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Current Protocols in Human Genetics最新文献

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Genetic Risk Scores 遗传风险评分
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.20
Jessica N. Cooke Bailey, Robert P. Igo Jr
{"title":"Genetic Risk Scores","authors":"Jessica N. Cooke Bailey,&nbsp;Robert P. Igo Jr","doi":"10.1002/cphg.20","DOIUrl":"10.1002/cphg.20","url":null,"abstract":"<p>The generation of genome-wide variation data has become commonplace. However, the potential for interpretation and application of these data for clinical assessment of outcomes of interest, and prediction of disease risk, is currently not fully realized. Many common, complex diseases now have numerous, well-established “risk” loci, and likely harbor many genetic determinants with effects too small to be detected at genome-wide levels of statistical significance. A simple and intuitive approach for converting genetic data to a predictive measure of disease susceptibility is to aggregate the risk effects of these loci into a single genetic risk score. Here, some common methods and software packages for calculating genetic risk scores, with focus on studies of common, complex diseases, are described. The basic information needed as well as important considerations for constructing genetic risk scores, including specific requirements for phenotypic and genetic data, and limitations in their application is reviewed. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.20","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84243265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 71
High-Risk Screening of Fabry Disease: Analysis of Fifteen Urinary Methylated and Non-Methylated Gb3 Isoforms Using Tandem Mass Spectrometry 法布里病的高风险筛查:使用串联质谱分析15种尿甲基化和非甲基化Gb3亚型
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.24
Mona Abaoui, Michel Boutin, Pamela Lavoie, Christiane Auray-Blais
{"title":"High-Risk Screening of Fabry Disease: Analysis of Fifteen Urinary Methylated and Non-Methylated Gb3 Isoforms Using Tandem Mass Spectrometry","authors":"Mona Abaoui,&nbsp;Michel Boutin,&nbsp;Pamela Lavoie,&nbsp;Christiane Auray-Blais","doi":"10.1002/cphg.24","DOIUrl":"10.1002/cphg.24","url":null,"abstract":"<p>Fabry disease is a multisystemic, X-linked lysosomal storage disorder caused by mutations in the <i>GLA</i> gene, leading to α-galactosidase A deficiency and resulting in the accumulation of glycosphingolipids in different tissues and biological fluids. Glycosphingolipid biomarkers, such as globotriaosylceramide (Gb<sub>3</sub>) isoforms, globotriaosylsphingosine (lyso-Gb<sub>3</sub>) and related analogs, and galabiosylceramide (Ga<sub>2</sub>) isoforms and analogs, are found to be abnormally increased in urine and in plasma of Fabry patients and have the potential to be used as specific biomarkers of the disease. This unit presents a protocol for the relative quantification of fifteen urinary isoforms of Gb<sub>3</sub> analyzed simultaneously with creatinine by ultra-performance liquid chromatography (UPLC) coupled to tandem mass spectrometry (MS/MS). In order to purify urine samples, a liquid-liquid extraction is performed and samples are analyzed by MS/MS in positive electrospray ionization mode. These biomarkers are useful for screening, diagnosis, and long-term monitoring of Fabry disease patients. We have shown that the methylated Gb<sub>3</sub> isoforms are particularly useful for screening Fabry patients who present with late-onset cardiac variant mutations. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.24","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90756405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Analysis of Heritability Using Genome-Wide Data 利用全基因组数据分析遗传力
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.25
Jacob B. Hall, William S. Bush
{"title":"Analysis of Heritability Using Genome-Wide Data","authors":"Jacob B. Hall,&nbsp;William S. Bush","doi":"10.1002/cphg.25","DOIUrl":"10.1002/cphg.25","url":null,"abstract":"<p>Most analyses of genome-wide association data consider each variant independently without considering or adjusting for the genetic background present in the rest of the genome. New approaches to genome analysis use representations of genomic sharing to better account for confounding factors like population stratification or to directly approximate heritability through the estimated sharing of individuals in a dataset. These approaches use mixed linear models, which relate genotypic sharing to phenotypic sharing, and rely on the efficient computation of genetic sharing among individuals in a dataset. This unit describes the principles and practical application of mixed models for the analysis of genome-wide association study data. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.25","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74568103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Acylglycine Analysis by Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS) 超高效液相色谱-串联质谱(UPLC-MS/MS)分析酰甘氨酸
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.19
Judith A. Hobert, Aiping Liu, Marzia Pasquali
{"title":"Acylglycine Analysis by Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS)","authors":"Judith A. Hobert,&nbsp;Aiping Liu,&nbsp;Marzia Pasquali","doi":"10.1002/cphg.19","DOIUrl":"10.1002/cphg.19","url":null,"abstract":"Quantitative analysis of urine acylglycines has shown to be a highly sensitive and specific method with proven clinical utility for the diagnosis of several inherited metabolic disorders including: medium chain acyl‐CoA dehydrogenase deficiency, multiple acyl‐CoA dehydrogenase deficiency, short chain acyl‐CoA dehydrogenase deficiency, 3‐methylcrotonyl‐CoA carboxylase deficiency, 2‐methylbutyryl‐CoA dehydrogenase deficiency, isovaleric acidemia, propionic academia, and isobutyryl‐CoA dehydrogenase deficiency. Here, a method that is currently performed using ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC‐MS/MS) is described. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76332709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Microscopy and Image Analysis 显微镜和图像分析
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.42
George McNamara, Michael Difilippantonio, Thomas Ried, Frederick R. Bieber
{"title":"Microscopy and Image Analysis","authors":"George McNamara,&nbsp;Michael Difilippantonio,&nbsp;Thomas Ried,&nbsp;Frederick R. Bieber","doi":"10.1002/cphg.42","DOIUrl":"10.1002/cphg.42","url":null,"abstract":"<div>\u0000 \u0000 <p>This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy—we briefly point to these new opportunities. © 2017 by John Wiley &amp; Sons, Inc.</p></div>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"94 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.42","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35158820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Pronuclear Injection-Based Targeted Transgenesis 基于原核注射的靶向转基因
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.23
Samantha L.P. Schilit, Masato Ohtsuka, Rolen M. Quadros, Channabasavaiah B. Gurumurthy
{"title":"Pronuclear Injection-Based Targeted Transgenesis","authors":"Samantha L.P. Schilit,&nbsp;Masato Ohtsuka,&nbsp;Rolen M. Quadros,&nbsp;Channabasavaiah B. Gurumurthy","doi":"10.1002/cphg.23","DOIUrl":"10.1002/cphg.23","url":null,"abstract":"<p>Microinjection of DNA expression cassettes into fertilized zygotes has been a standard method for generating transgenic animal models. While efficient, the injected DNA integrates randomly into the genome, leading to potential disruption of endogenous genes or regulatory elements, variation in copy number, or integration into heterochromatic regions that inhibit transgene expression. A recently developed method addresses such pitfalls of traditional transgenesis by targeting the transgene to predetermined sites in the genome that can safely harbor exogenous DNA. This method, called Pronuclear Injection-based Targeted Transgenesis (PITT), employs an enzymatic transfer of exogenous DNA from a donor vector to a previously created landing-pad site in the mouse genome. DNA transfer is achieved using molecular tools such as the Cre-<i>LoxP</i> recombinase and PhiC31-<i>attB</i>/<i>P</i> integrase systems. Here, we provide protocols for performing PITT and an overview of the current PITT tools available to the research community. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88406639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Mammalian Cell Tissue Culture 哺乳动物细胞组织培养
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.41
Katy Phelan, Kristin M. May
{"title":"Mammalian Cell Tissue Culture","authors":"Katy Phelan,&nbsp;Kristin M. May","doi":"10.1002/cphg.41","DOIUrl":"10.1002/cphg.41","url":null,"abstract":"<p>Cultured mammalian cells are used extensively in the field of human genetics. It requires a number of special skills in order to be able to preserve the structure, function, behavior, and biology of the cells in culture. This unit describes the basic skills required to maintain and preserve cell cultures: maintaining aseptic technique, preparing media with the appropriate characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"94 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.41","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35158821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Co-Differentiation of Human Pluripotent Stem Cells-Derived Cardiomyocytes and Endothelial Cells from Cardiac Mesoderm Provides a Three-Dimensional Model of Cardiac Microtissue 人类多能干细胞来源的心肌细胞和心脏中胚层内皮细胞的共分化提供了心脏显微组织的三维模型
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.46
Elisa Giacomelli, Milena Bellin, Valeria V. Orlova, Christine L. Mummery
{"title":"Co-Differentiation of Human Pluripotent Stem Cells-Derived Cardiomyocytes and Endothelial Cells from Cardiac Mesoderm Provides a Three-Dimensional Model of Cardiac Microtissue","authors":"Elisa Giacomelli,&nbsp;Milena Bellin,&nbsp;Valeria V. Orlova,&nbsp;Christine L. Mummery","doi":"10.1002/cphg.46","DOIUrl":"10.1002/cphg.46","url":null,"abstract":"<p>The formation of cardiac mesodermal subtypes is highly regulated in time and space during heart development. <i>In vitro</i> models based on human pluripotent stem cells (hPS cells) provide opportunities to study mechanisms underlying fate choices governing lineage specification from common cardiovascular progenitors in human embryos. The generation of cardiac endothelial cells in particular allows the creation of complex models of cardiovascular disorders in which either cardiomyocytes or endothelial cells are affected. Here, a protocol for co-differentiation of cardiomyocytes and endothelial cells from cardiac mesoderm using hPS cells is described. Precise details for the enrichment of each cell population from heterogeneous-differentiated cultures, a description of how to maintain and dissociate enriched cardiomyocytes, and the expansion and cryopreservation of enriched endothelial cells are all provided. The generation and culture of three-dimensional cardiac microtissues from these cell populations is described and guidelines for the characterization of microtissues by immunofluorescent staining and re-plating for downstream applications are provided. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.46","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35525812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 23
Molecular Diagnosis of Myotonic Dystrophy 强直性肌营养不良的分子诊断
Current Protocols in Human Genetics Pub Date : 2018-02-13 DOI: 10.1002/cphg.22
Sujata Chakraborty, Matteo Vatta, Linda L. Bachinski, Ralf Krahe, Stephen Dlouhy, Shaochun Bai
{"title":"Molecular Diagnosis of Myotonic Dystrophy","authors":"Sujata Chakraborty,&nbsp;Matteo Vatta,&nbsp;Linda L. Bachinski,&nbsp;Ralf Krahe,&nbsp;Stephen Dlouhy,&nbsp;Shaochun Bai","doi":"10.1002/cphg.22","DOIUrl":"10.1002/cphg.22","url":null,"abstract":"<p>Myotonic dystrophy types 1 (DM1) and 2 (DM2) are autosomal dominant, microsatellite repeat expansion disorders that affect muscle function. Myotonic dystrophy type 1 is caused by CTG repeat expansion in the 3′ UTR region of the <i>DMPK</i> gene. Patients with DM2 have expansion of CCTG repeats in intron 1 of the <i>CNBP</i> gene. In this unit, we review and discuss the clinical phenotypes, genetic mutations causing the diseases, and the molecular diagnostic approaches and tools that are used to determine repeat sizes in DM1/2. In summary, the goal of this chapter is to provide the reader with a basic understanding of the clinical, genetic and diagnostic aspects of these disorders. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83970699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
CRISPR/Cas9-Mediated Fluorescent Tagging of Endogenous Proteins in Human Pluripotent Stem Cells CRISPR/ cas9介导的人多能干细胞内源蛋白的荧光标记
Current Protocols in Human Genetics Pub Date : 2018-01-24 DOI: 10.1002/cphg.52
Arun Sharma, Christopher N. Toepfer, Tarsha Ward, Lauren Wasson, Radhika Agarwal, David A. Conner, Johnny H. Hu, Christine E. Seidman
{"title":"CRISPR/Cas9-Mediated Fluorescent Tagging of Endogenous Proteins in Human Pluripotent Stem Cells","authors":"Arun Sharma,&nbsp;Christopher N. Toepfer,&nbsp;Tarsha Ward,&nbsp;Lauren Wasson,&nbsp;Radhika Agarwal,&nbsp;David A. Conner,&nbsp;Johnny H. Hu,&nbsp;Christine E. Seidman","doi":"10.1002/cphg.52","DOIUrl":"10.1002/cphg.52","url":null,"abstract":"<p>Human induced pluripotent stem cells (hiPSCs) can be used to mass produce surrogates of human tissues, enabling new advances in drug screening, disease modeling, and cell therapy. Recent developments in clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing technology use homology-directed repair (HDR) to efficiently generate custom hiPSC lines harboring a variety of genomic insertions and deletions. Thus, hiPSCs that encode an endogenous protein fused to a fluorescent reporter protein can be rapidly created by employing CRISPR/Cas9 genome editing, enhancing HDR efficiency and optimizing homology arm length. These fluorescently tagged hiPSCs can be used to visualize protein function and dynamics in real time as cells proliferate and differentiate. Given that nearly any intracellular protein can be fluorescently tagged, this system serves as a powerful tool to facilitate new discoveries across many biological disciplines. In this unit, we present protocols for the design, generation, and monoclonal expansion of genetically customized hiPSCs encoding fluorescently tagged endogenous proteins. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":40007,"journal":{"name":"Current Protocols in Human Genetics","volume":"96 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cphg.52","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35763626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 51
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