Detection of chromosomal aneuploidy in ancient genomes

Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in t...

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Veröffentlicht in:Communications biology 2024-01, Vol.7 (1), p.14-9, Article 14
Hauptverfasser: Anastasiadou, Kyriaki, Silva, Marina, Booth, Thomas, Speidel, Leo, Audsley, Tony, Barrington, Christopher, Buckberry, Jo, Fernandes, Diana, Ford, Ben, Gibson, Mark, Gilardet, Alexandre, Glocke, Isabelle, Keefe, Katie, Kelly, Monica, Masters, Mackenzie, McCabe, Jesse, McIntyre, Lauren, Ponce, Paola, Rowland, Stephen, Ruiz Ventura, Jordi, Swali, Pooja, Tait, Frankie, Walker, David, Webb, Helen, Williams, Mia, Witkin, Annsofie, Holst, Malin, Loe, Louise, Armit, Ian, Schulting, Rick, Skoglund, Pontus
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Sprache:eng
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Zusammenfassung:Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits. A sex chromosome identification method for ancient DNA revealed six individuals who lived with chromosomal aneuploidies in Britain from ~ 2,500 to 250 years ago. Genomic and osteological information was combined to shed light on their lives.
ISSN:2399-3642
2399-3642
DOI:10.1038/s42003-023-05642-z