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Current Protocols in Human Genetics

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https://www.readbyqxmd.com/read/30516347/using-electronic-health-records-to-generate-phenotypes-for-research
#1
Sarah A Pendergrass, Dana C Crawford
Electronic health records contain patient-level data collected during and for clinical care. Data within the electronic health record include diagnostic billing codes, procedure codes, vital signs, laboratory test results, clinical imaging, and physician notes. With repeated clinic visits, these data are longitudinal, providing important information on disease development, progression, and response to treatment or intervention strategies. The near universal adoption of electronic health records nationally has the potential to provide population-scale real-world clinical data accessible for biomedical research, including genetic association studies...
December 5, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30387919/strategies-for-pathway-analysis-using-gwas-and-wgs-data
#2
Marquitta J White, Brian L Yaspan, Olivia J Veatch, Pagé Goddard, Oona S Risse-Adams, Maria G Contreras
Single-allele study designs, commonly used in genome-wide association studies (GWAS) as well as the more recently developed whole genome sequencing (WGS) studies, are a standard approach for investigating the relationship of common variation within the human genome to a given phenotype of interest. However, single-allele association results published for many GWAS studies represent only the tip of the iceberg for the information that can be extracted from these datasets. The primary analysis strategy for GWAS entails association analysis in which only the single nucleotide polymorphisms (SNPs) with the strongest p-values are declared statistically significant due to issues arising from multiple testing and type I errors...
November 2, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30335217/obtaining-a-genetic-family-history-using-computer-based-tools
#3
Weilong Li, Michael F Murray, Monica A Giovanni
Family health history has long been known to be a powerful predictor of individual disease risk. It can be obtained prior to DNA sequencing in order to examine inheritance patterns, to be used as a proxy for genetic information, or as a tool to guide decision-making on the utility of diagnostic genetic testing. Increasingly, it is also being obtained retrospectively from sequenced individuals to examine familial disease penetrance and to identify at-risk relatives for cascade testing. The collection of adequate family history information to screen patients for disease risk and guide decision-making is a time-consuming process that is difficult to accomplish exclusively through discussion between patients and their providers...
October 18, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30335214/glucose-responsiveness-of-pancreatic-%C3%AE-like-grp-%C3%AE-l-cells-generated-from-human-pluripotent-stem-cells
#4
Bahareh Rajaei, Mohammad Massumi, Michael Wheeler
The International Diabetic Federation estimated that 415 million adults currently have diabetes and 318 million adults had impaired glucose tolerance, putting them at high risk of developing diabetes in the future. In Type 1 Diabetes (T1D), the β cells are lost because of autoimmune reactions. Although islet transplantation has been a promising therapy for T1D, it is greatly limited by pancreatic donors. Here, we describe a protocol to generate glucose- responsive pancreatic β-like (GRPβ-L) cells from human-induced pluripotent stem (iPS) cells...
October 18, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30253059/quantification-of-muscle-contraction-in-vitro-and-in-vivo-using-musclemotion-software-from-stem-cell-derived-cardiomyocytes-to-zebrafish-and-human-hearts
#5
Berend J van Meer, Luca Sala, Leon G J Tertoolen, Godfrey L Smith, Francis L Burton, Christine L Mummery
Quantification of contraction is essential to the study of cardiac diseases, injury, and responses to drugs. While there are many techniques to assess contractility, most rely on costly, dedicated hardware and advanced informatics, and can only be used in specific experimental models. We have developed an automated open-source software tool (MUSCLEMOTION) for use with standard imaging equipment, to assess contractility in vitro and in vivo and quantify responses to drugs and diseases. We describe high-speed and disturbance-free acquisition of images from either electrically paced or non-paced human pluripotent stem cell-derived cardiomyocytes, isolated adult cardiomyocytes, zebrafish hearts, and human echocardiograms...
October 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30215889/multicolor-fluorescence-in-situ-hybridization-fish-approaches-for-simultaneous-analysis-of-the-entire-human-genome
#6
Chengsheng Zhang, Eliza Cerveira, Willem Rens, Fengtang Yang, Charles Lee
Analysis of the organization of the human genome is vital for understanding genetic diversity, human evolution, and disease pathogenesis. A number of approaches, such as multicolor fluorescence in situ hybridization (FISH) assays, cytogenomic microarray (CMA), and next-generation sequencing (NGS) technologies, are available for simultaneous analysis of the entire human genome. Multicolor FISH-based spectral karyotyping (SKY), multiplex FISH (M-FISH), and Rx-FISH may provide rapid identification of interchromosomal and intrachromosomal rearrangements as well as the origin of unidentified extrachromosomal elements...
October 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30215878/microrna-isolation-from-plasma-for-real-time-qpcr-array
#7
Isabel Witvrouwen, Andreas B Gevaert, Emeline M Van Craenenbroeck, Amaryllis H Van Craenenbroeck
MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level by mRNA degradation or suppression of translation. Their stability in plasma makes them attractive biomarkers. Since many plasma microRNA isolation procedures exist and the yield can be highly variable, we recently optimized the microRNA isolation and preamplification procedure using the mirVana PARIS kit (Thermo Fisher Scientific) for miRNA quantification with TaqMan Low Density Arrays in plasma samples. The method here is slightly modified from the original procedure supplied by Thermo Fisher...
October 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30199150/a-guided-protocol-for-array-based-t2c-a-high-quality-selective-high-resolution-high-throughput-chromosome-interaction-capture
#8
Tobias A Knoch
After now more than 170 years of research the dynamic three-dimensional chromatin architecture of genomes and the co-evolved interaction networks of regulatory elements which create genome function - i.e. the storage, expression, and finally replication of genetic information - involves ever more investigative efforts in respect to not only the pure understanding of living organisms, but also diagnosis, treatment, and even future genome engineering. To study genomic interactions, we developed a novel and superior high-quality selective high-resolution, high-throughput chromosome interaction capture method - T2C (targeted chromatin capture) - which allows to arbitrarily balance resolution, frequency range of interactions, and the investigated general genetic region or single interactions in a highly cost-effective manner in respect to the obtainable result and compared to other techniques...
October 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30192441/pancreatic-beta-cell-differentiation-from-human-pluripotent-stem-cells
#9
Lina Sui, Rudolph L Leibel, Dieter Egli
Insulin-expressing beta cells are crucial for the maintenance of systemic glucose homeostasis. Elucidation of the molecular and cellular mechanisms of beta cell development, expansion, survival, and function are required for full understanding of the molecular pathogenesis of diabetes. However, access to human beta cells for such studies is limited by virtue of the logistics of acquisition, prior medical status of donor, and imperfect culture systems for maintaining beta cell identity and function after isolation from human pancreas...
October 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29989334/assessing-skewed-x-chromosome-inactivation
#10
Thomas Liehr, Monika Ziegler, Sharon Löhmer, Anja Weise
We describe a simple and straightforward method for detection and characterization of X-chromosome inactivation in females and/or individuals with more than one X chromosome. The X-chromosome inactivation pattern is visualized on a single-cell level using 5-ethynyl-2-deoxyuridine (EdU) instead of the previously widely applied 5-bromo-2'-deoxyuridine (BUdR). The fluorochrome-labeled nucleoside analog EdU is incorporated into late-replication chromosomal regions of living blood cells in vitro; thus, it can also be used to specifically highlight the inactive X chromosome within a cytogenetic preparation...
July 10, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29979828/reporting-of-clinical-genome-sequencing-results
#11
Cui Song, Hatice Duzkale, Jun Shen
High-throughput sequencing and high-performance computing technologies have become powerful tools in clinical genetic diagnosis of hereditary disorders and genetic screening of healthy individuals to provide information for the diagnosis, treatment, and prevention of diseases or impairment and assessment of health. For patients with undiagnosed disorders, including many rare disorders, the whole-genome sequencing (WGS) test may end the diagnostic odyssey, ultimately guiding clinical care for them and their families...
July 6, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29979824/efficient-differentiation-of-human-pluripotent-stem-cells-to-endothelial-cells
#12
Mingxia Gu
Endothelial cells (ECs) line the interior surface of blood and lymphatic vessels, and play a key role in a variety of physiological or pathological processes such as thrombosis, inflammation, or vascular wall remodeling. Human-induced pluripotent stem cell (iPSCs)-derived ECs provide a new opportunity for vascular regeneration and serve as a model to study the mechanism and to screen for novel therapies. We use developmental cues in a monolayer differentiation approach to efficiently generate mesoderm cells from iPSCs via small-molecule activation of WNT signaling in chemically defined medium for 4 days, and subsequent EC specification using vascular endothelial growth factor and fibroblast growth factor for another 4 days...
July 6, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29979818/capture-hi-c-library-generation-and-analysis-to-detect-chromatin-interactions
#13
Giulia Orlando, Ben Kinnersley, Richard S Houlston
Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. The recently implemented modification, in situ Hi-C, maintains nuclear integrity during digestion and ligation steps, reducing random ligation of Hi-C fragments. Although Hi-C allows for genome-wide characterization of chromatin contacts, it requires high-depth sequencing to discover significant contacts...
July 6, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29975818/using-xcavator-and-excavator2-to-identify-cnvs-from-wgs-wes-and-ts-data
#14
Romina D'Aurizio, Roberto Semeraro, Alberto Magi
Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation but also associated with many disease states. In recent years, the identification of CNVs from high-throughput sequencing experiments has become a common practice for both research and clinical purposes. Several computational methods have been developed so far. In this unit, we describe and give instructions on how to run two read count-based tools, XCAVATOR and EXCAVATOR2, which are tailored for the detection of both germline and somatic CNVs from different sequencing experiments (whole-genome, whole-exome, and targeted) in various disease contexts and population genetic studies...
July 5, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29953168/preparation-culture-and-analysis-of-amniotic-fluid-samples
#15
Patricia Minehart Miron
Amniotic fluid obtained via amniocentesis provides a source of fetal material used in prenatal diagnosis. The fluid may be used directly for biochemical analyses, fluorescence in situ hybridization (FISH), and isolation of DNA for molecular studies, including chromosomal microarray analysis (CMA). The fluid is typically cultured as a source of metaphase cells for chromosome analysis and to provide additional material for biochemical and DNA-based testing. This unit describes an in situ method for the preparation, culture, and harvest of amniotic fluid samples for metaphase chromosome analysis...
June 28, 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30040223/pedigree-selection-and-information-content
#16
Badri N Vardarajan, Gary W Beecham, Jonathan L Haines
In this article, we discuss strategies for selection of families and family members for genetic studies. We will evaluate strategies to sample large families with multiply affected members, sibships, and nuclear families. In addition, we have added a section to discuss sub-sampling within pedigrees for large sequencing studies, particularly when genome-wide SNP chips are available on all members of a pedigree. The type of family sampled for a study will determine the statistical analyses and power of discovery of genetic findings...
April 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30040209/droplet-digital-pcr-with-evagreen-assay-confirmational-analysis-of-structural-variants
#17
Angela C Tai, Michael Parfenov, Joshua M Gorham
DNA structural variants can be analyzed by droplet digital PCR (ddPCR), a water-oil microfluidics and fluorescence technology to quantify target nucleic acids with extreme precision and sensitivity. Traditional ddPCR uses expensive fluorescent oligonucleotide probes that require extensive optimization. Here we describe a variation of ddPCR using a DNA-binding dye (EvaGreen), whose properties allow target products to be effectively quantified at a significantly lower cost. © 2018 by John Wiley & Sons, Inc...
April 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30040203/plink-key-functions-for-data-analysis
#18
Susan H Slifer
Genetic data analysis of large numbers of single nucleotide variants (SNVs), including genome-wide association studies (GWAS), exome chips, and whole exome (WES) or whole-genome (WGS) sequencing data, requires well defined processing steps. As a result, several freely available analytic toolkits have been developed to streamline these processes. Among these, PLINK is the most comprehensive in terms of its quality control and analytic modules, although its focus remains on SNVs. PLINK fulfills two analytic needs-aiding the process of performing quality control (QC) on large data sets and providing basic statistical tools to analyze the variants in genetic models...
April 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30038699/computational-prediction-of-position-effects-of-human-chromosome-rearrangements
#19
Cinthya J Zepeda-Mendoza, Shreya Menon, Cynthia C Morton
Balanced and apparently balanced chromosome abnormalities (BCAs) have long been known to generate disease through position effects, either by altering local networks of gene regulation or positioning genes in architecturally different chromosome domains. Despite these observations, identification of distally affected genes by BCAs is oftentimes neglected, especially when predicted gene disruptions are found elsewhere in the genome. In this unit, we provide detailed instructions on how to run a computational pipeline that identifies relevant candidates of non-coding BCA position effects...
April 2018: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/30038698/in-vivo-and-in-vitro-methods-to-identify-dna-sequence-variants-that-alter-rna-splicing
#20
Parth N Patel, Joshua M Gorham, Kaoru Ito, Christine E Seidman
Identification of sequence variants that create or eliminate splice sites has proven to be a significant challenge and represents one of many roadblocks in the clinical interpretation of rare genetic variation. Current methods of identifying splice altering sequence variants exist, however, these are limited by an imperfect understanding of splice signals and cumbersome functional assays. We have recently developed a computational tool that prioritizes putative splice-altering sequence variants, and a moderate-throughput minigene assay that confirms the variants which alter splicing...
April 2018: Current Protocols in Human Genetics
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