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1. Experience of a 2-year spinal muscular atrophy NBS pilot study in Italy: Towards specific guidelines and standard operating procedures for the molecular diagnosis

Author

Abiusi, Emanuela, Vaisfeld, Alessandro, Fiori, Simona, Novelli, A., Spartano, Serena, Faggiano, M. V., Giovanniello, T., Angeloni, A., Vento, Giovanni, Santoloci, Roberta, Gigli, Francesca, D'Amico, A., Costa, S., Porzi, A., Panella, M., Ticci, C., Daniotti, M., Sacchini, M., Boschi, I., Dani, C., Agostiniani, R., Bertini, Enrico Silvio, Lanzone, Antonio, Lamarca, G., Genuardi, Maurizio, Pane, Marika, Donati, M. A., Mercuri, Eugenio Maria, Tiziano, Francesco Danilo, Abiusi E. (ORCID:0000-0001-9028-012X), Vaisfeld A., Fiori S., Spartano S., Vento G. (ORCID:0000-0002-8132-5127), Santoloci R., Gigli F., Bertini E., Lanzone A. (ORCID:0000-0003-4119-414X), Genuardi M. (ORCID:0000-0002-7410-8351), Pane M. (ORCID:0000-0002-4851-6124), Mercuri E. (ORCID:0000-0002-9851-5365), Tiziano F. D. (ORCID:0000-0002-5545-6158), Abiusi, Emanuela, Vaisfeld, Alessandro, Fiori, Simona, Novelli, A., Spartano, Serena, Faggiano, M. V., Giovanniello, T., Angeloni, A., Vento, Giovanni, Santoloci, Roberta, Gigli, Francesca, D'Amico, A., Costa, S., Porzi, A., Panella, M., Ticci, C., Daniotti, M., Sacchini, M., Boschi, I., Dani, C., Agostiniani, R., Bertini, Enrico Silvio, Lanzone, Antonio, Lamarca, G., Genuardi, Maurizio, Pane, Marika, Donati, M. A., Mercuri, Eugenio Maria, Tiziano, Francesco Danilo, Abiusi E. (ORCID:0000-0001-9028-012X), Vaisfeld A., Fiori S., Spartano S., Vento G. (ORCID:0000-0002-8132-5127), Santoloci R., Gigli F., Bertini E., Lanzone A. (ORCID:0000-0003-4119-414X), Genuardi M. (ORCID:0000-0002-7410-8351), Pane M. (ORCID:0000-0002-4851-6124), Mercuri E. (ORCID:0000-0002-9851-5365), and Tiziano F. D. (ORCID:0000-0002-5545-6158)

Abstract

Background Spinal muscular atrophy (SMA) is due to the homozygous absence of SMN1 in around 97% of patients, independent of the severity (classically ranked into types I-III). The high genetic homogeneity, coupled with the excellent results of presymptomatic treatments of patients with each of the three disease-modifying therapies available, makes SMA one of the golden candidates to genetic newborn screening (NBS) (SMA-NBS). The implementation of SMA in NBS national programmes occurring in some countries is an arising new issue that the scientific community has to address. We report here the results of the first Italian SMA-NBS project and provide some proposals for updating the current molecular diagnostic scenario. Methods The screening test was performed by an in-house-developed qPCR assay, amplifying SMN1 and SMN2. Molecular prognosis was assessed on fresh blood samples. Results We found 15 patients/90885 newborns (incidence 1:6059) having the following SMN2 genotypes: 1 (one patient), 2 (eight patients), 2+c.859G>C variant (one patient), 3 (three patients), 4 (one patient) or 6 copies (one patient). Six patients (40%) showed signs suggestive of SMA at birth. We also discuss some unusual cases we found. Conclusion The molecular diagnosis of SMA needs to adapt to the new era of the disease with specific guidelines and standard operating procedures. In detail, SMA diagnosis should be felt as a true medical urgency due to therapeutic implications; SMN2 copy assessment needs to be standardised; commercially available tests need to be improved for higher SMN2 copies determination; and the SMN2 splicing-modifier variants should be routinely tested in SMA-NBS.

Published
2023

3. List of Contributors

Author

Aas, M., primary, Abalo, R., additional, Abdel-Salam, O.M.E., additional, Abilio, V.C., additional, Adelli, G.R., additional, Ahmed, M.H., additional, Alhouayek, M., additional, Allen, J., additional, Allsop, D.J., additional, Almada, R.C., additional, Almeida, V., additional, Aloway, A., additional, Amanullah, S., additional, Ames, S.L., additional, Annaheim, B., additional, Appendino, G., additional, Aramaki, H., additional, Arias-Horcajadas, F., additional, Ariza, C., additional, Arnold, J.C., additional, Asmaro, D., additional, Auwärter, V., additional, Bachmann, S., additional, Baker, A., additional, Balter, R.E., additional, Baraldi, P.G., additional, Barber, P.A., additional, Barbería, E., additional, Bar-Sela, G., additional, Bastiani, L., additional, Basu, D., additional, Basurte, I., additional, Beck, O., additional, Behrendt, S., additional, Bergen-Cico, D., additional, Berrendero, F., additional, Bhagav, P., additional, Bhattacharyya, S., additional, Bioque, M., additional, Bolkent, S., additional, Boman, J.H., additional, Bondallaz, P., additional, Bonnet, U., additional, Borges, R.S., additional, Borowiak, K., additional, Boschi, I., additional, Brents, L.K., additional, Bridts, C.H., additional, Bruno, A., additional, Burrows, B.T., additional, Busatto, G.F., additional, Callaghan, R.C., additional, Campos, A.C., additional, Camsari, U.M., additional, Canfield, A., additional, Carra, E., additional, Carrillo-Salinas, F.-J., additional, Cascini, F., additional, Castelli, M.P., additional, Cawich, S.O., additional, Cawston, E.E., additional, Cedro, C., additional, Chagas, M.H.N., additional, Chen, C., additional, Chisari, C., additional, Chtioui, H., additional, Cico, R.D., additional, Ciechomska, I.A., additional, Coimbra, N.C., additional, Cole, J., additional, Cookey, J., additional, Copeland, J., additional, Coskun, Z.M., additional, Crano, W.D., additional, Crippa, J.A.S., additional, Crocker, C.E., additional, Cuesta, M.J., additional, Cunha, P.J., additional, Cutando, L., additional, da Silva, A.B.F., additional, da Silva, J.A., additional, da Silva, V.K., additional, Dan, D., additional, De Boni, R.B., additional, Rodríguez de Fonseca, F., additional, Gómez de Heras, R., additional, de Oliveira, A.C.P., additional, de Souza Crippa, A.C., additional, de Souza Crippa, J.A., additional, Degenhardt, F., additional, Degenhardt, L., additional, Deiana, S., additional, Deonarine, U., additional, Di Forti, M., additional, dos Anjos-Garcia, T., additional, Guimarães dos Santos, R., additional, Drozd, M., additional, Duran, F.L.S., additional, Earleywine, M., additional, Ebo, D.G., additional, Egashira, N., additional, Egnatios, J., additional, Ellert-Miklaszewska, A., additional, ElShebiney, S.A., additional, ElSohly, M.A., additional, Evren, C., additional, Fañanás, L., additional, Faber, M.M., additional, Farag, S., additional, Farré, A., additional, Farré, M., additional, Fatjó-Vilas, M., additional, Favrat, B., additional, Feingold, D., additional, Feliú, A., additional, Fernández, A.A., additional, Fernández-Artamendi, S., additional, Ferrari, A.J., additional, Ferraro, L., additional, Fichna, J., additional, Finlay, D.B., additional, Fiz, J., additional, Flores, Á., additional, Fogel, J.S., additional, Fornari, E., additional, Fortunato, L., additional, Fyfe, T., additional, Gaafar, A.E.D.M., additional, Gade, S., additional, Gaffal, E., additional, Galal, A.F., additional, Gandhi, R., additional, Gates, P., additional, Gatley, J.M., additional, Giroud, C., additional, Glass, M., additional, Goldberg, S.R., additional, González-Ortega, I., additional, González-Pinto, A., additional, Guaza, C., additional, Guillon, V., additional, Guimarães, F.S., additional, Gul, W., additional, Guven, F.M., additional, Hall, W.D., additional, Hallak, J.E.C., additional, Hamerle, M., additional, Haney, M., additional, Harding, H.E., additional, Hassan, S., additional, Haugland, K., additional, Healey, A., additional, Heck, C., additional, Helander, A., additional, Hernandez-Folgado, L., additional, Herzig, D.A., additional, Hesse, M., additional, Hill, M.G., additional, Hirst, R., additional, Hjorthøj, C.R., additional, Hoch, E., additional, Holder, M.D., additional, Holtkamp, M., additional, Hunter, M.R., additional, Ikeda, E., additional, Izumi, Y., additional, Janus, T., additional, Kaminska, B., additional, Kanaan, A.S., additional, Karinen, R., additional, Karl, T., additional, Katsu, T., additional, Kay-Lambkin, F., additional, Kayser, O., additional, Kells, M., additional, Kelly, B.C., additional, Kelly, T.H., additional, Kokona, A., additional, Kumar, A., additional, Kumar, P., additional, La Barbera, D., additional, Lagerberg, T.V., additional, Lahat, A., additional, Larsen, H.J., additional, Laun, A.S., additional, Lecomte, T., additional, Legleye, S., additional, Lev-Ran, S., additional, Lile, J.A., additional, Limberger, R.P., additional, Linares, I.M.P., additional, Lisdahl, K.M., additional, Little, M., additional, Liu, W., additional, Loflin, M.J., additional, Lorente-Omeñaca, R., additional, Lorenzetti, V., additional, Lu, D., additional, Mørland, J., additional, Müller-Vahl, K.R., additional, Machoy-Mokrzyńska, A., additional, Maeder, P., additional, Majumdar, S., additional, Maldonado, R., additional, Maple, K.E., additional, Marrón, T., additional, Martínez-Cengotitabengoa, M., additional, Martín-Fontelles, M. Isabel, additional, Martín-Santos, R., additional, Masuda, K., additional, McRae-Clark, A.L., additional, Mecha, M., additional, Medallo, J., additional, Melle, I., additional, Menahem, S., additional, Mendes-Gomes, J., additional, Mesías, B., additional, Miller, S., additional, Mizrahi, R., additional, Molinaro, S., additional, Moore, C., additional, Moraes, M.F., additional, Moreira, F.A., additional, Moreno-Izco, L., additional, Morris, H.A., additional, Muñoz, E., additional, Muccioli, G.G., additional, Muscatello, M.R.A., additional, Nada, S.A., additional, Naraynsingh, V., additional, Narimatsu, S., additional, Nogueira-Filho, G., additional, Nordentoft, M., additional, Oguz, G., additional, Øiestad, Å.M.L., additional, Øiestad, E.L., additional, Okazaki, H., additional, Olive, M.F., additional, Orio, L., additional, Ozaita, A., additional, Pérez, A., additional, Panagis, G., additional, Pandolfo, G., additional, Panlilio, L.V., additional, Paquin, K., additional, Parakh, P., additional, Parker, L.A., additional, Patel, V.B., additional, Pawson, M., additional, Peres, F.F., additional, Petras, H., additional, Pollastro, F., additional, Porcu, A., additional, Potente, R., additional, Potter, D.E., additional, Potvin, S., additional, Prats, C., additional, Preedy, V.R., additional, Rajendram, R., additional, Rathke, L., additional, Reed, K.L., additional, Repka, M.A., additional, Rigter, H., additional, Rock, E.M., additional, Rohrbacher, H., additional, Rosa, P.G.P., additional, Sánchez-Martínez, F., additional, Sánchez-Torres, A.M., additional, Sałaga, M., additional, Sabato, V., additional, Sanders, A.N., additional, Santos, L.C., additional, Scalese, M., additional, Schaufelberger, M.S., additional, Schröder, N., additional, Scimeca, G., additional, Secades-Villa, R., additional, Selvarajah, D., additional, Senormanci, O., additional, Shivakumar, K., additional, Shrier, L.A., additional, Siciliano, V., additional, Sideli, L., additional, Siegel, J.T., additional, Sleem, A.A., additional, Sobczyński, J., additional, Sodos, L., additional, Solowij, N., additional, Song, Z.-H., additional, Stacy, A.W., additional, Stehle, F., additional, Stogner, J.M., additional, Sussman, S., additional, Swift, W., additional, Szerman, N., additional, Tüting, T., additional, Aghazadeh Tabrizi, M., additional, Taglialatela-Scafati, O., additional, Takahashi, R.N., additional, Takeda, S., additional, Tarricone, I., additional, Tashkin, D.P., additional, Tellioğlu, T., additional, Tellioğlu, Z., additional, Tesfaye, S., additional, Thornton, L., additional, Thylstrup, B., additional, Tibbo, P.G., additional, Todd, G., additional, Torrens, M., additional, Tsai, J., additional, Tseng, H.-H., additional, Turner, A., additional, Tuv, S.S., additional, Ullah, F., additional, Van der Linden, T., additional, Van Gasse, A.L., additional, Vega, P., additional, Vera, G., additional, Verdichevski, M., additional, Vieira Sousa, T.R., additional, Vilela, L.R., additional, Vindenes, V., additional, Walsh, Z., additional, Watanabe, K., additional, Watterson, L.R., additional, White, J.M., additional, Wright, N.E., additional, Yücel, M., additional, Yamamoto, I., additional, Yamaori, S., additional, Zalesky, A., additional, Zalman, D., additional, Zhang, J., additional, Zhang, Y., additional, Zoccali, R., additional, Zorumski, C.F., additional, and Zuardi, A.W., additional

Published
2017
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5. Experience of a 2-year spinal muscular atrophy NBS pilot study in Italy: towards specific guidelines and standard operating procedures for the molecular diagnosis

Author

Abiusi, Emanuela, Vaisfeld, Alessandro, Fiori, Simona, Novelli, A, Spartano, Serena, Faggiano, Maria Vittoria, Giovanniello, T, Angeloni, A, Vento, Giovanni, Santoloci, Roberta, Gigli, Francesca, D'Amico, A, Costa, S, Porzi, A, Panella, M, Ticci, C, Daniotti, M, Sacchini, M, Boschi, I, Bertini, Enrico Silvio, Lanzone, Antonio, Lamarca, G, Genuardi, Maurizio, Pane, Marika, Donati, Ma, Mercuri, Eugenio Maria, Tiziano, Francesco Danilo, Abiusi E (ORCID:0000-0001-9028-012X), Vaisfeld A, Fiori S, Spartano S, Faggiano MV, Vento G (ORCID:0000-0002-8132-5127), Santoloci R, Gigli F, Bertini E, Lanzone A (ORCID:0000-0003-4119-414X), Genuardi M (ORCID:0000-0002-7410-8351), Pane M (ORCID:0000-0002-4851-6124), Mercuri E (ORCID:0000-0002-9851-5365), Tiziano FD (ORCID:0000-0002-5545-6158), Abiusi, Emanuela, Vaisfeld, Alessandro, Fiori, Simona, Novelli, A, Spartano, Serena, Faggiano, Maria Vittoria, Giovanniello, T, Angeloni, A, Vento, Giovanni, Santoloci, Roberta, Gigli, Francesca, D'Amico, A, Costa, S, Porzi, A, Panella, M, Ticci, C, Daniotti, M, Sacchini, M, Boschi, I, Bertini, Enrico Silvio, Lanzone, Antonio, Lamarca, G, Genuardi, Maurizio, Pane, Marika, Donati, Ma, Mercuri, Eugenio Maria, Tiziano, Francesco Danilo, Abiusi E (ORCID:0000-0001-9028-012X), Vaisfeld A, Fiori S, Spartano S, Faggiano MV, Vento G (ORCID:0000-0002-8132-5127), Santoloci R, Gigli F, Bertini E, Lanzone A (ORCID:0000-0003-4119-414X), Genuardi M (ORCID:0000-0002-7410-8351), Pane M (ORCID:0000-0002-4851-6124), Mercuri E (ORCID:0000-0002-9851-5365), and Tiziano FD (ORCID:0000-0002-5545-6158)

Abstract

Background: Spinal muscular atrophy (SMA) is due to the homozygous absence of SMN1 in around 97% of patients, independent of the severity (classically ranked into types I-III). The high genetic homogeneity, coupled with the excellent results of presymptomatic treatments of patients with each of the three disease-modifying therapies available, makes SMA one of the golden candidates to genetic newborn screening (NBS) (SMA-NBS). The implementation of SMA in NBS national programmes occurring in some countries is an arising new issue that the scientific community has to address. We report here the results of the first Italian SMA-NBS project and provide some proposals for updating the current molecular diagnostic scenario. Methods: The screening test was performed by an in-house-developed qPCR assay, amplifying SMN1 and SMN2. Molecular prognosis was assessed on fresh blood samples. Results: We found 15 patients/90885 newborns (incidence 1:6059) having the following SMN2 genotypes: 1 (one patient), 2 (eight patients), 2+c.859G>C variant (one patient), 3 (three patients), 4 (one patient) or 6 copies (one patient). Six patients (40%) showed signs suggestive of SMA at birth. We also discuss some unusual cases we found. Conclusion: The molecular diagnosis of SMA needs to adapt to the new era of the disease with specific guidelines and standard operating procedures. In detail, SMA diagnosis should be felt as a true medical urgency due to therapeutic implications; SMN2 copy assessment needs to be standardised; commercially available tests need to be improved for higher SMN2 copies determination; and the SMN2 splicing-modifier variants should be routinely tested in SMA-NBS. Keywords: Genetic Testing; Genetics, Population; Neonatal Screening; Neuromuscular Diseases.

Published
2022

6. Cellular and molecular immune responses of the sea bass ( Dicentrarchus labrax) experimentally infected with betanodavirus

Author

Scapigliati, G., Buonocore, F., Randelli, E., Casani, D., Meloni, S., Zarletti, G., Tiberi, M., Pietretti, D., Boschi, I., Manchado, M., Martin-Antonio, B., Jimenez-Cantizano, R., Bovo, G., Borghesan, F., Lorenzen, N., Einer-Jensen, K., Adams, S., Thompson, K., Alonso, C., Bejar, J., Cano, I., Borrego, J.J., and Alvarez, M.C.

Published
2010
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10. 2006 GEP-ISFG collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures

Author

Prieto, L., Alonso, A., Alves, C., Crespillo, M., Montesino, M., Picornell, A., Brehm, A., Ramírez, J.L., Whittle, M.R., Anjos, M.J., Boschi, I., Buj, J., Cerezo, M., Cardoso, S., Cicarelli, R., Comas, D., Corach, D., Doutremepuich, C., Espinheira, R.M., Fernández-Fernández, I., Filippini, S., Garcia-Hirschfeld, Julia, González, A., Heinrichs, B., Hernández, A., Leite, F.P.N., Lizarazo, R.P., López-Parra, A.M., López-Soto, M., Lorente, J.A., Mechoso, B., Navarro, I., Pagano, S., Pestano, J.J., Puente, J., Raimondi, E., Rodríguez-Quesada, A., Terra-Pinheiro, M.F., Vidal-Rioja, L., Vullo, C., and Salas, A.

Published
2008
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11. A multi-perspective view of genetic variation in Cameroon

Author

Coia, V., Brisighelli, F., Donati, F., Pascali, V., Boschi, I., Luiselli, D., Battaggia, C., Batini, C., Taglioli, L., Cruciani, F., Paoli, G., Capelli, C., Spedini, G., and Destro-Bisol, G.

Subjects
Biological diversity -- Analysis, Biological diversity -- Genetic aspects, Mitochondrial DNA -- Analysis, Mitochondrial DNA -- Genetic aspects, Genetic research -- Analysis, Genetic research -- Genetic aspects, Anthropology/archeology/folklore
Abstract

In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration Nv rario that was more than double in the northern part of the country. The combined effect of the propensity to interpopulational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon. KEY WORDS microsatellites; autosomes; Y-chromosome; mtDNA; language; geography DOI 10.1002/ajpa.21088

Published
2009

16. Highly predictive genetic markers distinguish drug-type from fiber-type cannabis sativa L

Author

Cascini, F., Farcomeni, A., Migliorini, D., Baldassarri, L., Boschi, I., Martello, S., Amaducci, S., Lucini, L., Bernardi, J., Cascini F. (ORCID:0000-0001-6499-0734), Baldassarri L., Martello S., Amaducci S. (ORCID:0000-0002-6184-9257), Lucini L. (ORCID:0000-0002-5133-9464), Bernardi J., Cascini, F., Farcomeni, A., Migliorini, D., Baldassarri, L., Boschi, I., Martello, S., Amaducci, S., Lucini, L., Bernardi, J., Cascini F. (ORCID:0000-0001-6499-0734), Baldassarri L., Martello S., Amaducci S. (ORCID:0000-0002-6184-9257), Lucini L. (ORCID:0000-0002-5133-9464), and Bernardi J.

Abstract

Genetic markers can be used in seeds and in plants to distinguish drug-type from fiber-type Cannabis Sativa L. varieties even at early stages, including pre-germination when cannabinoids are not accumulated yet. With this aim, this paper reports sequencing results for tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes from 21 C. sativa L. varieties. Taking into account that THCAS-and CBDAS-derived enzymes compete for the same substrate, the novelty of this work relies in the identification of markers based on both THCAS and CBDAS rather than THCAS alone. Notably, in our panel, we achieved an adequate degree of discrimination (AUC 100%) between drug-type and fiber-type cannabis samples. Our sequencing approach allowed identifying multiple genetic markers (single-nucleotide polymorphisms—SNPs—and a deletion/insertion) that effectively discriminate between the two subgroups of cannabis, namely fiber type vs. drug type. We identified four functional SNPs that are likely to induce decreased THCAS activity in the fiber-type cannabis plants. We also report the finding on a deletion in the CBDAS gene sequence that produces a truncated protein, possibly resulting in loss of function of the enzyme in the drug-type varieties. Chemical analyses for the actual concentration of cannabinoids confirmed the identification of drug-type rather than fiber-type genotypes. Genetic markers permit an early identification process for forensic applications while simplifying the procedures related to detection of therapeutic or industrial hemp.

Published
2019

17. Highly predictive genetic markers distinguish drug-type from fiber-type cannabis sativa L

Author

Cascini, Fidelia, Farcomeni, A., Migliorini, D., Baldassarri, Laura, Boschi, I., Martello, Simona, Amaducci, Stefano, Lucini, Luigi, Bernardi, Jamila, Cascini F. (ORCID:0000-0001-6499-0734), Baldassarri L., Martello S., Amaducci S. (ORCID:0000-0002-6184-9257), Lucini L. (ORCID:0000-0002-5133-9464), Bernardi J., Cascini, Fidelia, Farcomeni, A., Migliorini, D., Baldassarri, Laura, Boschi, I., Martello, Simona, Amaducci, Stefano, Lucini, Luigi, Bernardi, Jamila, Cascini F. (ORCID:0000-0001-6499-0734), Baldassarri L., Martello S., Amaducci S. (ORCID:0000-0002-6184-9257), Lucini L. (ORCID:0000-0002-5133-9464), and Bernardi J.

Abstract

Genetic markers can be used in seeds and in plants to distinguish drug-type from fiber-type Cannabis Sativa L. varieties even at early stages, including pre-germination when cannabinoids are not accumulated yet. With this aim, this paper reports sequencing results for tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes from 21 C. sativa L. varieties. Taking into account that THCAS- and CBDAS-derived enzymes compete for the same substrate, the novelty of this work relies in the identification of markers based on bothTHCASandCBDASrather than THCAS alone. Notably, in our panel, we achieved an adequate degree of discrimination (AUC 100%) between drug-type and fiber-type cannabis samples. Our sequencing approach allowed identifying multiple genetic markers (single-nucleotide polymorphisms—SNPs—and a deletion/insertion) that effectively discriminate between the two subgroups of cannabis, namely fiber type vs. drug type. We identified four functional SNPs that are likely to induce decreased THCAS activity in the fiber-type cannabis plants. We also report the finding on a deletion in the CBDAS gene sequence that produces a truncated protein, possibly resulting in loss of function of the enzyme in the drug-type varieties. Chemical analyses for the actual concentration of cannabinoids confirmed the identification of drug-type rather than fiber-type genotypes. Genetic markers permit an early identification process for forensic applications while simplifying the procedures related to detection of therapeutic or industrial hemp.

Published
2019

21. Linguistic, geographic and genetic isolation: a collaborative study of Italian populations

Author

Capocasa, M, Anagnostou, P, Bachis, V, Battaggia, C, Bertoncini, S, Biondi, G, Boattini, A, Boschi, I, Brisighelli, F, Calò, C, Carta, M, Coia, V, Corrias, L, Crivellaro, F, De Fanti, S, Dominici, V, Ferri, G, Francalacci, P, Franceschi, Z, Luiselli, D, Morelli, L, Paoli, G, Rickards, O, Robledo, R, Sanna, D, Sanna, E, Sarno, S, Sineo, L, Taglioli, L, Tagarelli, G, Tofanelli, S, Vona, G, Pettener, D, Destro Bisol, G, Capocasa M, Anagnostou P, Bachis V, Battaggia C, Bertoncini S, Biondi G, Boattini A, Boschi I, Brisighelli F, Calò CM, Carta M, Coia V, Corrias L, Crivellaro F, De Fanti S, Dominici V, Ferri GM, Francalacci P, Franceschi ZA, Luiselli D, Morelli L, Paoli G, Rickards O, Robledo R, Sanna D, Sanna E, Sarno S, Sineo L, Taglioli L, Tagarelli G, Tofanelli S, Vona G, Pettener D, Destro-Bisol G, Capocasa,M, Anagnostou, P, Bachis, V, Battaggia, C, Bertoncini,S, Biondi, G, Boattini, A, Boschi, I, Brisighelli, F, Calò, CM, Carta, M, Coia, V, Corrias, L, Crivellaro, F, De Fanti,S, Dominici, V, Ferri Paolo G, Francalacci, P, Franceschi, ZA, Luiselli, D, Morelli, L, Paoli, G, Rickards, O, Robledo, R, Sanna, D, Sanna,E, Sarno, S, Sineo, L, Taglioli, L, Tagarelli, G, Tofanelli, S, Vona, G, and Destro Bisol, G

Subjects
Gene Flow, Chromosomes, Human, Y, Reproductive Isolation, Minority languages, Linguistic diversity, Settore BIO/08 - ANTROPOLOGIA, Genetic structure, Linguistic diversity, Minority languages, Linguistic islands, Linguistics, Settore BIO/08, Linguistic, Isolates, Minority language, DNA, Mitochondrial, White People, Genetics, Population, Italy, Anthropology, Ethnicity, Linguistic islands, Humans, Genetic structure, Linguistic diversity, Minority languages,Linguistic islands, Genetic structure, linguistic islands, minority languages, linguistic diversity, genetic structure
Abstract

Summary - The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity of Italian populations in the European context. The human genetic diversity of our country was found to be greater than observed throughout the continent at short (0-200 km) and intermediate (700-800km) distances, and accounted for most of the highest values of genetic distances observed at all geographic ranges. Interestingly, an important contribution to this pattern comes from the “linguistic islands” (e.g. German speaking groups of Sappada and Luserna from the Eastern Italian Alps), further proof of the importance of considering social and cultural factors when studying human genetic variation.

Published
2014

23. Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors

Author

DESTRO-BISOL, Giovanni, Donati, Francesco, Coia, Valentina, Boschi, I., Verginelli, F., Caglia', Alessandra, Caglia, A., Tofanelli, S., Spedini, Gabriella, and Capelli, C.

Subjects
Male, Mitochondrial DNA, mtdna, Population, Biology, hunter-gatherers, Social Environment, Y chromosome, DNA, Mitochondrial, Haplogroup, Gene flow, Evolution, Molecular, Genetic drift, Genetic variation, Ethnicity, Genetics, Humans, education, Molecular Biology, Africa South of the Sahara, Ecology, Evolution, Behavior and Systematics, education.field_of_study, y chromosome, food producers, sub-saharan africa, sociocultural factors, Chromosomes, Human, Y, Cultural Characteristics, Models, Genetic, Genetic Variation, Genetics, Population, Haplotypes, Genetic structure, Female, Microsatellite Repeats
Abstract

In this paper, we present a study of genetic variation in sub-Saharan Africa, which is based on published and unpublished data on fast-evolving (hypervariable region 1 of mitochondrial DNA and six microsatellites of Y chromosome) and slow-evolving (haplogroup frequencies) polymorphisms of mtDNA and Y chromosome. Our study reveals a striking difference in the genetic structure of food-producer (Bantu and Sudanic speakers) and hunter-gatherer populations (Pygmies, Kung, and Hadza). In fact, the ratio of mtDNA to Y-chromosome Nupsilon is substantially higher in food producers than in hunter-gatherers as determined by fast-evolving polymorphisms (1.76 versus 0.11). This finding indicates that the two population groups differ substantially in female and male migration rate and/or effective size. The difference also persists when linguistically homogeneous populations are used and outlier populations are eliminated (1.78 vs 0.19) or when the jacknife procedure is applied to a paired population data set (1.32 to 7.84 versus 0.14 to 0.66). The higher ratio of mtDNA to Y-chromosome Nnu in food producers than in hunter-gatherers is further confirmed by the use of slow-evolving polymorphisms (1.59 to 7.91 versus 0.12 to 0.35). To explain these results, we propose a model that integrates demographic and genetic aspects and incorporates ethnographic knowledge. In such a model, the asymmetric gene flow, polyginy, and patrilocality play an important role in differentiating the genetic structure of sub-Saharan populations. The existence of an asymmetric gene flow is supported by the phylogeographic features of mtDNA and Y-chromosome haplogroups found in the two population groups. The role of polyginy and patrilocality is sustained by the evidence of a differential pressure of genetic drift and gene flow on maternal and paternal lineages of food producers and hunter-gatherers that is revealed through the analysis of mitochondrial and Y-chromosomal intrapopulational variation.

Published
2016
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24. A repository of 13 PCR-loci Italian gene frequencies in the world wide web.

Author

Maviglia, R., Dobosz, M., Boschi, I., Caglia, Alessandra, Hall, D., Capelli, Cristian, d'Aloja, E., Pescarmona, M., Moscetti, A., Pascali, V.L., and Destro-Bisol, G.

Subjects
Italians -- Physiological aspects, Gene frequency -- Analysis, Human population genetics -- Methods, Forensic genetics -- Methods, Polymerase chain reaction -- Methods
Published
2001

25. Human biodiversity in Italy: micro-evolutionary patterns. A national collaborative project (PRIN 2009-2011)

Author

Capocasa M, Bachis V, Battaggia C, Boschi I, Brisighelli F, Calò CM, Coia C, Corrias L, Crivellaro F, Destro Bisol G, Ferri G, Francalacci P, Morelli L, Robledo R, Sanna D, Sanna E, Tofanelli S, Vona G, ANAGNOSTOU, PAOLO, BERTONCINI, STEFANIA, BOATTINI, ALESSIO, CARTA, MARILISA, FRANCESCHI, ZELDA ALICE, LUISELLI, DONATA, SARNO, STEFANIA, PETTENER, DAVIDE, Capocasa M, Anagnostou P, Bachis V, Battaggia C, Bertoncini S, Boattini A, Boschi I, Brisighelli F, Calò CM, Carta M, Coia C, Corrias L, Crivellaro F, Destro Bisol G, Ferri G, Francalacci P, Franceschi ZA, Luiselli D, Morelli L, Robledo R, Sanna D, Sanna E, Sarno S, Tofanelli S, Vona G, and Pettener D

Abstract

Due to their low genetic complexity and relative environmental and socio-cultural uniformity, geographical and/or cultural isolates provide an unique opportunity to reconstruct processes shaping human biodiversity. Groups with remarkable historic and linguistic peculiarities, often living in a mountainous setting, are widely dispersed in the Italian territory from the Alps to the main islands. Following and developing previous work by the same research network, the project initiative “Human biodiversity in Italy: micro-evolutionary patterns” is aimed at achieving an extensive genetic characterization of these populations and studying the relations between patterns of genetic diversity and cultural, historical and demographic factors. To this purpose, research units from the Universities of Bologna, Cagliari, Pisa and Roma Sapienza are collaborating in a multidisciplinary framework. The innovative aspects of this project are represented by: i) an accurate sampling strategy based on the history and the demographic structure of the populations; ii) a complete genotyping of uniparental and autosomal markers; iii) a participative involvement of the interested communities.

Published
2012

26. mtDNA hypervariable region-1 variation in Central Africa

Author

COIA, V., DESTRO-BISOL, G., SPEDINI, G., BELLEDI, M., BOSCHI, I., CAGLIA, A., VERGINELLI, F., and CALAFELL, F.

Subjects
Central Africa -- Research, Genetic research -- Analysis, Pygmies -- Genetic aspects, Biological diversity -- Genetic aspects, Bantu-speaking peoples -- Genetic aspects, Anthropology/archeology/folklore
Abstract

As a part of along term project on molecular variation in Central Africa (www.scienzemfn.uniroma1.it/labantro), we have sequenced the hypervariable region-1 of mitochondrial DNA in a Pygmy population from the Central African Republic (C.A.R), the Mbenzele Pygmies, and two Bantu-speaking 51 populations, the Bamileke and Ewondo from Cameroon. Concerning intrapopulational diversity, two results are worth noting. Firstly, the Mbenzele Pygmies have one of lowest within-population variability reported to date. In fact, smaller values of gene diversity have been reported only for the Hadza, Herero and the !Kung. A possible explanation is in the fact that mtDNA gene flow between Pygmies and neighbouring populations occurs mostly by marriages between a Pygmy female and a Bantu male, an event favored by the low bride price that the husband must pay. Thus, while the relatively small size of Pygmy make them prone to the loss of genetic variability, this is not counterbalanced by gene flow from external populations. Secondly, the examined groups differ substantially in their subsistence economy, since Pygmies are hunter-gatherers, while the two groups from Cameroon are descendants from farmers and pastoralists. As a matter of fact, this difference is reflected by their patterns of nucleotide pairwise differences. The most striking results provided by the analysis of interpopulational diversity is in the marked genetic differentiation between the Ewondo and Bamileke. This finding is in contrast to a previous microsatellite study. Pygmy-to-Bantu gene flow seems to play a role in this finding. In fact, there are three mtDNA lineages shared between Ewondo and Mbenzele. All these sequences are much more frequent in the Pygmy than 10) in the Bantu population and considering other Africans they are found only in the Biaka Pygmies from C.A.R. On the other hand, the Ewondo live in south Cameroon near the Cameroon Pygmies (who are closely related to the C.A.R. Pygmies) and they traditionally have no taboos against mixed marriages. By contrast, Bamileke and Mbenzele Pygmies shared no mtDNA sequence. This is to be expected since ethnic endogamy is rigid in the Bamileke and prevents mixed marriages with other Pygmy and Bantu groups.

Published
2001

29. The Arabs in Europe: Estimating medieval North Africa male legacy into Southern Europe

Author

CAPELLI C, ONOFRI V, BRISIGHELLI F, BOSCHI I, SCARNICCI F, MASULLO M, TOFANELLI S, TAGLIABRACCI A, GUSMAO L, AMORIM A, GATTO F, BRION MARTINEZ M, BLANCO VEREA A, PASCALI V., FERRI, Giuseppe, ROMANO, Valentino, CALI', Filippo, CAPELLI C, ONOFRI V, BRISIGHELLI F, BOSCHI I, SCARNICCI F, MASULLO M, FERRI G, TOFANELLI S, TAGLIABRACCI A, GUSMAO L, AMORIM A, GATTO F, BRION MARTINEZ M, BLANCO VEREA A, ROMANO V, CALI F, and PASCALI V

Published
2008

30. The 2011 GeFI collaborative exercise. Concordance study, proficiency testing and Italian population data on the new ENFSI/EDNAP loci D1S1656, D2S441, D10S1248, D12S391, D22S1045

Author

Previderè, C., Grignani, P., Alessandrini, F., Alù, M., Biondo, R., Boschi, I., Caenazzo, L., Carboni, I., Carnevali, E., De Stefano, F., Domenici, R., Fabbri, M., Giardina, E., Inturri, S., Pelotti, S., Piccinini, A., Piglionica, M., Resta, N., Turrina, S., Verzeletti, A., and Presciuttini, S.

Published
2013
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35. Patterns of Y-STR variation in Italy

Author

Brisighelli, Francesca, Blanco Verea, A, Boschi, I, Garagnani, P, Pascali, Vincenzo Lorenzo, Carracedo, A, Capelli, Cristian, Salas, A., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224), Brisighelli, Francesca, Blanco Verea, A, Boschi, I, Garagnani, P, Pascali, Vincenzo Lorenzo, Carracedo, A, Capelli, Cristian, Salas, A., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), and Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224)

Abstract

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR Yfiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 292 samples from seven Italian regions. Population comparisons with other European samples were undertaken; for this purpose, two databases were collated from the literature: (a) 19 population samples including >2900 Yfiler profiles, and (b) 67 population samples including >15,000 minimum haplotype profiles. A total of 276 different Yfiler haplotypes were observed in Italy, and only one of them was shared among our seven population samples. The overall haplotype diversity (0.9996) was comparable to other European samples. AMOVA indicates that among population variance depends on the amount of Y-STRs used, being higher when using minimal haplotypes. This is probably due to the fact that Yfiler profiles are represented by singleton haplotypes in all the population samples raising the diversity values to the maximum theoretical value. AMOVA results seems to depend even more strongly on the amount of population samples used, the among population variance in Italy ranging from 2.82% to 11.03% (using 15 and 32 Italian populations samples, respectively). Variance is not as strongly stratified geographically within Italy, although it is notorious that latitude is more important than longitude in the distribution of variance. The results also indicated that Italy is less stratified than other European samples. The present study contributes to enrich the Y-chromosome databases regarding high-resolution Y-chromosome data sets and demonstrates that extended Y-STR profiles substantially increases the discriminatory capacity in individual identification for forensic purposes.

Published
2012

45. mtDNA analysis does not detect Asian lineages in Cameroon

Author

Coia, V., Destro-Bisol, G., Boschi, I., Verginelli, F., Spedini, G., Cruciani, F., Comas, D., and Calafell, F.

Subjects
Human evolution -- Genetic aspects, Mitochondrial DNA -- Identification and classification, Anthropology/archeology/folklore
Abstract

In a recent high-resolution study of Y-chromosome variation it has been observed that the haplotype 117 (belonging to the haplogroup IX) occurs at a frequency ranging from 0% to 95% in northern Cameroon. This finding is of particular interest since the 117 haplotype seems to have been involved in a back migration from Asia to Africa. As a logical development of this study, we have analyzed mitochondrial variation in the same populations analyzed for Y chromosomes (Bakaka, Bamileke, Daba, Ewondo, Fali, Fulbe, Ouldeme and Tali) and in four additional populations (Bassa, Mandara, Tupuri and Podokwo). We analyzed the hypervariable region-1 by a standard sequencing method and 4 nucleotide positions of the mtDNA coding region (10400, 12308 and 12705, 10873) using the Snapshot method in a total of 439 individuals. We observed five different haplogroups, three of which ate sub-Saharan (L1, L2, L3), one northern African (U6) and one European (U5). The presence of the northern African haplogroup (among Podokwo and Uldeme) could be due to recent gene flow from north-eastern Africa. The U5 haplogroup was found only in one Fulbe individual. The lack of Asian haplogroups in Cameroon suggests that the migratory flow which spread the 117 haplotype was conducted predominantly by males and that the female contribution, ir present, was not as large to escape extinction by genetic drift.

Published
2003

48. Variation of the hypervariable region-1 of mitochondrial DNA in central-eastern Italy

Author

Verginelli, F., Donati, F., Coia, Valentina, Boschi, I., Palmirotta, R., Battista, P., Mariani Costantini, R., Costantini, R. M., and DESTRO-BISOL, Giovanni

Subjects
abruzzo, hypervariable region-1, mitochondrial dna, forensic science, Mitochondrial DNA, Genetic Variation, Sequence Analysis, DNA, Biology, DNA Fingerprinting, DNA, Mitochondrial, Pathology and Forensic Medicine, Hypervariable region, Variation (linguistics), Genetics, Population, Haplotypes, Italy, Evolutionary biology, Genetics, Humans

49. Archeologia della morte o archeologia dei morti?

Author

G. Lepore, F. Boschi, I. Venanzoni, and G. Lepore

Subjects
Archeologia della morte, necropoli, rituali funerari
Abstract

Il contributo fa il punto sullo stato delle conoscenze attuali nell'ambito della cd "Archeologia della morte"

Published
2021

50. Verso la mostra. Il progetto ArcheoNevola tra ricerca, archeologia preventiva e formazione

Author

Federica Boschi, F. Boschi, I. Venanzoni, and Federica Boschi

Subjects
Formazione, Mostra archeologica, ArcheoNevola, Archeologia Preventiva, Principe di Corinaldo
Abstract

Introduzione alla mostra e al relativo catalogo "Il tesoro ritrovato. La Tomba del Principe di Corinaldo", inaugurata presso la Pinacoteca comunale C. Ridolfi di Corinaldo e visitabile dal 25 luglio 2021 al 30 gennaio 2022.

Published
2021

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