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Related Concept Videos

Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
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.
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The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Nucleotide Excision Repair01:38

Nucleotide Excision Repair

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...
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Overview of DNA Repair02:25

Overview of DNA Repair

In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
06:18

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Published on: November 30, 2021

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Hákon Jónsson1, Aurélien Ginolhac, Mikkel Schubert

  • 1Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 København K, Denmark. jonsson.hakon@gmail.com

Bioinformatics (Oxford, England)
|April 25, 2013
PubMed
Summary

mapDamage 2.0 introduces a statistical model for ancient DNA (aDNA) damage, enabling quantitative comparisons of DNA degradation patterns. This tool aids in authenticating ancient sequences and understanding evolutionary history.

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Area of Science:

  • Paleogenomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Ancient DNA (aDNA) analysis is crucial for evolutionary biology, revealing past epidemics and population dynamics.
  • Challenges include distinguishing endogenous DNA from microbial contamination and accurately assessing post-mortem DNA damage.
  • Existing tools like mapDamage identify damage patterns but lack formal statistical modeling for quantitative comparisons.

Purpose of the Study:

  • To introduce mapDamage 2.0, an enhanced version of the mapDamage package.
  • To incorporate a statistical model for DNA damage to enable rigorous quantitative comparisons across ancient DNA samples.
  • To provide accurate estimates of key aDNA degradation features.

Main Methods:

  • Development of a Bayesian statistical framework to model DNA damage.
  • The model assumes damage events depend on sequencing position and post-mortem deamination.
  • Estimation of parameters including overhang length, nick frequency, and cytosine deamination rates.

Main Results:

  • mapDamage 2.0 provides quantitative estimates of DNA damage features (λ, ν, , ).
  • The model allows for rescaling base quality scores based on damage probability.
  • The software efficiently handles next-generation sequencing datasets and is compatible with various library protocols.

Conclusions:

  • mapDamage 2.0 offers a statistically robust method for analyzing ancient DNA damage.
  • The tool facilitates more reliable authentication of ancient sequences and deeper insights into evolutionary processes.
  • Enhanced quantitative analysis of DNA degradation patterns is now possible.