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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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Sanger Sequencing01:57

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Related Experiment Video

Updated: May 25, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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Published on: September 3, 2009

Analysis of high-throughput ancient DNA sequencing data.

Martin Kircher1

  • 1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. Martin.Kircher@eva.mpg.de

Methods in Molecular Biology (Clifton, N.J.)
|January 13, 2012
PubMed
Summary

High-throughput sequencing revolutionizes ancient DNA (aDNA) analysis, enabling comprehensive data generation. This study outlines essential primary data analysis workflows for accurate aDNA characterization.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput sequencing technologies have transformed ancient DNA (aDNA) research.
  • aDNA presents unique challenges including short fragments, damage, and low copy numbers.
  • Traditional methods are insufficient for comprehensive aDNA characterization.

Purpose of the Study:

  • To describe primary data analysis workflows for high-throughput aDNA sequencing.
  • To address specific limitations of aDNA data analysis.
  • To enable accurate characterization of aDNA extracts.

Main Methods:

  • Sample separation in multiplexed experiments.
  • Removal of library artifacts and adapter sequences.
  • Quality filtering, contamination quantification, and identification of endogenous molecules.
  • Handling of clonal amplification products.

Main Results:

  • Established workflows for processing high-throughput aDNA sequencing data.
  • Methods to mitigate issues like chimeric sequences, errors, and damage.
  • Techniques for distinguishing endogenous DNA from environmental contamination.
  • Strategies for assessing library complexity and removing artifacts.

Conclusions:

  • Standardized primary data analysis is crucial for reliable aDNA studies.
  • High-throughput sequencing, coupled with appropriate workflows, allows for complete aDNA characterization.
  • These methods enhance the accuracy and scope of ancient DNA research.