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HuConTest: Testing Human Contamination in Great Ape Samples.

Martin Kuhlwilm1, Claudia Fontsere1, Sojung Han1

  • 1Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.

Genome Biology and Evolution
|May 26, 2021
PubMed
Summary

Detecting modern human DNA contamination is crucial in ancient DNA studies and also affects great ape research. A new tool, HuConTest, effectively identifies human contamination in short-read sequencing data from various species, especially complex samples.

Keywords:
ancient DNAcontaminationfecal DNAnext-generation sequencingnonhuman primates

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Area of Science:

  • Genomics
  • Primate Biology
  • Ancient DNA Research

Background:

  • Modern human DNA contamination is a significant challenge in ancient DNA (aDNA) studies.
  • This contamination issue extends to studies involving great apes, our closest living relatives, particularly with noninvasive samples.
  • Existing methods may not be sufficient for complex sample types with low endogenous DNA content.

Purpose of the Study:

  • To introduce a straightforward method for detecting human contamination in short-read sequencing data from various species.
  • To validate the effectiveness of this new method, termed HuConTest, across different sample types.
  • To provide a valuable tool for researchers working with challenging samples like museum specimens and noninvasive collections.

Main Methods:

  • Development of a simple detection tool named HuConTest.
  • Application of HuConTest to short-read sequencing data.
  • Testing the method on blood and tissue samples from great apes.

Main Results:

  • Demonstrated the feasibility and effectiveness of HuConTest in detecting human contamination.
  • Confirmed the presence of human contamination in great ape samples, including noninvasive ones.
  • Showcased the utility of HuConTest for complex samples with limited endogenous DNA.

Conclusions:

  • HuConTest is a reliable and simple method for identifying human contamination in sequencing data.
  • The tool is particularly beneficial for analyzing degraded or low-quantity DNA samples, such as those from museum or noninvasive sources.
  • Addressing human contamination is essential for accurate genetic studies of great apes and other species.