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.

Porphyria Diagnostics-Part 1: A Brief Overview of the Porphyrias.
Authors: Ramanujam VM, Anderson KE Abstract Porphyria diseases are a group of metabolic disorders caused by abnormal functioning of heme biosynthesis enzymes and characterized by excessive accumulation and excretion of porphyrins and their precursors. Precisely which of these chemicals builds up depends on the type of porphyria. Porphyria is not a single disease but a group of nine disorders: acute intermittent porphyria (AIP), hereditary coproporphyria (HCP), variegate porphyria (VP), δ-aminolevulinic acid dehydratase deficiency porphyria (ADP), porphyria cutanea tarda (PCT), hepatoerythropoietic porphyr...
Source: Current Protocols in Human Genetics - July 5, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Finding Pathogenic Nucleic Acid Sequences in Next Generation Sequencing Data.
Authors: Parfenov M, Seidman JG Abstract Viruses and bacteria are established as one of the main causes of human diseases from hepatitis to cancer. Recently, the presence of such pathogens has been extensively studied using human whole genome and transcriptome sequencing data. However, detecting and studying pathogens via next generation sequencing data is a challenging task in terms of time and computational resources. In this protocol we give instructions for a simple and quick method to find pathogenic DNA or RNA and detect possible integration of the pathogen genome into the host genome. © 2015 by Joh...
Source: Current Protocols in Human Genetics - July 5, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Probe-Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA-Seq Libraries.
Authors: Archer SK, Shirokikh NE, Preiss T Abstract Most applications for RNA-seq require the depletion of abundant transcripts to gain greater coverage of the underlying transcriptome. The sequences to be targeted for depletion depend on application and species and in many cases may not be supported by commercial depletion kits. This unit describes a method for generating RNA-seq libraries that incorporates probe-directed degradation (PDD), which can deplete any unwanted sequence set, with the low-bias split-adapter method of library generation (although many other library generation methods are in princi...
Source: Current Protocols in Human Genetics - April 4, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Neural stem cell-mediated delivery of oncolytic adenovirus.
Authors: Kim JW, Kane JR, Young JS, Chang AL, Kanojia D, Qian S, Spencer DA, Ahmed AU, Lesniak MS Abstract The use of stem cells (SCs) as carriers for therapeutic agents has now progressed to early clinical trials. These clinical trials exploring SC-mediated delivery of oncolytic adenoviruses will commence in the near future, hopefully yielding meritorious results that can provoke further scientific inquiry. Preclinical animal studies have demonstrated that SCs can be successfully loaded with conditionally-replicative adenoviruses and delivered to the tumor, whereupon they may evoke pronounced therapeutic ...
Source: Current Protocols in Human Genetics - April 4, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Use of affymetrix arrays in the diagnosis of gene copy-number variation.
Authors: Zahir FR, Marra MA Abstract Diagnosing constitutional pathogenic copy number variants (CNVs) requires detecting submicroscopic segmental chromosomal imbalances. The Affymetrix GeneChip mapping array was one of the initial microarray platforms used to measure duplication and deletion of genetic material in DNA samples. Unlike oligonucleotide microarrays from NimbleGen and Agilent, developed around the same time to infer copy number status for the DNA sequence covered by the probe, the Affymetrix GeneChip system used 25-mer oligonucleotide probes designed to interrogate SNPs. Thus, it was possible t...
Source: Current Protocols in Human Genetics - April 4, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Diagnosis of fanconi anemia by diepoxybutane analysis.
Authors: Auerbach AD Abstract Fanconi anemia (FA) is a genetically and phenotypically heterogeneous disorder characterized by congenital malformations, progressive bone marrow failure, and predisposition to cancer, particularly hematological malignancies and solid tumors of the head and neck. The main role of FA proteins is in the repair of DNA interstrand crosslinks (ICLs). FA results from pathogenic variants in at least sixteen distinct genes, causing genomic instability. Although the highly variable phenotype makes accurate diagnosis on the basis of clinical manifestations difficult in some patients, di...
Source: Current Protocols in Human Genetics - April 4, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Preparation of Amniocytes for Interphase Fluorescence In Situ Hybridization (FISH).
Authors: Schwartz S Abstract FISH has been used to detect and clarify deletions and/or other structural rearrangements, and also has applications in interphase analysis. This unit describes preparation of uncultured amniotic fluid cells for FISH analysis. Cells are swollen, and then slides are prepared by standard methods. The cells are then fixed and permeabilized for subsequent FISH. An alternate protocol describes attachment of amniocytes to a glass or plastic surface followed by hypotonic swelling, fixation, and permeabilization for subsequent FISH. Interphase FISH analysis of amniotic fluid cells is a...
Source: Current Protocols in Human Genetics - April 4, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Statistical methods for genome-wide and sequencing association studies of complex traits in related samples.
Authors: Thornton TA Abstract Genome-wide association studies (GWAS) and sequencing studies are routinely conducted for the identification of genetic variants that are associated with complex traits. Many genetic studies for association mapping include related individuals. When relatives are included in an association analysis, familial correlations must be appropriately taken into account to ensure correct type I error and to increase power. This unit provides an overview of statistical methods that are available for GWAS and sequencing association studies of complex traits in samples with related individ...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Stranded Whole Transcriptome RNA-Seq for All RNA Types.
Authors: Miller DF, Yan PX, Fang F, Buechlein A, Ford JB, Tang H, Huang TH, Burow ME, Liu Y, Rusch DB, Nephew KP Abstract Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libra...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Diagnosing lysosomal storage disorders: mucopolysaccharidosis type i.
Authors: Johnson BA, Dajnoki A, Bodamer OA Abstract Mucopolysaccharidosis type I (MPS I) is a lysosomal storage disorder due to deficiency of alpha iduronidase (IDUA). Progressive storage of dermatan and heparan sulfate throughout the body lead to a multiorgan presentation including short stature, dysostosis multiplex, corneal clouding, hearing loss, coarse facies, hepatosplenomegaly, and intellectual disability. Diagnosis of MPS I is based on IDUA enzyme analysis in leukocytes or dried blood spots (DBS) followed by molecular confirmation of the IDUA gene mutations in individuals with low enzyme activity. ...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Molecular cytogenetic analysis of telomere rearrangements.
Authors: Martin CL, Ledbetter DH Abstract Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an int...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Noninvasive prenatal testing using cell-free fetal DNA in maternal plasma.
Authors: Dharajiya N, Zwiefelhofer T, Guan X, Angkachatchai V, Saldivar JS Abstract Noninvasive prenatal testing (NIPT) represents an outstanding example of how novel scientific discoveries can be quickly and successfully developed into hugely impactful clinical diagnostic tests. Since the introduction of NIPT to detect trisomy 21 in late 2011, the technology has rapidly advanced to analyze other autosomal and sex chromosome aneuploidies, and now includes the detection of subchromosomal deletion and duplication events. Here we provide a brief overview of how noninvasive prenatal testing using next-generati...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Preparation of Cells from Formalin-Fixed, Paraffin-Embedded Tissue for Use in Fluorescence In Situ Hybridization (FISH) Experiments.
Authors: Weremowicz S Abstract Numerical and structural chromosome abnormalities can be accurately detected in cells from archived tissues using fluorescence in situ hybridization (FISH). This unit describes two common approaches to performing FISH in formalin-fixed, paraffin-embedded tissue. The first approach utilizes 4 to 6 μm tissue sections in cases for which preserving tissue morphology is necessary, and the second involves extraction of intact nuclei from 50-μm tissue sections. To interpret FISH results using 4 to 6 μm sections, an adequate number of nuclei must be evaluated to perform statistica...
Source: Current Protocols in Human Genetics - January 21, 2015 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Histochemical methods for the diagnosis of mitochondrial diseases.
Authors: De Paepe B, De Bleecker JL, Van Coster R Abstract Through the process of oxidative phosphorylation (OXPHOS), mitochondria provide cells with required energy in the form of ATP. The organelle possesses its own genome (mtDNA), which encodes for part of the components needed (37 genes encoding either OXPHOS structural subunits or tRNAs and rRNAs). Nonetheless, the majority of structural OXPHOS components (as well as accessory proteins and proteins required for maintenance, replication, and expression of the mtDNA) are encoded by nuclear genes. Due to the dual genetic control and the large number of p...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research

Evaluation of the mitochondrial respiratory chain and oxidative phosphorylation system using polarography and spectrophotometric enzyme assays.
Authors: Barrientos A, Fontanesi F, Díaz F Abstract The oxidative phosphorylation (OXPHOS) system consists of five multimeric complexes embedded in the mitochondrial inner membrane. They work in concert to drive the aerobic synthesis of ATP. Mitochondrial and nuclear DNA mutations affecting the accumulation and function of these enzymes are the most common cause of mitochondrial diseases and have also been associated with neurodegeneration and aging. For this reason, several approaches for the assessment of the OXPHOS system enzymes have been developed. Based on the methods described elsewhere, the assays...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research