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Detection of chromosomal aneuploidy in ancient genomes.

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posted on 2024-01-12, 12:39 authored by Kyriaki Anastasiadou, Marina Silva, Thomas Booth, Leo Speidel, Tony Audsley, Christopher Barrington, Jo Buckberry, Diana Fernandes, Ben Ford, Mark Gibson, Alexandre Gilardet, Isabelle Glocke, Katie Keefe, Monica Kelly, Mackenzie Masters, Jesse McCabe, Lauren McIntyre, Paola Ponce, Stephen Rowland, Jordi Ruiz Ventura, Pooja Swali, Frankie Tait, David Walker, Helen Webb, Mia Williams, Annsofie Witkin, Malin Holst, Louise Loe, Ian Armit, Rick Schulting, Pontus Skoglund
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.


Crick (Grant ID: CC1107, Grant title: STP Bioinformatics & Biostatistics) Crick (Grant ID: CC2109, Grant title: Skoglund CC2109) Wellcome Trust (Grant ID: 217223/Z/19/Z, Grant title: WT 217223/Z/19/Z) The Bert L & N Kuggie Vallee Foundation (Grant title: Vallee Scholar) European Molecular Biology Organization (Grant ID: 4990, Grant title: EMBO Young Investigator) European Research Council (Grant ID: 852558, Grant title: ERC 852558 - AGRICON)


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