ArticleBioinformatics (Oxford, England)2026
ChASM: a statistically rigorous method for the detection of chromosomal aneuploidies in ancient DNA studies.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
motivationHow individuals with conditions, disabilities or abnormalities were treated gives us valuable insights into past societies. Chromosomal aneuploidies, the presence of an abnormal number of copies of the chromosomes, represent the most common large-scale chromosomal abnormalities in human populations. Chromosomal aneuploidies can affect autosomal chromosomes (e.g. Down syndrome) as well as the sex chromosomes (e.g. Klinefelter syndrome), with physical manifestations ranging from mild to severe. While simple to identify genetically, chromosomal aneuploidies are difficult to diagnose from skeletal remains alone, as they present skeletal pathologies consistent with many other conditions.
resultsHere we present ChASM (Chromosomal Aneuploidy Screening Methodology), a statistically rigorous Bayesian method for detecting full autosomal and sex chromosomal aneuploidies. The method leverages chromosome-wise read counts and takes into account differences in sequencing methodology, genetic coverage and condition rarity to produce posterior probability estimates for the screening of small and large databases of sequence data. AVAILABILITY AND IMPLEMENTATION: To facilitate the ease of use, ChASM has been implemented in R as the package RChASM. RChASM is available under MIT license on the Comprehensive R Archive Network.
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