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Getting started with microbiome analysis: sample acquisition to bioinformatics.
Authors: Kumar R, Eipers P, Little RB, Crowley M, Crossman DK, Lefkowitz EJ, Morrow CD Abstract Historically, in order to study microbes, it was necessary to grow them in the laboratory. It was clear though that many microbe communities were refractory to study because none of the members could be grown outside of their native habitat. The development of culture-independent methods to study microbiota using high-throughput sequencing of the 16S ribosomal RNA gene variable regions present in all prokaryotic organisms has provided new opportunities to investigate complex microbial communities. In this unit, ...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Digital Droplet PCR: CNV Analysis and Other Applications.
Authors: Mazaika E, Homsy J Abstract Digital droplet PCR (ddPCR) is an assay that combines state-of-the-art microfluidics technology with TaqMan-based PCR to achieve precise target DNA quantification at high levels of sensitivity and specificity. Because quantification is achieved without the need for standard assays in an easy to interpret, unambiguous digital readout, ddPCR is far simpler, faster, and less error prone than real-time qPCR. The basic protocol can be modified with minor adjustments to suit a wide range of applications, such as CNV analysis, rare variant detection, SNP genotyping, and transc...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Quality assurance and quality control in clinical cytogenetics.
Authors: Mikhail FM, Watson MS Abstract The goal of any clinical laboratory should be to provide patients with the most accurate test results possible. This is accomplished through various overlapping programs that continuously monitor and optimize all aspects of a test, including decisions by the laboratory to offer a test, the decision of providers to request the test, the testing itself, and the reporting of results to the referral source and patient. The levels at which test performance and accuracy can be optimized are encompassed under quality control (QC) and quality assurance (QA). The monitoring o...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Analysis of genetic linkage data for mendelian traits.
Authors: Dueker ND, Pericak-Vance MA Abstract This unit describes linkage analysis, an invaluable tool in mapping human disease genes. Linkage analysis is one of several methods used to map genes. Specifically, in linkage analysis, cosegregation of two or more genes (traits) is examined in a family unit to determine if they segregate independently of each other according to Mendel's laws or if they do not segregate independently because of their close physical proximity. The procedures outlined in this unit are not always straightforward, and a number of caveats are presented in the commentary regarding po...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.
Authors: Williams AG, Thomas S, Wyman SK, Holloway AK Abstract RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth. Common analysis steps in all RNA-seq experi...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Mouse Genome Editing Using the CRISPR/Cas System.
Authors: Harms DW, Quadros RM, Seruggia D, Ohtsuka M, Takahashi G, Montoliu L, Gurumurthy CB Abstract The availability of techniques to create desired genetic mutations has enabled the laboratory mouse as an extensively used model organism in biomedical research including human genetics. A new addition to this existing technical repertoire is the CRISPR/Cas system. Specifically, this system allows editing of the mouse genome much more quickly than the previously used techniques, and, more importantly, multiple mutations can be created in a single experiment. Here we provide protocols for preparation of CRI...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Diagnosing Lysosomal Storage Disorders: The GM2 Gangliosidoses.
Authors: Hall P, Minnich S, Teigen C, Raymond K Abstract The GM2 gangliosidoses are a group of autosomal recessive lysosomal storage disorders caused by defective β-hexosaminidase. There are three clinical conditions in this group: Tay-Sachs disease (TSD), Sandhoff disease (SD), and hexosaminidase activator deficiency. The three conditions are clinically indistinguishable. TSD and SD have been identified with infantile, juvenile, and adult onset forms. The activator deficiency is only known to present with infantile onset. Diagnosis of TSD and SD is based on decreased hexosaminidase activity and a change ...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Molecular diagnosis of duchenne muscular dystrophy.
Authors: Nallamilli BR, Ankala A, Hegde M Abstract Duchenne Muscular Dystrophy (DMD) is an X-linked inherited neuromuscular disorder caused by mutations in the dystrophin gene (DMD; locus Xp21.2). The mutation spectrum of DMD is unique in that 65% of causative mutations are intragenic deletions, with intragenic duplications and point mutations (along with other sequence variants) accounting for 6% to 10% and 30% to 35%, respectively. The strategy for molecular diagnostic testing for DMD involves initial screening for deletions/duplications using microarray-based comparative genomic hybridization (array-CGH...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research