Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA

The study of how past societies responded to disease, particularly those with physical and mental manifestations impacting daily life, is crucial in biological anthropology. Analyzing pathologies in skeletal remains is a direct approach, but osteological examinations are limited to skeletal tissue manifestations, and diagnosis can be complex. Rare diseases are often under-represented. This multidisciplinary study integrates genetic, anthropological, and archaeological data to understand the prevalence and societal perception of trisomies in prehistoric and historic populations. Chromosomal trisomy, characterized by three copies of a chromosome instead of two, is a common genetic aberration. Full autosomal trisomies are rarely survivable except for trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). Trisomy 13 and 18 rarely survive childhood without medical intervention. Each trisomy presents characteristic physical and neurodevelopmental symptoms, some potentially recognizable in past societies. While there are few documented historical cases, particularly of trisomies 13 and 18, a recent study identified a Neolithic Irish case of Down syndrome. The scarcity of identified cases is likely due to low prevalence rates (1:705 for Down syndrome, 1:2500 for Edwards syndrome, and 1:471 for Patau syndrome in live births) and analytical challenges in analyzing ancient DNA (aDNA) for copy number variations. This study uses a novel Bayesian method to analyze aDNA at low coverage, enabling the first systematic genetic screening and osteological description of trisomies in premodern samples.

The literature review highlights the challenges in diagnosing ancient diseases based solely on skeletal remains, emphasizing the limitations of osteological analyses in identifying the causes of skeletal lesions. Existing bioarchaeological literature shows an underrepresentation of rare diseases due to taphonomic factors, methodological issues, and public visibility. The lack of genetically identified historical and prehistoric cases of chromosomal trisomies is attributed to the low prevalence rates of these conditions in modern populations and the difficulty of analyzing ancient DNA (aDNA) for copy number variations using traditional methods. The study addresses this gap by utilizing a novel approach to aDNA analysis and integrating genetic data with osteological and archaeological information.

This study analyzed Illumina shotgun sequencing data from 9,855 prehistoric and historic individuals. The authors employed a novel Bayesian method designed for use with low-coverage aDNA data to screen for trisomy. This method can be applied to data with as few as 1000 reads mapped to the human genome. The method accounts for overdispersion in the data due to various factors such as different library protocols, sequencing runs, and DNA preservation. Beta-binomial distributions were used to model the proportion of reads mapping to each chromosome, and Z-scores were calculated to identify significant deviations from the expected proportion. Genetic sex was estimated by comparing the fraction of reads mapping to X and Y chromosomes. Osteological analyses were conducted by reviewing previously published findings, photographs, and reports. The age-at-death of infants was estimated using multiple skeletal indicators. Data availability includes proportions of reads mapping to autosomes and total read counts available on GitHub. The study adhered to ethical guidelines for archaeogenetic research and obtained the necessary permissions for sample collection.

The study identified six cases of Down syndrome (trisomy 21) and one case of Edwards syndrome (trisomy 18) among the 9,855 individuals analyzed. The positive cases for Down syndrome showed an approximately 1.5-fold higher proportion of reads mapping to chromosome 21 compared to negative cases. The case of Edwards syndrome showed a 1.47-fold increase in reads mapping to chromosome 18. All normalized posterior probabilities for the positive cases were one. The study also confirmed a previously published case of trisomy 21. The individuals with Down syndrome ranged in date from 5000 to 2400 years ago, with burials in settled urban or necropolis contexts, except for one 18th-century CE case from a Finnish church cemetery. The Edwards syndrome case (CRU013) was from Alto de la Cruz, Navarra, Spain (600-400 BCE). Osteological analysis, while noting that no single marker is pathognomonic, revealed overlapping markers consistent with trisomies in several individuals. These included porosity in cranial bones, abnormal growth on the occipital bone, and other features such as enamel hypoplasia. The individuals were interred with care, suggesting societal acceptance rather than stigmatization. The observed frequency of Down syndrome was lower than the modern rate, possibly due to non-random sampling and differential preservation of remains. Three Down syndrome cases were found at two nearby Iron Age sites in Spain, suggesting a potentially higher frequency in those specific communities.

The findings of this study offer insights into the prevalence and societal perception of trisomies in past communities. The identification of multiple cases of trisomy 21 and one case of trisomy 18 across different time periods and geographic locations, even with limitations of sample preservation, demonstrates that these conditions occurred in prehistoric and historic populations. The careful burial practices observed suggest that these individuals were not stigmatized and were likely acknowledged as members of their communities. The higher-than-expected cluster of trisomy 21 cases at two geographically close Iron Age sites warrants further investigation. The study emphasizes the importance of integrating genetic and osteological data with archaeological context to gain a more comprehensive understanding of past health and societal attitudes towards individuals with genetic disorders. The lower prevalence of Down syndrome compared to modern rates may be due to various factors including differential preservation and the fact that many of the cases occurred in stillbirths or very young infants.

This study successfully demonstrates the utility of applying a novel Bayesian method for identifying trisomies from ancient DNA at low coverage. The discovery of six cases of trisomy 21 and one case of trisomy 18 in ancient human remains, along with the observed burial practices, sheds light on the prevalence and social acceptance of these conditions in past populations. The unexpected clustering of trisomy 21 cases in Iron Age Spain highlights the need for further research into potential cultural factors influencing this observation. Future research could focus on expanding the analysis to larger datasets of ancient DNA, developing more sophisticated methods for detecting rare genetic conditions, and exploring additional archaeological contexts to gain a broader perspective on the experiences of individuals with genetic disorders in different societies throughout history.

The study acknowledges limitations related to sample preservation, which may affect the identification and interpretation of skeletal markers. The lower than expected frequency of Down Syndrome might be due to non-random sampling of the population. The age estimation of infants based on skeletal development has inherent uncertainties. While integrating genetic, anthropological, and archeological data significantly improves the understanding of trisomy in ancient populations, potential biases associated with the analysis methods and the inherent limitations of aDNA analysis should be considered.