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Pseudogenes

Overview of attention for book
Cover of 'Pseudogenes'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Pseudogene Redux with New Biological Significance
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    Chapter 2 Contribution of Pseudogenes to Sequence Diversity
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    Chapter 3 Computational Methods for Pseudogene Annotation Based on Sequence Homology
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    Chapter 4 Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content.
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    Chapter 5 Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation
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    Chapter 6 Whole-Genome Identification of Neutrally Evolving Pseudogenes Using the Evolutionary Measure dN/dS
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    Chapter 7 Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach.
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    Chapter 8 Methods for Detecting Transcribed Pseudogenes: PCR on Regions of High Sequence Similarity Followed by Cloning and Sequencing
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    Chapter 9 RNA Amplification for Pseudogene Detection Using RNA-Seq.
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    Chapter 10 GENCODE Pseudogenes
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    Chapter 11 Methods to Detect Transcribed Pseudogenes: RNA-Seq Discovery Allows Learning Through Features
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    Chapter 12 Proteomics techniques for the detection of translated pseudogenes.
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    Chapter 13 Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation.
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    Chapter 14 Pseudogenes: A Novel Source of trans-Acting Antisense RNAs
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    Chapter 15 Pseudogene-Derived Endogenous siRNAs and Their Function
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    Chapter 16 Methods to Study Translated Pseudogenes: In Vitro Translation, Fusion with a Tag/Reporter Gene, and Complementation Assay
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    Chapter 17 Targeted and robust amplification of mitochondrial DNA in the presence of nuclear-encoded mitochondrial pseudogenes using φ29 DNA polymerases.
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    Chapter 18 Pseudogenes
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    Chapter 19 Mutational Analysis of CYP21A2 Gene and CYP21A1P Pseudogene: Long-range PCR on Genomic DNA.
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    Chapter 20 PMS2 Gene Mutational Analysis: Direct cDNA Sequencing to Circumvent Pseudogene Interference
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    Chapter 21 Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era
Attention for Chapter 21: Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era
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Chapter title
Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era
Chapter number 21
Book title
Pseudogenes
Published in
Methods in molecular biology, April 2014
DOI 10.1007/978-1-4939-0835-6_21
Pubmed ID
24823787
Book ISBNs
978-1-4939-0834-9, 978-1-4939-0835-6
Authors

Claes, Kathleen B. M., De Leeneer, Kim, Kathleen B. M. Claes Ph.D., Kim De Leeneer, Kathleen B. M. Claes

Editors

Laura Poliseno

Abstract

In this chapter, we focus on issues related to the application of next-generation sequencing (NGS) strategies for the analysis of genes with pseudogenes in a clinical setting. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences, which are characterized by higher mutation rates than their functional parental genes. For the target enrichment strategies, we describe advantages and disadvantages of PCR- and capture-based enrichment methodologies. For the mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some concrete examples of genes with known pseudogenes and associated with Mendelian disorders that were analyzed by NGS on various platforms and starting from different library preparations.

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X Demographics

X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 46 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Norway 1 2%
Unknown 45 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 28%
Researcher 6 13%
Student > Bachelor 4 9%
Student > Master 4 9%
Other 3 7%
Other 6 13%
Unknown 10 22%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 13 28%
Agricultural and Biological Sciences 11 24%
Medicine and Dentistry 5 11%
Mathematics 2 4%
Neuroscience 2 4%
Other 2 4%
Unknown 11 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 27 October 2014.
All research outputs
#18,381,794
of 22,768,097 outputs
Outputs from Methods in molecular biology
#7,871
of 13,090 outputs
Outputs of similar age
#164,099
of 227,114 outputs
Outputs of similar age from Methods in molecular biology
#53
of 145 outputs
Altmetric has tracked 22,768,097 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,090 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 24th percentile – i.e., 24% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 227,114 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 14th percentile – i.e., 14% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 145 others from the same source and published within six weeks on either side of this one. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.

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