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.High-throughput multiplex sequencing of miRNA.
Authors: Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G
Abstract
Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Biochemical genetics. Introduction.
Authors: Sharer JD, Korf BR
PMID: 22470143 [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
Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).
Authors: Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, Stephens RM
Abstract
This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mir...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Searching Online Mendelian Inheritance in Man (OMIM) for information on genetic loci involved in human disease.
Authors: Baxevanis AD
Abstract
Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of information on human genes and genetic disorders, with a particular emphasis on the interplay between observed phenotypes and underlying genotypes. This unit focuses on the basic methodology for formulating OMIM searches and illustrates the types of information that can be retrieved from OMIM, including descriptions of clinical manifestations resulting from genetic abnormalities. This unit also provides information on additional relevant medical and molecular biology databases. A basic knowledge of OM...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Population-based case-control association studies.
Authors: Hancock DB, Scott WK
Abstract
This unit provides an overview of the design and analysis of population-based case-control studies of genetic risk factors for complex disease. Considerations specific to genetic studies are emphasized. The unit reviews basic study designs differentiating case-control studies from others, presents different genetic association strategies (candidate gene, genome-wide association, and high-throughput sequencing), introduces basic methods of statistical analysis for case-control data and approaches to combining case-control studies, and discusses measures of association ...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Molecular analysis of the human mitochondrial DNA control region for forensic identity testing.
Authors: Holland MM
Abstract
This unit highlights methods used to perform PCR amplification and sequence analysis of mitochondrial DNA (mtDNA) on pristine and highly degraded biological material. The focus is on applications to forensic casework, and a number of case examples are provided. Any laboratory working with DNA from old or "ancient" samples will benefit from this information.
PMID: 22786611 [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
Morphology antibody chromosome technique for determining phenotype and genetic status of the same cell.
Authors: Knuutila S, Mustjoki S
Abstract
The morphology antibody chromosome (MAC) technique is a combination of methods that permits analysis of both phenotypic and genetic evaluation on a single interphase or mitotic cell as a basis for lineage analysis of neoplastic and normal cells. This unit describes MAC with sequential phenotypic analysis using antibody and an alkaline phosphatase anti-alkaline phosphatase (APAAP) complex and genotypic analysis using in situ hybridization with either enzymatic or fluorescence detection. Alternate methods for phenotypic analysis are also described, which include the u...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Oligonucleotide microarrays for clinical diagnosis of copy number variation and zygosity status.
Authors: Miller DT, Shen Y, Wu BL
Abstract
Detection of submicroscopic genomic copy number variation is now considered the first-tier clinical test-in place of standard G-banded karyotyping-in the evaluation of children with unexplained developmental delay, intellectual disability, autism spectrum disorders, or congenital anomalies. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variants (CNVs), but microarray-based comparative genomic hybridization (array CGH) has a much higher diagnostic yield for these patients when compared t...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Preparation, culture, and analysis of amniotic fluid samples.
Authors: Miron PM
Abstract
Amniotic fluid obtained via amniocentesis provides a source of fetal material used in prenatal diagnosis. The fluid is used directly for biochemical analyses and as a source of fetal cells for biochemical assays, DNA testing, and chromosome studies. This unit describes an in situ method for the preparation, culture, and harvest of amniotic fluid samples for chromosome analysis. Cells are grown, harvested for metaphase spreads, and analyzed on glass coverslips. The unit also describes methods to obtain cells for additional studies (such as molecular genetic analyses) by growing ce...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Model-free tests for genetic linkage.
Authors: Amos CI, Schnell A, Chen WV, Elston RC
Abstract
This unit covers statistical methods of linkage analysis that do not require the assumption of a detailed genetic model, as is required for standard lod score analysis. The unit has been updated to include the latest methods in sib-pair analysis, including updates to using the software program SIBPAL as well as the relative-pair analysis software applications GENEHUNTER, GENEHUNTER PLUS, and Merlin.
PMID: 23074068 [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
Diagnosing lysosomal storage disorders: Pompe disease.
Authors: Bodamer OA, Dajnoki A
Abstract
Pompe disease is a lysosomal storage disorder caused by a deficiency of acid alpha glucosidase (GAA). Diagnosis of Pompe disease is typically based on an enzyme analysis of blood or tissues, such as fibroblasts, followed by confirmation through molecular testing. The advent of fluorometric and mass spectrometry methods for enzyme analysis in dried blood spots (DBS) has simplified the diagnostic approach for Pompe disease, facilitating high-throughput screening of at-risk populations and newborn infants. The following unit will provide the detailed analytical protocol...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Discovery of rare homozygous mutations from studies of consanguineous pedigrees.
Authors: Alkuraya FS
Abstract
The unmasking of recessive mutations by virtue of biparental inheritance of the same ancestral haplotype on which they reside (autozygosity) has provided human geneticists with one of their most powerful tools in unraveling the genetic basis of autosomal recessive disorders. This has historically been achieved by tracking the blocks of homozygosity as surrogates of autozygosity using polymorphic microsatellite markers. Mapping the entire set of autozygous blocks per individual (autozygome) at high resolution became possible with the advent of high-density SNP arrays. The more ...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
A survey of copy-number variation detection tools based on high-throughput sequencing data.
Authors: Xi R, Lee S, Park PJ
Abstract
Copy-number variation (CNV) is a major class of genomic variation with potentially important functional consequences in both normal and diseased populations. Remarkable advances in development of next-generation sequencing (NGS) platforms provide an unprecedented opportunity for accurate, high-resolution characterization of CNVs. In this unit, we give an overview of available computational tools for detection of CNVs and discuss comparative advantages and disadvantages of different approaches.
PMID: 23074071 [PubMed - indexed for MEDLINE] (Source: Current Prot...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Preparation of chorionic villus samples for metaphase chromosome analysis and chromosomal microarray analysis.
Authors: Breman A, Patel A
Abstract
Chorionic villi are composed of an outer layer of trophoblastic cells and an inner mesenchymal cell core. They can be prepared for chromosome analysis using a culture method wherein villi are disaggregated by mechanical and enzymatic methods and the resulting cell suspension is used to establish primary cultures. Mesenchymal cells of the villus core are released by this procedure and the fibroblasts are actively proliferative in tissue culture. Cultures can be used for cytogenetic analysis after ∼1 week. Slides prepared by this technique can be stained using trypsin-Gi...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
Overview of admixture mapping.
Authors: Shriner D
Abstract
Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to African Americans who trace ancestry to Europeans and West Africans. Recent developments in admixture mapping include improvements in methods to take advantage of higher densities of genetic variants, as well as extensions to admixed populations with three or more ancestral populations, such as Latino Americans. In this unit, the author outlines the key concepts of admixture mapping. The author describes several a...
Source: Current Protocols in Human Genetics - November 25, 2014 Category: Genetics & Stem Cells Tags: Curr Protoc Hum Genet Source Type: research
