasing inflammatory cytokines and clearing Aβ. Therefore, building up a landscape of these risk genes in microglia, based on current preclinical studies and in the context of their pathogenic or protective effects, would largely help us to understand the complex etiology of AD and provide new insight into the unmet need for effective treatment.

Published
2021
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28. Behavioural change during dispersal and its relationship to survival and reproduction in a cooperative breeder

Author

Andre Ganswindt, Tim H. Clutton-Brock, Paul J. Haverkamp, Gabriele Cozzi, Marta B. Manser, Arpat Ozgul, Natasha D. Harrison, Nino Maag, Harrison, Natasha D [0000-0001-5779-0187], Maag, Nino [0000-0002-1818-0674], Haverkamp, Paul J [0000-0002-3756-0795], Ganswindt, André [0000-0002-1474-7602], Ozgul, Arpat [0000-0001-7477-2642], Cozzi, Gabriele [0000-0002-1744-1940], Apollo - University of Cambridge Repository, University of Zurich, and Harrison, Natasha D

Subjects
0106 biological sciences, Evolution, Herpestidae, media_common.quotation_subject, Foraging, Biology, survival, 010603 evolutionary biology, 01 natural sciences, foraging, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, vigilance, reproductive skew, medicine, Animals, dispersal, Glucocorticoids, Research Articles, Ecology, Evolution, Behavior and Systematics, Behavioural Ecology, Demography, 030304 developmental biology, media_common, faecal glucocorticoid metabolites, Suricata suricatta, 0303 health sciences, Ecology, Aggression, Reproduction, 15. Life on land, 1105 Ecology, Evolution, Behavior and Systematics, Vigilance (behavioural ecology), behavioural response, 570 Life sciences, biology, 590 Animals (Zoology), Biological dispersal, Female, Animal Science and Zoology, Population Ecology, 1103 Animal Science and Zoology, medicine.symptom, FOS: Medical biotechnology, Research Article
Abstract

Funder: University of Zurich; Id: http://dx.doi.org/10.13039/501100006447, Funder: MAVA Foundation, Funder: Mammal Research Institute at the University of Pretoria, The ability of dispersing individuals to adjust their behaviour to changing conditions is instrumental in overcoming challenges and reducing dispersal costs, consequently increasing overall dispersal success. Understanding how dispersers' behaviour and physiology change during the dispersal process, and how they differ from resident individuals, can shed light on the mechanisms by which dispersers increase survival and maximise reproduction. By analysing individual behaviour and concentrations of faecal glucocorticoid metabolites (fGCM), a stress-associated biomarker, we sought to identify the proximate causes behind differences in survival and reproduction between dispersing and resident meerkats Suricata suricatta. We used data collected on 67 dispersing and 108 resident females to investigate (a) which individual, social and environmental factors are correlated to foraging and vigilance, and whether the role of such factors differs among dispersal phases, and between dispersers and residents; (b) how time allocated to either foraging or vigilance correlated to survival in dispersers and residents and (c) the link between aggression and change in fGCM concentration, and their relationship with reproductive rates in dispersing groups and resident groups with either long-established or newly established dominant females. Time allocated to foraging increased across dispersal phases, whereas time allocated to vigilance decreased. Time allocated to foraging and vigilance correlated positively and negatively, respectively, with dispersers' group size. We did not find a group size effect for residents. High proportions of time allocated to foraging correlated with high survival, and more so in dispersers, suggesting that maintaining good physical condition may reduce mortality during dispersal. Furthermore, while subordinate individuals rarely reproduced in resident groups, the conception rate of subordinates in newly formed dispersing groups was equal to that of their dominant individuals. Mirroring conception rates, in resident groups, fGCM concentrations were lower in subordinates than in dominants, whereas in disperser groups, fGCM concentrations did not differ between subordinates and dominants. Our results, which highlight the relationship between behavioural and physiological factors and demographic rates, provide insights into some of the mechanisms that individuals of a cooperative species can use to increase overall dispersal success.

Published
2021
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29. A likely association of damselflies with the habitat heterogeneity provided by the freshwater swamp lily,Ottelia ovalifolia, in Eyre Peninsula granite rock-holes, with a review of potential threats to this ephemeral habitat

Author

Philip Weinstein, John G. Conran, Gary S. Taylor, Chris P. Madden, Andrew D. Austin, and Brock A. Hedges

Subjects
biology, Ottelia ovalifolia, Swamp lily, Ecology, Ephemeral key, Paleontology, Hydrocharitaceae, biology.organism_classification, Odonata, Spatial heterogeneity, Geography, Habitat, Eyre peninsula, Anthropology, General Agricultural and Biological Sciences, General Environmental Science
Abstract

The granite rock-holes (sometimes called gnammas) across northern Eyre Peninsula (EP), South Australia, are a unique but poorly studied ephemeral freshwater habitat containing a complex invertebrat...

Published
2021
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30. Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma

Author

W. G. Li, Matthew D. Ringel, Sandya Liyanarachchi, Pearlly S. Yan, Albert de la Chapelle, Daniel F. Comiskey, Huiling He, Ralf Bundschuh, Altan M. Turkoglu, and Pamela Brock

Subjects
Male, 0301 basic medicine, Cell biology, endocrine system, endocrine system diseases, Carcinogenesis, Science, Thyroid Gland, Apoptosis, Pathogenesis, Biology, medicine.disease_cause, Article, Thyroid carcinoma, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Gene expression, Genetics, medicine, Humans, Thyroid cancer, Aged, Cell Proliferation, Multidisciplinary, Gene Expression Profiling, Thyroid, fungi, Computational Biology, Cancer, Middle Aged, Microarray Analysis, medicine.disease, Neoplasm Proteins, Gene Expression Regulation, Neoplastic, 030104 developmental biology, medicine.anatomical_structure, Thyroid Cancer, Papillary, 030220 oncology & carcinogenesis, Cancer research, Medicine, Female, Lymphocytic Thyroiditis
Abstract

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The molecular characteristics of histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed total RNA sequencing with fresh frozen thyroid tissues from a cohort of three categories of samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex or the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 256 coding genes and 5 noncoding genes have been reported as cancer genes involved in cell proliferation, apoptosis, and/or tumorigenesis. Bioinformatics analysis with Ingenuity Pathway Analysis software revealed that “Cancer, Organismal Injury and Abnormalities, Cellular Response to Therapeutics, and Cellular Movement” were major dysregulated pathways in the NAT tissues. This study provides improved insight into the complexity of gene expression changes in the thyroid glands of patients with PTC.

Published
2021

31. Context-dependent effects of whole-genome duplication during mammary tumor recurrence

Author

James V. Alvarez, Emily Dean, Brock McKinney, and Rachel Newcomb

Subjects
0301 basic medicine, Receptor, ErbB-2, Science, Context (language use), Mice, Transgenic, Biology, Article, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Mice, 0302 clinical medicine, Breast cancer, Chromosome instability, Cell Line, Tumor, Chromosomal Instability, Gene Duplication, Gene duplication, medicine, Animals, Humans, Cancer genetics, In Situ Hybridization, Fluorescence, Cell Proliferation, Mammary tumor, Multidisciplinary, Cancer, Mammary Neoplasms, Experimental, medicine.disease, 030104 developmental biology, Tumor progression, 030220 oncology & carcinogenesis, Karyotyping, Cancer research, Medicine, Female, Ploidy
Abstract

Whole-genome duplication (WGD) generates polyploid cells possessing more than two copies of the genome and is among the most common genetic abnormalities in cancer. The frequency of WGD increases in advanced and metastatic tumors, and WGD is associated with poor prognosis in diverse tumor types, suggesting a functional role for polyploidy in tumor progression. Experimental evidence suggests that polyploidy has both tumor-promoting and suppressing effects, but how polyploidy regulates tumor progression remains unclear. Using a genetically engineered mouse model of Her2-driven breast cancer, we explored the prevalence and consequences of whole-genome duplication during tumor growth and recurrence. While primary tumors in this model are invariably diploid, nearly 40% of recurrent tumors undergo WGD. WGD in recurrent tumors was associated with increased chromosomal instability, decreased proliferation and increased survival in stress conditions. The effects of WGD on tumor growth were dependent on tumor stage. Surprisingly, in recurrent tumor cells WGD slowed tumor formation, growth rate and opposed the process of recurrence, while WGD promoted the growth of primary tumors. These findings highlight the importance of identifying conditions that promote the growth of polyploid tumors, including the cooperating genetic mutations that allow cells to overcome the barriers to WGD tumor cell growth and proliferation.

Published
2021

32. Using camera traps to estimate ungulate abundance: a comparison of mark–resight methods

Author

Jericho C. Whiting, Brock R. McMillan, Steven B. Bates, Jace C. Taylor, and Randy T. Larsen

Subjects
Technology, remote cameras, Ungulate, Ecology, biology, symbols.heraldic_supporter, bighorn sheep, biology.organism_classification, motion sensor cameras, Geography, population monitoring, Abundance (ecology), symbols, ungulates, Ovis canadensis, Computers in Earth Sciences, Mark resight, QH540-549.5, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

Many global wildlife populations are experiencing unprecedented declines. Estimates of population abundance are needed to effectively manage common species and to conserve vulnerable species. Camera traps have advanced as wildlife monitoring tools for ungulates and can provide improved methods of estimating population abundance. Little is known, however, about how camera traps set for ungulates compare with traditional methods (e.g., ground and aerial surveys) used simultaneously. From 2012 to 2014, we captured and radio collared 34 female and 32 male bighorn sheep (Ovis canadensis) in a closed population in Utah, USA. Each collar had a unique letter and number combination. We then estimated number of young, females and yearlings, males and population abundance using multiple methods simultaneously: helicopter surveys, resight surveys performed from the ground, camera trap surveys using marked but not individually identifiable individuals and camera trap surveys using marked and individually identifiable animals. All methods estimated similar abundance. Across years, ages and sexes, however, camera trap surveys produced the most consistent and precise estimates of abundance for adult females and yearlings, lambs and the population. That method was less intrusive and safer than helicopter surveys. Our results indicate that camera trap surveys using photographs of marked animals in which the majority of the population visits a specific resource can produce precise estimates of abundance that are safer, as well as less intrusive and expensive than traditional methods. Using camera traps also creates a permanent record of photographs that can be archived and reanalyzed to answer future ecological and population questions. Finally, this method of estimating abundance can be used in other areas with ungulates that congregate around resources (e.g., watering sites or mineral licks).

Published
2021
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33. Does condition of adult male cervids reflect condition of adult females? A test with mule deer

Author

Jon C. Boren, Louis C. Bender, S. H. Cox, and Brock D. Hoenes

Subjects
education.field_of_study, Rump, Adult male, Adult female, Population, Biology, Subcutaneous fat, Body condition score, Animal ecology, Animal Science and Zoology, education, Ecology, Evolution, Behavior and Systematics, Body condition, Demography
Abstract

Body condition integrates the effects of habitat on individuals and consequently population performance of cervids. However, most condition data is likely to come from harvested males, which may not reflect absolute condition of, or habitat quality for, adult females because of basic ecological differences. To test whether condition of males reflected condition of females, we compared three indices of nutritional condition (rump body condition score, maximum subcutaneous fat thickness, and percent body fat) of adult male, lactating adult female, and dry adult female mule deer over multiple years in 2 sites in New Mexico, USA. Males consistently achieved significantly higher levels of condition than females for all indices of condition, regardless of whether indices for males were scaled for metabolic size or not. Because population productivity and rate-of-increase is driven by condition and consequent performance of females, population monitoring strategies that assess only condition of males may not reflect absolute condition of females and thus habitat quality as it fundamentally relates to population dynamics of cervids. Condition of males, however, can likely index relative habitat quality if not absolute.

Published
2021
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34. Single-cell analysis can define distinct evolution of tumor sites in follicular lymphoma

Author

Hojoon Lee, Hanlee P. Ji, Michael S. Binkley, Grady Day, Sarah Haebe, Steven R. Long, Brock A. Martin, Ronald Levy, Debra K. Czerwinski, Susan M. Grimes, Tanaya Shree, and Anuja Sathe

Subjects
Male, 0301 basic medicine, Follicular lymphoma, Biochemistry, 0302 clinical medicine, Single-cell analysis, Tumor Microenvironment, Gene Rearrangement, B-Lymphocyte, Light Chain, RNA, Neoplasm, Lymphoma, Follicular, Phylogeny, medicine.diagnostic_test, breakpoint cluster region, DNA, Neoplasm, Hematology, Middle Aged, Flow Cytometry, Neoplasm Proteins, Disease Progression, Biomarker (medicine), Female, Single-Cell Analysis, Adult, T Follicular Helper Cells, Biopsy, Fine-Needle, CD40 Ligand, Immunology, Biology, Gene Rearrangement, T-Lymphocyte, Flow cytometry, Clonal Evolution, 03 medical and health sciences, Lymphocytes, Tumor-Infiltrating, Antigens, Neoplasm, Sequence Homology, Nucleic Acid, medicine, Humans, CD40 Antigens, Aged, Tumor microenvironment, T-cell receptor, Cell Biology, medicine.disease, Lymphoma, 030104 developmental biology, Cancer research, Lymph Nodes, Transcriptome, Sequence Alignment, 030215 immunology
Abstract

Tumor heterogeneity complicates biomarker development and fosters drug resistance in solid malignancies. In lymphoma, our knowledge of site-to-site heterogeneity and its clinical implications is still limited. Here, we profiled 2 nodal, synchronously acquired tumor samples from 10 patients with follicular lymphoma (FL) using single-cell RNA, B-cell receptor (BCR) and T-cell receptor sequencing, and flow cytometry. By following the rapidly mutating tumor immunoglobulin genes, we discovered that BCR subclones were shared between the 2 tumor sites in some patients, but in many patients, the disease had evolved separately with limited tumor cell migration between the sites. Patients exhibiting divergent BCR evolution also exhibited divergent tumor gene-expression and cell-surface protein profiles. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper (Tfh) cell abundance. We further observed enrichment of particular ligand-receptor pairs between tumor and Tfh cells, including CD40 and CD40LG, and a significant correlation between tumor CD40 expression and Tfh proliferation. Our study may explain discordant responses to systemic therapies, underscores the difficulty of capturing a patient’s disease with a single biopsy, and furthers our understanding of tumor-immune networks in FL.

Published
2021
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35. Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma

Author

Dadong Zhang, Jeremy Gresham, David G. Kirsch, Andrea R. Daniel, Isibel Caraballo, Lixia Luo, Chang-Lung Lee, Alexander B. Sibley, Stephanie Hasapis, Xiaodi Qin, Kennedy Davis Brock, Kouros Owzar, and Matthew J. Hilton

Subjects
Male, Cancer Research, Lymphoma, Somatic cell, Biology, medicine.disease_cause, Article, Mice, hemic and lymphatic diseases, Exome Sequencing, medicine, Animals, Receptor, Notch1, Exome sequencing, Thymic Lymphoma, Wild type, Thymus Neoplasms, medicine.disease, Transplantation, Disease Models, Animal, Thymocyte, Oncology, Cancer research, Female, Tumor Suppressor Protein p53, Carcinogenesis
Abstract

Mouse models of radiation-induced thymic lymphoma are widely used to study the development of radiation-induced blood cancers and to gain insights into the biology of human T-cell lymphoblastic leukemia/lymphoma. Here we aimed to identify key oncogenic drivers for the development of radiation-induced thymic lymphoma by performing whole-exome sequencing using tumors and paired normal tissues from mice with and without irradiation. Thymic lymphomas from irradiated wild-type (WT), p53+/−, and KrasLA1 mice were not observed to harbor significantly higher numbers of nonsynonymous somatic mutations compared with thymic lymphomas from unirradiated p53−/− mice. However, distinct patterns of recurrent mutations arose in genes that control the Notch1 signaling pathway based on the mutational status of p53. Preferential activation of Notch1 signaling in p53 WT lymphomas was also observed at the RNA and protein level. Reporter mice for activation of Notch1 signaling revealed that total-body irradiation (TBI) enriched Notch1hi CD44+ thymocytes that could propagate in vivo after thymocyte transplantation. Mechanistically, genetic inhibition of Notch1 signaling in immature thymocytes prevented formation of radiation-induced thymic lymphoma in p53 WT mice. Taken together, these results demonstrate a critical role of activated Notch1 signaling in driving multistep carcinogenesis of thymic lymphoma following TBI in p53 WT mice. Significance: These findings reveal the mutational landscape and key drivers in murine radiation-induced thymic lymphoma, a classic animal model that has been used to study radiation carcinogenesis for over 70 years.

Published
2021
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36. Associations of Osteocalcin Forms With Metabolic Syndrome and Its Individual Components in Older Men: The Health In Men Study

Author

Leon Flicker, Bu B. Yeap, Itamar Levinger, Tara C. Brennan-Speranza, Xiaoying Liu, Kaye E. Brock, and Jonathan Golledge

Subjects
Blood Glucose, Male, medicine.medical_specialty, Waist, Endocrinology, Diabetes and Metabolism, Osteocalcin, Clinical Biochemistry, Hydroxyapatite binding, Blood Pressure, Context (language use), Type 2 diabetes, Lower risk, Biochemistry, Endocrinology, Insulin resistance, Internal medicine, medicine, Humans, Triglycerides, Aged, Metabolic Syndrome, biology, business.industry, Cholesterol, HDL, Biochemistry (medical), Western Australia, Middle Aged, medicine.disease, Cross-Sectional Studies, biology.protein, Waist Circumference, Metabolic syndrome, business, Biomarkers
Abstract

Context The osteoblast-derived polypeptide, osteocalcin (OC), has been associated with lower risk of type 2 diabetes and metabolic syndrome (MetS) in several epidemiological studies. Animal studies have indicated the undercarboxylated form of OC (ucOC) drives its association with metabolic outcomes. Objective We compared associations of ucOC and carboxylated OC (cOC) with MetS and its components in older men. Methods A cross-sectional analysis of 2575 men aged ≥70 years and older resident in Perth, Western Australia. ucOC was assayed using a hydroxyapatite-binding method, and cOC calculated by subtracting ucOC from total OC. Main outcome measures were MetS and its components. Results Both lower serum ucOC and cOC levels, and the proportion of cOC (%cOC) were associated with less favorable metabolic parameters (higher waist circumference, triglyceride, glucose, blood pressure, and lower high-density lipoprotein cholesterol), whereas inverse associations were found with %ucOC. Men in the lowest quintile of ucOC had higher risk of MetS compared to men in the highest quintile (Q1 ≤ 7.7 vs Q5 > 13.8 ng/mL; OR = 2.4; 95% CI, 1.8-3.2). Men in the lowest quintile of cOC had higher risk of MetS compared to those in the highest quintile (≤ 5.8 vs > 13.0 ng/mL; OR = 2.4; 95% CI, 1.8-3.2). Conclusion Lower concentrations of serum ucOC or cOC were associated with less favorable metabolic parameters and a higher risk of MetS. In contrast, a lower proportion of ucOC was associated with better metabolic parameters and lower MetS risk. Further research is warranted to determine whether ucOC and cOC are suitable biomarkers for cardiometabolic risk in men.

Published
2021
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37. Constitutive activation of MEK5 promotes a mesenchymal and migratory cell phenotype in triple negative breast cancer

Author

Aaron Buechlein, Hope E. Burks, Van T. Hoang, Courtney K. Brock, Jane E. Cavanaugh, Jacqueline La, Steven Elliott, Patrick T. Flaherty, Matthew E. Burow, Margarite D. Matossian, Douglas B. Rusch, Kenneth P. Nephew, Bridgette M. Collins-Burow, and Akshita B. Bhatt

Subjects
MAPK/ERK pathway, Cancer Research, cell migration, Cell growth, Mesenchymal stem cell, Cell, epithelial to mesenchymal transition, Cell migration, Biology, ERK5, medicine.anatomical_structure, Oncology, triple negative breast cancer, Cancer research, medicine, Epithelial–mesenchymal transition, Signal transduction, MEK5, Triple-negative breast cancer, Research Paper
Abstract

Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited targeted therapeutic options. A defining feature of TNBC is the propensity to metastasize and acquire resistance to cytotoxic agents. Mitogen activated protein kinase (MAPK) and extracellular regulated kinase (ERK) signaling pathways have integral roles in cancer development and progression. While MEK5/ERK5 signaling drives mesenchymal and migratory cell phenotypes in breast cancer, the specific mechanisms underlying these actions remain under-characterized. To elucidate the mechanisms through which MEK5 regulates the mesenchymal and migratory phenotype, we generated stably transfected constitutively active MEK5 (MEK5-ca) TNBC cells. Downstream signaling pathways and candidate targets of MEK5-ca cells were based on RNA sequencing and confirmed using qPCR and Western blot analyses. MEK5 activation drove a mesenchymal cell phenotype independent of cell proliferation effects. Transwell migration assays demonstrated MEK5 activation significantly increased breast cancer cell migration. In this study, we provide supporting evidence that MEK5 functions through FRA-1 to regulate the mesenchymal and migratory phenotype in TNBC.

Published
2021
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38. Comment on 'Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species'

Author

Bryan C. Carstens, M. Brock Fenton, Nancy B. Simmons, and Ariadna E. Morales

Subjects
0106 biological sciences, 0303 health sciences, biology, Myotis evotis, Population genetics, Zoology, Myotis keenii, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Long-eared myotis, 03 medical and health sciences, Single species, Animal Science and Zoology, Genetic exchange, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Genetic exchange and hybridization appear common among the western long-eared bats from North America. Multiple sources of evidence indicate that lineages within this group are evolving independently, despite genetic exchange. However, evidence of gene flow raises questions about the species-level status of some lineages. C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279) proposed that Myotis evotis (H. Allen, 1864) (long-eared myotis) and Myotis keenii (Merriam, 1895) (Keen’s myotis) are one species, not two. This conclusion is based on analyses of cytochrome b and microsatellite data suggesting gene flow between these taxa. Microsatellites are not reliable markers for identifying species because homoplasy can be a major confounding factor, which appears to be true in this case. We reanalyzed the dataset of C.L. Lausen et al. (2019) and show that it is not reliable to distinguish between gene flow or homoplasy, and that these data do not support the conclusion that M. evotis and M. keenii represent a single species. Previous morphological and genomic studies indicate that these are separate species despite previous genetic exchange between them. Failing to recognize that gene flow can occur between independently evolving lineages is counterproductive for conservation because it can lead to neglect of important independent lineages, and likewise failing to use proper tools to delimit species is counterproductive to efforts to quantify biodiversity and design conservation strategies.

Published
2021
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39. Recruitment dynamics of non-native largemouth bass within the Sacramento–San Joaquin Delta

Author

Brock M. Huntsman, Joseph E. Kirsch, James A. Hobbs, Brian Mahardja, Matthew J. Young, Swee J. Teh, Frederick Feyrer, and Shawn Acuña

Subjects
Fishery, Delta, Bass (fish), food.ingredient, food, biology, Habitat, Micropterus, Aquatic Science, San Joaquin, biology.organism_classification, Ecology, Evolution, Behavior and Systematics, Early life
Abstract

Largemouth bass (LMB; Micropterus salmoides) recruitment is limited by a critical developmental period during early life stages, but this mechanism may be less important within non-native habitats. We conducted boat electrofishing surveys in four tidal lakes of California’s Sacramento–San Joaquin Delta (SSJD) from 2010 to 2011 to describe introduced LMB recruitment dynamics. We evaluated growth, proximate composition, and health indices of young-of-the-year (YOY) LMB among tidal lakes and developed an integrated count model to determine how factors known to affect LMB recruitment shape SSJD population structure. Our results show a mismatch among growth, nutrition, and YOY abundance, where the tidal lake with the most abundant and fastest-growing LMB had the poorest nutritional status. The warm winter water temperatures and lack of a hatching-cohort growth advantage suggests overwinter starvation plays a less important role in SSJD LMB recruitment than in many native LMB habitats. Collectively, our results suggest that habitat characteristics (submerged aquatic vegetation) and not overwinter mortality shapes SSJD LMB population structure, a mechanism consistent with contemporary hypotheses about the altered fish community structure of the SSJD.

Published
2021
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40. Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation

Author

Jenna A. Lee, Adam C. Martiny, Nicola A. Wiseman, Melissa L. Brock, J. Keith Moore, Lucas J. Ustick, Alyse A. Larkin, Catherine A. Garcia, and Nathan S. Garcia

Subjects
Nitrogen, Iron, Oceans and Seas, Phosphates, Iron assimilation, Phosphorus metabolism, Nutrient, Stress, Physiological, Nitrogen Fixation, Phytoplankton, Seawater, Atlantic Ocean, Indian Ocean, Nitrogen cycle, Prochlorococcus, Nitrates, Pacific Ocean, Multidisciplinary, biology, Ecology, Phosphorus, Nutrients, biology.organism_classification, Adaptation, Physiological, Genes, Bacterial, Metagenomics, Metagenome, Environmental science, Hydrography
Abstract

Genomes reveal nutrient stress patterns Within the surface ocean, nitrogen, iron, and phosphorous can all be limiting nutrients for phytoplankton depending on location. Ustick et al. used the prevalence of Prochlorococcus genes involved in nutrient acquisition to develop maps of inferred nutrient stress across the global ocean (see the Perspective by Coleman). They found broad patterns of limitation consistent with an Earth system model and nutrient addition experiments. Leveraging metagenomic data in this manner is an appealing approach that will help to expand our understanding of the biogeochemistry in the vast open ocean. Science , this issue p. 287 ; see also p. 239

Published
2021
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41. SARS-CoV-2 Cardiac Involvement in Young Competitive Athletes

Author

Nathaniel Moulson, Bradley J. Petek, Jonathan A. Drezner, Kimberly G. Harmon, Stephanie A. Kliethermes, Manesh R. Patel, Aaron L. Baggish, Irfan M. Asif, James Borchers, Katherine M. Edenfield, Michael S. Emery, Kyle Goerl, Brian Hainline, Jonathan H. Kim, William E. Kraus, Rachel Lampert, Matthew Leiszler, Benjamin D. Levine, Matthew W. Martinez, Francis G. O’Connor, Dermot Phelan, Lawrence D. Rink, Herman A. Taylor, Carl Ade, Aryan Aiyer, Jarrah Alfadhli, Chloe Amaradio, Scott Anderson, Stephanie Arlis-Mayor, Jonathan S. Aubry, Andrea Austin, Timothy Beaver, Nicolas Benitez, Brant Berkstresser, Thomas M. Best, Tiffany Bohon, Jonathan P. Bonnet, Elizabeth Boyington, James Bray, Jenna Bryant, Sean Carnahan, Rachel Chamberlain, Samantha Charters, Timothy W. Churchill, Douglas Comeau, Laura E. Cook, Deanna Corey, Amy Costa, Marshall Crowther, Tarun Dalia, Craig Davidson, Kaitlin Davitt, Annabelle De St Maurice, Peter N. Dean, Katelyn DeZenzo, Courtney Dimitris, Jeanne Doperak, Calvin Duffaut, Craig Fafara, Katherine Fahy, Jason Ferderber, Megan Finn, Angelo Galante, Todd Gerlt, Amy Gest, Carla Gilson, Jeffrey Goldberger, Joshua Goldman, Erich Groezinger, Jonathan R. Guin, Heather Halseth, Joshua Hare, Beth Harness, Nicolas Hatamiya, Julie Haylett, Neal Hazen, Yeun Hiroi, Amy Hockenbrock, Amanda Honsvall, Jennifer Hopp, Julia Howard, Samantha Huba, Mustafa Husaini, Lindsay Huston, Calvin Hwang, Laura Irvin, Val Gene Iven, Robert Jones, Donald Joyce, Kristine Karlson, Christian Klein, Chris Klenck, Michele Kirk, Jordan Knight, Laura Knippa, Madeleine Knutson, Louis E. Kovacs, Yumi Kuscher, Andrea Kussman, Chrissy Landreth, Amy Leu, Dylan Lothian, Maureen Lowery, Andrew Lukjanczuk, John M. MacKnight, Lawrence M. Magee, Marja-Liisa Magnuson, Aaron V. Mares, Anne Marquez, Grant McKinley, Megan Meier, Christopher Miles, Emily Miller, Hannah Miller, Raul Mitrani, Robert J. Myerburg, Greg Mytyk, Andrew Narver, Aurelia Nattiv, Laika Nur, Brooke E. Organ, Meredith Pendergast, Frank A. Pettrone, Sourav K. Poddar, Diana Priestman, Ian Quinn, Fred Reifsteck, Morgan Restivo, James B. Robinson, Ryan Roe, Thomas Rosamond, Carrie Rubertino Shearer, Miguel Rueda, Takamasa Sakamoto, Brock Schnebel, Ankit B. Shah, Alan Shahtaji, Kevin Shannon, Polly Sheridan-Young, Siobhan M. Statuta, Mark Stovak, Andrei Tarsici, Kenneth S. Taylor, Kim Terrell, Matt Thomason, Jason Tso, Daniel Vigil, Francis Wang, Jennifer Winningham, and Susanna T. Zorn

Subjects
medicine.medical_specialty, 2019-20 coronavirus outbreak, Myocarditis, Coronavirus disease 2019 (COVID-19), Adverse outcomes, Hospitalized patients, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Competitive athletes, 030204 cardiovascular system & hematology, 03 medical and health sciences, 0302 clinical medicine, Physiology (medical), Internal medicine, Original Research Articles, medicine, Humans, 030212 general & internal medicine, biology, Athletes, business.industry, SARS-CoV-2, COVID-19, medicine.disease, biology.organism_classification, Return to Sport, athletes, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, myocarditis, Cardiology and Cardiovascular Medicine, business
Abstract

Supplemental Digital Content is available in the text., Background: Cardiac involvement among hospitalized patients with severe coronavirus disease 2019 (COVID-19) is common and associated with adverse outcomes. This study aimed to determine the prevalence and clinical implications of COVID-19 cardiac involvement in young competitive athletes. Methods: In this prospective, multicenter, observational cohort study with data from 42 colleges and universities, we assessed the prevalence, clinical characteristics, and outcomes of COVID-19 cardiac involvement among collegiate athletes in the United States. Data were collected from September 1, 2020, to December 31, 2020. The primary outcome was the prevalence of definite, probable, or possible COVID-19 cardiac involvement based on imaging definitions adapted from the Updated Lake Louise Imaging Criteria. Secondary outcomes included the diagnostic yield of cardiac testing, predictors for cardiac involvement, and adverse cardiovascular events or hospitalizations. Results: Among 19 378 athletes tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 3018 (mean age, 20 years [SD, 1 year]; 32% female) tested positive and underwent cardiac evaluation. A total of 2820 athletes underwent at least 1 element of cardiac triad testing (12-lead ECG, troponin, transthoracic echocardiography) followed by cardiac magnetic resonance imaging (CMR) if clinically indicated. In contrast, primary screening CMR was performed in 198 athletes. Abnormal findings suggestive of SARS-CoV-2 cardiac involvement were detected by ECG (21 of 2999 [0.7%]), cardiac troponin (24 of 2719 [0.9%]), and transthoracic echocardiography (24 of 2556 [0.9%]). Definite, probable, or possible SARS-CoV-2 cardiac involvement was identified in 21 of 3018 (0.7%) athletes, including 15 of 2820 (0.5%) who underwent clinically indicated CMR (n=119) and 6 of 198 (3.0%) who underwent primary screening CMR. Accordingly, the diagnostic yield of CMR for SARS-CoV-2 cardiac involvement was 4.2 times higher for a clinically indicated CMR (15 of 119 [12.6%]) versus a primary screening CMR (6 of 198 [3.0%]). After adjustment for race and sex, predictors of SARS-CoV-2 cardiac involvement included cardiopulmonary symptoms (odds ratio, 3.1 [95% CI, 1.2, 7.7]) or at least 1 abnormal triad test result (odds ratio, 37.4 [95% CI, 13.3, 105.3]). Five (0.2%) athletes required hospitalization for noncardiac complications of COVID-19. During clinical surveillance (median follow-up, 113 days [interquartile range=90 146]), there was 1 (0.03%) adverse cardiac event, likely unrelated to SARS-CoV-2 infection. Conclusions: SARS-CoV-2 infection among young competitive athletes is associated with a low prevalence of cardiac involvement and a low risk of clinical events in short-term follow-up.

Published
2021

42. Neofusicoccum caryigenum, a new species causing leaf dieback disease of pecan (Carya illinoinensis)

Author

Cynthia T. Chan, Bhabesh Dutta, L J Grauke, Courtney J Cameron, Marin Talbot Brewer, Ronald D. Gitaitis, Jason Brock, and Timothy B. Brenneman

Subjects
0106 biological sciences, Species complex, Physiology, 010603 evolutionary biology, 01 natural sciences, 030308 mycology & parasitology, 03 medical and health sciences, food, Botany, Genetics, medicine, Internal transcribed spacer, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 0303 health sciences, biology, Carya illinoinensis, Juglandaceae, Cell Biology, General Medicine, Pecan scab, Botryosphaeriaceae, biology.organism_classification, medicine.disease, food.food, Neofusicoccum, Conidiomata
Abstract

Neofusicoccum species are endophytes and pathogens of woody hosts and members of the Botryosphaeriaceae. Leaf dieback is a new disease resulting in death of compound leaves and extensive defoliation of pecan trees (Carya illinoinensis) throughout the southeastern United States. Currently, the disease is consistently most severe on trees that are not managed with fungicides for pecan scab. Preliminary observations of the fungus isolated from symptomatic leaves indicated that it was a member of the genus Neofusicoccum. Our objectives were to confirm that this is the causal organism of leaf dieback disease of pecan and to determine whether this disease is caused by a new or previously described species of Neofusicoccum. Morphological observations of pure cultures, conidiomata, conidiogenous cells, and conidia were consistent with members of the genus Neofusicoccum. Using Koch's postulates, we established that Neofusicoccum sp. isolated from symptomatic leaves caused the disease. We sequenced the internal transcribed spacer of the rDNA (ITS), elongation factor 1-α (EF1-α), the second largest subunit of RNA polymerase II (RPB2), and β-tubulin (TUB2) of 11 isolates collected from Georgia and Texas. Phylogenetic and network analyses of these sequences combined with publicly available sequences of 40 members of the N. parvum-N. ribis species complex and the outgroup N. australe revealed that this fungus is a member of the species complex but is genetically distinct from previously described species. We determined that leaf dieback of pecan is caused by a novel species, named herein N. caryigenum.

Published
2021
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43. Identification of a foetal epigenetic compartment in adult human kidney

Author

Devin C. Koestler, John K. Wiencke, Brock C. Christensen, Karl T. Kelsey, Lucas A. Salas, Annette M. Molinaro, and Ze Zhang

Subjects
0301 basic medicine, Cancer Research, Kidney Disease, Renal and urogenital, Nephron, Medical Biochemistry and Metabolomics, Biology, Regenerative Medicine, Kidney, Epigenesis, Genetic, Mice, 03 medical and health sciences, Fetus, 0302 clinical medicine, Genetic, Genetics, medicine, Renal medulla, Homeobox, foetal stem cells, Animals, Humans, Compartment (development), stem cell niche, Epigenetics, Molecular Biology, Renal stem cell, Homeodomain Proteins, Mammals, DNA methylation, epigenetics, Genes, Homeobox, DNA Methylation, Stem Cell Research, Rats, Cell biology, 030104 developmental biology, medicine.anatomical_structure, Genes, 030220 oncology & carcinogenesis, Generic health relevance, Biochemistry and Cell Biology, Stem cell, Epigenesis, Developmental Biology, Research Paper
Abstract

The mammalian kidney has extensive repair capacity; however, identifying adult renal stem cells has proven elusive. We applied an epigenetic marker of foetal cell origin (FCO) in diverse human tissues as a probe for developmental cell persistence, finding a 5.4-fold greater FCO proportion in kidney. Normal kidney FCO proportions averaged 49% with extensive interindividual variation. FCO proportions were significantly negatively correlated with immune-related gene expression and positively correlated with genes expressed in the renal medulla, including those involved in renal organogenesis (e.g., FGF2, PAX8, and HOXB7). FCO associated genes also mapped to medullary nephron segments in mouse and rat, suggesting evolutionary conservation of this cellular compartment. Renal cancer patients whose tumours contained non-zero FCO scores survived longer. The kidney appears unique in possessing substantial foetal epigenetic features. Further study of FCO-related gene methylation may elucidate regenerative regulatory programmes in tissues without apparent discrete stem cell compartments.

Published
2021
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44. Tandem Fluorescence Measurements of Organic Matter and Bacteria Released in Sea Spray Aerosols

Author

Brock A. Mitts, Kimberly A. Prather, Lucia B. Cancelada, Julie Dinasquet, Ke’La A. Kimble, Alexia N. Moore, Francesca Malfatti, Matthew A. Pendergraft, Mitchell V. Santander, Christopher T. Lee, Santander, M. V., Mitts, B. A., Pendergraft, M. A., Dinasquet, J., Lee, C., Moore, A. N., Cancelada, L. B., Kimble, K. A., Malfatti, F., and Prather, K. A.

Subjects
aerosol, 010501 environmental sciences, complex mixtures, 01 natural sciences, marine microbe, Environmental Chemistry, Seawater, Organic matter, 0105 earth and related environmental sciences, Aerosols, chemistry.chemical_classification, marine microbes, Bacteria, biology, Tandem, Atmosphere, Spectrum Analysis, General Chemistry, respiratory system, Sea spray, biology.organism_classification, ocean, Fluorescence, Aerosol, stomatognathic diseases, chemistry, Environmental chemistry, Environmental science, fluorescence, sense organs
Abstract

Biological aerosols, typically identified through their fluorescence properties, strongly influence clouds and climate. Sea spray aerosol (SSA) particles are a major source of biological aerosols, but detection in the atmosphere is challenging due to potential interference from other sources. Here, the fluorescence signature of isolated SSA, produced using laboratory-based aerosol generation methods, was analyzed and compared with two commonly used fluorescence techniques: excitation-emission matrix spectroscopy (EEMS) and the wideband integrated bioaerosol sensor (WIBS). A range of dynamic biological ocean scenarios were tested to compare EEMS and WIBS analyses of SSA. Both techniques revealed similar trends in SSA fluorescence intensity in response to changes in ocean microbiology, demonstrating the potential to use the WIBS to measure fluorescent aerosols alongside EEMS bulk solution measurements. Together, these instruments revealed a unique fluorescence signature of isolated, nascent SSA and, for the first time, a size-segregated emission of fluorescent species in SSA. Additionally, the fluorescence signature of aerosolized marine bacterial isolates was characterized and showed similar fluorescence peaks to those of SSA, suggesting that bacteria are a contributor to SSA fluorescence. Through investigation of isolated SSA, this study provides a reference for future identification of marine biological aerosols in a complex atmosphere.

Published
2021
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45. Three New Species of Burmeistera (Campanulaceae) Endemic to Ecuador

Author

Nathan Muchhala and Brock Mashburn

Subjects
Campanulaceae, Burmeistera, biology, Zoology, Plant Science, biology.organism_classification, Ecology, Evolution, Behavior and Systematics
Abstract

Three species of Burmeistera discovered during fieldwork in Ecuador are described here. Burmeistera velutina and Burmeistera catulum are unusual in being nearly completely covered in indumentum, short and velvety in the former and remarkably long (up to 4 mm) and silky in the latter. Burmeistera jostii possesses bright red corollas, rare in a genus typically characterized by dull green flowers, and yellow to tan strigose hairs. We provide a discussion of each species’ etymology, phenology, and ecology, a list of all specimens examined, and distribution maps and photos.

Published
2021
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46. Room Temperature Intrinsic Emission Ratio of BSA Correlates With Percent Aggregates During Long-Term Storage

Author

Zakiya K. Powell, Cynthia Franklin, Joel D. Manrrique, Adeola O. Coker, and Ryan M. Brock

Subjects
Circular dichroism, biology, Chemistry, Size-exclusion chromatography, Temperature, Analytical chemistry, Pharmaceutical Science, Serum Albumin, Bovine, 02 engineering and technology, Protein aggregation, 021001 nanoscience & nanotechnology, 030226 pharmacology & pharmacy, Emission intensity, Fluorescence, Fluorescence spectroscopy, Excipients, 03 medical and health sciences, 0302 clinical medicine, Drug Stability, Chromatography, Gel, biology.protein, Bovine serum albumin, 0210 nano-technology, Thermal analysis
Abstract

Successful formulation development hinges on the ability to screen and identify excipients that stabilize drug products during long-term storage. Biophysical and accelerated stability studies are used to screen for excipients that stabilize protein drug products. However, these studies are not always predictive of aggregation during long-term storage. In this study, we used multivariate experimentation to compare the effectiveness of intrinsic fluorescence and size exclusion chromatography accelerated stability parameters to predict excipients that stabilized bovine serum albumin (BSA) against aggregation on long-term storage at 4 °C. Emission intensity ratio (IR330/350) data was more sensitive than emission maxima (λmax) or intensity measurements in identifying significant factors and interactions. We observed the expected inverse correlation between the mid-points of fluorescence thermal transitions (Tms) and insoluble aggregates at 4 and 40 °C. However, there were positive correlations between Tms and % aggregates at 4 °C, indicating that if Tm was used as a predictive tool, it would select formulations that promoted soluble aggregates on long-term storage. Ambient temperature IR330/350 measurements identified excipients that reduced BSA soluble aggregates on long-term storage. The results show ambient temperature emission ratio measurements can be useful for protein formulation development.

Published
2021
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48. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Author

Bailey M. H., Meyerson W. U., Dursi L. J., Wang L. -B., Dong G., Liang W. -W., Weerasinghe A., Li S., Li Y., Kelso S., Akbani R., Anur P., Buchanan A., Chiotti K., Covington K., Creason A., Ding L., Ellrott K., Fan Y., Foltz S., Getz G., Hale W., Haussler D., Hess J. M., Hutter C. M., Kandoth C., Kasaian K., Kasapi M., Larson D., Leshchiner I., Letaw J., Ma S., McLellan M. D., Men Y., Mills G. B., Niu B., Peto M., Radenbaugh A., Reynolds S. M., Saksena G., Sofia H., Stewart C., Struck A. J., Stuart J. M., Wang W., Weinstein J. N., Wheeler D. A., Wong C. K., Xi L., Ye K., Bieg M., Boutros P. C., Buchhalter I., Butler A. P., Chen K., Chong Z., Drechsel O., Jonathan Dursi L., Eils R., Espiritu S. M. G., Fulton R. S., Gao S., Gelpi J. L., Gerstein M. B., Gonzalez S., Gut I. G., Hach F., Heinold M. C., Hinton J., Hu T., Huang V., Huang Y., Hutter B., Jones D. R., Jung J., Jager N., Kim H. -L., Kleinheinz K., Kumar S., Kumar Y., Lalansingh C. M., Letunic I., Livitz D., Ma E. Z., Maruvka Y. E., Mashl R. J., Menzies A., Milovanovic A., Nielsen M. M., Ossowski S., Paramasivam N., Pedersen J. S., Perry M. D., Puiggros M., Raine K. M., Rheinbay E., Royo R., Sahinalp S. C., Sarrafi I., Schlesner M., Simpson J. T., Stebbings L., Stobbe M. D., Teague J. W., Tiao G., Torrents D., Wala J. A., Wang J., Waszak S. M., Weischenfeldt J., Wendl M. C., Werner J., Wu Z., Xue H., Yakneen S., Yamaguchi T. N., Yellapantula V. D., Yung C. K., Zhang J., Aaltonen L. A., Abascal F., Abeshouse A., Aburatani H., Adams D. J., Agrawal N., Ahn K. S., Ahn S. -M., Aikata H., Akdemir K. C., Al-Ahmadie H., Al-Sedairy S. T., Al-Shahrour F., Alawi M., Albert M., Aldape K., Alexandrov L. B., Ally A., Alsop K., Alvarez E. G., Amary F., Amin S. B., Aminou B., Ammerpohl O., Anderson M. J., Ang Y., Antonello D., Aparicio S., Appelbaum E. L., Arai Y., Aretz A., Arihiro K., Ariizumi S. -I., Armenia J., Arnould L., Asa S., Assenov Y., Atwal G., Aukema S., Auman J. T., Aure M. R., Awadalla P., Aymerich M., Bader G. D., Baez-Ortega A., Bailey P. J., Balasundaram M., Balu S., Bandopadhayay P., Banks R. E., Barbi S., Barbour A. P., Barenboim J., Barnholtz-Sloan J., Barr H., Barrera E., Bartlett J., Bartolome J., Bassi C., Bathe O. F., Baumhoer D., Bavi P., Baylin S. B., Bazant W., Beardsmore D., Beck T. A., Behjati S., Behren A., Bell C., Beltran S., Benz C., Berchuck A., Bergmann A. K., Bergstrom E. N., Berman B. P., Berney D. M., Bernhart S. H., Beroukhim R., Berrios M., Bersani S., Bertl J., Betancourt M., Bhandari V., Bhosle S. G., Biankin A. V., Bigner D., Binder H., Birney E., Birrer M., Biswas N. K., Bjerkehagen B., Bodenheimer T., Boice L., Bonizzato G., De Bono J. S., Boot A., Bootwalla M. S., Borg A., Borkhardt A., Boroevich K. A., Borozan I., Borst C., Bosenberg M., Bosio M., Boultwood J., Bourque G., Bova G. S., Bowen D. T., Bowlby R., Bowtell D. D. L., Boyault S., Boyce R., Boyd J., Brazma A., Brennan P., Brewer D. S., Brinkman A. B., Bristow R. G., Broaddus R. R., Brock J. E., Brock M., Broeks A., Brooks A. N., Brooks D., Brors B., Brunak S., Bruxner T. J. C., Bruzos A. L., Buchholz C., Bullman S., Burke H., Burkhardt B., Burns K. H., Busanovich J., Bustamante C. D., Butte A. J., Byrne N. J., Borresen-Dale A. -L., Caesar-Johnson S. J., Cafferkey A., Cahill D., Calabrese C., Caldas C., Calvo F., Camacho N., Campbell P. J., Campo E., Cantu C., Cao S., Carey T. E., Carlevaro-Fita J., Carlsen R., Cataldo I., Cazzola M., Cebon J., Cerfolio R., Chadwick D. E., Chakravarty D., Chalmers D., Chan C. W. Y., Chan K., Chan-Seng-Yue M., Chandan V. S., Chang D. K., Chanock S. J., Chantrill L. A., Chateigner A., Chatterjee N., Chayama K., Chen H. -W., Chen J., Chen Y., Chen Z., Cherniack A. D., Chien J., Chiew Y. -E., Chin S. -F., Cho J., Cho S., Choi J. K., Choi W., Chomienne C., Choo S. P., Chou A., Christ A. N., Christie E. L., Chuah E., Cibulskis C., Cibulskis K., Cingarlini S., Clapham P., Claviez A., Cleary S., Cloonan N., Cmero M., Collins C. C., Connor A. A., Cooke S. L., Cooper C. S., Cope L., Corbo V., Cordes M. G., Cordner S. M., Cortes-Ciriano I., Cowin P. A., Craft B., Craft D., Creighton C. J., Cun Y., Curley E., Cutcutache I., Czajka K., Czerniak B., Dagg R. A., Danilova L., Davi M. V., Davidson N. R., Davies H., Davis I. J., Davis-Dusenbery B. N., Dawson K. J., De La Vega F. M., De Paoli-Iseppi R., Defreitas T., Dei Tos A. P., Delaneau O., Demchok J. A., Demeulemeester J., Demidov G. M., Demircioglu D., Dennis N. M., Denroche R. E., Dentro S. C., Desai N., Deshpande V., Deshwar A. G., Desmedt C., Deu-Pons J., Dhalla N., Dhani N. C., Dhingra P., Dhir R., DiBiase A., Diamanti K., Ding S., Dinh H. Q., Dirix L., Doddapaneni H. V., Donmez N., Dow M. T., Drapkin R., Drews R. M., Serge S., Dudderidge T., Dueso-Barroso A., Dunford A. J., Dunn M., Duthie F. R., Dutton-Regester K., Eagles J., Easton D. F., Edmonds S., Edwards P. A., Edwards S. E., Eeles R. A., Ehinger A., Eils J., El-Naggar A., Eldridge M., Erkek S., Escaramis G., Estivill X., Etemadmoghadam D., Eyfjord J. E., Faltas B. M., Fan D., Faquin W. C., Farcas C., Fassan M., Fatima A., Favero F., Fayzullaev N., Felau I., Fereday S., Ferguson M. L., Ferretti V., Feuerbach L., Field M. A., Fink J. L., Finocchiaro G., Fisher C., Fittall M. W., Fitzgerald A., Fitzgerald R. C., Flanagan A. M., Fleshner N. E., Flicek P., Foekens J. A., Fong K. M., Fonseca N. A., Foster C. S., Fox N. S., Fraser M., Frazer S., Frenkel-Morgenstern M., Friedman W., Frigola J., Fronick C. C., Fujimoto A., Fujita M., Fukayama M., Fulton L. A., Furuta M., Futreal P. A., Fullgrabe A., Gabriel S. B., Gallinger S., Gambacorti Passerini C., Gao J., Garraway L., Garred O., Garrison E., Garsed D. W., Gehlenborg N., George J., Gerhard D. S., Gerhauser C., Gershenwald J. E., Gerstung M., Ghori M., Ghossein R., Giama N. H., Gibbs R. A., Gill A. J., Gill P., Giri D. D., Glodzik D., Gnanapragasam V. J., Goebler M. E., Goldman M. J., Gomez C., Gonzalez-Perez A., Gordenin D. A., Gossage J., Gotoh K., Govindan R., Grabau D., Graham J. S., Grant R. C., Green A. R., Green E., Greger L., Grehan N., Grimaldi S., Grimmond S. M., Grossman R. L., Grundhoff A., Gundem G., Guo Q., Gupta M., Gupta S., Gut M., Goke J., Ha G., Haake A., Haan D., Haas S., Haase K., Haber J. E., Habermann N., Haider S., Hama N., Hamdy F. C., Hamilton A., Hamilton M. P., Han L., Hanna G. B., Hansmann M., Haradhvala N. J., Harismendy O., Harliwong I., Harmanci A. O., Harrington E., Hasegawa T., Hawkins S., Hayami S., Hayashi S., Hayes D. N., Hayes S. J., Hayward N. K., Hazell S., He Y., Heath A. P., Heath S. C., Hedley D., Hegde A. M., Heiman D. I., Heins Z., Heisler L. E., Hellstrom-Lindberg E., Helmy M., Heo S. G., Hepperla A. J., Heredia-Genestar J. M., Herrmann C., Hersey P., Hilmarsdottir H., Hirano S., Hiraoka N., Hoadley K. A., Hobolth A., Hodzic E., Hoell J. I., Hoffmann S., Hofmann O., Holbrook A., Holik A. Z., Hollingsworth M. A., Holmes O., Holt R. A., Hong C., Hong E. P., Hong J. H., Hooijer G. K., Hornshoj H., Hosoda F., Hou Y., Hovestadt V., Howat W., Hoyle A. P., Hruban R. H., Hu J., Hua X., Huang K. -L., Huang M., Huang M. N., Huber W., Hudson T. J., Hummel M., Hung J. A., Huntsman D., Hupp T. R., Huse J., Huska M. R., Hubschmann D., Iacobuzio-Donahue C. A., Imbusch C. D., Imielinski M., Imoto S., Isaacs W. B., Isaev K., Ishikawa S., Iskar M., Islam S. M. A., Ittmann M., Ivkovic S., Izarzugaza J. M. G., Jacquemier J., Jakrot V., Jamieson N. B., Jang G. H., Jang S. J., Jayaseelan J. C., Jayasinghe R., Jefferys S. R., Jegalian K., Jennings J. L., Jeon S. -H., Jerman L., Ji Y., Jiao W., Johansson P. A., Johns A. L., Johns J., Johnson R., Johnson T. A., Jolly C., Joly Y., Jonasson J. G., Jones C. D., Jones D. T. W., Jones N., Jones S. J. M., Jonkers J., Ju Y. S., Juhl H., Juul M., Juul R. I., Juul S., Kabbe R., Kahles A., Kahraman A., Kaiser V. B., Kakavand H., Kalimuthu S., von Kalle C., Kang K. J., Karaszi K., Karlan B., Karlic R., Karsch D., Kassahn K. S., Katai H., Kato M., Katoh H., Kawakami Y., Kay J. D., Kazakoff S. H., Kazanov M. D., Keays M., Kebebew E., Kefford R. F., Kellis M., Kench J. G., Kennedy C. J., Kerssemakers J. N. A., Khoo D., Khoo V., Khuntikeo N., Khurana E., Kilpinen H., Kim H. K., Kim H. -Y., Kim H., Kim J., Kim J. K., Kim Y., King T. A., Klapper W., Klimczak L. J., Knappskog S., Kneba M., Knoppers B. M., Koh Y., Jan Komorowski, Komura D., Komura M., Kong G., Kool M., Korbel J. O., Korchina V., Korshunov A., Koscher M., Koster R., Kote-Jarai Z., Koures A., Kovacevic M., Kremeyer B., Kretzmer H., Kreuz M., Krishnamurthy S., Kube D., Kumar K., Kumar P., Kundra R., Kubler K., Kuppers R., Lagergren J., Lai P. H., Laird P. W., Lakhani S. R., Lalonde E., Lamaze F. C., Lambert A., Lander E., Landgraf P., Landoni L., Langerod A., Lanzos A., Larsimont D., Larsson E., Lathrop M., Lau L. M. S., Lawerenz C., Lawlor R. T., Lawrence M. S., Lazar A. J., Le X., Lee D., Lee E. A., Lee H. J., Lee J. J. -K., Lee J. -Y., Lee J., Lee M. T. M., Lee-Six H., Lehmann K. -V., Lehrach H., Lenze D., Leonard C. R., Leongamornlert D. A., Letourneau L., Levine D. A., Lewis L., Ley T., Li C., Li C. H., Li H. I., Li J., Li L., Li X., Liang H., Liang S. -B., Lichter P., Lin P., Lin Z., Linehan W. M., Lingjaerde O. C., Liu D., Liu E. M., Liu F. -F., Liu F., Liu J., Liu X., Livingstone J., Livni N., Lochovsky L., Loeffler M., Long G. V., Lopez-Guillermo A., Lou S., Louis D. N., Lovat L. B., Lu Y., Lu Y. -J., Luchini C., Lungu I., Luo X., Luxton H. J., Lynch A. G., Lype L., Lopez C., Lopez-Otin C., Ma Y., MacGrogan G., MacRae S., Macintyre G., Madsen T., Maejima K., Mafficini A., Maglinte D. T., Maitra A., Majumder P. P., Malcovati L., Malikic S., Malleo G., Mann G. 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Subjects
Science, MEDLINE, Medizin, General Physics and Astronomy, Pain, 610 Medicine & health, 1600 General Chemistry, Computational biology, Biology, 10 kHz spinal cord stimulation, Genome, responders, MC3 Working Group, General Biochemistry, Genetics and Molecular Biology, whole exome sequencing, Machine Learning, 1300 General Biochemistry, Genetics and Molecular Biology, PCAWG novel somatic mutation calling methods working group, medicine, cancer, Genome mutation, Exome, Exome sequencing, Whole genome sequencing, whole genome sequencing, Multidisciplinary, Published Erratum, Cancer, PCAWG Consortium, General Chemistry, medicine.disease, 3100 General Physics and Astronomy, oncology, 10032 Clinic for Oncology and Hematology, Prediction
Abstract

Weitere Nicht-UDE-Autoren sind nicht genannt. Originalpublikation: 10.1038/s41467-020-18151-y. CA extern The original version of this Article omitted from the author list the 9th author Yize Li, who is from the ‘The McDonnell Genome Institute at Washington University, St. Louis, MO 63108, USA and Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA’. This has been corrected in both the PDF and HTML versions of the Article. © 2020, The Author(s).

Published
2020

49. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Author

Bailey, Matthew H, Meyerson, William U, Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Shantao, Li, Kelso, Sean, Saksena, Gordon, Ellrott, Kyle, Wendl, Michael C, Wheeler, David A, Getz, Gad, Simpson, Jared T, Gerstein, Mark B, Ding, Lirehan, Akbani, Pavana, Anur, Matthew, H Bailey, Alex, Buchanan, Kami, Chiotti, Kyle, Covington, Allison, Creason, Ding, Li, Kyle, Ellrott, Fan, Yu, Steven, Foltz, Gad, Getz, Walker, Hale, David, Haussler, Julian, M Hess, Carolyn, M Hutter, Cyriac, Kandoth, Katayoon, Kasaian, Melpomeni, Kasapi, Dave, Larson, Ignaty, Leshchiner, John, Letaw, Singer, Ma, Michael, D McLellan, Yifei, Men, Gordon, B Mills, Beifang, Niu, Myron, Peto, Amie, Radenbaugh, Sheila, M Reynolds, Gordon, Saksena, Heidi, Sofia, Chip, Stewart, Adam, J Struck, Joshua, M Stuart, Wenyi, Wang, John, N Weinstein, David, A Wheeler, Christopher, K Wong, Liu, Xi, Kai, Ye, Matthias, Bieg, Paul, C Boutros, Ivo, Buchhalter, Adam, P Butler, Ken, Chen, Zechen, Chong, Oliver, Drechsel, Lewis Jonathan Dursi, Roland, Eils, Shadrielle M, G Espiritu, Robert, S Fulton, Shengjie, Gao, Josep L, L Gelpi, Mark, B Gerstein, Santiago, Gonzalez, Ivo, G Gut, Faraz, Hach, Michael, C Heinold, Jonathan, Hinton, Taobo, Hu, Vincent, Huang, Huang, Yi, Barbara, Hutter, David, R Jones, Jongsun, Jung, Natalie, Jäger, Hyung-Lae, Kim, Kortine, Kleinheinz, Sushant, Kumar, Yogesh, Kumar, Christopher, M Lalansingh, Ivica, Letunic, Dimitri, Livitz, Eric, Z Ma, Yosef, E Maruvka, R Jay Mashl, Andrew, Menzies, Ana, Milovanovic, Morten Muhlig Nielsen, Stephan, Ossowski, Nagarajan, Paramasivam, Jakob Skou Pedersen, Marc, D Perry, Montserrat, Puiggròs, Keiran, M Raine, Esther, Rheinbay, Romina, Royo, S Cenk Sahinalp, Iman, Sarrafi, Matthias, Schlesner, Jared, T Simpson, Lucy, Stebbings, Miranda, D Stobbe, Jon, W Teague, Grace, Tiao, David, Torrents, Jeremiah, A Wala, Jiayin, Wang, Sebastian, M Waszak, Joachim, Weischenfeldt, Michael, C Wendl, Johannes, Werner, 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Chan-Seng-Yue, Vishal, S Chandan, David, K Chang, Stephen, J Chanock, Lorraine, A Chantrill, Aurélien, Chateigner, Nilanjan, Chatterjee, Kazuaki, Chayama, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Chen, Andrew, D Cherniack, Jeremy, Chien, Yoke-Eng, Chiew, Suet-Feung, Chin, Juok, Cho, Sunghoon, Cho, Jung Kyoon Choi, Wan, Choi, Christine, Chomienne, Su Pin Choo, Angela, Chou, Angelika, N Christ, Elizabeth, L Christie, Eric, Chuah, Carrie, Cibulskis, Kristian, Cibulskis, Sara, Cingarlini, Peter, Clapham, Alexander, Claviez, Sean, Cleary, Nicole, Cloonan, Marek, Cmero, Colin, C Collins, Ashton, A Connor, Susanna, L Cooke, Colin, S Cooper, Leslie, Cope, Corbo, Vincenzo, Matthew, G Cordes, Stephen, M Cordner, Isidro, Cortés-Ciriano, Prue, A Cowin, Brian, Craft, David, Craft, Chad, J Creighton, Yupeng, Cun, Erin, Curley, Ioana, Cutcutache, Karolina, Czajka, Bogdan, Czerniak, Rebecca, A Dagg, Ludmila, Danilova, Maria Vittoria Davi, Natalie, R Davidson, Helen, Davies, Ian, J Davis, 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Yamamoto, S, Yamaue, H, Yang, F, Yang, H, Yang, J, Yang, L, Yang, S, Yang, T, Yang, Y, Yao, X, Yaspo, M, Yates, L, Yau, C, Ye, C, Yoon, C, Yoon, S, Yousif, F, Yu, J, Yu, K, Yu, W, Yu, Y, Yuan, K, Yuan, Y, Yuen, D, Zaikova, O, Zamora, J, Zapatka, M, Zenklusen, J, Zenz, T, Zeps, N, Zhang, C, Zhang, F, Zhang, H, Zhang, X, Zhang, Y, Zhang, Z, Zhao, Z, Zheng, L, Zheng, X, Zhou, W, Zhou, Y, Bin, Z, Zhu, H, Zhu, J, Zhu, S, Zou, L, Zou, X, Defazio, A, van As, N, van Deurzen, C, van de Vijver, M, van't Veer, L, von Mering, C, Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Tampere University, BioMediTech, TAYS Cancer Centre, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, University of St Andrews. Statistics, University of St Andrews. School of Medicine, University of Zurich, Gerstein, Mark B, Ding, Li, Bailey, Matthew H [0000-0003-4526-9727], Wheeler, David A [0000-0002-9056-6299], Gerstein, Mark B [0000-0002-9746-3719], Faculty of Economic and Social Sciences and Solvay Business School, Lauri Antti Aaltonen / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Medical and Clinical Genetics, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Information Technology, Institute of Biotechnology, Bioinformatics, Department of Computer Science, Faculty of Medicine, and HUS Helsinki and Uusimaa Hospital District

Subjects
VARIANTS, 0302 clinical medicine, 706/648/697/129/2043, Databases, Genetic, Cancer genomics, SOMATIC POINT MUTATIONS, Càncer, lcsh:Science, Exome, Exome sequencing, Cancer, Base Composition, Neoplasms -- genetics, 1184 Genetics, developmental biology, physiology, 3100 General Physics and Astronomy, 3. Good health, 030220 oncology & carcinogenesis, Science & Technology - Other Topics, Transformació genètica, Genetic databases, Erfðarannsóknir, Human, GENES, Science, 1600 General Chemistry, General Biochemistry, Genetics and Molecular Biology, RC0254, 03 medical and health sciences, Genetic, SDG 3 - Good Health and Well-being, 1300 General Biochemistry, Genetics and Molecular Biology, Exome Sequencing, Genetics, Humans, Author Correction, Retrospective Studies, Whole genome sequencing, Comparative genomics, Science & Technology, RC0254 Neoplasms. Tumors. Oncology (including Cancer), INSERTIONS, DNA, PERFORMANCE, Human genetics, Communication and replication, Cancérologie, 692/4028/67/69, Genòmica, 030104 developmental biology, Mutation, Genome mutation, Human genome, lcsh:Q, COMPREHENSIVE CHARACTERIZATION, Genètica, 0301 basic medicine, Medizin, General Physics and Astronomy, Genome, Whole Exome Sequencing, Genetic transformation, International Cancer Genome Consortium, Neoplasms, 631/114/2399, Genamengi, Medicine and Health Sciences, Medicine(all), Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Multidisciplinary, 318 Medical biotechnology, Exome -- genetics, article, Exons, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Multidisciplinary Sciences, CAPTURE, 1181 Ecology, evolutionary biology, oncology, DNA, Intergenic, 139, Medical Genetics, Biotechnology, ICGC/TCGA Pan-Cancer Analysis, 3122 Cancers, 610 Medicine & health, 45/23, QH426 Genetics, Biology, MC3 Working Group, Databases, Germline mutation, PCAWG novel somatic mutation calling methods working group, Krabbameinsrannsóknir, Cancer Genome Atlas, Genome, Human -- genetics, ddc:610, QH426, Medicinsk genetik, Krabbamein, Intergenic, Whole Genome Sequencing, Genome, Human, Human Genome, PCAWG Consortium, DAS, General Chemistry, DELETIONS, Good Health and Well Being, 10032 Clinic for Oncology and Hematology, 3111 Biomedicine, 631/1647/2217/748
Abstract

MC3 Working Group: Rehan Akbani21, Pavana Anur22, Matthew H. Bailey1,2,3, Alex Buchanan9, Kami Chiotti9, Kyle Covington12,23, Allison Creason9, Li Ding1,2,3,20, Kyle Ellrott9, Yu Fan21, Steven Foltz1,2, Gad Getz8,14,15,16, Walker Hale12, David Haussler24,25, Julian M. Hess8,26, Carolyn M. Hutter27, Cyriac Kandoth28, Katayoon Kasaian29,30, Melpomeni Kasapi27, Dave Larson1 , Ignaty Leshchiner8, John Letaw31, Singer Ma32, Michael D. McLellan1,3,20, Yifei Men32, Gordon B. Mills33,34, Beifang Niu35, Myron Peto22, Amie Radenbaugh24, Sheila M. Reynolds36, Gordon Saksena8, Heidi Sofia27, Chip Stewart8, Adam J. Struck31, Joshua M. Stuart24,37, Wenyi Wang21, John N. Weinstein38, David A. Wheeler12,13, Christopher K. Wong24,39, Liu Xi12 & Kai Ye40,41 21Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 22Molecular and Medical Genetics, OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. 23Castle Biosciences Inc, Friendswood, TX 77546, USA. 24UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 25Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 26Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02114, USA. 27National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA. 28Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. 29Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada. 30Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada. 31Computational Biology Program, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA. 32DNAnexus Inc, Mountain View, CA 94040, USA. 33Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA. 34Precision Oncology, OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. 35Computer Network Information Center, Chinese Academy of Sciences, Beijing, China. 36Institute for Systems Biology, Seattle, WA 98109, USA. 37Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 38Department of Bioinformatics and Computational Biology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 39Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 40School of Elect, PCAWG novel somatic mutation calling methods working group: Matthew H. Bailey1,2,3, Beifang Niu35, Matthias Bieg42,43, Paul C. Boutros6,44,45,46, Ivo Buchhalter43,47,48, Adam P. Butler49, Ken Chen50, Zechen Chong51, Li Ding1,2,3,20, Oliver Drechsel52,53, Lewis Jonathan Dursi6,7, Roland Eils47,48,54,55, Kyle Ellrott9, Shadrielle M. G. Espiritu6, Yu Fan21, Robert S. Fulton1,3,20, Shengjie Gao56, Josep L. l. Gelpi57,58, Mark B. Gerstein5,18,19, Gad Getz8,14,15,16, Santiago Gonzalez59,60, Ivo G. Gut52,61, Faraz Hach62,63, Michael C. Heinold47,48, Julian M. Hess8,26, Jonathan Hinton49, Taobo Hu64, Vincent Huang6, Yi Huang65,66, Barbara Hutter43,67,68, David R. Jones49, Jongsun Jung69, Natalie Jäger47, Hyung-Lae Kim70, Kortine Kleinheinz47,48, Sushant Kumar5,19, Yogesh Kumar64, Christopher M. Lalansingh6, Ignaty Leshchiner8, Ivica Letunic71, Dimitri Livitz8, Eric Z. Ma64, Yosef E. Maruvka8,26,72, R. Jay Mashl1,2, Michael D. McLellan1,3,20, Andrew Menzies49, Ana Milovanovic57, Morten Muhlig Nielsen73, Stephan Ossowski52,53,74, Nagarajan Paramasivam43,47, Jakob Skou Pedersen73,75, Marc D. Perry76,77, Montserrat Puiggròs57, Keiran M. Raine49, Esther Rheinbay8,14,72, Romina Royo57, S. Cenk Sahinalp62,78,79, Gordon Saksena8, Iman Sarrafi62,78, Matthias Schlesner47,80, Jared T. Simpson6,17, Lucy Stebbings49, Chip Stewart8, Miranda D. Stobbe52,61, Jon W. Teague49, Grace Tiao8, David Torrents57,81, Jeremiah A. Wala8,14,82, Jiayin Wang1,40,66, Wenyi Wang21, Sebastian M. Waszak60, Joachim Weischenfeldt60,83,84, Michael C. Wendl1,10,11, Johannes Werner47,85, Zhenggang Wu64, Hong Xue64, Sergei Yakneen60, Takafumi N. Yamaguchi6, Kai Ye40,41, Venkata D. Yellapantula20,86, Christina K. Yung76 & Junjun Zhang76, PCAWG Consortium: Lauri A. Aaltonen87, Federico Abascal49, Adam Abeshouse88, Hiroyuki Aburatani89, David J. Adams49, Nishant Agrawal90, Keun Soo Ahn91, Sung-Min Ahn92, Hiroshi Aikata93, Rehan Akbani21, Kadir C. Akdemir50, Hikmat Al-Ahmadie88, Sultan T. Al-Sedairy94, Fatima Al-Shahrour95, Malik Alawi96,97, Monique Albert98, Kenneth Aldape99,100, Ludmil B. Alexandrov49,101,102, Adrian Ally30, Kathryn Alsop103, Eva G. Alvarez104,105,106, Fernanda Amary107, Samirkumar B. Amin108,109,110, Brice Aminou76, Ole Ammerpohl111,112, Matthew J. Anderson113, Yeng Ang114, Davide Antonello115, Pavana Anur22, Samuel Aparicio116, Elizabeth L. Appelbaum1,117, Yasuhito Arai118, Axel Aretz119, Koji Arihiro93, Shun-ichi Ariizumi120, Joshua Armenia121, Laurent Arnould122, Sylvia Asa123,124, Yassen Assenov125, Gurnit Atwal6,126,127, Sietse Aukema112,128, J. Todd Auman129, Miriam R. Aure130, Philip Awadalla6,126, Marta Aymerich131, Gary D. Bader126, Adrian Baez-Ortega132, Matthew H. Bailey1,2,3, Peter J. Bailey133, Miruna Balasundaram30, Saianand Balu134, Pratiti Bandopadhayay8,135,136, Rosamonde E. Banks137, Stefano Barbi138, Andrew P. Barbour139,140, Jonathan Barenboim6, Jill Barnholtz-Sloan141,142, Hugh Barr143, Elisabet Barrera59, John Bartlett98,144, Javier Bartolome57, Claudio Bassi115, Oliver F. Bathe145,146, Daniel Baumhoer147, Prashant Bavi148, Stephen B. Baylin149,150, Wojciech Bazant59, Duncan Beardsmore151, Timothy A. Beck152,153, Sam Behjati49, Andreas Behren154, Beifang Niu35, Cindy Bell155, Sergi Beltran52,61, Christopher Benz156, Andrew Berchuck157, Anke K. Bergmann158, Erik N. Bergstrom101,102, Benjamin P. Berman159,160,161, Daniel M. Berney162, Stephan H. Bernhart163,164,165, Rameen Beroukhim8,14,82, Mario Berrios166, Samantha Bersani167, Johanna Bertl73,168, Miguel Betancourt169, Vinayak Bhandari6,44, Shriram G. Bhosle49, Andrew V. Biankin133,170,171,172, Matthias Bieg42,43, Darell Bigner173, Hans Binder163,164, Ewan Birney59, Michael Birrer72, Nidhan K. Biswas174, Bodil Bjerkehagen147,175, Tom Bodenheimer134, Lori Boice176, Giada Bonizzato177, Johann S. De Bono178, Arnoud Boot179,180, Moiz S. Bootwalla166, Ake Borg181, Arndt Borkhardt182, Keith A. Boroevich183,184, Ivan Borozan6, Christoph Borst185, Marcus Bosenberg186, Mattia Bosio52,53,57, Jacqueline Boultwood187, Guillaume Bourque188,189, Paul C. Boutros6,44,45,46, G. Steven Bova190, David T. Bowen49,191, Reanne Bowlby30, David D. L. Bowtell103, Sandrine Boyault192, Rich Boyce59, Jeffrey Boyd193, Alvis Brazma59, Paul Brennan194, Daniel S. Brewer195,196, Arie B. Brinkman197, Robert G. Bristow44,198,199,200,201, Russell R. Broaddus99, Jane E. Brock202, Malcolm Brock203, Annegien Broeks204, Angela N. Brooks8,24,37,82, Denise Brooks30, Benedikt Brors67,205,206, Søren Brunak207,208, Timothy J. C. Bruxner113,209, Alicia L. Bruzos104,105,106, Alex Buchanan9, Ivo Buchhalter43,47,48, Christiane Buchholz210, Susan Bullman8,82, Hazel Burke211, Birgit Burkhardt212, Kathleen H. Burns213,214, John Busanovich8,215, Carlos D. Bustamante216,217, Adam P. Butler49, Atul J. Butte218, Niall J. Byrne76, Anne-Lise Børresen-Dale130,219, Samantha J. Caesar-Johnson220, Andy Cafferkey59, Declan Cahill221, Claudia Calabrese59,60, Carlos Caldas222,223, Fabien Calvo224, Niedzica Camacho178, Peter J. Campbell49,225, Elias Campo226,227, Cinzia Cantù177, Shaolong Cao21, Thomas E. Carey228, Joana Carlevaro-Fita229,230,231, Rebecca Carlsen30, Ivana Cataldo167,177, Mario Cazzola232, Jonathan Cebon154, Robert Cerfolio233, Dianne E. Chadwick234, Dimple Chakravarty235, Don Chalmers236, Calvin Wing Yiu Chan47,237, Kin Chan238, Michelle Chan-Seng-Yue148, Vishal S. Chandan239, David K. Chang133,170, Stephen J. Chanock240, Lorraine A. Chantrill170,241, Aurélien Chateigner76,242, Nilanjan Chatterjee149,243, Kazuaki Chayama93, Hsiao-Wei Chen114,121, Jieming Chen218, Ken Chen50, Yiwen Chen21, Zhaohong Chen244, Andrew D. Cherniack8,82, Jeremy Chien245, Yoke-Eng Chiew246,247, Suet-Feung Chin222,223, Juok Cho8, Sunghoon Cho248, Jung Kyoon Choi249, Wan Choi250, Christine Chomienne251, Zechen Chong51, Su Pin Choo252, Angela Chou170,246, Angelika N. Christ113, Elizabeth L. Christie103, Eric Chuah30, Carrie Cibulskis8, Kristian Cibulskis8, Sara Cingarlini253, Peter Clapham49, Alexander Claviez254, Sean Cleary148,255, Nicole Cloonan256, Marek Cmero257,258,259, Colin C. Collins62, Ashton A. Connor255,260, Susanna L. Cooke133, Colin S. Cooper178,196,261, Leslie Cope149, Vincenzo Corbo138,177, Matthew G. Cordes1,262, Stephen M. Cordner263, Isidro Cortés-Ciriano264,265,266, Kyle Covington12,23, Prue A. Cowin267, Brian Craft24, David Craft8,268, Chad J. Creighton269, Yupeng Cun270, Erin Curley271, Ioana Cutcutache179,180, Karolina Czajka272, Bogdan Czerniak99,273, Rebecca A. Dagg274, Ludmila Danilova149, Maria Vittoria Davi275, Natalie R. Davidson276,277,278,279,280, Helen Davies49,281,282, Ian J. Davis283, Brandi N. Davis-Dusenbery284, Kevin J. Dawson49, Francisco M. De La Vega216,217,285, Ricardo De Paoli-Iseppi211, Timothy Defreitas8, Angelo P. Dei Tos286, Olivier Delaneau287,288,289, John A. Demchok220, Jonas Demeulemeester290,291, German M. Demidov52,53,74, Deniz Demircioğlu292,293, Nening M. Dennis221, Robert E. Denroche148, Stefan C. Dentro49,290,294, Nikita Desai76, Vikram Deshpande72, Amit G. Deshwar295, Christine Desmedt296,297, Jordi Deu-Pons298,299, Noreen Dhalla30, Neesha C. Dhani300, Priyanka Dhingra301,302, Rajiv Dhir303, Anthony DiBiase304, Klev Diamanti305, Li Ding1,2,3,20, Shuai Ding306, Huy Q. Dinh159, Luc Dirix307, HarshaVardhan Doddapaneni12, Nilgun Donmez62,78, Michelle T. Dow244, Ronny Drapkin308, Oliver Drechsel52,53, Ruben M. Drews223, Serge Serge49, Tim Dudderidge150,221, Ana Dueso-Barroso57, Andrew J. Dunford8, Michael Dunn309, Lewis Jonathan Dursi6,7, Fraser R. Duthie133,310, Ken Dutton-Regester311, Jenna Eagles272, Douglas F. Easton312,313, Stuart Edmonds314, Paul A. Edwards223,315, Sandra E. Edwards178, Rosalind A. Eeles178,221, Anna Ehinger316, Juergen Eils54,55, Roland Eils47,48,54,55, Adel El-Naggar99,273, Matthew Eldridge223, Kyle Ellrott9, Serap Erkek60, Georgia Escaramis53,317,318, Shadrielle M. G. Espiritu6, Xavier Estivill53,319, Dariush Etemadmoghadam103, Jorunn E. Eyfjord320, Bishoy M. Faltas280, Daiming Fan321, Yu Fan21, William C. Faquin72, Claudiu Farcas244, Matteo Fassan322, Aquila Fatima323, Francesco Favero324, Nodirjon Fayzullaev76, Ina Felau220, Sian Fereday103, Martin L. Ferguson325, Vincent Ferretti76,326, Lars Feuerbach205, Matthew A. Field327, J. Lynn Fink57,113, Gaetano Finocchiaro328, Cyril Fisher221, Matthew W. Fittall290, Anna Fitzgerald329, Rebecca C. Fitzgerald282, Adrienne M. Flanagan330, Neil E. Fleshner331, Paul Flicek59, John A. Foekens332, Kwun M. Fong333, Nuno A. Fonseca59,334, Christopher S. Foster335,336, Natalie S. Fox6, Michael Fraser6, Scott Frazer8, Milana Frenkel-Morgenstern337, William Friedman338, Joan Frigola298, Catrina C. Fronick1,262, Akihiro Fujimoto184, Masashi Fujita184, Masashi Fukayama339, Lucinda A. Fulton1 , Robert S. Fulton1,3,20, Mayuko Furuta184, P. Andrew Futreal340, Anja Füllgrabe59, Stacey B. Gabriel8, Steven Gallinger148,255,260, Carlo Gambacorti-Passerini341, Jianjiong Gao121, Shengjie Gao56, Levi Garraway82, Øystein Garred342, Erik Garrison49, Dale W. Garsed103, Nils Gehlenborg8,343, Josep L. l. Gelpi57,58, Joshy George110, Daniela S. Gerhard344, Clarissa Gerhauser345, Jeffrey E. Gershenwald346,347, Mark B. Gerstein5,18,19, Moritz Gerstung59,60, Gad Getz8,14,15,16, Mohammed Ghori49, Ronald Ghossein348, Nasra H. Giama349, Richard A. Gibbs12, Anthony J. Gill170,350, Pelvender Gill351, Dilip D. Giri348, Dominik Glodzik49, Vincent J. Gnanapragasam352,353, Maria Elisabeth Goebler354, Mary J. Goldman24, Carmen Gomez355, Santiago Gonzalez59,60, Abel Gonzalez-Perez298,299,356, Dmitry A. Gordenin357, James Gossage358, Kunihito Gotoh359, Ramaswamy Govindan3, Dorthe Grabau360, Janet S. Graham133,361, Robert C. Grant148,260, Anthony R. Green315, Eric Green27, Liliana Greger59, Nicola Grehan282, Sonia Grimaldi177, Sean M. Grimmond362, Robert L. Grossman363, Adam Grundhoff97,364, Gunes Gundem88, Qianyun Guo75, Manaswi Gupta8, Shailja Gupta365, Ivo G. Gut52,61, Marta Gut52,61, Jonathan Göke292,366, Gavin Ha8, Andrea Haake111, David Haan37, Siegfried Haas185, Kerstin Haase290, James E. Haber367, Nina Habermann60, Faraz Hach62,63, Syed Haider6, Natsuko Hama118, Freddie C. Hamdy351, Anne Hamilton267, Mark P. Hamilton368, Leng Han369, George B. Hanna370, Martin Hansmann371, Nicholas J. Haradhvala8,72, Olivier Harismendy102,372, Ivon Harliwong113, Arif O. Harmanci5,373, Eoghan Harrington374, Takanori Hasegawa375, David Haussler24,25, Steve Hawkins223, Shinya Hayami376, Shuto Hayashi375, D. Neil Hayes134,377,378, Stephen J. Hayes379,380, Nicholas K. Hayward211,311, Steven Hazell221, Yao He381, Allison P. Heath382, Simon C. Heath52,61, David Hedley300, Apurva M. Hegde38, David I. Heiman8, Michael C. Heinold47,48, Zachary Heins88, Lawrence E. Heisler152, Eva Hellstrom-Lindberg383, Mohamed Helmy384, Seong Gu Heo385, Austin J. Hepperla134, José María Heredia-Genestar386, Carl Herrmann47,48,387, Peter Hersey211, Julian M. Hess8,26, Holmfridur Hilmarsdottir320, Jonathan Hinton49, Satoshi Hirano388, Nobuyoshi Hiraoka389, Katherine A. Hoadley134,390, Asger Hobolth75,168, Ermin Hodzic78, Jessica I. Hoell182, Steve Hoffmann163,164,165,391, Oliver Hofmann392, Andrea Holbrook166, Aliaksei Z. Holik53, Michael A. Hollingsworth393, Oliver Holmes209,311, Robert A. Holt30, Chen Hong205,237, Eun Pyo Hong385, Jongwhi H. Hong394, Gerrit K. Hooijer395, Henrik Hornshøj73, Fumie Hosoda118, Yong Hou56,396, Volker Hovestadt397, William Howat352, Alan P. Hoyle134, Ralph H. Hruban149, Jianhong Hu12, Taobo Hu64, Xing Hua240, Kuan-lin Huang1,398, Mei Huang176, Mi Ni Huang179,180, Vincent Huang6, Yi Huang65,66, Wolfgang Huber60, Thomas J. Hudson272,399, Michael Hummel400, Jillian A. Hung246,247, David Huntsman401, Ted R. Hupp402, Jason Huse88, Matthew R. Huska403, Barbara Hutter43,67,68, Carolyn M. Hutter27, Daniel Hübschmann48,54,404,405,406, Christine A. Iacobuzio-Donahue348, Charles David Imbusch205, Marcin Imielinski407,408, Seiya Imoto375, William B. Isaacs409, Keren Isaev6,44, Shumpei Ishikawa410, Murat Iskar397, S. M. Ashiqul Islam244, Michael Ittmann411,412,413, Sinisa Ivkovic284, Jose M. G. Izarzugaza414, Jocelyne Jacquemier415, Valerie Jakrot211, Nigel B. Jamieson133,172,416, Gun Ho Jang148, Se Jin Jang417, Joy C. Jayaseelan12, Reyka Jayasinghe1 , Stuart R. Jefferys134, Karine Jegalian418, Jennifer L. Jennings419, Seung-Hyup Jeon250, Lara Jerman60,420, Yuan Ji421,422, Wei Jiao6, Peter A. Johansson311, Amber L. Johns170, Jeremy Johns272, Rory Johnson230,423, Todd A. Johnson183, Clemency Jolly290, Yann Joly424, Jon G. Jonasson320, Corbin D. Jones425, David R. Jones49, David T. W. Jones426,427, Nic Jones428, Steven J. M. Jones30, Jos Jonkers204, Young Seok Ju49,249, Hartmut Juhl429, Jongsun Jung69, Malene Juul73, Randi Istrup Juul73, Sissel Juul374, Natalie Jäger47, Rolf Kabbe47, Andre Kahles276,277,278,279,430, Abdullah Kahraman431,432,433, Vera B. Kaiser434, Hojabr Kakavand211, Sangeetha Kalimuthu148, Christof von Kalle405, Koo Jeong Kang91, Katalin Karaszi351, Beth Karlan435, Rosa Karlić436, Dennis Karsch437, Katayoon Kasaian29,30, Karin S. Kassahn113,438, Hitoshi Katai439, Mamoru Kato440, Hiroto Katoh410, Yoshiiku Kawakami93, Jonathan D. Kay117, Stephen H. Kazakoff209,311, Marat D. Kazanov441,442,443, Maria Keays59, Electron Kebebew444,445, Richard F. Kefford446, Manolis Kellis8,447, James G. Kench170,350,448, Catherine J. Kennedy246,247, Jules N. A. Kerssemakers47, David Khoo273, Vincent Khoo221, Narong Khuntikeo115,449, Ekta Khurana301,302,450,451, Helena Kilpinen117, Hark Kyun Kim452, Hyung-Lae Kim70, Hyung-Yong Kim415, Hyunghwan Kim250, Jaegil Kim8, Jihoon Kim453, Jong K. Kim454, Youngwook Kim455,456, Tari A. King457,458,459, Wolfram Klapper128, Kortine Kleinheinz47,48, Leszek J. Klimczak460, Stian Knappskog49,461, Michael Kneba437, Bartha M. Knoppers424, Youngil Koh462,463, Jan Komorowski305,464, Daisuke Komura410, Mitsuhiro Komura375, Gu Kong415, Marcel Kool426,465, Jan O. Korbel59,60, Viktoriya Korchina12, Andrey Korshunov465, Michael Koscher465, Roelof Koster466, Zsofia Kote-Jarai178, Antonios Koures244, Milena Kovacevic284, Barbara Kremeyer49, Helene Kretzmer164,165, Markus Kreuz467, Savitri Krishnamurthy99,468, Dieter Kube469, Kiran Kumar8, Pardeep Kumar221, Sushant Kumar5,19, Yogesh Kumar64, Ritika Kundra114,121, Kirsten Kübler8,14,72, Ralf Küppers470, Jesper Lagergren383,471, Phillip H. Lai166, Peter W. Laird472, Sunil R. Lakhani473, Christopher M. Lalansingh6, Emilie Lalonde6, Fabien C. Lamaze6, Adam Lambert351, Eric Lander8, Pablo Landgraf474,475, Luca Landoni115, Anita Langerød130, Andrés Lanzós230,231,423, Denis Larsimont476, Erik Larsson477, Mark Lathrop189, Loretta M. S. Lau478, Chris Lawerenz55, Rita T. Lawlor177, Michael S. Lawrence8,72,183, Alexander J. Lazar99,108, Xuan Le479, Darlene Lee30, Donghoon Lee5, Eunjung Alice Lee480, Hee Jin Lee417, Jake June-Koo Lee264,266, Jeong-Yeon Lee481, Juhee Lee482, Ming Ta Michael Lee340, Henry Lee-Six49, Kjong-Van Lehmann276,277,278,279,430, Hans Lehrach483, Dido Lenze400, Conrad R. Leonard209,311, Daniel A. Leongamornlert49,178, Ignaty Leshchiner8, Louis Letourneau484, Ivica Letunic71, Douglas A. Levine88,485, Lora Lewis12, Tim Ley486, Chang Li56,396, Constance H. Li6,44, Haiyan Irene Li30, Jun Li21, Lin Li56, Shantao Li5, Siliang Li56,396, Xiaobo Li56,396, Xiaotong Li5, Xinyue Li56, Yilong Li49, Han Liang21, Sheng-Ben Liang234, Peter Lichter68,397, Pei Lin8, Ziao Lin8,487, W. M. Linehan488, Ole Christian Lingjærde489, Dongbing Liu56,396, Eric Minwei Liu88,301,302, Fei-Fei Liu201,490, Fenglin Liu381,491, Jia Liu492, Xingmin Liu56,396, Julie Livingstone6, Dimitri Livitz8, Naomi Livni221, Lucas Lochovsky5,19,110, Markus Loeffler467, Georgina V. Long211, Armando Lopez-Guillermo493, Shaoke Lou5,19, David N. Louis72, Laurence B. Lovat117, Yiling Lu38, Yong-Jie Lu162,494, Youyong Lu495,496,497, Claudio Luchini167, Ilinca Lungu144,148, Xuemei Luo152, Hayley J. Luxton117, Andy G. Lynch223,315,498, Lisa Lype36, Cristina López111,112, Carlos López-Otín499, Eric Z. Ma64, Yussanne Ma30, Gaetan MacGrogan500, Shona MacRae501, Geoff Macintyre223, Tobias Madsen73, Kazuhiro Maejima184, Andrea Mafficini177, Dennis T. Maglinte166,502, Arindam Maitra174, Partha P. Majumder174, Luca Malcovati232, Salem Malikic62,78, Giuseppe Malleo115, Graham J. Mann211,246,503, Luisa Mantovani-Löffler504, Kathleen Marchal505,506, Giovanni Marchegiani115, Elaine R. Mardis1,193,507, Adam A. Margolin31, Maximillian G. Marin37, Florian Markowetz223,315, Julia Markowski403, Jeffrey Marks508, Tomas Marques-Bonet61,81,386,509, Marco A. Marra30, Luke Marsden351, John W. M. Martens332, Sancha Martin49,510, Jose I. Martin-Subero81,511, Iñigo Martincorena49, Alexander Martinez-Fundichely301,302,451 Yosef E. Maruvka8,26,72, R. Jay Mashl1,2, Charlie E. Massie223, Thomas J. Matthew37, Lucy Matthews178, Erik Mayer221,512, Simon Mayes513, Michael Mayo30, Faridah Mbabaali272, Karen McCune514, Ultan McDermott49, Patrick D. McGillivray19, Michael D. McLellan1,3,20, John D. McPherson148,272,515, John R. McPherson179,180, Treasa A. McPherson260, Samuel R. Meier8, Alice Meng516, Shaowu Meng134, Andrew Menzies49, Neil D. Merrett115,517, Sue Merson178, Matthew Meyerson8,14,82, William U. Meyerson4,5, Piotr A. Mieczkowski518, George L. Mihaiescu76, Sanja Mijalkovic284, Ana Mijalkovic Mijalkovic-Lazic284, Tom Mikkelsen519, Michele Milella253, Linda Mileshkin103, Christopher A. Miller1 , David K. Miller113,170, Jessica K. Miller272, Gordon B. Mills33,34, Ana Milovanovic57, Sarah Minner520, Marco Miotto115, Gisela Mir Arnau267, Lisa Mirabello240, Chris Mitchell103, Thomas J. Mitchell49,315,352, Satoru Miyano375, Naoki Miyoshi375, Shinichi Mizuno521, Fruzsina Molnár-Gábor522, Malcolm J. Moore300, Richard A. Moore30, Sandro Morganella49, Quaid D. Morris127,490, Carl Morrison523,524, Lisle E. Mose134, Catherine D. Moser349, Ferran Muiños298,299, Loris Mularoni298,299, Andrew J. Mungall30, Karen Mungall30, Elizabeth A. Musgrove133, Ville Mustonen525,526,527, David Mutch528, Francesc Muyas52,53,74, Donna M. Muzny12, Alfonso Muñoz59, Jerome Myers529, Ola Myklebost461, Peter Möller530, Genta Nagae89, Adnan M. Nagrial170, Hardeep K. Nahal-Bose76, Hitoshi Nakagama531, Hidewaki Nakagawa184, Hiromi Nakamura118, Toru Nakamura388, Kaoru Nakano184, Tannistha Nandi532, Jyoti Nangalia49, Mia Nastic284, Arcadi Navarro61,81,386, Fabio C. P. Navarro19, David E. Neal223,352, Gerd Nettekoven533, Felicity Newell209,311, Steven J. Newhouse59, Yulia Newton37, Alvin Wei Tian Ng534, Anthony Ng535, Jonathan Nicholson49, David Nicol221, Yongzhan Nie321,536, G. Petur Nielsen72, Morten Muhlig Nielsen73, Serena Nik-Zainal49,281,282,537, Michael S. Noble8, Katia Nones209,311, Paul A. Northcott538, Faiyaz Notta148,539, Brian D. O’Connor76,540, Peter O’Donnell541, Maria O’Donovan282, Sarah O’Meara49, Brian Patrick O’Neill542, J. Robert O’Neill543, David Ocana59, Angelica Ochoa88, Layla Oesper544, Christopher Ogden221, Hideki Ohdan93, Kazuhiro Ohi375, Lucila Ohno-Machado244, Karin A. Oien523,545, Akinyemi I. Ojesina546,547,548, Hidenori Ojima549, Takuji Okusaka550, Larsson Omberg551, Choon Kiat Ong552, Stephan Ossowski52,53,74, German Ott553, B. F. Francis Ouellette76,554, Christine P’ng6, Marta Paczkowska6, Salvatore Paiella115, Chawalit Pairojkul523, Marina Pajic170, Qiang Pan-Hammarström56,555, Elli Papaemmanuil49, Irene Papatheodorou59, Nagarajan Paramasivam43,47, Ji Wan Park385, Joong-Won Park556, Keunchil Park557,558, Kiejung Park559, Peter J. Park264,266, Joel S. Parker518, Simon L. Parsons124, Harvey Pass560, Danielle Pasternack272, Alessandro Pastore276, Ann-Marie Patch209,311, Iris Pauporté251, Antonio Pea115, John V. Pearson209,311, Chandra Sekhar Pedamallu8,14,82, Jakob Skou Pedersen73,75, Paolo Pederzoli115, Martin Peifer270, Nathan A. Pennell561, Charles M. Perou129,518, Marc D. Perry76,77, Gloria M. Petersen562, Myron Peto22, Nicholas Petrelli563, Robert Petryszak59, Stefan M. Pfister426,465,564, Mark Phillips424, Oriol Pich298,299, Hilda A. Pickett478, Todd D. Pihl565, Nischalan Pillay566, Sarah Pinder567, Mark Pinese170, Andreia V. Pinho568, Esa Pitkänen60, Xavier Pivot569, Elena Piñeiro-Yáñez95, Laura Planko533, Christoph Plass345, Paz Polak8,14,15, Tirso Pons570, Irinel Popescu571, Olga Potapova572, Aparna Prasad52, Shaun R. Preston573, Manuel Prinz47, Antonia L. Pritchard311, Stephenie D. Prokopec6, Elena Provenzano574, Xose S. Puente499, Sonia Puig176, Montserrat Puiggròs57, Sergio Pulido-Tamayo505,506, Gulietta M. Pupo246, Colin A. Purdie575, Michael C. Quinn209,311, Raquel Rabionet52,53,576, Janet S. Rader577, Bernhard Radlwimmer397, Petar Radovic284, Benjamin Raeder60, Keiran M. Raine49, Manasa Ramakrishna49, Kamna Ramakrishnan49, Suresh Ramalingam578, Benjamin J. Raphael579, W. Kimryn Rathmell580, Tobias Rausch60, Guido Reifenberger475, Jüri Reimand6,44, Jorge Reis-Filho348, Victor Reuter348, Iker Reyes-Salazar298, Matthew A. Reyna579, Sheila M. Reynolds36, Esther Rheinbay8,14,72, Yasser Riazalhosseini189, Andrea L. Richardson323, Julia Richter111,128, Matthew Ringel581, Markus Ringnér181, Yasushi Rino582, Karsten Rippe405, Jeffrey Roach583, Lewis R. Roberts349, Nicola D. Roberts49, Steven A. Roberts584, A. Gordon Robertson30, Alan J. Robertson113, Javier Bartolomé Rodriguez57, Bernardo Rodriguez-Martin104,105,106, F. Germán Rodríguez-González83,332, Michael H. A. Roehrl44,123,148,234,585,586, Marius Rohde587, Hirofumi Rokutan440, Gilles Romieu588, Ilse Rooman170, Tom Roques262, Daniel Rosebrock8, Mara Rosenberg8,72, Philip C. Rosenstiel589, Andreas Rosenwald590, Edward W. Rowe221,591, Romina Royo57, Steven G. Rozen179,180,592, Yulia Rubanova17,127, Mark A. Rubin423,593,594,595,596, Carlota Rubio-Perez298,299,597, Vasilisa A. Rudneva60, Borislav C. Rusev177, Andrea Ruzzenente598, Gunnar Rätsch276,277,278,279,280,430, Radhakrishnan Sabarinathan298,299,599, Veronica Y. Sabelnykova6, Sara Sadeghi30, S. Cenk Sahinalp62,78,79, Natalie Saini357, Mihoko Saito-Adachi440, Gordon Saksena8, Adriana Salcedo6, Roberto Salgado600, Leonidas Salichos5,19, Richard Sallari8, Charles Saller601, Roberto Salvia115, Michelle Sam272, Jaswinder S. Samra115,602, Francisco Sanchez-Vega114,121, Chris Sander276,603,604, Grant Sanders134, Rajiv Sarin605, Iman Sarrafi62,78, Aya Sasaki-Oku184, Torill Sauer489, Guido Sauter520, Robyn P. M. Saw211, Maria Scardoni167, Christopher J. Scarlett170,606, Aldo Scarpa177, Ghislaine Scelo194, Dirk Schadendorf68,607, Jacqueline E. Schein30, Markus B. Schilhabel589, Matthias Schlesner47,80, Thorsten Schlomm84,608, Heather K. Schmidt1 , Sarah-Jane Schramm246, Stefan Schreiber609, Nikolaus Schultz121, Steven E. Schumacher8,323, Roland F. Schwarz59,403,405,610, Richard A. Scolyer211,448,602, David Scott428, Ralph Scully611, Raja Seethala612, Ayellet V. Segre8,613, Iris Selander260, Colin A. Semple434, Yasin Senbabaoglu276, Subhajit Sengupta614, Elisabetta Sereni115, Stefano Serra585, Dennis C. Sgroi72, Mark Shackleton103, Nimish C. Shah352, Sagedeh Shahabi234, Catherine A. Shang329, Ping Shang211, Ofer Shapira8,323, Troy Shelton271, Ciyue Shen603,604, Hui Shen615, Rebecca Shepherd49, Ruian Shi490, Yan Shi134, Yu-Jia Shiah6, Tatsuhiro Shibata118,616, Juliann Shih8,82, Eigo Shimizu375, Kiyo Shimizu617, Seung Jun Shin618, Yuichi Shiraishi375, Tal Shmaya285, Ilya Shmulevich36, Solomon I. Shorser6, Charles Short59, Raunak Shrestha62, Suyash S. Shringarpure217, Craig Shriver619, Shimin Shuai6,126, Nikos Sidiropoulos83, Reiner Siebert112,620, Anieta M. Sieuwerts332, Lina Sieverling205,237, Sabina Signoretti202,621, Katarzyna O. Sikora177, Michele Simbolo138, Ronald Simon520, Janae V. Simons134, Jared T. Simpson6,17, Peter T. Simpson473, Samuel Singer115,458, Nasa Sinnott-Armstrong8,217, Payal Sipahimalani30, Tara J. Skelly390, Marcel Smid332, Jaclyn Smith622, Karen Smith-McCune514, Nicholas D. Socci276, Heidi J. Sofia27, Matthew G. Soloway134, Lei Song240, Anil K. Sood623,624,625, Sharmila Sothi626, Christos Sotiriou244, Cameron M. Soulette37, Paul N. Span627, Paul T. Spellman22, Nicola Sperandio177, Andrew J. Spillane211, Oliver Spiro8, Jonathan Spring628, Johan Staaf181, Peter F. Stadler163,164,165, Peter Staib629, Stefan G. Stark277,279,618,630, Lucy Stebbings49, Ólafur Andri Stefánsson631, Oliver Stegle59,60,632, Lincoln D. Stein6,126, Alasdair Stenhouse633, Chip Stewart8, Stephan Stilgenbauer634, Miranda D. Stobbe52,61, Michael R. Stratton49, Jonathan R. Stretch211, Adam J. Struck31, Joshua M. Stuart24,37, Henk G. Stunnenberg396,635, Hong Su56,396, Xiaoping Su99, Ren X. Sun6, Stephanie Sungalee60, Hana Susak52,53, Akihiro Suzuki89,636, Fred Sweep637, Monika Szczepanowski128, Holger Sültmann67,638, Takashi Yugawa617, Angela Tam30, David Tamborero298,299, Benita Kiat Tee Tan639, Donghui Tan518, Patrick Tan180,532,592,640, Hiroko Tanaka375, Hirokazu Taniguchi616, Tomas J. Tanskanen641, Maxime Tarabichi49,290, Roy Tarnuzzer220, Patrick Tarpey642, Morgan L. Taschuk152, Kenji Tatsuno89, Simon Tavaré223,643, Darrin F. Taylor113, Amaro Taylor-Weiner8, Jon W. Teague49, Bin Tean Teh180,592,640,644,645, Varsha Tembe246, Javier Temes104,105, Kevin Thai76, Sarah P. Thayer393, Nina Thiessen30, Gilles Thomas646, Sarah Thomas221, Alan Thompson221, Alastair M. Thompson633, John F. Thompson211, R. Houston Thompson647, Heather Thorne103, Leigh B. Thorne176, Adrian Thorogood424, Grace Tiao8, Nebojsa Tijanic284, Lee E. Timms272, Roberto Tirabosco648, Marta Tojo106, Stefania Tommasi649, Christopher W. Toon170, Umut H. Toprak48,650, David Torrents57,81, Giampaolo Tortora651,652, Jörg Tost653, Yasushi Totoki118, David Townend654, Nadia Traficante103, Isabelle Treilleux655,656, Jean-Rémi Trotta61, Lorenz H. P. Trümper469, Ming Tsao124,539, Tatsuhiko Tsunoda183,657,658,659, Jose M. C. Tubio104,105,106, Olga Tucker660, Richard Turkington661, Daniel J. Turner513, Andrew Tutt323, Masaki Ueno376, Naoto T. Ueno662, Christopher Umbricht151,213,663, Husen M. Umer305,664, Timothy J. Underwood665, Lara Urban59,60, Tomoko Urushidate616, Tetsuo Ushiku339, Liis Uusküla-Reimand666,667, Alfonso Valencia57,81, David J. Van Den Berg166, Steven Van Laere307, Peter Van Loo290,291, Erwin G. Van Meir668, Gert G. Van den Eynden307, Theodorus Van der Kwast123, Naveen Vasudev137, Miguel Vazquez57,669, Ravikiran Vedururu267, Umadevi Veluvolu518, Shankar Vembu490,670, Lieven P. C. Verbeke506,671, Peter Vermeulen307, Clare Verrill351,672, Alain Viari177, David Vicente57, Caterina Vicentini177, K. Vijay Raghavan365, Juris Viksna673, Ricardo E. Vilain674, Izar Villasante57, Anne Vincent-Salomon635, Tapio Visakorpi190, Douglas Voet8, Paresh Vyas311,351, Ignacio Vázquez-García49,86,675,676, Nick M. Waddell209, Nicola Waddell209,311, Claes Wadelius677, Lina Wadi6, Rabea Wagener111,112, Jeremiah A. Wala8,14,82, Jian Wang56, Jiayin Wang1,40,66, Linghua Wang12, Qi Wang465, Wenyi Wang21, Yumeng Wang21, Zhining Wang220, Paul M. Waring523, Hans-Jörg Warnatz483, Jonathan Warrell5,19, Anne Y. Warren352,678, Sebastian M. Waszak60, David C. Wedge49,294,679, Dieter Weichenhan345, Paul Weinberger680, John N. Weinstein38, Joachim Weischenfeldt60,83,84, Daniel J. Weisenberger166, Ian Welch681, Michael C. Wendl1,10,11, Johannes Werner47,85, Justin P. Whalley61,682, David A. Wheeler12,13, Hayley C. Whitaker117, Dennis Wigle683, Matthew D. Wilkerson518, Ashley Williams244, James S. Wilmott211, Gavin W. Wilson6,148, Julie M. Wilson148, Richard K. Wilson1,684, Boris Winterhoff685, Jeffrey A. Wintersinger17,127,384, Maciej Wiznerowicz686,687, Stephan Wolf688, Bernice H. Wong689, Tina Wong1,30, Winghing Wong690, Youngchoon Woo250, Scott Wood209,311, Bradly G. Wouters44, Adam J. Wright6, Derek W. Wright133,691, Mark H. Wright217, Chin-Lee Wu72, Dai-Ying Wu285, Guanming Wu692, Jianmin Wu170, Kui Wu56,396, Yang Wu179,180, Zhenggang Wu64, Liu Xi12, Tian Xia693, Qian Xiang76, Xiao Xiao66, Rui Xing497, Heng Xiong56,396, Qinying Xu209,311, Yanxun Xu694, Hong Xue64, Shinichi Yachida118,695, Sergei Yakneen60, Rui Yamaguchi375, Takafumi N. Yamaguchi6, Masakazu Yamamoto120, Shogo Yamamoto89, Hiroki Yamaue376, Fan Yang490, Huanming Yang56, Jean Y. Yang696, Liming Yang220, Lixing Yang697, Shanlin Yang306, Tsun-Po Yang270, Yang Yang369, Xiaotong Yao408,698, Marie-Laure Yaspo483, Lucy Yates49, Christina Yau156, Chen Ye56,396, Kai Ye40,41, Venkata D. Yellapantula20,86, Christopher J. Yoon249, Sung-Soo Yoon463, Fouad Yousif6, Jun Yu699, Kaixian Yu700, Willie Yu701, Yingyan Yu702, Ke Yuan223,510,703, Yuan Yuan21, Denis Yuen6, Takashi Yugawa617, Christina K. Yung76, Olga Zaikova704, Jorge Zamora49,104,105,106, Marc Zapatka397, Jean C. Zenklusen220, Thorsten Zenz67, Nikolajs Zeps705,706, Cheng-Zhong Zhang8,707, Fan Zhang381, Hailei Zhang8, Hongwei Zhang494, Hongxin Zhang121, Jiashan Zhang220, Jing Zhang5, Junjun Zhang76, Xiuqing Zhang56, Xuanping Zhang66,369, Yan Zhang5,708,709, Zemin Zhang381,710, Zhongming Zhao711, Liangtao Zheng381, Xiuqing Zheng381, Wanding Zhou615, Yong Zhou56, Bin Zhu240, Hongtu Zhu700,712, Jingchun Zhu24, Shida Zhu56,396, Lihua Zou713, Xueqing Zou49, Anna deFazio246,247,714, Nicholas van As221, Carolien H. M. van Deurzen715, Marc J. van de Vijver523, L. van’t Veer716 & Christian von Mering433,717, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.

Published
2020
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50. Sex differences in oncogenic mutational processes

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Li C. H., Prokopec S. D., Sun R. X., Yousif F., Schmitz N., Al-Shahrour F., Atwal G., Bailey P. J., Biankin A. V., Boutros P. C., Campbell P. J., Chang D. K., Cooke S. L., Deshpande V., Faltas B. M., Faquin W. C., Garraway L., Getz G., Grimmond S. M., Haider S., Hoadley K. A., Jiao W., Kaiser V. B., Karlic R., Kato M., Kubler K., Lazar A. J., Louis D. N., Margolin A., Martin S., Nahal-Bose H. K., Nielsen G. P., Nik-Zainal S., Omberg L., P'ng C., Perry M. D., Polak P., Rheinbay E., Rubin M. A., Semple C. A., Sgroi D. C., Shibata T., Siebert R., Smith J., Stein L. D., Stobbe M. D., Thai K., Wright D. W., Wu C. -L., Yuan K., Zhang J., Aaltonen L. A., Abascal F., Abeshouse A., Aburatani H., Adams D. J., Agrawal N., Ahn K. S., Ahn S. -M., Aikata H., Akbani R., Akdemir K. C., Al-Ahmadie H., Al-Sedairy S. T., Alawi M., Albert M., Aldape K., Alexandrov L. B., Ally A., Alsop K., Alvarez E. G., Amary F., Amin S. B., Aminou B., Ammerpohl O., Anderson M. J., Ang Y., Antonello D., Anur P., Aparicio S., Appelbaum E. L., Arai Y., Aretz A., Arihiro K., Ariizumi S. -I., Armenia J., Arnould L., Asa S., Assenov Y., Aukema S., Auman J. T., Aure M. R., Awadalla P., Aymerich M., Bader G. D., Baez-Ortega A., Bailey M. H., Balasundaram M., Balu S., Bandopadhayay P., Banks R. E., Barbi S., Barbour A. P., Barenboim J., Barnholtz-Sloan J., Barr H., Barrera E., Bartlett J., Bartolome J., Bassi C., Bathe O. F., Baumhoer D., Bavi P., Baylin S. B., Bazant W., Beardsmore D., Beck T. A., Behjati S., Behren A., Niu B., Bell C., Beltran S., Benz C., Berchuck A., Bergmann A. K., Bergstrom E. N., Berman B. P., Berney D. M., Bernhart S. H., Beroukhim R., Berrios M., Bersani S., Bertl J., Betancourt M., Bhandari V., Bhosle S. G., Bieg M., Bigner D., Binder H., Birney E., Birrer M., Biswas N. K., Bjerkehagen B., Bodenheimer T., Boice L., Bonizzato G., De Bono J. S., Boot A., Bootwalla M. S., Borg A., Borkhardt A., Boroevich K. A., Borozan I., Borst C., Bosenberg M., Bosio M., Boultwood J., Bourque G., Bova G. S., Bowen D. T., Bowlby R., Bowtell D. D. L., Boyault S., Boyce R., Boyd J., Brazma A., Brennan P., Brewer D. S., Brinkman A. B., Bristow R. G., Broaddus R. R., Brock J. E., Brock M., Broeks A., Brooks A. N., Brooks D., Brors B., Brunak S., Bruxner T. J. C., Bruzos A. L., Buchanan A., Buchhalter I., Buchholz C., Bullman S., Burke H., Burkhardt B., Burns K. H., Busanovich J., Bustamante C. D., Butler A. P., Butte A. J., Byrne N. J., Borresen-Dale A. -L., Caesar-Johnson S. J., Cafferkey A., Cahill D., Calabrese C., Caldas C., Calvo F., Camacho N., Campo E., Cantu C., Cao S., Carey T. E., Carlevaro-Fita J., Carlsen R., Cataldo I., Cazzola M., Cebon J., Cerfolio R., Chadwick D. E., Chakravarty D., Chalmers D., Chan C. W. Y., Chan K., Chan-Seng-Yue M., Chandan V. S., Chanock S. J., Chantrill L. A., Chateigner A., Chatterjee N., Chayama K., Chen H. -W., Chen J., Chen K., Chen Y., Chen Z., Cherniack A. D., Chien J., Chiew Y. -E., Chin S. -F., Cho J., Cho S., Choi J. K., Choi W., Chomienne C., Chong Z., Choo S. P., Chou A., Christ A. N., Christie E. L., Chuah E., Cibulskis C., Cibulskis K., Cingarlini S., Clapham P., Claviez A., Cleary S., Cloonan N., Cmero M., Collins C. C., Connor A. A., Cooper C. S., Cope L., Corbo V., Cordes M. G., Cordner S. M., Cortes-Ciriano I., Covington K., Cowin P. A., Craft B., Craft D., Creighton C. J., Cun Y., Curley E., Cutcutache I., Czajka K., Czerniak B., Dagg R. A., Danilova L., Davi M. V., Davidson N. R., Davies H., Davis I. J., Davis-Dusenbery B. N., Dawson K. J., De La Vega F. M., De Paoli-Iseppi R., Defreitas T., Dei Tos A. P., Delaneau O., Demchok J. A., Demeulemeester J., Demidov G. M., Demircioglu D., Dennis N. M., Denroche R. E., Dentro S. C., Desai N., Deshwar A. G., Desmedt C., Deu-Pons J., Dhalla N., Dhani N. C., Dhingra P., Dhir R., DiBiase A., Diamanti K., Ding L., Ding S., Dinh H. Q., Dirix L., Doddapaneni H. V., Donmez N., Dow M. T., Drapkin R., Drechsel O., Drews R. M., Serge S., Dudderidge T., Dueso-Barroso A., Dunford A. J., Dunn M., Dursi L. J., Duthie F. R., Dutton-Regester K., Eagles J., Easton D. F., Edmonds S., Edwards P. A., Edwards S. E., Eeles R. A., Ehinger A., Eils J., Eils R., El-Naggar A., Eldridge M., Ellrott K., Erkek S., Escaramis G., Espiritu S. M. G., Estivill X., Etemadmoghadam D., Eyfjord J. E., Fan D., Fan Y., Farcas C., Fassan M., Fatima A., Favero F., Fayzullaev N., Felau I., Fereday S., Ferguson M. L., Ferretti V., Feuerbach L., Field M. A., Fink J. L., Finocchiaro G., Fisher C., Fittall M. W., Fitzgerald A., Fitzgerald R. C., Flanagan A. M., Fleshner N. E., Flicek P., Foekens J. A., Fong K. M., Fonseca N. A., Foster C. S., Fox N. S., Fraser M., Frazer S., Frenkel-Morgenstern M., Friedman W., Frigola J., Fronick C. C., Fujimoto A., Fujita M., Fukayama M., Fulton L. A., Fulton R. S., Furuta M., Futreal P. A., Fullgrabe A., Gabriel S. B., Gallinger S., Gambacorti Passerini C., Gao J., Gao S., Garred O., Garrison E., Garsed D. W., Gehlenborg N., Gelpi J. L. L., George J., Gerhard D. S., Gerhauser C., Gershenwald J. E., Gerstein M., Gerstung M., Ghori M., Ghossein R., Giama N. H., Gibbs R. A., Gill A. J., Gill P., Giri D. D., Glodzik D., Gnanapragasam V. J., Goebler M. E., Goldman M. J., Gomez C., Gonzalez S., Gonzalez-Perez A., Gordenin D. A., Gossage J., Gotoh K., Govindan R., Grabau D., Graham J. S., Grant R. C., Green A. R., Green E., Greger L., Grehan N., Grimaldi S., Grossman R. L., Grundhoff A., Gundem G., Guo Q., Gupta M., Gupta S., Gut I. G., Gut M., Goke J., Ha G., Haake A., Haan D., Haas S., Haase K., Haber J. E., Habermann N., Hach F., Hama N., Hamdy F. C., Hamilton A., Hamilton M. P., Han L., Hanna G. B., Hansmann M., Haradhvala N. J., Harismendy O., Harliwong I., Harmanci A. O., Harrington E., Hasegawa T., Haussler D., Hawkins S., Hayami S., Hayashi S., Hayes D. N., Hayes S. J., Hayward N. K., Hazell S., He Y., Heath A. P., Heath S. C., Hedley D., Hegde A. M., Heiman D. I., Heinold M. C., Heins Z., Heisler L. E., Hellstrom-Lindberg E., Helmy M., Heo S. G., Hepperla A. J., Heredia-Genestar J. M., Herrmann C., Hersey P., Hess J. M., Hilmarsdottir H., Hinton J., Hirano S., Hiraoka N., Hobolth A., Hodzic E., Hoell J. I., Hoffmann S., Hofmann O., Holbrook A., Holik A. Z., Hollingsworth M. A., Holmes O., Holt R. A., Hong C., Hong E. P., Hong J. H., Hooijer G. K., Hornshoj H., Hosoda F., Hou Y., Hovestadt V., Howat W., Hoyle A. P., Hruban R. H., Hu J., Hu T., Hua X., Huang K. -L., Huang M., Huang M. N., Huang V., Huang Y., Huber W., Hudson T. J., Hummel M., Hung J. A., Huntsman D., Hupp T. R., Huse J., Huska M. R., Hutter B., Hutter C. M., Hubschmann D., Iacobuzio-Donahue C. A., Imbusch C. D., Imielinski M., Imoto S., Isaacs W. B., Isaev K., Ishikawa S., Iskar M., Islam S. M. A., Ittmann M., Ivkovic S., Izarzugaza J. M. G., Jacquemier J., Jakrot V., Jamieson N. B., Jang G. H., Jang S. J., Jayaseelan J. C., Jayasinghe R., Jefferys S. R., Jegalian K., Jennings J. L., Jeon S. -H., Jerman L., Ji Y., Johansson P. A., Johns A. L., Johns J., Johnson R., Johnson T. A., Jolly C., Joly Y., Jonasson J. G., Jones C. D., Jones D. R., Jones D. T. W., Jones N., Jones S. J. M., Jonkers J., Ju Y. S., Juhl H., Jung J., Juul M., Juul R. I., Juul S., Jager N., Kabbe R., Kahles A., Kahraman A., Kakavand H., Kalimuthu S., von Kalle C., Kang K. J., Karaszi K., Karlan B., Karsch D., Kasaian K., Kassahn K. S., Katai H., Katoh H., Kawakami Y., Kay J. D., Kazakoff S. H., Kazanov M. D., Keays M., Kebebew E., Kefford R. F., Kellis M., Kench J. G., Kennedy C. J., Kerssemakers J. N. A., Khoo D., Khoo V., Khuntikeo N., Khurana E., Kilpinen H., Kim H. K., Kim H. -L., Kim H. -Y., Kim H., Kim J., Kim J. K., Kim Y., King T. A., Klapper W., Kleinheinz K., Klimczak L. J., Knappskog S., Kneba M., Knoppers B. M., Koh Y., Komorowski J., Komura D., Komura M., Kong G., Kool M., Korbel J. O., Korchina V., Korshunov A., Koscher M., Koster R., Kote-Jarai Z., Koures A., Kovacevic M., Kremeyer B., Kretzmer H., Kreuz M., Krishnamurthy S., Kube D., Kumar K., Kumar P., Kumar S., Kumar Y., Kundra R., Kuppers R., Lagergren J., Lai P. H., Laird P. W., Lakhani S. R., Lalansingh C. M., Lalonde E., Lamaze F. C., Lambert A., Lander E., Landgraf P., Landoni L., Langerod A., Lanzos A., Larsimont D., Larsson E., Lathrop M., Lau L. M. S., Lawerenz C., Lawlor R. T., Lawrence M. S., Le X., Lee D., Lee E. A., Lee H. J., Lee J. J. -K., Lee J. -Y., Lee J., Lee M. T. M., Lee-Six H., Lehmann K. -V., Lehrach H., Lenze D., Leonard C. R., Leongamornlert D. A., Leshchiner I., Letourneau L., Letunic I., Levine D. A., Lewis L., Ley T., Li C., Li H. I., Li J., Li L., Li S., Li X., Li Y., Liang H., Liang S. -B., Lichter P., Lin P., Lin Z., Linehan W. M., Lingjaerde O. C., Liu D., Liu E. M., Liu F. -F., Liu F., Liu J., Liu X., Livingstone J., Livitz D., Livni N., Lochovsky L., Loeffler M., Long G. V., Lopez-Guillermo A., Lou S., Lovat L. B., Lu Y., Lu Y. -J., Luchini C., Lungu I., Luo X., Luxton H. J., Lynch A. G., Lype L., Lopez C., Lopez-Otin C., Ma E. Z., Ma Y., MacGrogan G., MacRae S., Macintyre G., Madsen T., Maejima K., Mafficini A., Maglinte D. T., Maitra A., Majumder P. P., Malcovati L., Malikic S., Malleo G., Mann G. J., Mantovani-Loffler L., Marchal K., Marchegiani G., Mardis E. R., Margolin A. A., Marin M. G., Markowetz F., Markowski J., Marks J., Marques-Bonet T., Marra M. A., Marsden L., Martens J. W. M., Martin-Subero J. I., Martincorena I., Martinez-Fundichely A., Maruvka Y. E., Mashl R. J., Massie C. E., Matthew T. J., Matthews L., Mayer E., Mayes S., Mayo M., Mbabaali F., McCune K., McDermott U., McGillivray P. D., McLellan M. D., McPherson J. D., McPherson J. R., McPherson T. A., Meier S. R., Meng A., Meng S., Menzies A., Merrett N. D., Merson S., Meyerson M., Meyerson W., Mieczkowski P. A., Mihaiescu G. L., Mijalkovic S., Mijalkovic-Lazic A. M., Mikkelsen T., Milella M., Mileshkin L., Miller C. A., Miller D. K., Miller J. K., Mills G. B., Milovanovic A., Minner S., Miotto M., Arnau G. M., Mirabello L., Mitchell C., Mitchell T. J., Miyano S., Miyoshi N., Mizuno S., Molnar-Gabor F., Moore M. J., Moore R. A., Morganella S., Morris Q. D., Morrison C., Mose L. E., Moser C. D., Muinos F., Mularoni L., Mungall A. J., Mungall K., Musgrove E. A., Mustonen V., Mutch D., Muyas F., Muzny D. M., Munoz A., Myers J., Myklebost O., Moller P., Nagae G., Nagrial A. M., Nakagama H., Nakagawa H., Nakamura H., Nakamura T., Nakano K., Nandi T., Nangalia J., Nastic M., Navarro A., Navarro F. C. P., Neal D. E., Nettekoven G., Newell F., Newhouse S. J., Newton Y., Ng A. W. T., Ng A., Nicholson J., Nicol D., Nie Y., Nielsen M. M., Noble M. S., Nones K., Northcott P. A., Notta F., O'Connor B. D., O'Donnell P., O'Donovan M., O'Meara S., O'Neill B. P., O'Neill J. R., Ocana D., Ochoa A., Oesper L., Ogden C., Ohdan H., Ohi K., Ohno-Machado L., Oien K. A., Ojesina A. I., Ojima H., Okusaka T., Ong C. K., Ossowski S., Ott G., Ouellette B. F. F., Paczkowska M., Paiella S., Pairojkul C., Pajic M., Pan-Hammarstrom Q., Papaemmanuil E., Papatheodorou I., Paramasivam N., Park J. W., Park J. -W., Park K., Park P. J., Parker J. S., Parsons S. L., Pass H., Pasternack D., Pastore A., Patch A. -M., Pauporte I., Pea A., Pearson J. V., Pedamallu C. S., Pedersen J. S., Pederzoli P., Peifer M., Pennell N. A., Perou C. M., Petersen G. M., Peto M., Petrelli N., Petryszak R., Pfister S. M., Phillips M., Pich O., Pickett H. A., Pihl T. D., Pillay N., Pinder S., Pinese M., Pinho A. V., Pitkanen E., Pivot X., Pineiro-Yanez E., Planko L., Plass C., Pons T., Popescu I., Potapova O., Prasad A., Preston S. R., Prinz M., Pritchard A. L., Provenzano E., Puente X. S., Puig S., Puiggros M., Pulido-Tamayo S., Pupo G. M., Purdie C. A., Quinn M. C., Rabionet R., Rader J. S., Radlwimmer B., Radovic P., Raeder B., Raine K. M., Ramakrishna M., Ramakrishnan K., Ramalingam S., Raphael B. J., Rathmell W. K., Rausch T., Reifenberger G., Reimand J., Reis-Filho J., Reuter V., Reyes-Salazar I., Reyna M. A., Reynolds S. M., Riazalhosseini Y., Richardson A. L., Richter J., Ringel M., Ringner M., Rino Y., Rippe K., Roach J., Roberts L. R., Roberts N. D., Roberts S. A., Robertson A. G., Robertson A. J., Rodriguez J. B., Rodriguez-Martin B., Rodriguez-Gonzalez F. G., Roehrl M. H. A., Rohde M., Rokutan H., Romieu G., Rooman I., Roques T., Rosebrock D., Rosenberg M., Rosenstiel P. C., Rosenwald A., Rowe E. W., Royo R., Rozen S. G., Rubanova Y., Rubio-Perez C., Rudneva V. A., Rusev B. C., Ruzzenente A., Ratsch G., Sabarinathan R., Sabelnykova V. Y., Sadeghi S., Sahinalp S. C., Saini N., Saito-Adachi M., Saksena G., Salcedo A., Salgado R., Salichos L., Sallari R., Saller C., Salvia R., Sam M., Samra J. S., Sanchez-Vega F., Sander C., Sanders G., Sarin R., Sarrafi I., Sasaki-Oku A., Sauer T., Sauter G., Saw R. P. M., Scardoni M., Scarlett C. J., Scarpa A., Scelo G., Schadendorf D., Schein J. E., Schilhabel M. B., Schlesner M., Schlomm T., Schmidt H. K., Schramm S. -J., Schreiber S., Schultz N., Schumacher S. E., Schwarz R. F., Scolyer R. A., Scott D., Scully R., Seethala R., Segre A. V., Selander I., Senbabaoglu Y., Sengupta S., Sereni E., Serra S., Shackleton M., Shah N. C., Shahabi S., Shang C. A., Shang P., Shapira O., Shelton T., Shen C., Shen H., Shepherd R., Shi R., Shi Y., Shiah Y. -J., Shih J., Shimizu E., Shimizu K., Shin S. J., Shiraishi Y., Shmaya T., Shmulevich I., Shorser S. I., Short C., Shrestha R., Shringarpure S. S., Shriver C., Shuai S., Sidiropoulos N., Sieuwerts A. M., Sieverling L., Signoretti S., Sikora K. O., Simbolo M., Simon R., Simons J. V., Simpson J. T., Simpson P. T., Singer S., Sinnott-Armstrong N., Sipahimalani P., Skelly T. J., Smid M., Smith-McCune K., Socci N. D., Sofia H. J., Soloway M. G., Song L., Sood A. K., Sothi S., Sotiriou C., Soulette C. M., Span P. N., Spellman P. T., Sperandio N., Spillane A. J., Spiro O., Spring J., Staaf J., Stadler P. F., Staib P., Stark S. G., Stebbings L., Stefansson O. A., Stegle O., Stenhouse A., Stewart C., Stilgenbauer S., Stratton M. R., Stretch J. R., Struck A. J., Stuart J. M., Stunnenberg H. G., Su H., Su X., Sungalee S., Susak H., Suzuki A., Sweep F., Szczepanowski M., Sultmann H., Yugawa T., Tam A., Tamborero D., Tan B. K. T., Tan D., Tan P., Tanaka H., Taniguchi H., Tanskanen T. J., Tarabichi M., Tarnuzzer R., Tarpey P., Taschuk M. L., Tatsuno K., Tavare S., Taylor D. F., Taylor-Weiner A., Teague J. W., Teh B. T., Tembe V., Temes J., Thayer S. P., Thiessen N., Thomas G., Thomas S., Thompson A., Thompson A. M., Thompson J. F., Thompson R. H., Thorne H., Thorne L. B., Thorogood A., Tiao G., Tijanic N., Timms L. E., Tirabosco R., Tojo M., Tommasi S., Toon C. W., Toprak U. H., Torrents D., Tortora G., Tost J., Totoki Y., Townend D., Traficante N., Treilleux I., Trotta J. -R., Trumper L. H. P., Tsao M., Tsunoda T., Tubio J. M. C., Tucker O., Turkington R., Turner D. J., Tutt A., Ueno M., Ueno N. T., Umbricht C., Umer H. M., Underwood T. J., Urban L., Urushidate T., Ushiku T., Uuskula-Reimand L., Valencia A., Van Den Berg D. J., Van Laere S., Van Loo P., Van Meir E. G., Van den Eynden G. G., Van der Kwast T., Vasudev N., Vazquez M., Vedururu R., Veluvolu U., Vembu S., Verbeke L. P. C., Vermeulen P., Verrill C., Viari A., Vicente D., Vicentini C., Raghavan K. V., Viksna J., Vilain R. E., Villasante I., Vincent-Salomon A., Visakorpi T., Voet D., Vyas P., Vazquez-Garcia I., Waddell N. M., Waddell N., Wadelius C., Wadi L., Wagener R., Wala J. A., Wang J., Wang L., Wang Q., Wang W., Wang Y., Wang Z., Waring P. M., Warnatz H. -J., Warrell J., Warren A. Y., Waszak S. M., Wedge D. C., Weichenhan D., Weinberger P., Weinstein J. N., Weischenfeldt J., Weisenberger D. J., Welch I., Wendl M. C., Werner J., Whalley J. P., Wheeler D. A., Whitaker H. C., Wigle D., Wilkerson M. D., Williams A., Wilmott J. S., Wilson G. W., Wilson J. M., Wilson R. K., Winterhoff B., Wintersinger J. A., Wiznerowicz M., Wolf S., Wong B. H., Wong T., Wong W., Woo Y., Wood S., Wouters B. G., Wright A. J., Wright M. H., Wu D. -Y., Wu G., Wu J., Wu K., Wu Y., Wu Z., Xi L., Xia T., Xiang Q., Xiao X., Xing R., Xiong H., Xu Q., Xu Y., Xue H., Yachida S., Yakneen S., Yamaguchi R., Yamaguchi T. N., Yamamoto M., Yamamoto S., Yamaue H., Yang F., Yang H., Yang J. Y., Yang L., Yang S., Yang T. -P., Yang Y., Yao X., Yaspo M. -L., Yates L., Yau C., Ye C., Ye K., Yellapantula V. D., Yoon C. J., Yoon S. -S., Yu J., Yu K., Yu W., Yu Y., Yuan Y., Yuen D., Yung C. K., Zaikova O., Zamora J., Zapatka M., Zenklusen J. C., Zenz T., Zeps N., Zhang C. -Z., Zhang F., Zhang H., Zhang X., Zhang Y., Zhang Z., Zhao Z., Zheng L., Zheng X., Zhou W., Zhou Y., Zhu B., Zhu H., Zhu J., Zhu S., Zou L., Zou X., deFazio A., van As N., van Deurzen C. H. M., van de Vijver M. J., Veer L., von Mering C., Lauri Antti Aaltonen / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Medical and Clinical Genetics, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Information Technology, Institute of Biotechnology, Bioinformatics, Department of Computer Science, Faculty of Medicine, HUS Helsinki and Uusimaa Hospital District, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, University of St Andrews. Statistics, University of St Andrews. School of Medicine, Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Li, C, Prokopec, S, Sun, R, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, P, Biankin, A, Boutros, P, Campbell, P, Chang, D, Cooke, S, Deshpande, V, Faltas, B, Faquin, W, Garraway, L, Getz, G, Grimmond, S, Haider, S, Hoadley, K, Jiao, W, Kaiser, V, Karlic, R, Kato, M, Kubler, K, Lazar, A, Louis, D, Margolin, A, Martin, S, Nahal-Bose, H, Nielsen, G, Nik-Zainal, S, Omberg, L, P'Ng, C, Perry, M, Polak, P, Rheinbay, E, Rubin, M, Semple, C, Sgroi, D, Shibata, T, Siebert, R, Smith, J, Stein, L, Stobbe, M, Thai, K, Wright, D, Wu, C, Yuan, K, Zhang, J, Aaltonen, L, Abascal, F, Abeshouse, A, Aburatani, H, Adams, D, Agrawal, N, Ahn, K, Ahn, S, Aikata, H, Akbani, R, Akdemir, K, Al-Ahmadie, H, Al-Sedairy, S, Alawi, M, Albert, M, Aldape, K, Alexandrov, L, Ally, A, Alsop, K, Alvarez, E, Amary, F, Amin, S, Aminou, B, Ammerpohl, O, Anderson, M, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, E, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, S, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, J, Aure, M, Awadalla, P, Aymerich, M, Bader, G, Baez-Ortega, A, Bailey, M, Balasundaram, M, Balu, S, Bandopadhayay, P, Banks, R, Barbi, S, Barbour, A, Barenboim, J, Barnholtz-Sloan, J, Barr, H, Barrera, E, Bartlett, J, Bartolome, J, Bassi, C, Bathe, O, Baumhoer, D, Bavi, P, Baylin, S, Bazant, W, Beardsmore, D, Beck, T, Behjati, S, Behren, A, Niu, B, Bell, C, Beltran, S, Benz, C, Berchuck, A, Bergmann, A, Bergstrom, E, Berman, B, Berney, D, Bernhart, S, Beroukhim, R, Berrios, M, Bersani, S, Bertl, J, Betancourt, M, Bhandari, V, Bhosle, S, Bieg, M, Bigner, D, Binder, H, Birney, E, Birrer, M, Biswas, N, Bjerkehagen, B, Bodenheimer, T, Boice, L, Bonizzato, G, De Bono, J, Boot, A, Bootwalla, M, Borg, A, Borkhardt, A, Boroevich, K, Borozan, I, Borst, C, Bosenberg, M, Bosio, M, Boultwood, J, Bourque, G, Bova, G, Bowen, D, Bowlby, R, Bowtell, D, Boyault, S, Boyce, R, Boyd, J, Brazma, A, Brennan, P, Brewer, D, Brinkman, A, Bristow, R, Broaddus, R, Brock, J, Brock, M, Broeks, A, Brooks, A, Brooks, D, Brors, B, Brunak, S, Bruxner, T, Bruzos, A, Buchanan, A, Buchhalter, I, Buchholz, C, Bullman, S, Burke, H, Burkhardt, B, Burns, K, Busanovich, J, Bustamante, C, Butler, A, Butte, A, Byrne, N, Borresen-Dale, A, Caesar-Johnson, S, Cafferkey, A, Cahill, D, Calabrese, C, Caldas, C, Calvo, F, Camacho, N, Campo, E, Cantu, C, Cao, S, Carey, T, Carlevaro-Fita, J, Carlsen, R, Cataldo, I, Cazzola, M, Cebon, J, Cerfolio, R, Chadwick, D, Chakravarty, D, Chalmers, D, Chan, C, Chan, K, Chan-Seng-Yue, M, Chandan, V, Chanock, S, Chantrill, L, Chateigner, A, Chatterjee, N, Chayama, K, Chen, H, Chen, J, Chen, K, Chen, Y, Chen, Z, Cherniack, A, Chien, J, Chiew, Y, Chin, S, Cho, J, Cho, S, Choi, J, Choi, W, Chomienne, C, Chong, Z, Choo, S, Chou, A, Christ, A, Christie, E, Chuah, E, Cibulskis, C, Cibulskis, K, Cingarlini, S, Clapham, P, Claviez, A, Cleary, S, 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Estivill, X, Etemadmoghadam, D, Eyfjord, J, Fan, D, Fan, Y, Farcas, C, Fassan, M, Fatima, A, Favero, F, Fayzullaev, N, Felau, I, Fereday, S, Ferguson, M, Ferretti, V, Feuerbach, L, Field, M, Fink, J, Finocchiaro, G, Fisher, C, Fittall, M, Fitzgerald, A, Fitzgerald, R, Flanagan, A, Fleshner, N, Flicek, P, Foekens, J, Fong, K, Fonseca, N, Foster, C, Fox, N, Fraser, M, Frazer, S, Frenkel-Morgenstern, M, Friedman, W, Frigola, J, Fronick, C, Fujimoto, A, Fujita, M, Fukayama, M, Fulton, L, Fulton, R, Furuta, M, Futreal, P, Fullgrabe, A, Gabriel, S, Gallinger, S, Gambacorti Passerini, C, Gao, J, Gao, S, Garred, O, Garrison, E, Garsed, D, Gehlenborg, N, Gelpi, J, George, J, Gerhard, D, Gerhauser, C, Gershenwald, J, Gerstein, M, Gerstung, M, Ghori, M, Ghossein, R, Giama, N, Gibbs, R, Gill, A, Gill, P, Giri, D, Glodzik, D, Gnanapragasam, V, Goebler, M, Goldman, M, Gomez, C, Gonzalez, S, Gonzalez-Perez, A, Gordenin, D, Gossage, J, Gotoh, K, Govindan, R, Grabau, D, Graham, J, Grant, R, Green, A, Green, E, Greger, L, Grehan, N, Grimaldi, S, Grossman, R, Grundhoff, A, Gundem, G, Guo, Q, Gupta, M, Gupta, S, Gut, I, Gut, M, Goke, J, Ha, G, Haake, A, Haan, D, Haas, S, Haase, K, Haber, J, Habermann, N, Hach, F, Hama, N, Hamdy, F, Hamilton, A, Hamilton, M, Han, L, Hanna, G, Hansmann, M, Haradhvala, N, Harismendy, O, Harliwong, I, Harmanci, A, Harrington, E, Hasegawa, T, Haussler, D, Hawkins, S, Hayami, S, Hayashi, S, Hayes, D, Hayes, S, Hayward, N, Hazell, S, He, Y, Heath, A, Heath, S, Hedley, D, Hegde, A, Heiman, D, Heinold, M, Heins, Z, Heisler, L, Hellstrom-Lindberg, E, Helmy, M, Heo, S, Hepperla, A, Heredia-Genestar, J, Herrmann, C, Hersey, P, Hess, J, Hilmarsdottir, H, Hinton, J, Hirano, S, Hiraoka, N, Hobolth, A, Hodzic, E, Hoell, J, Hoffmann, S, Hofmann, O, Holbrook, A, Holik, A, Hollingsworth, M, Holmes, O, Holt, R, Hong, C, Hong, E, Hong, J, Hooijer, G, Hornshoj, H, Hosoda, F, Hou, Y, Hovestadt, V, Howat, W, Hoyle, A, Hruban, R, Hu, J, Hu, T, Hua, X, Huang, K, Huang, M, 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[0000-0002-5487-7225], Prokopec, Stephenie D. [0000-0001-7936-8577], Boutros, Paul C. [0000-0003-0553-7520], Apollo - University of Cambridge Repository, Tampere University, BioMediTech, TAYS Cancer Centre, Basic (bio-) Medical Sciences, Li, Constance H [0000-0002-5487-7225], Prokopec, Stephenie D [0000-0001-7936-8577], Boutros, Paul C [0000-0003-0553-7520], and Medical Oncology

Subjects
sex differences, Male, Colorectal cancer, Kynferði, 02 engineering and technology, 0302 clinical medicine, DISPARITIES, Epidemiology of cancer, Cancer genomics, lcsh:Science, Càncer, Cancer genetics, Genome informatics, Cancer genomics, Oncogenes, Cancer genetics, Exome, Cancer, 0303 health sciences, Mutation, Neoplasms -- genetics, 1184 Genetics, developmental biology, physiology, Neoplasms/genetics, 3. Good health, 030220 oncology & carcinogenesis, Medical genetics, 0210 nano-technology, Human, Sex characteristics, medicine.medical_specialty, Science, Genomic Instability, General Biochemistry, Genetics and Molecular Biology, RC0254, Càncer -- Epidemiologia, Open Reading Frames, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Chromosomal Instability, Sex differences, Genetics, Humans, beta Catenin -- genetics, Sex organ, SIGNATURES, 45, RC0254 Neoplasms. Tumors. Oncology (including Cancer), Oncogenes, medicine.disease, 692/4028/67/69, Cancérologie, Genòmica, Logistic Models, 030104 developmental biology, lcsh:Q, PCAWG Tumour Subtypes and Clinical Translation, Human genome, 119, 0301 basic medicine, Medizin, General Physics and Astronomy, medicine.disease_cause, Bioinformatics, Genome informatics, Genome, Neoplasms, 38/23, Medicine and Health Sciences, Body Size, beta Catenin, Sex Characteristics, 318 Medical biotechnology, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Multidisciplinary, article, 3rd-DAS, 021001 nanoscience & nanotechnology, humanities, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Causality, oncology, 1181 Ecology, evolutionary biology, SURVIVAL, 631/114/2785, Female, Càncer -- Tractament, Oncogenes -- genetics, beta Catenin/genetics, 3122 Cancers, 610 Medicine & health, QH426 Genetics, Biology, Cancer epidemiology, Rare Diseases, 631/67/68, Krabbameinsrannsóknir, medicine, ddc:610, Gene, QH426, 030304 developmental biology, Krabbamein, Oncogenes/genetics, Genome, Human, Sex organs, Human Genome, PCAWG Consortium, General Chemistry, GENE, Good Health and Well Being, Estudis de gènere, oncogenic mutational processes, 692/4028/67/395, Diferències entre sexes, Gender studies, 3111 Biomedicine
Abstract

Publisher's version (útgefin grein), Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research., We thank all the members of the Boutros lab for insightful discussions. This study was conducted with the support of the Ontario Institute for Cancer Research to P.C.B. through funding provided by the Government of Ontario. This work was supported by the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada and the Canada Foundation for Innovation (CFI). P.C.B. was supported by a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award. This work was supported by an NSERC Discovery grant and by Canadian Institutes of Health Research, grant #SVB-145586, to P.C.B. This work was supported by the NIH/NCI under award number P30CA016042 and an operating grant from the National Cancer Institute Early Detection Research Network (1U01CA214194-01). We acknowledge the contributions of the many clinical networks across ICGC and TCGA who provided samples and data to the PCAWG Consortium, and the contributions of the Technical Working Group and the Germline Working Group of the PCAWG Consortium for collation, realignment and harmonised variant calling of the cancer genomes used in this study. We thank the patients and their families for their participation in the individual ICGC and TCGA projects.

Published
2020
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