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Related Concept Videos

Mutations in Microorganisms01:18

Mutations in Microorganisms

Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

Overview
Mutations01:39

Mutations

Overview
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...

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Related Experiment Video

Updated: Jul 6, 2026

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

TRAB: testing whether mutation frequencies are above an unknown background.

Giovanni Parmigiani1, Sining Chen

  • 1Johns Hopkins University, USA. gp@jhu.edu

Statistical Applications in Genetics and Molecular Biology
|April 4, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces TRAB, an R library for identifying cancer-driving genes by comparing mutation frequencies against controls. TRAB rigorously evaluates if gene mutation rates exceed normal levels using a Bayesian approach.

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Last Updated: Jul 6, 2026

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
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Area of Science:

  • Genomics
  • Cancer Research
  • Bioinformatics

Background:

  • Determining gene involvement in carcinogenesis necessitates comparing mutation prevalence to control frequencies in tumor DNA.
  • Existing methods may lack the rigor to definitively identify genes driving cancer development.

Purpose of the Study:

  • To develop a robust statistical approach for evaluating whether a gene's somatic mutation frequency is significantly higher than expected.
  • To introduce the TRAB R library, facilitating the rigorous assessment of gene alterations in carcinogenesis.

Main Methods:

  • A hypothesis testing framework comparing a gene's mutation frequency to a control group of gene frequencies.
  • Utilizing a hierarchical Bayesian approach to compute a posteriori probabilities and Bayes factors.
  • The R library TRAB implements this statistical methodology for practical application.

Main Results:

  • TRAB provides a quantitative measure (a posteriori probability and Bayes factor) to assess the significance of mutation frequencies.
  • The approach accounts for variability within the control mutation frequencies.
  • Enables researchers to more confidently identify genes potentially involved in cancer initiation and progression.

Conclusions:

  • TRAB offers a statistically sound method for identifying candidate genes in carcinogenesis.
  • The R library enhances the ability to analyze somatic mutation data for cancer research.
  • This tool aids in the rigorous determination of gene alterations contributing to tumor development.