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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Point and Frameshift Mutations01:30

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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Is it time to reassess variant annotation?

David C Samuels1, Hui Yu2, Yan Guo2

  • 1Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA.

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New variant annotation tools use real-world data, not just predictions, for better candidate selection. This shift, driven by large-scale genomics projects, improves the accuracy of variant analysis.

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Variant annotation is crucial for identifying significant genetic variations.
  • Traditional methods relied on theoretical predictions, limiting accuracy.
  • Advancements in functional genomics necessitate updated annotation strategies.

Purpose of the Study:

  • To highlight recent, empirically-based variant annotation methods.
  • To discuss the advantages and disadvantages of these novel approaches.
  • To inform the selection of genetic variants for further research.

Main Methods:

  • Review of current literature on empirically-based variant annotation tools.
  • Analysis of data generated by large national and international genomics consortia.
  • Comparative assessment of different annotation methodologies.

Main Results:

  • Empirically-based annotation leverages large-scale, validated experimental data.
  • These methods offer higher accuracy compared to purely predictive models.
  • Strengths include direct evidence, weaknesses may involve data accessibility or scope.

Conclusions:

  • The shift towards empirical data in variant annotation is a significant advancement.
  • These methods enhance the reliability of variant candidate selection.
  • Future research should focus on integrating diverse omics data for comprehensive annotation.