Real time PCR primer sequences of the genes studied.

<p>B2M – β2-microglobulin; PMM1 - phosphomannomutase 1; IL1B – interleukin-1β; IL6 – interleukin-6; TNF – tumor necrosis factor; TGFB1 – transforming growth factor β1; BMP – Bone morphogenetic protein; IGF1 – insulin growth factor-1; FGF2 – fibroblast growth factor 2; PDGFB – platelet derived growth factor β; OPG – osteoprotegerin; RANK – receptor activator of nuclear factor κB; RANKL – RANK ligand; CBFA1/RUNX2 – core binding factor α1/runt-related transcription factor 2; OSX – osterix; ALP – alkaline phosphatase; SOST – sclerostin; TRAP – tartrate-resistant acid phosphatase; CTSK – cathepsin K; ITGB3 – subunit β3 of the integrin αvβ3; ATP - ATPase H⁺ transporter.</p

Description of the study population divided between the event of fracture and surgery.

<p>Values represent mean±standard deviation.</p><p>Comparisons between groups performed with ANOVA or chi-square tests.</p

Comparison between the relative gene expression levels of patients submitted to hip replacement surgery due to low-energy fracture in relation to the days between fracture and surgery.

<p>Values represent median (Q1–Q3).</p><p>Comparisons between the 3 groups performed with Kruskall-Wallis H test.</p><p>*p-value for comparison between the 3 groups.</p><p>IL1B – interleukin-1β; IL6 – interleukin-6; TNF – tumor necrosis factor; TGFB1 – transforming growth factor β1; BMP – Bone morphogenetic protein; IGF1 – insulin growth factor-1; FGF2 – fibroblast growth factor 2; PDGFB – platelet derived growth factor β; OPG – osteoprotegerin; RANK – receptor activator of nuclear factor κB; RANKL – RANK ligand; CBFA1/RUNX2 – core binding factor α1/runt-related transcription factor 2; OSX – osterix; ALP – alkaline phosphatase; SOST – sclerostin; TRAP – tartrate-resistant acid phosphatase; CTSK – cathepsin K; ITGB3 – subunit β3 of the integrin αvβ3; ATP - ATPase H⁺ transporter.</p

Relative expression of inflammation and growth factors genes grouped according to the time between the event of fracture and the surgery.

<p>Each gene was normalized to the expression of the housekeeping genes <i>B2M</i> and <i>PMM1</i>. *p-value<0.05 for comparisons between the three groups. (Points represent median values). IL1B – interleukin-1β; IL6 – interleukin-6; TNF – tumor necrosis factor; IGF1 – insulin growth factor-1 ; FGF2 – fibroblast growth factor 2 ; PDGFB – platelet derived growth factor β; BMP – Bone morphogenetic protein; TGFB1 – transforming growth factor β1.</p

Relative expression of bone metabolism-related genes divided according to the time between the event of fracture and the surgery.

<p><i>RANK</i>, <i>RANKL</i> and <i>OPG</i> (<b>A</b>), osteoblast (<b>B</b>), osteocyte (<b>C</b>) and osteoclast-specific genes (<b>D</b>) were studied in the three study groups. Each gene was normalized to the expression of the housekeeping genes <i>B2M</i> and <i>PMM1</i>. *p-value<0.05 for comparisons between the three groups. (Points represent median values). RANK – receptor activator of nuclear factor κB; RANKL – RANK ligand; OPG – osteoprotegerin; CBFA1/RUNX2 – core binding factor α1/runt-related transcription factor 2; OSX – osterix; ALP – alkaline phosphatase; SOST – sclerostin; ITGB3 – subunit β3 of the integrin αvβ3; TRAP – tartrate-resistant acid phosphatase; ATP - ATPase H⁺ transporter; CTSK – cathepsin K.</p

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 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