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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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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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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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Sequences01:29

Sequences

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Updated: Jan 29, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Utilizing iVariantGuide for Variant Assessment of Next-Generation Sequencing.

Sophia R Chaudhry1, Michael A Tainsky1,2,3

  • 1Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan.

Current Protocols in Bioinformatics
|February 13, 2019
PubMed
Summary

iVariantGuide simplifies tertiary analysis of next-generation sequencing (NGS) data for personalized genetic testing. This tool aids in identifying disease-causing variants and understanding their biological impact, crucial for clinical applications.

Keywords:
clinical risk analysisnovel single nucleotide variantsvariant assessment

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Molecular genetic testing is essential for personalized medicine, enabling accurate disease prediction, diagnosis, and targeted treatments.
  • Variant assessment of next-generation sequencing (NGS) data is critical for clinicians to provide genetic counseling regarding patient risk and management strategies.

Purpose of the Study:

  • To provide a step-by-step guide for utilizing the iVariantGuide application for tertiary analysis of NGS data.
  • To demonstrate the application's capability in identifying novel genetic variants and assessing their impact on biological pathways and Gene Ontology (GO) terms.

Main Methods:

  • The iVariantGuide web-based application was employed for tertiary analysis.
  • A publicly available NGS dataset from high-risk serous ovarian cancer (OVCA) patient germline DNA was utilized.
  • The study focused on filtering variants and analyzing their pathway and GO term implications.

Main Results:

  • The iVariantGuide application facilitated the efficient filtering of NGS data to identify compelling novel variants.
  • The analysis successfully demonstrated the impact of identified variants on biological pathways and GO terms.
  • The study showcased the ease of use of iVariantGuide for complex genetic data analysis.

Conclusions:

  • iVariantGuide is a valuable tool for the tertiary analysis of NGS data, aiding in variant assessment and interpretation.
  • The application enhances the understanding of genetic variant impact on biological pathways and GO terms, supporting clinical decision-making.
  • This guide facilitates the adoption of iVariantGuide for researchers and clinicians involved in genetic testing and personalized medicine.