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Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291–1329 CE) indicates the first known case of late-onset Pompe disease

  • 1.

    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).

    CAS 
    Article 

    Google Scholar 

  • 2.

    Atoche, P. & Aufderheide, A. C. Mummies and Science World Mummies Research VI World Congress (Springer, 2008).

    Google Scholar 

  • 3.

    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).

    CAS 
    Article 

    Google Scholar 

  • 4.

    Napione, E. Il Corpo Del Principe: Ricerche su Cangrande della Scala (Springer, 2006).

    Google Scholar 

  • 5.

    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).

    CAS 
    Article 

    Google Scholar 

  • 6.

    Schulz, J. La morte di Cangrande I della Scala: Un caso da riaprire (Springer, 2015).

    Google Scholar 

  • 7.

    Parker, C. et al. A systematic investigation of human DNA preservation in medieval skeletons. Sci. Rep. 10, 18225 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 9.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 10.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 11.

    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).

    Article 

    Google Scholar 

  • 12.

    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).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 14.

    Gaudin, M. & Desnues, C. Hybrid capture-based next generation sequencing and its application to human infectious diseases. Front. Microbiol. 9, 27 (2018).

    Article 

    Google Scholar 

  • 15.

    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).

    Article 
    CAS 

    Google Scholar 

  • 16.

    Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 19.

    Mafessoni, F. et al. A high-coverage neandertal genome from chagyrskaya cave. Proc. Natl. Acad. Sci. USA. 117, 15132–15136 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Gravel, S. et al. Reconstructing native American migrations from whole-genome and whole-exome data. PLoS Genet. 9, 1004023 (2013).

    Article 
    CAS 

    Google Scholar 

  • 21.

    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).

    Article 
    CAS 

    Google Scholar 

  • 22.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 23.

    Olalde, I. et al. Genomic analysis of the blood attributed to Louis XVI (1754–1793), king of France. Sci. Rep. 4, 1–7 (2014).

    Google Scholar 

  • 24.

    Castellano, S. et al. Patterns of coding variation in the complete exomes of three Neandertals. Proc. Natl. Acad. Sci. USA. 111, 6666–6671 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 25.

    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).

    Article 
    CAS 

    Google Scholar 

  • 26.

    Cipolla, C. Le opere di Ferreto de’ Ferreti vicentino, III, De Scaligerorum origine poema (Springer, 1920).

    Google Scholar 

  • 27.

    Mussato, A. De gestis Italicorum Post Henricum VII Cesarem (Libri I-VII) (Springer, 2019).

    Google Scholar 

  • 28.

    Cipolla, C. Le opere di Ferreto de’ Ferreti Vicentino: Historia Rerum in Italia Gestarum ab Anno MCCL ad Annum Usque MCCCXVIII. (1914).

  • 29.

    Mussato, A. De Gestis Italicorum Post Henricum VII Cesarem, seu de Conflictu Domini Canis Grandis de Verona Apud Moenia Paduanae Civitatis. Liber XI. (1727).

  • 30.

    Pagnin, B. Guillelmi de Cortusiis Chronica de novitatibus Padue et Lombardie. (1941).

  • 31.

    Vaccari, R. Chronicon Veronense di Paride da Cerea e dei Suoi Continuatori (Il), II/1, La Continuazione Scaligera (1278–1375). (2014).

  • 32.

    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).

  • 33.

    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).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 34.

    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).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 35.

    Conzelmann, E. & Sandhoff, K. Partial enzyme deficiencies: Residual activities and the development of neurological disorders. Dev. Neurosci. 6, 58–71 (1983).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 36.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 37.

    Mehler, M. & Dimauro, S. Residual acid maltase activity in late-onset acid maltase deficiency. Neurology 27, 178 (1977).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 38.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Ballabio, A. & Bonifacino, J. S. Lysosomes as dynamic regulators of cell and organismal homeostasis. Nat. Rev. Mol. Cell Biol. 21, 101–118 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 40.

    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).

    Article 

    Google Scholar 

  • 41.

    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).

    Google Scholar 

  • 42.

    Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, 5448 (2010).

    Article 

    Google Scholar 

  • 43.

    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).

    Article 
    CAS 

    Google Scholar 

  • 44.

    Peltzer, A. et al. EAGER: Efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 45.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 46.

    Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    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).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 48.

    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).

    CAS 
    Article 

    Google Scholar 

  • 49.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 50.

    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).

    Article 

    Google Scholar 

  • 51.

    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.

  • 52.

    Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 53.

    van Oven, M. PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Sci. Int. Genet. Suppl. Ser. 5, e392–e394 (2015).

    Article 

    Google Scholar 

  • 54.

    Weissensteiner, H. et al. HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 55.

    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).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 56.

    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).

    Article 

    Google Scholar 

  • 57.

    Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 58.

    Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of next generation sequencing data. BMC Bioinform. 15, 356 (2014).

    Article 

    Google Scholar 

  • 59.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

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