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Abstract
INTRODUCTION Male factor infertility concerns 7-10% of men and among these 40-60% remain unexplained. SOURCES OF DATA This review is based on recent published literature regarding the genetic causes of male infertility. AREAS OF AGREEMENT Screening for karyotype abnormalities, biallelic pathogenic variants in the CFTR gene and Y-chromosomal microdeletions have been routine in andrology practice for >20 years, explaining ~10% of infertility cases. Rare specific conditions, such as congenital hypogonadotropic hypogonadism, disorders of sex development and defects of sperm morphology and motility, are caused by pathogenic variants in recurrently affected genes, which facilitate high diagnostic yield (40-60%) of targeted gene panel-based testing. AREAS OF CONTROVERSY Progress in mapping monogenic causes of quantitative spermatogenic failure, the major form of male infertility, has been slower. No 'recurrently' mutated key gene has been identified and worldwide, a few hundred patients in total have been assigned a possible monogenic cause. GROWING POINTS Given the high genetic heterogeneity, an optimal approach to screen for heterogenous genetic causes of spermatogenic failure is sequencing exomes or in perspective, genomes. Clinical guidelines developed by multidisciplinary experts are needed for smooth integration of expanded molecular diagnostics in the routine management of infertile men. AREAS TIMELY FOR DEVELOPING RESEARCH Di-/oligogenic causes, structural and common variants implicated in multifactorial inheritance may explain the 'hidden' genetic factors. It is also critical to understand how the recently identified diverse genetic factors of infertility link to general male health concerns across lifespan and how the clinical assessment could benefit from this knowledge.
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Affiliation(s)
- Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Laura Kasak
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Margus Punab
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia.,Andrology Centre, Tartu University Hospital, 50406 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
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2
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Abstract
Non-alcoholic fatty liver disease (NAFLD) is a continuous progression of pathophysiologic stages that is challenging to diagnose due to its inherent heterogeneity and poor standardization across a wide variety of diagnostic measures. NAFLD is heritable, and several loci have been robustly associated with various stages of disease. In the past few years, larger genetic association studies using new methodology have identified novel genes associated with NAFLD, some of which have shown therapeutic promise. This mini-review provides an overview of the heterogeneity in NAFLD phenotypes and diagnostic methods, discusses genetic associations in relation to the specific stages for which they were identified, and offers a perspective on the design of future genetic mapping studies to accelerate therapeutic target identification.
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Affiliation(s)
- Xiaomi Du
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Natalie DeForest
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Amit R. Majithia
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
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3
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Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo-Mesa A, Bosch E, Calafell F, Quintana-Murci L, Comas D. The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. Mol Biol Evol 2021; 38:2804-2817. [PMID: 33713133 PMCID: PMC8233508 DOI: 10.1093/molbev/msab070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Human Genomics and Evolution, Collège de France, Paris, France
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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4
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Kausthubham N, Shukla A, Gupta N, Bhavani GS, Kulshrestha S, Das Bhowmik A, Moirangthem A, Bijarnia-Mahay S, Kabra M, Puri RD, Mandal K, Verma IC, Bielas SL, Phadke SR, Dalal A, Girisha KM. A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians. Hum Mutat 2021; 42:e15-e61. [PMID: 33502066 PMCID: PMC10052794 DOI: 10.1002/humu.24172] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 12/16/2022]
Abstract
Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.
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Affiliation(s)
- Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gandham S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Aneek Das Bhowmik
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,ASPIRE (Diagnostics Facility), CSIR-Centre for Cellular & Molecular Biology, CCMB Annexe II, Hyderabad, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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5
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McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan R, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, Savojardo C, Martelli PL, Casadio R, Pal LR, Moult J, Brenner SE, Altman R. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat 2019; 40:1314-1320. [PMID: 31140652 DOI: 10.1002/humu.23825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 01/14/2023]
Abstract
Genetics play a key role in venous thromboembolism (VTE) risk, however established risk factors in European populations do not translate to individuals of African descent because of the differences in allele frequencies between populations. As part of the fifth iteration of the Critical Assessment of Genome Interpretation, participants were asked to predict VTE status in exome data from African American subjects. Participants were provided with 103 unlabeled exomes from patients treated with warfarin for non-VTE causes or VTE and asked to predict which disease each subject had been treated for. Given the lack of training data, many participants opted to use unsupervised machine learning methods, clustering the exomes by variation in genes known to be associated with VTE. The best performing method using only VTE related genes achieved an area under the ROC curve of 0.65. Here, we discuss the range of methods used in the prediction of VTE from sequence data and explore some of the difficulties of conducting a challenge with known confounders. In addition, we show that an existing genetic risk score for VTE that was developed in European subjects works well in African Americans.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California
| | - Roxana Daneshjou
- Department of Dermatology, Stanford School of Medicine, Stanford, California
| | - Panagiostis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology, Baylor College of Medicine, Houston, Texas.,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas
| | | | - Sadhna Rana
- Innovations Labs, Tata Consultancy Services, Hyderabad, India
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington
| | - Kymberleigh A Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Moses Stamboulian
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Yuxiang Jiang
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Emidio Capriotti
- BioFolD Unit, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Samuele Bovo
- Department of Pharmacy and Biotechnology, Bologna Biocomputing Group, University of Bologna, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, Bologna Biocomputing Group, University of Bologna, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, Bologna Biocomputing Group, University of Bologna, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, Bologna Biocomputing Group, University of Bologna, Italy.,Institute of Biomembrane and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Steven E Brenner
- Department of Plant and Microbial biology, University of California Berkeley, Berkeley, California
| | - Russ Altman
- Departments of Bioengineering, Biomedical Data Science, Genetics, and Medicine, Stanford University, Stanford, California
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6
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Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat 2017. [PMID: 28634997 DOI: 10.1002/humu.23280] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.
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Affiliation(s)
- Roxana Daneshjou
- Department of Genetics, Stanford School of Medicine, Stanford, California
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Samuele Bovo
- Biocomputing Group, BiGeA/CIG, "Luigi Galvani" Interdepartmental Center for Integrated Studies of Bioinformatics, Biophysics, and Biocomplexity, University of Bologna, Bologna, Italy
| | - Pier L Martelli
- Biocomputing Group, BiGeA/CIG, "Luigi Galvani" Interdepartmental Center for Integrated Studies of Bioinformatics, Biophysics, and Biocomplexity, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Biocomputing Group, BiGeA/CIG, "Luigi Galvani" Interdepartmental Center for Integrated Studies of Bioinformatics, Biophysics, and Biocomplexity, University of Bologna, Bologna, Italy
| | - Pietro Di Lena
- Biocomputing Group/Department of Computer Science and Engineering, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, BiGeA/CIG, "Luigi Galvani" Interdepartmental Center for Integrated Studies of Bioinformatics, Biophysics, and Biocomplexity, University of Bologna, Bologna, Italy.,"Giorgio Prodi" Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | - Matthew Edwards
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - David Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
| | - Laksshman Sundaram
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida, Gainesville, Florida
| | - Rajendra Rana Bhat
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida, Gainesville, Florida
| | - Xiaolin Li
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida, Gainesville, Florida
| | - Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Yuxiang Jiang
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana.,Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington
| | - Kymberleigh A Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Biao Li
- Gilead Sciences, Foster City, California
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Sohela Shah
- Qiagen Bioinformatics, Redwood City, California
| | - Marco Carraro
- Department of Biomedical Science, University of Padova, Padova, Italy
| | - Alessandra Gasparini
- Department of Biomedical Science, University of Padova, Padova, Italy.,Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Manuel Giollo
- Department of Biomedical Science, University of Padova, Padova, Italy.,Department of Information Engineering, University of Padova, Padova, Italy
| | - Carlo Ferrari
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Science, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
| | - Eran Bachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Johnathan R Azaria
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yanay Ofran
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Abhishek Niroula
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mauno Vihinen
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Billy Chang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Maggie H Wang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, N.T., Hong Kong.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Mehdi Pirooznia
- Department of Psychiatry, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - James B Potash
- Department of Psychiatry, University of Iowa, Iowa City, Iowa
| | - Russ B Altman
- Department of Genetics, Stanford School of Medicine, Stanford, California
| | - Teri E Klein
- Department of Genetics, Stanford School of Medicine, Stanford, California
| | - Roger A Hoskins
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
| | - Susanna Repo
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
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7
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Huang PJ, Lee CC, Tan BCM, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS, Liu H, Tang P. Vanno: a visualization-aided variant annotation tool. Hum Mutat 2015; 36:167-74. [PMID: 25196204 DOI: 10.1002/humu.22684] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/25/2014] [Indexed: 01/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have revolutionized the field of genetics and are trending toward clinical diagnostics. Exome and targeted sequencing in a disease context represent a major NGS clinical application, considering its utility and cost-effectiveness. With the ongoing discovery of disease-associated genes, various gene panels have been launched for both basic research and diagnostic tests. However, the fundamental inconsistencies among the diverse annotation sources, software packages, and data formats have complicated the subsequent analysis. To manage disease-associated NGS data, we developed Vanno, a Web-based application for in-depth analysis and rapid evaluation of disease-causative genome sequence alterations. Vanno integrates information from biomedical databases, functional predictions from available evaluation models, and mutation landscapes from TCGA cancer types. A highly integrated framework that incorporates filtering, sorting, clustering, and visual analytic modules is provided to facilitate exploration of oncogenomics datasets at different levels, such as gene, variant, protein domain, or three-dimensional structure. Such design is crucial for the extraction of knowledge from sequence alterations and translating biological insights into clinical applications. Taken together, Vanno supports almost all disease-associated gene tests and exome sequencing panels designed for NGS, providing a complete solution for targeted and exome sequencing analysis. Vanno is freely available at http://cgts.cgu.edu.tw/vanno.
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Affiliation(s)
- Po-Jung Huang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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8
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VanderWeele DJ, Brown CD, Taxy JB, Gillard M, Hatcher DM, Tom WR, Stadler WM, White KP. Low-grade prostate cancer diverges early from high grade and metastatic disease. Cancer Sci 2014; 105:1079-85. [PMID: 24890684 PMCID: PMC4317857 DOI: 10.1111/cas.12460] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/16/2014] [Accepted: 05/23/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding the developmental relationship between indolent and aggressive tumors is central to understanding disease progression and making treatment decisions. For example, most men diagnosed with prostate cancer have clinically indolent disease and die from other causes. Overtreatment of prostate cancer remains a concern. Here we use laser microdissection followed by exome sequencing of low- and high-grade prostate cancer foci from four subjects, and metastatic disease from two of those subjects, to evaluate the molecular relationship of coincident cancer foci. Seventy of 79 (87%) high-confidence somatic mutations in low-grade disease were private to low-grade foci. In contrast, high-grade foci and metastases harbored many of the same mutations. In cases in which there was a metastatic focus, 15 of 80 (19%) high-confidence somatic mutations in high-grade foci were private. Seven of the 80 (9%) were shared with low-grade foci and 65 (82%) were shared with metastatic foci. Notably, mutations in cancer-associated genes and the p53 signaling pathway were found exclusively in high-grade foci and metastases. The pattern of mutations is consistent with early divergence between low- and high-grade foci and late divergence between high-grade foci and metastases. These data provide insights into the development of high-grade and metastatic prostate cancer.
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Affiliation(s)
- David J VanderWeele
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA; Department of Medicine, University of Chicago, Chicago, Illinois, USA
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9
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O'Brien JE, Meisler MH. Sodium channel SCN8A (Nav1.6): properties and de novo mutations in epileptic encephalopathy and intellectual disability. Front Genet 2013; 4:213. [PMID: 24194747 PMCID: PMC3809569 DOI: 10.3389/fgene.2013.00213] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/04/2013] [Indexed: 11/13/2022] Open
Abstract
The sodium channel Nav1.6, encoded by the gene SCN8A, is one of the major voltage-gated channels in human brain. The sequences of sodium channels have been highly conserved during evolution, and minor changes in biophysical properties can have a major impact in vivo. Insight into the role of Nav1.6 has come from analysis of spontaneous and induced mutations of mouse Scn8a during the past 18 years. Only within the past year has the role of SCN8A in human disease become apparent from whole exome and genome sequences of patients with sporadic disease. Unique features of Nav1.6 include its contribution to persistent current, resurgent current, repetitive neuronal firing, and subcellular localization at the axon initial segment (AIS) and nodes of Ranvier. Loss of Nav1.6 activity results in reduced neuronal excitability, while gain-of-function mutations can increase neuronal excitability. Mouse Scn8a (med) mutants exhibit movement disorders including ataxia, tremor and dystonia. Thus far, more than ten human de novo mutations have been identified in patients with two types of disorders, epileptic encephalopathy and intellectual disability. We review these human mutations as well as the unique features of Nav1.6 that contribute to its role in determining neuronal excitability in vivo. A supplemental figure illustrating the positions of amino acid residues within the four domains and 24 transmembrane segments of Nav1.6 is provided to facilitate the location of novel mutations within the channel protein.
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Affiliation(s)
- Janelle E O'Brien
- Department of Human Genetics, University of Michigan Ann Arbor, MI, USA
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