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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Cancers Originate from Somatic Mutations in a Single Cell02:21

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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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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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Nucleotide Excision Repair01:38

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DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
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Updated: Nov 3, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Exonic variants undergoing allele-specific selection in cancers.

Qiyuan Li1,2, Yuanyuan Zeng3, Janet Wang4

  • 1Department of Hematology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361102, China.

BMC Medical Genomics
|June 1, 2021
PubMed
Summary

This study identifies specific genetic variants (SNPs) associated with allele imbalance (AI) in tumors. These variants are linked to cancer development and essential genes, offering a new method for cancer research.

Keywords:
Allelic imbalanceCancerCopy numberExonic variantsSomatic selection

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Area of Science:

  • Genomics
  • Cancer Biology
  • Molecular Genetics

Background:

  • Allelic imbalance (AI) in tumors arises from chromosomal alterations.
  • AI reflects gains and losses of genetic material within cancer cells.

Purpose of the Study:

  • To identify single nucleotide polymorphism (SNP) loci exhibiting allele specificity in tumor AI.
  • To investigate the relationship between allele-specific SNPs, population frequencies, and protein-damaging variants.
  • To explore the role of genes harboring allele-specific SNPs in cancer-related processes.

Main Methods:

  • Evaluated AI across 109,086 germline exonic SNP loci in four cancer types.
  • Compared allele frequencies in cancer versus healthy populations.
  • Assessed enrichment of predicted protein-damaging variants and cancer-related biological processes.

Main Results:

  • Identified SNPs with strong tumor allele specificity in AI events.
  • Allele-specific SNPs showed distinct frequencies in cancer patients vs. healthy individuals.
  • Genes with allele-specific SNPs were enriched for cancer relevance and essentiality in cancer cells.

Conclusions:

  • The study presents a novel method for identifying genes and variants crucial for carcinogenesis.
  • This approach complements existing methods in cancer variant discovery.