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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Genetic Variation01:25

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Related Experiment Video

Updated: Apr 18, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data.

Xi Chen, Xu Shi, Ayesha N Shajahan

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
    |January 9, 2015
    PubMed
    Summary
    This summary is machine-generated.

    We developed BSSV, a Bayesian framework for identifying somatic structural variations (SSVs) in cancer genomes. This method improves SSV detection accuracy and reduces false negatives, aiding in cancer gene discovery.

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    Last Updated: Apr 18, 2026

    Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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    Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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    Area of Science:

    • Genomics
    • Cancer Research
    • Bioinformatics

    Background:

    • High-coverage whole genome sequencing is crucial for identifying somatic structural variations (SSVs).
    • Simultaneous analysis of paired tumor and normal samples offers improved SSV detection resolution compared to subtracting shared variations.
    • Existing tools have limitations in identifying all SSV types and ranking their somatic significance.

    Purpose of the Study:

    • To develop a novel Bayesian framework, BSSV, for accurate and comprehensive SSV identification.
    • To integrate read alignment data from tumor and normal samples for robust SSV significance calculation.
    • To address the limitations of current tools in detecting all SSV types and assessing their somatic relevance.

    Main Methods:

    • Developed a Bayesian framework (BSSV) integrating read alignment information from paired tumor and normal samples.
    • Utilized simulated data to rigorously test and validate the BSSV framework's performance.
    • Applied the BSSV approach to analyze The Cancer Genome Atlas (TCGA) breast cancer dataset.

    Main Results:

    • BSSV demonstrates comparable precision to existing tools in SSV detection.
    • BSSV significantly reduces the false negative rate for SSV identification.
    • Successfully identified known breast cancer-associated mutated genes (e.g., RAD51, BRIP1, ER, PGR, PTPRD) in TCGA data.

    Conclusions:

    • BSSV provides a robust and accurate method for identifying somatic structural variations.
    • The framework enhances the detection of SSVs, particularly reducing false negatives.
    • BSSV aids in the discovery of cancer-specific mutated genes, advancing cancer genomics research.