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Principle of Digital Imaging Microscopy

A challenging problem of in situ hybridization is to visualize then localize genes or specifie sequences within the interphase nuclei or on chromosomes, as we now have at our disposai a large panel of probes. In addition, methods for probe labeling are continuously being improved to allow incre ...

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Detection of Chromosomal Aberrations in Interphase and Metaphase Cells in Prenatal and Postnatal Studies

The identification of numerical and structural chromosome abnormalities by routine and high resolution cytogenetic studies plays an important role in the diagnosis and treatment of various diseases. The analysis of structural aberrations is relatively gross and only permits t ...

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Characterization of Constitutive Marker Chromosomes in Humans

A marker chromosome is one that is morphologically different from any normal chromosome with its origin not being readily discernible by classical cytogenetic techniques. Marker chromosomes in neoplasia often represent the products of complex rearrangements and will not be disc ...

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Family-Based Linkage Disequilibrium Tests Using General Pedigrees

Linkage disequilibrium (LD) mapping has been established as a promising approach to identifying disease genes. The presence of a disease gene located near a marker locus may cause LD between the marker and the disease loci. In LD mapping, we assume that some of the affected individuals may have a comm ...

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Association Studies Using Familial Cases: An Efficient Strategy for Identifying Low-Penetrance Disease Alleles

Low-penetrance alleles are likely to contribute to inherited susceptibility to many complex traits. Such alleles will rarely generate multiple-case families and are therefore difficult or impossible to identify through genetic linkage analyses. The search for low-penetran ...

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Association Mapping Using Pooled DNA

The genetic dissection of complex disorders via genetic marker data has gained popularity in the postgenome era. Methods for typing genetic markers on human chromosomes continue to improve. Compared with the popular individual genotyping experiment, a pooled-DNA experiment (all ...

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Selecting Single-Nucleotide Polymorphisms for Association Studies With SNPbrowser Software

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage d ...

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Avoiding False Discoveries in Association Studies

We consider the problem of controlling false discoveries in association studies. We assume that the design of the study is adequate so that the “false discoveries” are potentially only because of random chance, not to confounding or other flaws. Under this premise, we review the statistical fr ...

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Gene Mapping in Asthma-Related Traits

In asthma, as in many other common multifactorial diseases, the identification of the susceptibility genes has been challenging because consistent results at the genome-wide significance level have been scarce. So far, genome-wide scans have been reported in 17 study populations. By m ...

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Identifying Susceptibility Variants for Type 2 Diabetes

The etiology of type 2 diabetes (T2D) is complex and remains poorly understood. Differences in individual susceptibility to this condition reflect the action of multiple variants, each of which confers a modest effect, and their interactions with a variety of environmental exposures. S ...

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Linkage Disequilibrium and Association Mapping: An Introduction

The basis for recent developments on the characterization of the linkage-disequilibrium structure of the genome and the application of association mapping to genes for common human diseases is described. Patterns of linkage disequilibrium are now understood, for a number of human po ...

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A History of Association Mapping

The current exciting developments in association mapping are founded on theory, which has been developed since the beginning of the last century. I hereby review these developments in their historical context.

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Linkage Disequilibrium Maps and Location Databases

Effective application of association mapping for complex traits requires characterization of linkage disequilibrium (LD) patterns that reflect the dominant process of recombination and its duration in addition to the more subtle influences of mutation, selection, and genet ...

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LDMAP: The Construction of High-Resolution Linkage Disequilibrium Maps of the Human Genome

The precise characterization of the linkage disequilibrium (LD) landscape from highdensity single-nucleotide polymorphism (SNP) data underpins the association mapping of diseases and other studies. We describe the algorithm and implementation of a powerful approach for co ...

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Linkage Disequilibrium as a Tool for Detecting Signatures of Natural Selection

Natural selection has been theoretically and empirically proven to alter patterns of linkage disequilibrium (LD). Reciprocally, recombination, the driving force behind LD, modifies the signature of natural selection by reintroducing variation in a punctuate manner across the ...

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The Genetic Basis of Complex Traits: Rare Variants or Common Gene, Common Disease

The goal of the Human Genome Project and the subsequent HapMap Project was to accelerate the pace at which genes for complex human traits were discovered. Elated by the early successes from cloning disease genes for monogenic disorders, the architects of the projects reasoned that complex hum ...

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Direct In Situ Single-Copy (DISC)-PCR

The physical mapping of functional genes and polymorphic markers is obviously important for understanding genome organization in higher organisms. Fluorescence in situ hybridization of labeled DNA to metaphase chromosome spreads has been a very effective means of accomplish ...

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In Situ PCR to Cells and to Wax Sections: An Alternative to In Situ Hybridization for the Detection of Low Copies of Human Papillomavirus and Cytomega

In situ hybridization and solution-phase PCR are suitable methods for DNA or RNA analysis. The first protocol for in situ hybridization was described almost 25 years ago (1). Since then, this technique has proven valuable to localize cellular DNA or mRNA. It has also been applied to detect viral DNA or R ...

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Reverse Transcriptase PCR In Situ on Cryopreserved Tissue Sections

The polymerase chain reaction (PCR) is an extraordinarily powerful tool that can amplify fragments of DNA or mRNA from a single cell (1). By combining PCR with other established methods, the reaction has been extended from isolated DNA in solution, to mRNA, to studies using tissue sections (2–5). In s ...

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Flow Cytometry Analysis of an In Situ PCR for the Detection of Human Immunodeficiency Virus Type-1 (HIV-1) Proviral DNA

The polymerase chain reaction (PCR) (1,2) is extremely sensitive and flexible, and in theory, will detect a single copy of a specific DNA (or retrotranscribed RNA) sequence either in cell cultures or in clinical samples (3). PCR technology has, therefore, been applied to the diagnosis of a wide range of ...

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