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

Improving ancient DNA read mapping against modern reference genomes.

Mikkel Schubert1, Aurelien Ginolhac, Stinus Lindgreen

  • 1Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 Øster Voldgade, 1350, Kobenhavns K, Denmark.

BMC Genomics
|May 12, 2012
PubMed
Summary
This summary is machine-generated.

Optimizing computational mapping parameters significantly improves ancient DNA (aDNA) identification from shotgun sequencing data. This enhanced accuracy aids in recovering more genuine aDNA fragments and increases genotyping accuracy for ancient specimens.

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Area of Science:

  • Paleogenomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-Generation Sequencing (NGS) enables ancient DNA (aDNA) research but faces challenges from DNA damage and contamination.
  • Mapping ancient DNA reads to modern genomes is hindered by platform-specific errors and post-mortem damage.
  • This limits the identification of endogenous ancient DNA fragments, reducing shotgun sequencing efficiency.

Purpose of the Study:

  • To compare computational methods for improving ancient DNA sequence identification accuracy and sensitivity.
  • To optimize mapping parameters for Illumina and Helicos sequencing platforms for aDNA analysis.
  • To assess strategies for increasing the recovery of genuine aDNA fragments and identifying contamination.

Main Methods:

  • Compared computational mapping methods for shotgun sequencing reads from Pleistocene horse DNA extracts.
  • Modified default parameters of the Burrows Wheeler Aligner (BWA) for platform-specific error profiles.
  • Evaluated read-trimming strategies for damaged DNA ends and best hit filtering for contamination identification.

Main Results:

  • Optimized BWA mapping parameters improved performance for Illumina GAIIx and Helicos Heliscope reads.
  • Platform-specific parameter adjustments and read trimming increased genuine aDNA fragment recovery.
  • Combined mapping and filtering approaches enhanced high-quality endogenous hit recovery by up to 33%.

Conclusions:

  • Illumina and Helicos aDNA sequences require optimized mapping parameters for efficient alignment to modern reference genomes.
  • Developed mapping guidelines improve the identification of genuine aDNA sequences, crucial for accurate ancient specimen genotyping.
  • The proposed framework enhances standard ancient genome characterization procedures, addressing challenges of contamination and low DNA yields.