Allentoft, M. E. et al. The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B Biol. Sci. 279, 4724–4733 (2012).
Google Scholar
Atoche, P. & Aufderheide, A. C. Mummies and Science World Mummies Research VI World Congress (Springer, 2008).
Fornaciari, G. et al. A medieval case of digitalis poisoning: The sudden death of Cangrande della Scala, lord of verona (1291–1329). J. Archaeol. Sci. 54, 162–167 (2015).
Google Scholar
Napione, E. Il Corpo Del Principe: Ricerche su Cangrande della Scala (Springer, 2006).
Perciaccante, A. et al. Lessons from the past: Some histories of alpha-1 antitrypsin deficiency before its discovery. COPD J. Chronic Obstr. Pulm. Dis. 15, 1–3 (2018).
Google Scholar
Schulz, J. La morte di Cangrande I della Scala: Un caso da riaprire (Springer, 2015).
Parker, C. et al. A systematic investigation of human DNA preservation in medieval skeletons. Sci. Rep. 10, 18225 (2020).
Google Scholar
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V. & Pääbo, S. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7, e34131 (2012).
Google Scholar
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110, 15758–15763 (2013).
Google Scholar
Ozga, A. T. et al. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. Am. J. Phys. Anthropol. 160, 220–228 (2016).
Google Scholar
Modi, A. et al. Combined methodologies for gaining much information from ancient dental calculus: Testing experimental strategies for simultaneously analysing DNA and food residues. Archaeol. Anthropol. Sci. 12, 1–11 (2020).
Google Scholar
Zhang, W. Q. et al. Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium. J. Genet. 94, 731–740 (2015).
Google Scholar
Napolitano, F. et al. Rare variants in autophagy and non-autophagy genes in late-onset pompe disease: Suggestions of their disease-modifying role in two Italian families. Int. J. Mol. Sci. 22, 3625 (2021).
Google Scholar
Gaudin, M. & Desnues, C. Hybrid capture-based next generation sequencing and its application to human infectious diseases. Front. Microbiol. 9, 27 (2018).
Google Scholar
Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 1–11 (2017).
Google Scholar
Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).
Google Scholar
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
Google Scholar
Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).
Google Scholar
Mafessoni, F. et al. A high-coverage neandertal genome from chagyrskaya cave. Proc. Natl. Acad. Sci. USA. 117, 15132–15136 (2020).
Google Scholar
Gravel, S. et al. Reconstructing native American migrations from whole-genome and whole-exome data. PLoS Genet. 9, 1004023 (2013).
Google Scholar
Keller, A. et al. New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 1–9 (2012).
Google Scholar
Gilissen, C., Hoischen, A., Brunner, H. G. & Veltman, J. A. Disease gene identification strategies for exome sequencing. Eur. J. Hum. Genet. 20, 490–497 (2012).
Google Scholar
Olalde, I. et al. Genomic analysis of the blood attributed to Louis XVI (1754–1793), king of France. Sci. Rep. 4, 1–7 (2014).
Castellano, S. et al. Patterns of coding variation in the complete exomes of three Neandertals. Proc. Natl. Acad. Sci. USA. 111, 6666–6671 (2014).
Google Scholar
Iadarola, B. et al. Shedding light on dark genes: Enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length. Sci. Rep. 10, 1–11 (2020).
Google Scholar
Cipolla, C. Le opere di Ferreto de’ Ferreti vicentino, III, De Scaligerorum origine poema (Springer, 1920).
Mussato, A. De gestis Italicorum Post Henricum VII Cesarem (Libri I-VII) (Springer, 2019).
Cipolla, C. Le opere di Ferreto de’ Ferreti Vicentino: Historia Rerum in Italia Gestarum ab Anno MCCL ad Annum Usque MCCCXVIII. (1914).
Mussato, A. De Gestis Italicorum Post Henricum VII Cesarem, seu de Conflictu Domini Canis Grandis de Verona Apud Moenia Paduanae Civitatis. Liber XI. (1727).
Pagnin, B. Guillelmi de Cortusiis Chronica de novitatibus Padue et Lombardie. (1941).
Vaccari, R. Chronicon Veronense di Paride da Cerea e dei Suoi Continuatori (Il), II/1, La Continuazione Scaligera (1278–1375). (2014).
Varanini, G. M. La Morte di Cangrande della Scala. Strategie di Comunicazione Intorno al Cadavere, in Cangrande della Scala. La Morte e il Corredo di un Principe nel Medioevo Europeo. (2004).
Montalvo, A. L. E. et al. Mutation profile of the GAA gene in 40 Italian patients with late onset glycogen storage disease type II. Hum. Mutat. 27, 999–1006 (2006).
Google Scholar
Swallow, D. M. et al. An investigation of the properties and possible clinical significance of the lysosomal?-glucosidase GAA 2 allele. Ann. Hum. Genet. 53, 177–184 (1989).
Google Scholar
Conzelmann, E. & Sandhoff, K. Partial enzyme deficiencies: Residual activities and the development of neurological disorders. Dev. Neurosci. 6, 58–71 (1983).
Google Scholar
Musumeci, O. et al. LOPED study: Looking for an early diagnosis in a late-onset Pompe disease high-risk population. J. Neurol. Neurosurg. Psychiatry 87, 5–11 (2016).
Google Scholar
Mehler, M. & Dimauro, S. Residual acid maltase activity in late-onset acid maltase deficiency. Neurology 27, 178 (1977).
Google Scholar
Settembre, C., Fraldi, A., Medina, D. L. & Ballabio, A. Signals from the lysosome: A control centre for cellular clearance and energy metabolism. Nat. Rev. Mol. Cell Biol. 14, 283–296 (2013).
Google Scholar
Ballabio, A. & Bonifacino, J. S. Lysosomes as dynamic regulators of cell and organismal homeostasis. Nat. Rev. Mol. Cell Biol. 21, 101–118 (2020).
Google Scholar
Samadelli, M., Roselli, G., Fernicola, V. C., Moroder, L. & Zink, A. R. Theoretical aspects of physical-chemical parameters for the correct conservation of mummies on display in museums and preserved in storage rooms. J. Cult. Herit. 14, 480–484 (2013).
Google Scholar
Llamas, B. et al. From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. Sci. Technol. Archaeol. Res. 3, 1–14 (2017).
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, 5448 (2010).
Google Scholar
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil DNA glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370, 2013624 (2015).
Google Scholar
Peltzer, A. et al. EAGER: Efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
Google Scholar
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
Google Scholar
Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013).
Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: Estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 776 (2015).
Google Scholar
Modi, A., Vai, S. & Posth, C. More data on ancient human mitogenome variability in Italy: New mitochondrial genome sequences from three Upper Palaeolithic burials. Submitted.
Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).
Google Scholar
van Oven, M. PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Sci. Int. Genet. Suppl. Ser. 5, e392–e394 (2015).
Google Scholar
Weissensteiner, H. et al. HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).
Google Scholar
Schubert, M. et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. 9, 1056–1082 (2014).
Google Scholar
Auwera, G. A. et al. From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinforma. 43, 11.10.1-11.10.33 (2013).
Google Scholar
Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
Google Scholar
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of next generation sequencing data. BMC Bioinform. 15, 356 (2014).
Google Scholar
Stenson, P. D. et al. The human gene mutation database (HGMD®): optimizing its use in a clinical diagnostic or research setting. Hum. Genet. 139, 1197–1207 (2020).
Google Scholar

