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Related Concept Videos

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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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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CoVaCS: a consensus variant calling system.

Matteo Chiara1, Silvia Gioiosa2,3, Giovanni Chillemi2

  • 1Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.

BMC Genomics
|February 7, 2018
PubMed
Summary
This summary is machine-generated.

CoVaCS is a new automated bioinformatics system for genotyping and variant annotation. It provides accurate and efficient analysis of human genome resequencing data, improving diagnostic capabilities for precision medicine.

Keywords:
Consensus methodGraphical user interfaceVariant annotationVariant callingVariant prioritizationWeb serverWorkflow

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) generates vast amounts of human genome data, driving personalized genomics and precision medicine.
  • The increasing volume of genome resequencing data necessitates efficient bioinformatics systems for accurate genotyping.
  • Genotyping is critical for identifying causal mutations in diagnostic genetic screening.

Purpose of the Study:

  • To present CoVaCS, a novel, automated system for genotyping and variant annotation.
  • To provide a user-friendly, web-based graphical interface for complex genomic analyses.
  • To enhance the accuracy and efficiency of human genome resequencing data analysis.

Main Methods:

  • Development of CoVaCS, a fully automated system with optimized pipelines for variant calling and annotation.
  • Integration of state-of-the-art tools for whole genome sequencing (WGS), whole-exome sequencing (WES), and target-gene sequencing (TGS) data.
  • Utilizing a high-performance computing (HPC) facility for rapid analysis of large sample cohorts.

Main Results:

  • CoVaCS demonstrates high accuracy and sensitivity, comparable to command-line approaches and superior to individual tools.
  • The system achieves higher specificity than equivalent commercial software.
  • Extensive testing on the NA12878 Illumina platinum genome benchmark dataset validates CoVaCS's performance.

Conclusions:

  • CoVaCS offers a valuable, automated, and reproducible solution for human genome resequencing studies.
  • The system's speed and accuracy make it suitable for large-scale genomic analyses.
  • CoVaCS is accessible via a web-based interface, facilitating its adoption in diagnostic and research settings.