Current Protocols in Human Genetics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.
This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc. PMID: 31479590 [PubMed - in process] (Source: Current Protocols in Human Genetics)
Source: Current Protocols in Human Genetics - September 4, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Best Practices for Illumina Library Preparation.
Authors: Bronner IF, Quail MA Abstract In this unit, we describe a set of protocols and recommendations for Illumina library preparation. We review best practices in template quantitation methods; template fragmentation methodologies; solid-phase reverse-immobilization cleanup, including buffer exchange and size selection; end repair, A-tailing, and adapter ligation; indexing strategies; considerations regarding whether to use polymerase chain reaction; final library quantification methodologies; and normalization and pooling strategies. These workflows are applicable to both high-throughput and low-throug...
Source: Current Protocols in Human Genetics - June 21, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Analytical Methods for Quantitative Plasma Carnitine Determination.
Authors: Zimmerman CN, Sharer JD Abstract Carnitine is an essential molecule for mitochondrial beta-oxidation of long-chain fatty acids and other cellular functions. Several rare, inherited disorders of carnitine metabolism occur in humans, and secondary carnitine deficiency is an important feature in a variety of clinical settings. Many of these conditions can be detected via quantitative analysis of free and esterified carnitine in plasma or urine, which thus offers an effective means for assessing the transport and initial processing of fatty acids. Here, we describe some of the methods most commonly em...
Source: Current Protocols in Human Genetics - June 21, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Genotype Imputation in Genome-Wide Association Studies.
This article reviews the general concepts behind imputation, describes imputation approaches and methods for various types of genotype data, including family-based data, and identifies web-based resources that can be used in different steps of the imputation process. For practical application, it provides a step-by-step guide to implementation of a two-step imputation process consisting of phasing of the study genotypes and the imputation of reference panel genotypes into the study haplotypes. In addition, this review describes recently developed haplotype reference panel resources and online imputation servers that are ca...
Source: Current Protocols in Human Genetics - June 21, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits.
Authors: Weissenkampen JD, Jiang Y, Eckert S, Jiang B, Li B, Liu DJ Abstract With the advent of Next Generation Sequencing (NGS) technologies, whole genome and whole exome DNA sequencing has become affordable for routine genetic studies. Coupled with improved genotyping arrays and genotype imputation methodologies, it is increasingly feasible to obtain rare genetic variant information in large datasets. Such datasets allow researchers to gain a more complete understanding of the genetic architecture of complex traits caused by rare variants. State-of-the-art statistical methods for the statistical genetics...
Source: Current Protocols in Human Genetics - March 10, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Conducting a Reproducible Mendelian Randomization Analysis Using the R Analytic Statistical Environment.
Authors: Rasooly D, Patel CJ Abstract Mendelian randomization (MR) is defined as the utilization of genetic variants as instrumental variables to assess the causal relationship between an exposure and an outcome. By leveraging genetic polymorphisms as proxy for an exposure, the causal effect of an exposure on an outcome can be assessed while addressing susceptibility to biases prone to conventional observational studies, including confounding and reverse causation, where the outcome causes the exposure. Analogous to a randomized controlled trial where patients are randomly assigned to subgroups based on di...
Source: Current Protocols in Human Genetics - January 17, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Simultaneous Targeted Methylation Sequencing (sTM-Seq).
Authors: Asmus N, Papale LA, Madrid A, Alisch RS Abstract Mapping patterns of DNA methylation throughout the epigenome are critical to our understanding of several important biological and regulatory functions, such as transcriptional regulation, genomic imprinting, and embryonic development. The development and rapid advancement of next-generation sequencing (NGS) technologies have provided clinicians and researchers with accurate and reliable read-outs of genomic and epigenomic information at the nucleotide level. Such improvements have significantly lowered the cost required for genome-wide sequencing, ...
Source: Current Protocols in Human Genetics - January 10, 2019 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Using Electronic Health Records To Generate Phenotypes For Research.
We describe here common and emerging electronic phenotyping approaches applied to electronic health records, as well as current limitations of both the approaches and the biases associated with these clinically collected data that impact their use in research. © 2018 by John Wiley & Sons, Inc. PMID: 30516347 [PubMed - as supplied by publisher] (Source: Current Protocols in Human Genetics)
Source: Current Protocols in Human Genetics - December 6, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Strategies for Pathway Analysis Using GWAS and WGS Data.
Authors: White MJ, Yaspan BL, Veatch OJ, Goddard P, Risse-Adams OS, Contreras MG Abstract 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 ...
Source: Current Protocols in Human Genetics - November 4, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Glucose-Responsiveness of Pancreatic β-Like (GRP β-L) Cells Generated from Human Pluripotent Stem Cells.
Authors: Rajaei B, Massumi M, Wheeler M Abstract 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. We recapit...
Source: Current Protocols in Human Genetics - October 20, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Obtaining a Genetic Family History Using Computer-Based Tools.
Authors: Li W, Murray MF, Giovanni MA Abstract 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...
Source: Current Protocols in Human Genetics - October 20, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Quantification of Muscle Contraction In Vitro and In Vivo Using MUSCLEMOTION Software: From Stem Cell-Derived Cardiomyocytes to Zebrafish and Human Hearts.
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. Recordings are then used as input for automated batch analysis by the MUSCLEMOTION software tool configured with specific settings and parameters tailored to the recording technique. Details on accuracy, interpretation, and troubleshooting are discussed. Acquisition duration depends on the experimental setup and aim, but quantification of drug or disease responses in an in vitro muscle mod...
Source: Current Protocols in Human Genetics - September 28, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

MicroRNA Isolation from Plasma for Real-Time qPCR Array.
Authors: Witvrouwen I, Gevaert AB, Van Craenenbroeck EM, Van Craenenbroeck AH Abstract 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 i...
Source: Current Protocols in Human Genetics - September 16, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome.
Authors: Zhang C, Cerveira E, Rens W, Yang F, Lee C Abstract 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 rearrangeme...
Source: Current Protocols in Human Genetics - September 16, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

A Guided Protocol for Array Based T2C: A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture.
Authors: Knoch TA Abstract 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...
Source: Current Protocols in Human Genetics - September 12, 2018 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research