Current Protocols in Human Genetics 
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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.Analysis of gene-gene interactions.
Authors: Gilbert-Diamond D, Moore JH
Abstract
The goal of this unit is to introduce gene-gene interactions (epistasis) as a significant complicating factor in the search for disease susceptibility genes. This unit begins with an overview of gene-gene interactions and why they are likely to be common. Then, it reviews several statistical and computational methods for detecting and characterizing genes with effects that are dependent on other genes. The focus of this unit is genetic association studies of discrete and quantitative traits because most of the methods for detecting gene-gene interactions have b...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
An overview of biochemical genetics.
Authors: Sharer JD
Abstract
Biochemical genetics focuses on the pathophysiology, diagnosis, and treatment of inherited metabolic disorders. While individually rare, the combined incidence of these diseases is likely greater than 1:3000 live births. These conditions may present in the neonatal period as an acute, life-threatening illness, or may manifest later in childhood with symptoms of progressive neurodegeneration, skeletal abnormalities, and/or dysmorphia. The purpose of this introductory unit is to provide an overview of the different clinical categories of metabolic disorders, modern diagnostic meth...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Diagnosis of copper transport disorders.
Authors: Møller LB, Hicks JD, Holmes CS, Goldstein DS, Brendl C, Huppke P, Kaler SG
Abstract
Techniques for the diagnosis of copper transport disorders are increasingly important due to recent recognition of previously unappreciated clinical phenotypes and emerging advances in the treatment of these conditions. Here, we collate the diagnostic approaches and techniques currently employed for biochemical and molecular assessment of at-risk individuals in whom abnormal copper metabolism is suspected.
PMID: 21735378 [PubMed - indexed for MEDLINE] (Source: Current Protocols in Human Genetics)
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Strategies for pathway analysis from GWAS data.
Authors: Yaspan BL, Veatch OJ
Abstract
Genome-wide association studies (GWAS) 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 mul...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Using the PhenX Toolkit to Add Standard Measures to a Study.
Authors: Hendershot T, Pan H, Haines J, Harlan WR, Junkins HA, Ramos EM, Hamilton CM
Abstract
The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) offers high-quality, well-established measures of phenotypes and exposures for use by the scientific community. The Toolkit contains 295 measures drawn from 21 research domains (fields of research). The measures were selected by Working Groups of domain experts using a consensus process that included input from the scientific community. The Toolkit provides a description of each PhenX measure, the rationale for incl...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
The UCSC Genome Browser.
Authors: Karolchik D, Hinrichs AS, Kent WJ
Abstract
The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation "tracks." The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy.
Authors: Huang T
Abstract
This protocol describes the methodology to characterize mitochondrial DNA (mtDNA) heteroplasmy by parallel sequencing. Mitochondria play an important role in essential cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. Mutant and wild-type mtDNA may co-exist as heteroplasmy, and cause human disease. The purpose of this protocol is to simultaneously determine mtDNA sequence and quantify the heteroplasmic level. This protocol includes a two-fragment mitochondrial genome DNA PCR amplification. The PCR product is then mixe...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Searching NCBI Databases Using Entrez.
Authors: Gibney G, Baxevanis AD
Abstract
One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simp...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Collection of clinical and epidemiological data for genetic linkage and association studies.
Authors: Farrer L, Logue M
Abstract
Modern gene-mapping can include linkage studies, which correlate the presence of disease to broad genomic regions in either small or large family units, and association studies, which can narrow the location of a disease-predisposing trait to a single gene using either case-control or family data. This unit provides an overview of key concepts and presents guidelines for collecting diagnostic, epidemiological, and genealogical data from potential study participants. The commentary discusses the use of publicly available data from online resources, methods for evaluating ...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Identifying functional annotation for noncoding genomic sequences.
Authors: Mortlock DP, Pregizer S
Abstract
The recent success of genome-wide association studies has generated a trove of biologically significant variants implicated in human disease. However, many, if not most, of these variants fall in noncoding regions that have traditionally lacked much functional annotation. New data sets and tools allow for a more detailed assessment of potential importance of noncoding genetic variants. An overview of types of regulatory annotation that are currently available, and approaches to analyzing this data are provided with emphasis on usage of the UCSC genome browser.
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Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Determination of sialylated and neutral oligosaccharides in urine by mass spectrometry.
Authors: Clements PR
Abstract
This protocol describes a method to allow for the detection of specific oligosaccharide fragments in urine by tandem mass spectrometry. The detection of fragments with specific masses indicates the presence of one of a number of diseases where the deficiency of lysosomal enzymes involved in the degradation of the glyco- moieties of glycoproteins is present in the patient. This method describes the derivatization of oligosaccharides present in urine with phenyl-1-methylpyrazolone, which renders them hydrophobic, thus allowing desalting with Combi cleanup columns prior to inject...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Interpretation of genomic copy number variants using DECIPHER.
Authors: Corpas M, Bragin E, Clayton S, Bevan P, Firth HV
Abstract
Many patients suffering from developmental disorders have submicroscopic deletions or duplications affecting the copy number of dosage-sensitive genes or disrupting normal gene expression. Many of these changes are novel or extremely rare, making clinical interpretation problematic and genotype/phenotype correlations difficult. Identification of patients sharing a genomic rearrangement and having phenotypes in common increases certainty in the diagnosis and allows characterization of new syndromes. The DECIPHER database is an online reposit...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Molecular diagnosis of hearing loss.
Authors: Brown KK, Rehm HL
Abstract
This unit discusses an approach to identifying a genetic etiology in an individual with nonsyndromic hearing loss. The unit begins with a discussion of the decision-making process that can be used to determine whether specific genes and/or a large gene panel should be used for molecular diagnosis of a patient presenting with nonsyndromic hearing loss. Next, two protocols are presented: (1) a full gene-sequencing assay to identify mutations in the GJB2 gene (encoding connexin 26), the most common cause of congenital hearing loss, and (2) an assay to detect the presence of...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Methods for detecting and correcting for population stratification.
We describe methods for detecting the presence of PS including global and local ancestry methods. We also describe approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. This is particularly important since many traits are being examined in minority populations, populations that may inherently feature PS.
PMID: 22470140 [PubMed - indexed for MEDLINE] (Source: Current Protocols in Human Genetics)
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Metaphase harvest and cytogenetic analysis of malignant hematological specimens.
Authors: Dal Cin P, McLaughlin C
Abstract
Cytogenetic analysis of malignant hematological disease is an important methodology used by clinicians and researchers, as observations of clonal chromosomal abnormalities have been shown to have both diagnostic and prognostic significance. The Basic Protocol describes culture, harvest, and preparation of chromosome spreads from bone marrow aspirates. Three alternate protocols describe adaptations of the Basic Protocol for preparation of specimens from chronic lymphocytic leukemia (CLL) blood/bone marrow, plasma cell disorders, mainly bone marrow multiple myeloma (...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
