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52. SMA - TREATMENT

Author

Mercuri, E., primary, Finkel, R., additional, Day, J., additional, Pascual, S. Pascual, additional, Ryan, M., additional, De Vivo, D., additional, Montes, J., additional, Gurgel-Giannetti, J., additional, Gambino, G., additional, Nuzzo, R., additional, Makepeace, C., additional, Garafalo, S., additional, and Berger, Z., additional

Published
2021
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57. Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine

Author

Dal Santo S., De Paoli E., Pagliarani C., Amato A., Celii M., Boccacci P., Zenoni S., Gambino G., and Perrone I

Subjects
embryogenic competence, food and beverages, transposon silencing, Vitis vinifera (grapevine), somatic embryogenesis, transcriptome
Abstract

Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species the SE competence is strongly genotype dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to non-embryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.

Published
2021

59. Modulating Long Term Memory at Late-Encoding Phase: An rTMS Study

Author

Giglia, G, Gambino, G, Cuffaro, L, Aleo, F, Sardo, P, Ferraro, G, Blandino, V, Brighina, F, Gangitano, M, Piccoli, T, Giglia Giuseppe, Gambino Giuditta, Cuffaro Luca, Aleo Fabio, Sardo Pierangelo, Ferraro Giuseppe, Blandino Valeria, Brighina Filippo, Gangitano Massimo, Piccoli T, Giglia, G, Gambino, G, Cuffaro, L, Aleo, F, Sardo, P, Ferraro, G, Blandino, V, Brighina, F, Gangitano, M, Piccoli, T, Giglia Giuseppe, Gambino Giuditta, Cuffaro Luca, Aleo Fabio, Sardo Pierangelo, Ferraro Giuseppe, Blandino Valeria, Brighina Filippo, Gangitano Massimo, and Piccoli T

Abstract

Despite a huge effort of the scientific community, the functioning of Long-Term Memory (LTM) processes is still debated and far from being elucidated. Functional and neurophysiological data point to an involvement of Dorsolateral Prefrontal Cortex (DLPFC) in both encoding and retrieval phases. However, the recently proposed Explicit/Implicit Memory Encoding and Retrieval (EIMER) model proposes that LTM at the encoding phase consists of anatomically and chronologically different sub-phases. On this basis, we aimed to investigate the role of right DLPFC during a late-encoding phase by means of low-frequency rTMS. Thirty right-handed healthy subjects were divided into three experimental groups. Inhibitory rTMS was applied over right-DLPFC immediately after the encoding phase (Late-Encoding Group) or before recognition phase (Pre-Recognition Group), 24 h after, of an LTM task. Both groups also received sham stimulation during the non-target phase, while the third group (Sham Group) received only sham stimulation in both phases. The Late-Encoding Group collected a lower number of correct responses compared with Sham Group (p = 0.00), while Pre-Retrieval Group increased accuracy as compared to the Sham Group (p = 0.0). rTMS-inhibition of the right DLPFC seems able to interfere with LTM memory performances when delivered at a late stage of the encoding phase, with opposite effects at the pre-retrieval phase.

Published
2021

60. ASO Author Reflections: How Long will We Perform Lymphadenectomy in Endometrial Cancer Patients?

Author

Capozzi, V. A., Sozzi, G., Rosati, A., Restaino, S., Gambino, G., Cianciolo, A., Ceccaroni, Marcello, Uccella, S., Franchi, M., Chiantera, V., Scambia, Giovanni, Fanfani, Francesco, Berretta, R., Ceccaroni M., Scambia G. (ORCID:0000-0003-2758-1063), Fanfani F. (ORCID:0000-0003-1991-7284), Capozzi, V. A., Sozzi, G., Rosati, A., Restaino, S., Gambino, G., Cianciolo, A., Ceccaroni, Marcello, Uccella, S., Franchi, M., Chiantera, V., Scambia, Giovanni, Fanfani, Francesco, Berretta, R., Ceccaroni M., Scambia G. (ORCID:0000-0003-2758-1063), and Fanfani F. (ORCID:0000-0003-1991-7284)

Published
2021

61. Predictive Score of Nodal Involvement in Endometrial Cancer Patients: A Large Multicentre Series

Author

Capozzi, V. A., Sozzi, G., Rosati, A., Restaino, S., Gambino, G., Cianciolo, A., Ceccaroni, M., Uccella, S., Franchi, M., Chiantera, V., Scambia, Giovanni, Fanfani, Francesco, Berretta, R., Scambia G. (ORCID:0000-0003-2758-1063), Fanfani F. (ORCID:0000-0003-1991-7284), Capozzi, V. A., Sozzi, G., Rosati, A., Restaino, S., Gambino, G., Cianciolo, A., Ceccaroni, M., Uccella, S., Franchi, M., Chiantera, V., Scambia, Giovanni, Fanfani, Francesco, Berretta, R., Scambia G. (ORCID:0000-0003-2758-1063), and Fanfani F. (ORCID:0000-0003-1991-7284)

Abstract

Background: Sentinel lymph node (SLN) biopsy is considered the standard of care in early-stage endometrial cancer (EC). For SLN failure, a side-specific lymphadenectomy is recommended. Nevertheless, most hemipelvises show no nodal involvement. The authors previously published a predictive score of lymphovascular involvement in EC. In case of a negative score (value 3–4), the risk of nodal metastases was extremely low. This multicenter study aimed to analyze a predictive score of nodal involvement in EC patients. Methods: The study enrolled patients with EC who had received comprehensive surgical staging with nodal assessment. A preoperative predictive score of nodal involvement was calculated for all the patients before surgery. The score included myometrial infiltration, tumor grading (G), tumor diameter, and Ca125 assessment. The STARD (standards for Reporting Diagnostic accuracy studies) guidelines were followed for score accuracy. Results: The study analyzed 1038 patients and detected 155 (14.9%) nodal metastases. The score was negative (3 or 4) for 475 patients and positive (5–7) for 563 of these patients. The score had a sensitivity of 83.2%, a specificity of 50.8%, a negative predictive value of 94.5%, and a diagnostic value of 55.7%. The area under the curve was 0.75. The logistic regression showed a significant correlation between a negative score and absence of nodal metastasis (odds ration [OR], 5.133, 95% confidence interval [CI], 3.30–7.98; p < 0.001). Conclusion: The proposed predictive score is a useful test to identify patients at low risk of nodal involvement. In case of SLN failure, the application of the current score in the SLN algorithm could allow avoidance of unnecessary lymphadenectomies.

Published
2021

63. Correction to :β adrenergic receptor kinase C-terminal peptide gene-therapy improves ß2-adrenergic receptor-dependent neoangiogenesis after hindlimb ischemia (Journal of Pharmacology and Experimental Therapeutics (2016) 356:2 (503–513) DOI: 10.1124/jpet.115.228411)

Author

Cannavo A., Liccardo D., Lymperopoulos A., Gambino G., D'Amico M. L., Rengo F., Koch W. J., Leosco D., Ferrara N., Rengo G., Cannavo, A., Liccardo, D., Lymperopoulos, A., Gambino, G., D'Amico, M. L., Rengo, F., Koch, W. J., Leosco, D., Ferrara, N., and Rengo, G.

Abstract

In the above article [Cannavo A, Liccardo D, Lymperopoulos A, Gambino G, D’Amico ML, Rengo F, Koch WJ, Leosco D, Ferrara N, and Rengo G (2016) J Pharmacol Exp Ther 356(2): 503–513; DOI: 10.1124/jpet.115.228411], the following funding information was omitted: This work was funded by the National Institutes of Health [Grant R37 HL061690]. The authors regret this error and any inconvenience it may have caused.

Published
2019

64. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

Author

Fachal, L., Aschard, H., Beesley, J., Barnes, D.R., Allen, J., Kar, S., Pooley, K.A., Dennis, J., Michailidou, K., Turman, C., Soucy, P., Lemaçon, A., Lush, M., Tyrer, J.P., Ghoussaini, M., Marjaneh, M.M., Jiang, X., Agata, S., Aittomäki, K., Alonso, M.R., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arason, A., Arndt, V., Aronson, K.J., Arun, B.K., Auber, B., Auer, P.L., Azzollini, J., Balmaña, J., Barkardottir, R.B., Barrowdale, D., Beeghly-Fadiel, A., Benitez, J., Bermisheva, M., Białkowska, K., Blanco, A.M., Blomqvist, C., Blot, W., Bogdanova, N.V., Bojesen, S.E., Bolla, M.K., Bonanni, B., Borg, A., Bosse, K., Brauch, H., Brenner, H., Briceno, I., Brock, I.W., Brooks-Wilson, A., Brüning, T., Burwinkel, B., Buys, S.S., Cai, Q., Caldés, T., Caligo, M.A., Camp, N.J., Campbell, I., Canzian, F., Carroll, J.S., Carter, B.D., Castelao, J.E., Chiquette, J., Christiansen, H., Chung, W.K., Claes, K.B.M., Clarke, C.L., Mari, V., Berthet, P., Castera, L., Vaur, D., Lallaoui, H., Bignon, Y.-J., Uhrhammer, N., Bonadona, V., Lasset, C., Révillion, F., Vennin, P., Muller, D., Gomes, D.M., Ingster, O., Coupier, I., Pujol, P., Collonge-Rame, M.-A., Mortemousque, I., Bera, O., Rose, M., Baurand, A., Bertolone, G., Faivre, L., Dreyfus, H., Leroux, D., Venat-Bouvet, L., Bézieau, S., Delnatte, C., Chiesa, J., Gilbert-Dussardier, B., Gesta, P., Prieur, F.P., Bronner, M., Sokolowska, J., Coulet, F., Boutry-Kryza, N., Calender, A., Giraud, S., Leone, M., Fert-Ferrer, S., Stoppa-Lyonnet, D., Jiao, Y., Lesueur, F.L., Mebirouk, N., Barouk-Simonet, E., Bubien, V., Longy, M., Sevenet, N., Gladieff, L., Toulas, C., Reimineras, A., Sobol, H., Paillerets, B.B.-D., Cabaret, O., Caron, O., Guillaud-Bataille, M., Rouleau, E., Belotti, M., Buecher, B., Caputo, S., Colas, C., Pauw, A.D., Fourme, E., Gauthier-Villars, M., Golmard, L., Moncoutier, V., Saule, C., Donaldson, A., Murray, A., Brady, A., Brewer, C., Pottinger, C., Miller, C., Gallagher, D., Gregory, H., Cook, J., Eason, J., Adlard, J., Barwell, J., Ong, K.-R., Snape, K., Walker, L., Izatt, L., Side, L., Tischkowitz, M., Rogers, M.T., Porteous, M.E., Ahmed, M., Morrison, P.J., Brennan, P., Eeles, R., Davidson, R., Collée, M., Cornelissen, S., Couch, F.J., Cox, A., Cross, S.S., Cybulski, C., Czene, K., Daly, M.B., de la Hoya, M., Devilee, P., Diez, O., Ding, Y.C., Dite, G.S., Domchek, S.M., Dörk, T., dos-Santos-Silva, I., Droit, A., Dubois, S., Dumont, M., Duran, M., Durcan, L., Dwek, M., Eccles, D.M., Engel, C., Eriksson, M., Evans, D.G., Fasching, P.A., Fletcher, O., Floris, G., Flyger, H., Foretova, L., Foulkes, W.D., Friedman, E., Fritschi, L., Frost, D., Gabrielson, M., Gago-Dominguez, M., Gambino, G., Ganz, P.A., Gapstur, S.M., Garber, J., García-Sáenz, J.A., Gaudet, M.M., Georgoulias, V., Giles, G., Glendon, G., Godwin, A.K., Goldberg, M.S., Goldgar, D.E., González-Neira, A., Tibiletti, M.G., Greene, M.H., Grip, M., Gronwald, J., Grundy, A., Guénel, P., Hahnen, E., Haiman, C.A., Håkansson, N., Hall, P., Hamann, U., Harrington, P.A., Hartikainen, J.M., Hartman, M., He, W., Healey, C.S., Heemskerk-Gerritsen, B.A.M., Heyworth, J., Hillemanns, P., Hogervorst, F.B.L., Hollestelle, A., Hooning, M., Hopper, J., Howell, A., Huang, G., Hulick, P.J., Imyanitov, E.N., Sexton, A., Christian, A., Trainer, A., Spigelman, A., Fellows, A., Shelling, A., Fazio, A.D., Blackburn, A., Crook, A., Meiser, B., Patterson, B., Clarke, C., Saunders, C., Hunt, C., Scott, C., Amor, D., Marsh, D., Edkins, E., Salisbury, E., Haan, E., Neidermayr, E., Macrea, F., Farshid, G., Lindeman, G., Chenevix-Trench, G., Mann, G., Gill, G., Thorne, H., Hickie, I., Winship, I., Flanagan, J., Kollias, J., Visvader, J., Stone, J., Taylor, J., Burke, J., Saunus, J., Forbes, J., Kirk, J., French, J., Tucker, K., Wu, K., Phillips, K., Lipton, L., Andrews, L., Lobb, L., Kentwell, M., Spurdle, M., Cummings, M., Gleeson, M., Harris, M., Jenkins, M., Young, M.A., Delatycki, M., Wallis, M., Burgess, M., Price, M., Brown, M., Southey, M., Bogwitz, M., Field, M., Friedlander, M., Gattas, M., Saleh, M., Hayward, N., Pachter, N., Cohen, P., Duijf, P., James, P., Simpson, P., Fong, P., Butow, P., Williams, R., Kefford, R., Scott, R., Milne, R.L., Balleine, R., Dawson, S.–J., Lok, S., O’Connell, S., Greening, S., Nightingale, S., Edwards, S., Fox, S., McLachlan, S.-A., Lakhani, S., Antill, Y., Aalfs, C., Meijers-Heijboer, H., van Engelen, K., Gille, H., Boere, I., van Deurzen, C., Obdeijn, I.-M., van den Ouweland, A., Seynaeve, C., Siesling, S., Verloop, J., van Asperen, C.J., van Cronenburg, T., Blok, R., de Boer, M., Garcia, E.G., Adank, M., Hogervorst, F., Jenner, D., van Leeuwen, F., Rookus, M., Russell, N., Schmidt, M., van den Belt-Dusebout, S., Kets, C., Mensenkamp, A., de Bock, T., van der Hout, A., Mourits, M., Oosterwijk, J., Ausems, M., Koudijs, M., Baxter, R., Yip, D., Carpenter, J., Davis, A., Pathmanathan, N., Graham, D., Sachchithananthan, M., Isaacs, C., Iwasaki, M., Jager, A., Jakimovska, M., Jakubowska, A., James, P.A., Janavicius, R., Jankowitz, R.C., John, E.M., Johnson, N., Jones, M.E., Jukkola-Vuorinen, A., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Karlan, B.Y., Keeman, R., Kerin, M.J., Khusnutdinova, E., Kiiski, J.I., Kitahara, C.M., Ko, Y.-D., Konstantopoulou, I., Kosma, V.-M., Koutros, S., Kubelka-Sabit, K., Kwong, A., Kyriacou, K., Laitman, Y., Lambrechts, D., Lee, E., Leslie, G., Lester, J., Lesueur, F., Lindblom, A., Lo, W.-Y., Long, J., Lophatananon, A., Loud, J.T., Lubiński, J., MacInnis, R.J., Maishman, T., Makalic, E., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, M.E., Matsuo, K., Maurer, T., Mavroudis, D., Mayes, R., McGuffog, L., McLean, C., Meindl, A., Miller, A., Miller, N., Montagna, M., Moreno, F., Muir, K., Mulligan, A.M., Muñoz-Garzon, V.M., Muranen, T.A., Narod, S.A., Nassir, R., Nathanson, K.L., Neuhausen, S.L., Nevanlinna, H., Neven, P., Nielsen, F.C., Nikitina-Zake, L., Norman, A., Offit, K., Olah, E., Olopade, O.I., Olsson, H., Orr, N., Osorio, A., Pankratz, V.S., Papp, J., Park, S.K., Park-Simon, T.-W., Parsons, M.T., Paul, J., Pedersen, I.S., Peissel, B., Peshkin, B., Peterlongo, P., Peto, J., Plaseska-Karanfilska, D., Prajzendanc, K., Prentice, R., Presneau, N., Prokofyeva, D., Pujana, M.A., Pylkäs, K., Radice, P., Ramus, S.J., Rantala, J., Rau-Murthy, R., Rennert, G., Risch, H.A., Robson, M., Romero, A., Rossing, M., Saloustros, E., Sánchez-Herrero, E., Sandler, D.P., Santamariña, M., Sawyer, E.J., Scheuner, M.T., Schmidt, D.F., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Schöttker, B., Schürmann, P., Scott, R.J., Senter, L., Seynaeve, C.M., Shah, M., Sharma, P., Shen, C.-Y., Shu, X.-O., Singer, C.F., Slavin, T.P., Smichkoska, S., Southey, M.C., Spinelli, J.J., Spurdle, A.B., Sutter, C., Swerdlow, A.J., Tamimi, R.M., Tan, Y.Y., Tapper, W.J., Taylor, J.A., Teixeira, M.R., Tengström, M., Teo, S.H., Terry, M.B., Teulé, A., Thomassen, M., Thull, D.L., Toland, A.E., Tollenaar, R.A.E.M., Tomlinson, I., Torres, D., Torres-Mejía, G., Troester, M.A., Truong, T., Tung, N., Tzardi, M., Ulmer, H.-U., Vachon, C.M., van der Kolk, L.E., van Rensburg, E.J., Vega, A., Viel, A., Vijai, J., Vogel, M.J., Wang, Q., Wappenschmidt, B., Weinberg, C.R., Weitzel, J.N., Wendt, C., Wildiers, H., Winqvist, R., Wolk, A., Wu, A.H., Yannoukakos, D., Zhang, Y., Zheng, W., Hunter, D., Pharoah, P.D.P., Chang-Claude, J., García-Closas, M., Schmidt, M.K., Kristensen, V.N., French, J.D., Edwards, S.L., Antoniou, A.C., Simard, J., Easton, D.F., Kraft, P., Dunning, A.M., Collaborators, GEMO Study, Collaborators, EMBRACE, Investigators, KConFab, Investigators, HEBON, Investigators, ABCTB, Fachal, Laura, Aschard, Hugues, Beesley, Jonathan, Barnes, Daniel R, Duijf, Pascal, Dunning, Alison M, GEMO Study Collaborators, EMBRACE Collaborators, KConFab Investigators, HEBON Investigators, ABCTB Investigators, MUMC+: MA Medische Oncologie (9), RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, Klinische Genetica, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Lab Centraal Lab (9), European Commission, Government of Canada, Canadian Institutes of Health Research, National Institutes of Health (US), Cancer Research UK, Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), QIMR Berghofer Medical Research Institute, University of Cambridge [UK] (CAM), NSCAD, University of Cyprus [Nicosia], Harvard T.H. Chan School of Public Health, This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement number 656144. Genotyping of the OncoArray was principally funded from three sources: the PERSPECTIVE project (funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the ‘Ministère de l’Économie de la Science et de l’Innovation du Québec’ (through Genome Québec) and the Quebec Breast Cancer Foundation), the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and the Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) project (NIH grants U19 CA148065 and X01HG007492), and Cancer Research UK (C1287/A10118, C8197/A16565 and C1287/A16563). BCAC is funded by Cancer Research UK (C1287/A16563), by the European Community’s Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) and by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 633784 (B-CAST) and 634935 (BRIDGES). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the ‘CIHR Team in Familial Risks of Breast Cancer’ program, and the Ministry of Economic Development, Innovation and Export Trade of Quebec (grant PSR-SIIRI-701). Combining of the GWAS data was supported in part by NIH Cancer Post-Cancer GWAS initiative grant U19 CA 148065 (DRIVE, part of the GAME-ON initiative). For a full description of funding and acknowledgments, see the Supplementary Note., We thank all of the individuals who took part in these studies, as well as all of the researchers, clinicians, technicians and administrative staff who enabled this work to be carried out, European Project: 656144,H2020,H2020-MSCA-IF-2014,RADIOGENFF(2016), European Project: 223175,EC:FP7:HEALTH,FP7-HEALTH-2007-B,COGS(2009), European Project: 633784,H2020,H2020-PHC-2014-two-stage,B-CAST(2015), European Project: 634935,H2020,H2020-PHC-2014-two-stage,BRIDGES(2015), Clinical Genetics, Medical Oncology, Pathology, Radiology & Nuclear Medicine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Cyprus [Nicosia] (UCY), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Life Course Epidemiology (LCE), Targeted Gynaecologic Oncology (TARGON), ​Basic and Translational Research and Imaging Methodology Development in Groningen (BRIDGE), Aschard, Hugues [0000-0002-7554-6783], Barnes, Daniel R [0000-0002-3781-7570], Dennis, Joe [0000-0003-4591-1214], Michailidou, Kyriaki [0000-0001-7065-1237], Lemaçon, Audrey [0000-0002-1817-7029], Andrulis, Irene L [0000-0002-4226-6435], Arason, Adalgeir [0000-0003-0480-886X], Arndt, Volker [0000-0001-9320-8684], Auber, Bernd [0000-0003-1880-291X], Azzollini, Jacopo [0000-0002-9364-9778], Bojesen, Stig E [0000-0002-4061-4133], Bonanni, Bernardo [0000-0003-3589-2128], Brauch, Hiltrud [0000-0001-7531-2736], Campbell, Ian [0000-0002-7773-4155], Carroll, Jason S [0000-0003-3643-0080], Claes, Kathleen BM [0000-0003-0841-7372], Collée, J Margriet [0000-0002-9272-9346], Devilee, Peter [0000-0002-8023-2009], Dörk, Thilo [0000-0002-9458-0282], Dwek, Miriam [0000-0001-7184-2932], Fletcher, Olivia [0000-0001-9387-7116], Floris, Giuseppe [0000-0003-2391-5425], Foulkes, William D [0000-0001-7427-4651], García-Sáenz, José A [0000-0001-6880-0301], Greene, Mark H [0000-0003-1852-9239], Guénel, Pascal [0000-0002-8359-518X], Heemskerk-Gerritsen, Bernadette AM [0000-0002-9724-6693], Hollestelle, Antoinette [0000-0003-1166-1966], Hulick, Peter J [0000-0001-8397-4078], Jakimovska, Milena [0000-0002-1506-0669], Jakubowska, Anna [0000-0002-5650-0501], James, Paul A [0000-0002-4361-4657], Jones, Michael E [0000-0001-7479-3451], Kapoor, Pooja Middha [0000-0001-5503-8215], Keeman, Renske [0000-0002-5452-9933], Konstantopoulou, Irene [0000-0002-0470-0309], Leslie, Goska [0000-0001-5756-6222], Lesueur, Fabienne [0000-0001-7404-4549], Matsuo, Keitaro [0000-0003-1761-6314], McLean, Catriona [0000-0002-0302-5727], Miller, Austin [0000-0001-9739-8462], Muir, Kenneth [0000-0001-6429-988X], Muranen, Taru A [0000-0002-5895-1808], Nathanson, Katherine L [0000-0002-6740-0901], Nevanlinna, Heli [0000-0002-0916-2976], Olopade, Olufunmilayo I [0000-0002-9936-1599], Orr, Nick [0000-0003-2866-942X], Pankratz, V Shane [0000-0002-3742-040X], Parsons, Michael T [0000-0003-3242-8477], Paul, James [0000-0001-7367-5816], Peshkin, Beth [0000-0002-2997-4701], Peterlongo, Paolo [0000-0001-6951-6855], Peto, Julian [0000-0002-1685-8912], Plaseska-Karanfilska, Dijana [0000-0001-8877-2416], Pylkäs, Katri [0000-0002-2449-0521], Radice, Paolo [0000-0001-6298-4111], Rennert, Gad [0000-0002-8512-068X], Robson, Mark [0000-0002-3109-1692], Romero, Atocha [0000-0002-1634-7397], Saloustros, Emmanouil [0000-0002-0485-0120], Scott, Christopher [0000-0003-1340-0647], Scott, Rodney J [0000-0001-7724-3404], Spurdle, Amanda B [0000-0003-1337-7897], Stone, Jennifer [0000-0001-5077-0124], Sutter, Christian [0000-0003-4051-5888], Tan, Yen Yen [0000-0003-1063-5352], Teixeira, Manuel R [0000-0002-4896-5982], Toland, Amanda E [0000-0002-0271-1792], Tomlinson, Ian [0000-0003-3037-1470], Viel, Alessandra [0000-0003-2804-0840], Vijai, Joseph [0000-0002-7933-151X], Wolk, Alicja [0000-0001-7387-6845], Yannoukakos, Drakoulis [0000-0001-7509-3510], Pharoah, Paul DP [0000-0001-8494-732X], Schmidt, Marjanka K [0000-0002-2228-429X], Milne, Roger L [0000-0001-5764-7268], Edwards, Stacey L [0000-0001-7428-4139], Simard, Jacques [0000-0001-6906-3390], Easton, Douglas F [0000-0003-2444-3247], Kraft, Peter [0000-0002-4472-8103], Dunning, Alison M [0000-0001-6651-7166], Apollo - University of Cambridge Repository, Academic Medical Center, ARD - Amsterdam Reproduction and Development, Human genetics, CCA - Cancer biology and immunology, Molecular cell biology and Immunology, Medicum, Kristiina Aittomäki / Principal Investigator, HUSLAB, Department of Medical and Clinical Genetics, University of Helsinki, HUS Comprehensive Cancer Center, Department of Oncology, Clinicum, Doctoral Programme in Clinical Research, Staff Services, INDIVIDRUG - Individualized Drug Therapy, HUS Gynecology and Obstetrics, and Department of Obstetrics and Gynecology

Subjects
CHROMATIN, Linkage disequilibrium, Genome-wide association study, Regulatory Sequences, Nucleic Acid, Genome-wide association studies, Linkage Disequilibrium, Basic medicine, 0302 clinical medicine, Breast cancer, MESH: Risk Factors, Risk Factors, COMPREHENSIVE MOLECULAR PORTRAITS, 11 Medical and Health Sciences, HEBON Investigators, Genetics & Heredity, 0303 health sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], PROTEIN FUNCTION, Tumor, breast tumor, MESH: Polymorphism, Single Nucleotide, 1184 Genetics, developmental biology, physiology, MESH: Genetic Predisposition to Disease, apoptosis, Chromosome Mapping, Single Nucleotide, 3. Good health, MESH: Linkage Disequilibrium, Female, MESH: Biomarkers, Tumor, Biomarkers, Tumor/genetics, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Life Sciences & Biomedicine, SUSCEPTIBILITY LOCI, MESH: Bayes Theorem, Quantitative Trait Loci, ABCTB Investigators, INTEGRATIVE ANALYSIS, Breast Neoplasms, Computational biology, Biology, Quantitative trait locus, Breast Neoplasms/genetics, Polymorphism, Single Nucleotide, Article, ENHANCER, GEMO Study Collaborators, 03 medical and health sciences, breast cancer, SDG 3 - Good Health and Well-being, REVEALS, Genetics, Biomarkers, Tumor, MESH: Regulatory Sequences, Nucleic Acid, Humans, Genetic Predisposition to Disease, Polymorphism, GENOME-WIDE ASSOCIATION, FUNCTIONAL VARIANTS, EMBRACE Collaborators, Gene, 030304 developmental biology, Genetic association, Bayes Theorem, Genome-Wide Association Study, MESH: Humans, Science & Technology, Nucleic Acid, gene mapping, 06 Biological Sciences, MESH: Quantitative Trait Loci, DNA binding site, ESTROGEN-RECEPTOR, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Clinical medicine, Expression quantitative trait loci, MESH: Genome-Wide Association Study, Human genome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, KConFab Investigators, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Chromosome Mapping, Chromosome Mapping/methods, Regulatory Sequences, MESH: Female, Biomarkers, 030217 neurology & neurosurgery, MESH: Breast Neoplasms, Developmental Biology
Abstract

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes., This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement number 656144. Genotyping of the OncoArray was principally funded from three sources: the PERSPECTIVE project (funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the ‘Ministère de l’Économie de la Science et de l’Innovation du Québec’ (through Genome Québec) and the Quebec Breast Cancer Foundation); the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and the Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) project (NIH grants U19 CA148065 and X01HG007492); and Cancer Research UK (C1287/A10118, C8197/A16565 and C1287/A16563). BCAC is funded by Cancer Research UK (C1287/A16563), by the European Community’s Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) and by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 633784 (B-CAST) and 634935 (BRIDGES). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the ‘CIHR Team in Familial Risks of Breast Cancer’ program, and the Ministry of Economic Development, Innovation and Export Trade of Quebec (grant PSR-SIIRI-701). Combining of the GWAS data was supported in part by NIH Cancer Post-Cancer GWAS initiative grant U19 CA 148065 (DRIVE; part of the GAME-ON initiative).

Published
2020

65. Identificazione delle varietà nel vino

Author

Gambino G. and Boccacci P.

Subjects
vino, Vite, Nebbiolo, SNP genotyping, mosti
Abstract

Negli ultimi anni la qualità e la sicurezza dei prodotti agroalimentari sono diventate un requisito essenziale a garanzia dei consumatori. Il vino è una delle bevande economicamente più importanti e può essere soggetto a frodi ed errori di etichettatura, sebbene esistano regole europee specifiche e rigorose a tutela della sua autenticità. Le tecniche utilizzate per l'identificazione varietale delle uve utilizzate nella produzione di mosti e vini si basano tradizionalmente su parametri chimici e biochimici, quali profili di proteine ed aminoacidi, oligoelementi e isotopi, nonché composti aromatici. Tuttavia, tali metodi richiedono lunghi tempi di analisi e sono spesso influenzati dalle pratiche culturali, dalle condizioni ambientali e dal processo di vinificazione. L'analisi del DNA, affermatasi come tecnica per l'identificazione genetica delle cultivar di vite grazie al suo alto potere discriminante ed a costi relativamente bassi, rappresenta una valida alternativa in quanto non influenzata dai suddetti fattori esterni ed altamente riproducibile. I recenti sviluppi della genomica, grazie soprattutto alle sempre più evolute tecniche di sequenziamento di interi genomi, hanno permesso di selezionare e caratterizzare una nuova generazione di marcatori molecolari: i single nucleotide polymorphisms (SNPs), altamente frequenti nei genomi ed in grado di discriminare gli individui sulla base di singole mutazioni. Il protocollo messo a punto per SNP genotyping basato sulle sonde TaqMan® ha dimostrato di essere semplice e altamente promettente per l'identificazione varietale nei vini a base Nebbiolo. I vantaggi della tecnica sono: (i) alta sensibilità e specificità nella rilevazione del DNA; (ii) quantificazione di eventuali tagli fraudolenti (fino all' 1% in mosti e 10-20% in vini sperimentali); (iii) tempo di analisi estremamente ridotto; e (iv) interpretazione diretta dei risultati, anche in laboratori non specializzati.

Published
2020

67. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes.

Author

Ramus S.J., Carroll J.S., Schneeweiss A., Schoemaker M.J., Schottker B., Schurmann P., Scott C., Scott R.J., Senter L., Shah M., Sharma P., Shen C.-Y., Shu X.-O., Singer C.F., Slavin T.P., Smichkoska S., Spinelli J.J., Spurdle A.B., Sutter C., Swerdlow A.J., Tamimi R.M., Tan Y.Y., Tapper W.J., Taylor J., Teixeira M.R., Tengstrom M., Teo S.H., Terry M.B., Teule A., Thomassen M., Thull D.L., Toland A.E., Tollenaar R.A.E.M., Tomlinson I., Torres D., Torres-Mejia G., Troester M.A., Truong T., Tung N., Tzardi M., Ulmer H.-U., Vachon C.M., van der Kolk L.E., van Rensburg E.J., Vega A., Viel A., Vijai J., Vogel M.J., Wang Q., Wappenschmidt B., Weinberg C.R., Weitzel J.N., Wendt C., Wildiers H., Winqvist R., Wolk A., Wu A.H., Yannoukakos D., Zhang Y., Zheng W., Hunter D., Pharoah P.D.P., Chang-Claude J., Garcia-Closas M., Schmidt M.K., Kristensen V.N., French J.D., Antoniou A.C., Chenevix-Trench G., Simard J., Easton D.F., Kraft P., Allen J., Harris M., Fachal L., Aschard H., Beesley J., Barnes D.R., Kar S., Pooley K.A., Dennis J., Michailidou K., Turman C., Soucy P., Lemacon A., Lush M., Tyrer J.P., Ghoussaini M., Marjaneh M.M., Jiang X., Agata S., Aittomaki K., Alonso M.R., Andrulis I.L., Anton-Culver H., Antonenkova N.N., Arason A., Arndt V., Aronson K.J., Arun B.K., Auber B., Auer P.L., Azzollini J., Balmana J., Barkardottir R.B., Barrowdale D., Beeghly-Fadiel A., Benitez J., Bermisheva M., Bialkowska K., Blanco A.M., Blomqvist C., Blot W., Bogdanova N.V., Bojesen S.E., Bolla M.K., Bonanni B., Borg A., Bosse K., Brauch H., Brenner H., Briceno I., Brock I.W., Brooks-Wilson A., Bruning T., Burwinkel B., Buys S.S., Cai Q., Caldes T., Caligo M.A., Camp N.J., Campbell I., Carter B.D., Castelao J.E., Chiquette J., Christiansen H., Chung W.K., Claes K.B.M., Clarke C.L., Mari V., Berthet P., Castera L., Vaur D., Lallaoui H., Bignon Y.-J., Uhrhammer N., Bonadona V., Lasset C., Revillion F., Vennin P., Muller D., Gomes D.M., Ingster O., Coupier I., Pujol P., Collonge-Rame M.-A., Mortemousque I., Bera O., Rose M., Baurand A., Bertolone G., Faivre L., Dreyfus H., Leroux D., Venat-Bouvet L., Bezieau S., Delnatte C., Chiesa J., Gilbert-Dussardier B., Gesta P., Prieur F.P., Bronner M., Sokolowska J., Coulet F., Boutry-Kryza N., Calender A., Giraud S., Leone M., Fert-Ferrer S., Stoppa-Lyonnet D., Jiao Y., Lesueur F.L., Mebirouk N., Barouk-Simonet E., Bubien V., Longy M., Sevenet N., Gladieff L., Toulas C., Reimineras A., Sobol H., Paillerets B.B.-D., Cabaret O., Caron O., Guillaud-Bataille M., Rouleau E., Belotti M., Buecher B., Caputo S., Colas C., Pauw A.D., Fourme E., Gauthier-Villars M., Golmard L., Moncoutier V., Saule C., Donaldson A., Murray A., Brady A., Brewer C., Pottinger C., Miller C., Gallagher D., Gregory H., Cook J., Eason J., Adlard J., Barwell J., Ong K.-R., Snape K., Walker L., Izatt L., Side L., Tischkowitz M., Rogers M.T., Porteous M.E., Ahmed M., Morrison P.J., Brennan P., Eeles R., Davidson R., Collee J.M., Cornelissen S., Couch F.J., Cox A., Cross S.S., Cybulski C., Czene K., Daly M.B., de la Hoya M., Devilee P., Diez O., Ding Y.C., Dite G.S., Domchek S.M., Dork T., dos-Santos-Silva I., Droit A., Dubois S., Dumont M., Duran M., Durcan L., Dwek M., Eccles D.M., Engel C., Eriksson M., Evans D.G., Fasching P.A., Fletcher O., Floris G., Flyger H., Foretova L., Foulkes W.D., Friedman E., Fritschi L., Frost D., Gabrielson M., Gago-Dominguez M., Gambino G., Ganz P.A., Gapstur S.M., Garber J., Garcia-Saenz J.A., Gaudet M.M., Georgoulias V., Giles G., Glendon G., Godwin A.K., Goldberg M.S., Goldgar D.E., Gonzalez-Neira A., Tibiletti M.G., Greene M.H., Grip M., Gronwald J., Grundy A., Guenel P., Hahnen E., Haiman C.A., Hakansson N., Hall P., Hamann U., Harrington P.A., Hartikainen J.M., Hartman M., He W., Healey C.S., Heemskerk-Gerritsen B.A.M., Heyworth J., Hillemanns P., Hogervorst F.B.L., Hollestelle A., Hooning M., Hopper J., Howell A., Huang G., Hulick P.J., Imyanitov E.N., Sexton A., Christian A., Trainer A., Spigelman A., Fellows A., Shelling A., Fazio A.D., Blackburn A., Crook A., Meiser B., Patterson B., Clarke C., Saunders C., Hunt C., Amor D., Marsh D., Edkins E., Salisbury E., Haan E., Neidermayr E., Macrea F., Farshid G., Lindeman G., Trench G., Mann G., Gill G., Thorne H., Hickie I., Winship I., Flanagan J., Kollias J., Visvader J., Stone J., Burke J., Saunus J., Forbes J., French J., Tucker K., Wu K., Phillips K., Lipton L., Andrews L., Lobb L., Kentwell M., Spurdle M., Cummings M., Gleeson M., Jenkins M., Young M.A., Delatycki M., Wallis M., Burgess M., Price M., Brown M., Southey M., Bogwitz M., Field M., Friedlander M., Gattas M., Saleh M., Hayward N., Pachter N., Cohen P., Duijf P., James P., Simpson P., Fong P., Butow P., Williams R., Kefford R., Scott R., Milne R.L., Balleine R., Dawson S.-J., Lok S., O'Connell S., Greening S., Nightingale S., Edwards S., Fox S., McLachlan S.-A., Lakhani S., Antill Y., Aalfs C., Meijers-Heijboer H., van Engelen K., Gille H., Boere I., Collee M., van Deurzen C., Obdeijn I.-M., van den Ouweland A., Seynaeve C., Siesling S., Verloop J., van Asperen C., van Cronenburg T., Blok R., de Boer M., Garcia E.G., Adank M., Hogervorst F., Jenner D., van Leeuwen F., Rookus M., Russell N., Schmidt M., van den Belt-Dusebout S., Kets C., Mensenkamp A., de Bock T., van der Hout A., Mourits M., Oosterwijk J., Ausems M., Koudijs M., Baxter R., Yip D., Carpenter J., Davis A., Pathmanathan N., Graham D., Sachchithananthan M., Isaacs C., Iwasaki M., Jager A., Jakimovska M., Jakubowska A., Janavicius R., Jankowitz R.C., John E.M., Johnson N., Jones M.E., Jukkola-Vuorinen A., Jung A., Kaaks R., Kang D., Kapoor P.M., Karlan B.Y., Keeman R., Kerin M.J., Khusnutdinova E., Kiiski J.I., Kirk J., Kitahara C.M., Ko Y.-D., Konstantopoulou I., Kosma V.-M., Koutros S., Kubelka-Sabit K., Kwong A., Kyriacou K., Laitman Y., Lambrechts D., Lee E., Leslie G., Lester J., Lesueur F., Lindblom A., Lo W.-Y., Long J., Lophatananon A., Loud J.T., Lubinski J., MacInnis R.J., Maishman T., Makalic E., Mannermaa A., Manoochehri M., Manoukian S., Margolin S., Martinez M.E., Matsuo K., Maurer T., Mavroudis D., Mayes R., McGuffog L., McLean C., Meindl A., Miller A., Miller N., Montagna M., Moreno F., Muir K., Mulligan A.M., Munoz-Garzon V.M., Muranen T.A., Narod S.A., Nassir R., Nathanson K.L., Neuhausen S.L., Nevanlinna H., Neven P., Nielsen F.C., Nikitina-Zake L., Norman A., Offit K., Olah E., Olopade O.I., Olsson H., Orr N., Osorio A., Pankratz V.S., Papp J., Park S.K., Park-Simon T.-W., Parsons M.T., Paul J., Pedersen I.S., Peissel B., Peshkin B., Peterlongo P., Peto J., Plaseska-Karanfilska D., Prajzendanc K., Prentice R., Presneau N., Prokofyeva D., Pujana M.A., Pylkas K., Radice P., Canzian F., Rantala J., Rau-Murthy R., Rennert G., Risch H.A., Robson M., Romero A., Rossing M., Saloustros E., Sanchez-Herrero E., Sandler D.P., Santamarina M., Sawyer E.J., Scheuner M.T., Schmidt D.F., Schmutzler R.K., Ramus S.J., Carroll J.S., Schneeweiss A., Schoemaker M.J., Schottker B., Schurmann P., Scott C., Scott R.J., Senter L., Shah M., Sharma P., Shen C.-Y., Shu X.-O., Singer C.F., Slavin T.P., Smichkoska S., Spinelli J.J., Spurdle A.B., Sutter C., Swerdlow A.J., Tamimi R.M., Tan Y.Y., Tapper W.J., Taylor J., Teixeira M.R., Tengstrom M., Teo S.H., Terry M.B., Teule A., Thomassen M., Thull D.L., Toland A.E., Tollenaar R.A.E.M., Tomlinson I., Torres D., Torres-Mejia G., Troester M.A., Truong T., Tung N., Tzardi M., Ulmer H.-U., Vachon C.M., van der Kolk L.E., van Rensburg E.J., Vega A., Viel A., Vijai J., Vogel M.J., Wang Q., Wappenschmidt B., Weinberg C.R., Weitzel J.N., Wendt C., Wildiers H., Winqvist R., Wolk A., Wu A.H., Yannoukakos D., Zhang Y., Zheng W., Hunter D., Pharoah P.D.P., Chang-Claude J., Garcia-Closas M., Schmidt M.K., Kristensen V.N., French J.D., Antoniou A.C., Chenevix-Trench G., Simard J., Easton D.F., Kraft P., Allen J., Harris M., Fachal L., Aschard H., Beesley J., Barnes D.R., Kar S., Pooley K.A., Dennis J., Michailidou K., Turman C., Soucy P., Lemacon A., Lush M., Tyrer J.P., Ghoussaini M., Marjaneh M.M., Jiang X., Agata S., Aittomaki K., Alonso M.R., Andrulis I.L., Anton-Culver H., Antonenkova N.N., Arason A., Arndt V., Aronson K.J., Arun B.K., Auber B., Auer P.L., Azzollini J., Balmana J., Barkardottir R.B., Barrowdale D., Beeghly-Fadiel A., Benitez J., Bermisheva M., Bialkowska K., Blanco A.M., Blomqvist C., Blot W., Bogdanova N.V., Bojesen S.E., Bolla M.K., Bonanni B., Borg A., Bosse K., Brauch H., Brenner H., Briceno I., Brock I.W., Brooks-Wilson A., Bruning T., Burwinkel B., Buys S.S., Cai Q., Caldes T., Caligo M.A., Camp N.J., Campbell I., Carter B.D., Castelao J.E., Chiquette J., Christiansen H., Chung W.K., Claes K.B.M., Clarke C.L., Mari V., Berthet P., Castera L., Vaur D., Lallaoui H., Bignon Y.-J., Uhrhammer N., Bonadona V., Lasset C., Revillion F., Vennin P., Muller D., Gomes D.M., Ingster O., Coupier I., Pujol P., Collonge-Rame M.-A., Mortemousque I., Bera O., Rose M., Baurand A., Bertolone G., Faivre L., Dreyfus H., Leroux D., Venat-Bouvet L., Bezieau S., Delnatte C., Chiesa J., Gilbert-Dussardier B., Gesta P., Prieur F.P., Bronner M., Sokolowska J., Coulet F., Boutry-Kryza N., Calender A., Giraud S., Leone M., Fert-Ferrer S., Stoppa-Lyonnet D., Jiao Y., Lesueur F.L., Mebirouk N., Barouk-Simonet E., Bubien V., Longy M., Sevenet N., Gladieff L., Toulas C., Reimineras A., Sobol H., Paillerets B.B.-D., Cabaret O., Caron O., Guillaud-Bataille M., Rouleau E., Belotti M., Buecher B., Caputo S., Colas C., Pauw A.D., Fourme E., Gauthier-Villars M., Golmard L., Moncoutier V., Saule C., Donaldson A., Murray A., Brady A., Brewer C., Pottinger C., Miller C., Gallagher D., Gregory H., Cook J., Eason J., Adlard J., Barwell J., Ong K.-R., Snape K., Walker L., Izatt L., Side L., Tischkowitz M., Rogers M.T., Porteous M.E., Ahmed M., Morrison P.J., Brennan P., Eeles R., Davidson R., Collee J.M., Cornelissen S., Couch F.J., Cox A., Cross S.S., Cybulski C., Czene K., Daly M.B., de 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Abstract

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.Copyright © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

Published
2020

69. Molecular modeling of interactions between L-lysine and functionalized quartz surfaces

Author

Gambino, G.. Laura, Grassi, Antonio, and Marletta, Giovanni

Subjects
Lysine -- Chemical properties, Lysine -- Structure, Quartz -- Chemical properties, Molecules -- Models, Molecules -- Methods, Chemicals, plastics and rubber industries
Abstract

Molecular modeling techniques are used to investigate the interaction of L-lysine in aqueous medium with silanol and methyl sites onto quartz substrates. The structure of water shells around L-lysine molecules is strongly affected by the relative hydrophilic/hydrophobic character of the surfaces, where the order is almost completely lost for partially hydrophilic surfaces, while well-defined hydration shells around L-lysine are obtained for hydrophobic surfaces.

Published
2006

73. SMA – THERAPY

Author

Finkel, R., primary, Castro, D., additional, Farrar, M., additional, Tulinius, M., additional, Krosschell, K., additional, Saito, K., additional, Gambino, G., additional, Foster, R., additional, Ramirez-Schrempp, D., additional, Wong, J., additional, Kandinov, B., additional, and Farwell, W., additional

Published
2020
Full Text
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74. SMA – THERAPY

Author

Mercuri, E., primary, Darras, B., additional, Chiriboga, C., additional, Farrar, M., additional, Kirschner, J., additional, Kuntz, N., additional, Acsadi, G., additional, Tulinius, M., additional, Montes, J., additional, Gambino, G., additional, Foster, R., additional, Ramirez-Schrempp, D., additional, Garafolo, S., additional, and Farwell, W., additional

Published
2020
Full Text
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75. SMA – THERAPY

Author

Montes, J., primary, Krasinski, D., additional, Foster, R., additional, Gambino, G., additional, Paradis, A., additional, Garafalo, S., additional, and Johnson, N., additional

Published
2020
Full Text
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76. SMA - CLINICAL

Author

Young, S. Dunaway, primary, Montes, J., additional, Glanzman, A., additional, Gee, R., additional, Day, J., additional, Finkel, R., additional, Darras, B., additional, De Vivo, D., additional, Gambino, G., additional, Foster, R., additional, Wong, J., additional, Kandinov, B., additional, and Berger, Z., additional

Published
2020
Full Text
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77. Glomerular filtration rate: A prognostic marker in atrial fibrillation—A subanalysis of the AntiThrombotic Agents Atrial Fibrillation

Author

Proietti, Riccardo, Gonzini, Lucio, Pizzimenti, Giovanni, Ledda, Antonietta, Sanna, Pietro, Alturki, Ahmed, Russo, Vincenzo, Lencioni, Mauro, Siciliano, R., Boffa, M., Bazzanini, F., Di Nucci, G., Fonti, S., De Franceschi, T., Davio, P., Alagna, G., Cipollini, F., Arma, P., Gunnellini, M. G., Dottori, M., Paulillo, D., Giudice, M., Sicuro, M., Lenti, S., Iannelli, G., Notarstefano, P., Galiotto, M., Apolloni, Enzo, Molini, G., Massarelli, L., Di Iorio, P., Scandurra, F., Candelmo, F., Iodice, P., Laureano, R., Perlangeli, S., Praticò, A., Lucchesi, Q., Conese, V., Scalera, G., Palma, F., De Antoni, M. E., Beltramello, G., Carbonella, M., Capone, A., Bianchi, V., Zerella, F., Masina, M., Boggian, G., Pancaldi, L. G., Brucato, A. L., Scialfa, S., Ferrari, P., Gavazzi, A., Santoro, E., Bertinieri, G., Caragnano, V., Zaccaroni, S., Marchetti, G., Urbinati, S., Belmonte, G., Giannoni, C., Panuccio, D., Pedone, V., Colletta, M., Di Pasquale, G., Cemin, R., Paffoni, P. R. C., Pezzotti, Chiara, Capretti, M., Lamari, A. L., Maugeri, S., Moretti, R., Ganga, R., Mascia, P., Caddori, A., Cusumano, S., Alletto, M., DE VINCENZO, Ciro, Musacchio, E., Stendardo, A., Cantarella, SALVATORE ALFREDO, Ferrari, V., Bassano, F., PERRONE CAPANO, Carla, Piccinni, G. C., Catanzaro, M., Vinciguerra, A., Lusiani, L., De Caro, G., Scarcia, M., Scarcia, Aurora, Losi, E., Gaddi, O., Lo Sciuto, A., Cascio Ingurgio, N., Vignai, E., Romano, M., Borzì, V., Bellanuova, I. A., Felis, S., Gulizia, M. M., Francese, G. M., Artale, S., Mazzuca, S., Perticone, F., Tirotta, D., Talini, E., Ventrella, F., Iosa, G., Cuccurullo, O., Bertello, P. D., Benemio, G., Garognoli, O., Arcelli, G., Prosciutti, L., De Matthaeis, G., Quattrini, C., Calcagno, S., Canestrini, S., Franco, A., Pastorelli, R., Acquati, F., Botto, G. L., Sitta, N., Migliacci, R., Cosmi, F., Tarquini, B., Chiappetta, P., Sprovieri, M. F., Macrì, G., Bertolazzi, S., Spotti, Alessia, Pirelli, S., Marasco, M. F., Elia, Martina, Gambino, G. M., Fenoglio, L., Gelmini, G. P., Ziacchi, V., Rigon, N., Petix, N. R., Zipoli, A., Caiolo, A., Marino, E., Scattolin, G., Gerini, S., Parisi, G., Tavernese, G., Conti, Alessandro, Ferrante, Federico, Morettini, A., Alterini, B., Rocchi, Federico, Nozzoli, C., Goedecke, L., Seravalle, C., Cuomo, A., Panettieri, I., Pellegrino, P., Di Biase, M., Savarese, G., Patriarchi, F., Bondì, Giuseppina, Rossini, Elena, Nello, S., Ranieri, A. T., Gelonesi, F. N., Costantini, M., Dugnani, M., Ria, L., Mussardo, V., Zanini, G., Morgante, O., Fazio, G., Lo, G., Castello, C., Moroni, L. A., Costa, S., Domenicucci, S., Venzano, C., Loiacono, L., Ortuso, R., Esposito, L., Cuzzucrea, D. G., Fiammengo, F., Selva, E., Gestra, R., Alessandri, M., Nuzzi, G., Porrino, L., Parise, P., Capponi, E. A., Mandorla, S., Politi, Caterina, Olivieri, Claudia, Gurioli, L., Agostinelli, P., Striuli, R., Petrarca, Massimo, Corsini, Francesca, Orlandini, F., Badolati, S., Colarusso, D., Vertullo, V., Pelaggi, P., Campagna, G., Haupt, E., Parente, F., Milanese, G., Magliari, F., Morando, G., Guarise, P., Mazzone, A., Palumbo, G., Lambelet, P., Camaiti, A., Pasquinelli, P., Frediani, L., Vituliano, A., Brunelleschi, G., Lisi, C., La Torre, P. P. A., Villella, A., Rimoldi, A., Russo, V., Di Summa, F., Reggiani, A., Raimondo, F. C., Disalvo, D., Borrello, V. M., Magnante, A., Stellitano, E., Procopio, L., Franculli, F., Serafini, Filippo, Tondo, C., Fiorentini, C., Manfredini, R., Robbiolo, L., Pizzimenti, G., VASQUEZ LOPEZ, LUIDER FERNEY, Piangiamore, A., Tosi, P., Donà, G., Bacchiega, E., Malavasi, V., Modena, M. G., Divella, C., Marengo, C., Montanari, P., Manicardi, V., Abate, L., Cuccuini, A., Magni, S., Vincenti, A., Spinelli, M., Mortara, A., Specchia, G., Silvestri, N., Silvestri, Oriana, Piscopo, G., Muscherà, R., Gallucci, F., Cannavale, A., Bresciani, A., Perrone Filardi, P., Fontanella, Andrea, Iannuzzo, D., Lucà, S., Zuccoli, A., Rinaldi, P., Ferri, G., Barbieri, E., Grasselli, S., Rossi, A., Agosti, S., Sanna, GIAN PAOLO, Casu, G., Orecchioni, G., Da Silva Carvalho, P. C., POZZI MUCELLI, Roberto, Salvati, Fabio, Bendini, M. G., Giordano, G., Pellegrini, F., Pighini, G., Tremolada, F., Zanin, L., Ledda, A., Floresta, A. M., Enia, F., Nicolosi, G., Ingrillì, F., D'Angelo, A., Musacchio, D., Savastano, Silvia, Magnani, Leonardo, Capitelli, M., Cioni, Giovanni, Aloisi, B., De Finis, A., Vacri, A., Costantini, V., Guercini, F., Zingarini, G., Nardoni, M. C., Teghini, L., Panigada, G., Di Marco, S., Vergoni, W., Paonessa, K., Artom, A., Bigliardi, M., Riccardi, R., Riva, L., Marandino, A., Barsotti, L., Ginocchio, G., Marchese, Dario, Tintori, G., Annese, M., Breschi, R., Manini, M., Scopelliti, Giulia, Pastore, A., Spirito, G., Amato, A., Del Bianco, F., Ongari, M., Fiorencis, R., Querci, F., Martone, V. D., Molero, U., Fiusti, R., Giovannini, T., D'Arienzo, E., Cellamare, G., Placci, A., Gulli, G., Ruggeri, A., Pulitanò, G., Iori, I., Ingianni, N., Saporito, D., Marconi, GIAN MARIA, Grossi, Alice, Grosseto, D., Ciamei, M., Mete, F., Russo, F., Bianchi, C., Costantino, S., Manfellotto, D., Risa, M. P., Azzolini, P., Conversano, L., Santini, M., Macchiusi, A., Francia, P., Pietrantonio, F., Biscione, F., Magliano, G., Fedele, Francesca, Salituri, S., Salituri, F., Zamboni, S., Rossetti, C., Roncon, Leonora, Delucchi, M., De Benedictis, M., Vitolo, A., Anselmi, Michela, Celino, T., Moretti, V., Cuccurullo, M., Castelli, G., Martino, G., Pierandrei, G., Carella, A. M., Tonizzo, M., Nassi, R., Tarducci, R., Fronticelli Baldelli, M., Commisso, B., Lazzarini, D., Matarazzo, M. M., Novati, P., Petacchi, R., Maninchedda, P., Melandri, F., Bellesi, P., Sacchetti, C., Grandi, M., Cattana, A., Tassara, R., Menardo, G., Aykut, V., Chesi, G., Reverzani, A., Galgano, Angela, Bartone, B., Stornello, M., Muscio, G., Gemmiti, M. P., Alfonsi, F., Fontana, D., Astarita, C., Gaspardo, G., La Brocca, A., Rillo, M., Pascente, T., Pirozzi, M. 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R., Zipoli, A., Caiolo, A., Marino, E., Scattolin, G., Gerini, S., Parisi, G., Tavernese, G., Conti, A., Ferrante, F., Morettini, A., Alterini, B., Rocchi, F., Nozzoli, C., Goedecke, L., Seravalle, C., Cuomo, A., Panettieri, I., Pellegrino, P., Di Biase, M., Savarese, G., Patriarchi, F., Bondi, G., Rossini, E., Nello, S., Ranieri, A. T., Gelonesi, F. N., Costantini, M., Dugnani, M., Ria, L., Mussardo, V., Zanini, G., Morgante, O., Fazio, G., Lo, G., Castello, C., Moroni, L. A., Costa, S., Domenicucci, S., Venzano, C., Loiacono, L., Ortuso, R., Esposito, L., Cuzzucrea, D. G., Fiammengo, F., Selva, E., Gestra, R., Alessandri, M., Nuzzi, G., Porrino, L., Parise, P., Capponi, E. A., Mandorla, S., Politi, C., Olivieri, C., Gurioli, L., Agostinelli, P., Striuli, R., Petrarca, M., Corsini, F., Orlandini, F., Badolati, S., Colarusso, D., Vertullo, V., Pelaggi, P., Campagna, G., Haupt, E., Parente, F., Milanese, G., Magliari, F., Morando, G., Guarise, P., Mazzone, A., Palumbo, G., Lambelet, P., Camaiti, A., Pasquinelli, P., Frediani, L., Vituliano, A., Brunelleschi, G., Lisi, C., La Torre, P. P. A., Villella, A., Rimoldi, A., Russo, V., Di Summa, F., Reggiani, A., Raimondo, F. C., Disalvo, D., Borrello, V. M., Magnante, A., Stellitano, E., Procopio, L., Franculli, F., Serafini, F., Tondo, C., Fiorentini, C., Manfredini, R., Robbiolo, L., Pizzimenti, G., Vasquez, L., Piangiamore, A., Tosi, P., Donà, G., Bacchiega, E., Malavasi, V., Modena, M. G., Divella, C., Marengo, C., Montanari, P., Manicardi, V., Abate, L., Cuccuini, A., Magni, S., Vincenti, A., Spinelli, M., Mortara, A., Specchia, G., Silvestri, N., Silvestri, O., Piscopo, G., Muscherà, R., Gallucci, F., Cannavale, A., Bresciani, A., Perrone Filardi, P., Fontanella, A., Iannuzzo, D., Lucà, S., Zuccoli, A., Rinaldi, P., Ferri, G., Barbieri, E., Grasselli, S., Rossi, A., Agosti, S., Sanna, P., Casu, G., Orecchioni, G., Da Silva Carvalho, P. C., Pozzi, R., Salvati, F., Bendini, M. G., Giordano, G., Pellegrini, F., Pighini, G., Tremolada, F., Zanin, L., Ledda, A., Floresta, A. M., Enia, F., Nicolosi, G., Ingrillì, F., D'Angelo, A., Musacchio, D., Savastano, S., Magnani, L., Capitelli, M., Cioni, G., Aloisi, B., De Finis, A., Vacri, A., Costantini, V., Guercini, F., Zingarini, G., Nardoni, M. C., Teghini, L., Panigada, G., Di Marco, S., Vergoni, W., Paonessa, K., Artom, A., Bigliardi, M., Riccardi, R., Riva, L., Marandino, A., Barsotti, L., Ginocchio, G., Marchese, D., Tintori, G., Annese, M., Breschi, R., Manini, M., Scopelliti, G., Pastore, A., Spirito, G., Amato, A., Del Bianco, F., Ongari, M., Fiorencis, R., Querci, F., Martone, V. D., Molero, U., Fiusti, R., Giovannini, T., D'Arienzo, E., Cellamare, G., Placci, A., Gulli, G., Ruggeri, A., Pulitanò, G., Iori, I., Ingianni, N., Saporito, D., Marconi, M., Grossi, A., Grosseto, D., Ciamei, M., Mete, F., Russo, F., Bianchi, C., Costantino, S., Manfellotto, D., Risa, M. P., Azzolini, P., Conversano, L., Santini, M., Macchiusi, A., Francia, P., Pietrantonio, F., Biscione, F., Magliano, G., Fedele, F., Salituri, S., Salituri, F., Zamboni, S., Rossetti, C., Roncon, L., Delucchi, M., De Benedictis, M., Vitolo, A., Anselmi, M., Celino, T., Moretti, V., Cuccurullo, M., Castelli, G., Martino, G., Pierandrei, G., Carella, A. M., Tonizzo, M., Nassi, R., Tarducci, R., Fronticelli Baldelli, M., Commisso, B., Lazzarini, D., Matarazzo, M. M., Novati, P., Petacchi, R., Maninchedda, P., Melandri, F., Bellesi, P., Sacchetti, C., Grandi, M., Cattana, A., Tassara, R., Menardo, G., Aykut, V., Chesi, G., Reverzani, A., Galgano, A., Bartone, B., Stornello, M., Muscio, G., Gemmiti, M. P., Alfonsi, F., Fontana, D., Astarita, C., Gaspardo, G., La Brocca, A., Rillo, M., Pascente, T., Pirozzi, M. R., Addis, L., De Siati, P., Beato, E., Iannaccone, V., Barabani, M., Castronuovo, M., Battaia, L., Biscottini, B., Boccali, A., Marengo, S., Dallerba, R., Diana, A., Coser, A., Pauletto, P., Calzolari, V., Olivari, Z., De Masi De Luca, G., Accogli, M., Gerloni, R., Cattin, L., Vitali Serdoz, L., Sinagra, G., Bulfoni, A., De Biasio, M., Proclemer, A., Miserocchi, F., Marazzi, R., Salerno Uriarte, J. A., Levantesi, G., Olivetti, P., Capuano, A., Bertoncelli, M. C., Molinaro, N., Anastasio, L., Teti, G., Vescovo, G. A., Muriago, M., Incao, F., Lettica, G. V., Nieswandt, V., Osti, R., and Tafi, A.

Subjects
Male, medicine.medical_specialty, Time Factors, Clinical Investigations, Renal function, 030204 cardiovascular system & hematology, Risk Assessment, 03 medical and health sciences, 0302 clinical medicine, Fibrinolytic Agents, Risk Factors, atrial fibrillation, glomerular filtration rate, mortality, Cardiology and Cardiovascular Medicine, Internal medicine, Antithrombotic, medicine, Humans, In patient, 030212 general & internal medicine, Renal Insufficiency, Cardiovascular mortality, Aged, Retrospective Studies, business.industry, Incidence, Atrial fibrillation, General Medicine, medicine.disease, Prognosis, Survival Rate, Italy, Hospital admission, Atrial Fibrillation, Female, Follow-Up Studies, Glomerular Filtration Rate, Morbidity, Cardiology, business
Abstract

OBJECTIVE: An increased cardiovascular mortality and morbidity has been widely reported in patients with atrial fibrillation (AF). In this study, a subanalysis of the AntiThrombotic Agents Atrial Fibrillation (ATA‐AF) is performed with the aim to evaluate estimated glomerular filtration rate (eGFR) as an independent prognostic marker of cardiovascular mortality and morbidity in patients with AF. METHODS AND RESULTS: The ATA‐AF study enrolled 7148 patients with AF, in 360 Italian centers. The eGFR was calculated from data reported in patient notes or hospital database. This post‐hoc analysis included 1097 AF patients with eGFR data available and 1‐year clinical follow‐up. The endpoint was assessed as cardiovascular mortality and/or hospital admission for cardiovascular causes at follow‐up. Patients were also divided in two groups according to the eGFR (

Published
2018

80. Composti non convenzionali per la lotta all'oidio in vite: analisi degli effetti sul fillobioma e sulle risposte endogene di difesa

Author

Nerva L., Pagliarani C., Pugliese M., Monchiero M., Gonthier S. Gullino M.L., Gambino G., and Chitarra W

Subjects
vite, Fillobioma, composti antifungini
Abstract

La viticultura rappresenta un settore trainante nell'economia agroindustriale nazionale e la gestione delle malattie fungine in vigneto (peronospora e oidio in primis) ha un costo notevole, sia dal punto di vista economico che ambientale. Gli agrofarmaci utilizzati in viticoltura sono numerosi così come il numero di trattamenti applicati ogni stagione. Tuttavia, molti dei composti utilizzati sono sostanze che possono presentare dei rischi per l'uomo e per l'ambiente. Nel presente lavoro è stato indagato, mediante approcci multidisciplinari, l'effetto dell'applicazione di composti non convenzionali per il contenimento dell'oidio. Composti a base di laminarina e di fosfonato di potassio sono stati confrontati con l'acibenzolar-S-metile, un induttore di resistenza convenzionale. Per valutare l'impatto dei composti applicati, sono stati adottati approcci molecolari (analisi del viroma e della comunità fungina in foglia), biochimici (quantificazione degli stilbeni e delle cere cuticolari fogliari) e microbiologici (Biolog EcoplatesTM per definire il profilo fisiologico della comunità batterica in foglia). Dei composti applicati, il trattamento con Bion e la Laminarina sono risultati i più efficaci nel contenimento dell'oidio. L'analisi della comunità fungina e della fisiologia funzionale batterica non mostra differenze significative all'interno della stessa varietà, di conseguenza i composti applicati non impattano negativamente le comunità dei microorganismi residenti. Le indagini sulla comunità fungina condotte mediante sequenziamento evidenziano una netta riduzione della quantità di Erysiphe in 'Moscato' (a conferma dei risultati sull'incidenza della malattia) ed in generale una maggiore biodiversità microbica rispetto al 'Nebbiolo'. Questo studio si inserisce in un contesto di mutamenti climatici e nella necessità, in viticultura, di studiare nuovi interventi di lotta sostenibile contro l'oidio che siano a basso impatto per l'ambiente, per la pianta in sé e per i microorganismi ad essa associati, utili per la corretta funzionalità fisiologica e biochimica della vite.

Published
2019

82. Two integrated platforms to detect source-sink carbon movements in grapevine

Author

Patono D.L., Said Pullicino D., Alcantrao L.E., Ivaldi G., Firbus A., Craveri L., Gambino G., Ricauda D., Celi L., and Lovisolo C.

Subjects
fungi, food and beverages, drought, C allocation kinetics, grapevine
Abstract

"To study the allocation kinetics of carbon in the different sinks competing in grapevines, a plant growth chamber for stable isotope labeling has been set in an environmental control system (light intensity, temperature and relative humidity of the air, pot water content) in order to simulate different climate scenarios. Basing on pulse-chasing isotopic strategy, the isotope acted as a tracer of carbon phloem flows. Furthermore, an open-air plant/soil growth system consisting in twelve independent plant/pot balloons with computing-adjustable air flows allowing continuous gas exchange detection between plants / soil and atmosphere has been set. The two platforms have been coordinated and used before, during and after induction of drought stress. Photosynthetic assimilation, stomatal regulation and respiration have been checked in the various phases to size 13CO2 enrichment flows in the chamber for stable isotope labeling. Maximum assimilation ranged from 9 to 12 ?mol m-2 s-1, reduced by stomatal control 3 o 4 times at the end of the drought period. Saturation of net photosynthesis occurred around 1000 ?mol m-2 s-1 PPFD: thereafter photoinhibition impairment started in old leaves, whereas young leaves experienced half of maximum assimilation without drastic photoinhibition. An in-vineyard parallel trial of measurements was used to calibrate and reference pot measurements. "

Published
2019

84. Interim report on the safety and efficacy of longer-term treatment with nusinersen in later-onset spinal muscular atrophy (SMA): results from the SHINE study

Author

Kirschner, J, Darras, B, Farrar, M, Mercuri, E, Chiriboga, C, Kuntz, N, Shieh, P, Tulinius, M, Montes, J, Reyna, S, Gambino, G, Foster, R, Bhan, I, Wong, J, Farwell, W, Kirschner, J, Darras, B, Farrar, M, Mercuri, E, Chiriboga, C, Kuntz, N, Shieh, P, Tulinius, M, Montes, J, Reyna, S, Gambino, G, Foster, R, Bhan, I, Wong, J, and Farwell, W

Published
2019

85. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification.

Author

Feroce I., Schoenwiese U., Seggewiss J., Solanes A., Steinemann D., Stiller M., Stoppa-Lyonnet D., Sullivan K.J., Susman R., Sutter C., Tavtigian S.V., Teo S.H., Teule A., Thomassen M., Tibiletti M.G., Tischkowitz M., Tognazzo S., Toland A.E., Tornero E., Torngren T., Torres-Esquius S., Toss A., Trainer A.H., Tucker K.M., van Asperen C.J., van Mackelenbergh M.T., Varesco L., Vargas-Parra G., Varon R., Vega A., Velasco A., Vesper A.-S., Viel A., Vreeswijk M.P.G., Wagner S.A., Waha A., Walker L.C., Walters R.J., Wang-Gohrke S., Weber B.H.F., Weichert W., Wieland K., Wiesmuller L., Witzel I., Wockel A., Woodward E.R., Zachariae S., Zampiga V., Zeder-Goss C., Investigators K., Lazaro C., De Nicolo A., Radice P., Engel C., Schmutzler R.K., Goldgar D.E., Spurdle A.B., Harris M., Parsons M.T., Tudini E., Li H., Hahnen E., Wappenschmidt B., Feliubadalo L., Aalfs C.M., Agata S., Aittomaki K., Alducci E., Alonso-Cerezo M.C., Arnold N., Auber B., Austin R., Azzollini J., Balmana J., Barbieri E., Bartram C.R., Blanco A., Blumcke B., Bonache S., Bonanni B., Borg A., Bortesi B., Brunet J., Bruzzone C., Bucksch K., Cagnoli G., Caldes T., Caliebe A., Caligo M.A., Calvello M., Capone G.L., Caputo S.M., Carnevali I., Carrasco E., Caux-Moncoutier V., Cavalli P., Cini G., Clarke E.M., Concolino P., Cops E.J., Cortesi L., Couch F.J., Darder E., de la Hoya M., Dean M., Debatin I., Del Valle J., Delnatte C., Derive N., Diez O., Ditsch N., Domchek S.M., Dutrannoy V., Eccles D.M., Ehrencrona H., Enders U., Evans D.G., Farra C., Faust U., Felbor U., Fine M., Foulkes W.D., Galvao H.C.R., Gambino G., Gehrig A., Gensini F., Gerdes A.-M., Germani A., Giesecke J., Gismondi V., Gomez C., Gomez Garcia E.B., Gonzalez S., Grau E., Grill S., Gross E., Guerrieri-Gonzaga A., Guillaud-Bataille M., Gutierrez-Enriquez S., Haaf T., Hackmann K., Hansen T.V.O., Hauke J., Heinrich T., Hellebrand H., Herold K.N., Honisch E., Horvath J., Houdayer C., Hubbel V., Iglesias S., Izquierdo A., James P.A., Janssen L.A.M., Jeschke U., Kaulfuss S., Keupp K., Kiechle M., Kolbl A., Krieger S., Kruse T.A., Kvist A., Lalloo F., Larsen M., Lattimore V.L., Lautrup C., Ledig S., Leinert E., Lewis A.L., Lim J., Loeffler M., Lopez-Fernandez A., Lucci-Cordisco E., Maass N., Manoukian S., Marabelli M., Matricardi L., Meindl A., Michelli R.D., Moghadasi S., Moles-Fernandez A., Montagna M., Montalban G., Monteiro A.N., Montes E., Mori L., Moserle L., Muller C.R., Mundhenke C., Naldi N., Nathanson K.L., Navarro M., Nevanlinna H., Nichols C.B., Niederacher D., Nielsen H.R., Ong K.-R., Pachter N., Palmero E.I., Papi L., Pedersen I.S., Peissel B., Perez-Segura P., Pfeifer K., Pineda M., Pohl-Rescigno E., Poplawski N.K., Porfirio B., Quante A.S., Ramser J., Reis R.M., Revillion F., Rhiem K., Riboli B., Ritter J., Rivera D., Rofes P., Rump A., Salinas M., Sanchez de Abajo A.M., Schmidt G., Feroce I., Schoenwiese U., Seggewiss J., Solanes A., Steinemann D., Stiller M., Stoppa-Lyonnet D., Sullivan K.J., Susman R., Sutter C., Tavtigian S.V., Teo S.H., Teule A., Thomassen M., Tibiletti M.G., Tischkowitz M., Tognazzo S., Toland A.E., Tornero E., Torngren T., Torres-Esquius S., Toss A., Trainer A.H., Tucker K.M., van Asperen C.J., van Mackelenbergh M.T., Varesco L., Vargas-Parra G., Varon R., Vega A., Velasco A., Vesper A.-S., Viel A., Vreeswijk M.P.G., Wagner S.A., Waha A., Walker L.C., Walters R.J., Wang-Gohrke S., Weber B.H.F., Weichert W., Wieland K., Wiesmuller L., Witzel I., Wockel A., Woodward E.R., Zachariae S., Zampiga V., Zeder-Goss C., Investigators K., Lazaro C., De Nicolo A., Radice P., Engel C., Schmutzler R.K., Goldgar D.E., Spurdle A.B., Harris M., Parsons M.T., Tudini E., Li H., Hahnen E., Wappenschmidt B., Feliubadalo L., Aalfs C.M., Agata S., Aittomaki K., Alducci E., Alonso-Cerezo M.C., Arnold N., Auber B., Austin R., Azzollini J., Balmana J., Barbieri E., Bartram C.R., Blanco A., Blumcke B., Bonache S., Bonanni B., Borg A., Bortesi B., Brunet J., Bruzzone C., Bucksch K., Cagnoli G., Caldes T., Caliebe A., Caligo M.A., Calvello M., Capone G.L., Caputo S.M., Carnevali I., Carrasco E., Caux-Moncoutier V., Cavalli P., Cini G., Clarke E.M., Concolino P., Cops E.J., Cortesi L., Couch F.J., Darder E., de la Hoya M., Dean M., Debatin I., Del Valle J., Delnatte C., Derive N., Diez O., Ditsch N., Domchek S.M., Dutrannoy V., Eccles D.M., Ehrencrona H., Enders U., Evans D.G., Farra C., Faust U., Felbor U., Fine M., Foulkes W.D., Galvao H.C.R., Gambino G., Gehrig A., Gensini F., Gerdes A.-M., Germani A., Giesecke J., Gismondi V., Gomez C., Gomez Garcia E.B., Gonzalez S., Grau E., Grill S., Gross E., Guerrieri-Gonzaga A., Guillaud-Bataille M., Gutierrez-Enriquez S., Haaf T., Hackmann K., Hansen T.V.O., Hauke J., Heinrich T., Hellebrand H., Herold K.N., Honisch E., Horvath J., Houdayer C., Hubbel V., Iglesias S., Izquierdo A., James P.A., Janssen L.A.M., Jeschke U., Kaulfuss S., Keupp K., Kiechle M., Kolbl A., Krieger S., Kruse T.A., Kvist A., Lalloo F., Larsen M., Lattimore V.L., Lautrup C., Ledig S., Leinert E., Lewis A.L., Lim J., Loeffler M., Lopez-Fernandez A., Lucci-Cordisco E., Maass N., Manoukian S., Marabelli M., Matricardi L., Meindl A., Michelli R.D., Moghadasi S., Moles-Fernandez A., Montagna M., Montalban G., Monteiro A.N., Montes E., Mori L., Moserle L., Muller C.R., Mundhenke C., Naldi N., Nathanson K.L., Navarro M., Nevanlinna H., Nichols C.B., Niederacher D., Nielsen H.R., Ong K.-R., Pachter N., Palmero E.I., Papi L., Pedersen I.S., Peissel B., Perez-Segura P., Pfeifer K., Pineda M., Pohl-Rescigno E., Poplawski N.K., Porfirio B., Quante A.S., Ramser J., Reis R.M., Revillion F., Rhiem K., Riboli B., Ritter J., Rivera D., Rofes P., Rump A., Salinas M., Sanchez de Abajo A.M., and Schmidt G.

Abstract

The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.Copyright © 2019 Wiley Periodicals, Inc.

Published
2019

86. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Author

Parsons, MT, Tudini, E, Li, H, Hahnen, E, Wappenschmidt, B, Feliubadalo, L, Aalfs, CM, Agata, S, Aittomaki, K, Alducci, E, Concepcion Alonso-Cerezo, M, Arnold, N, Auber, B, Austin, R, Azzollini, J, Balmana, J, Barbieri, E, Bartram, CR, Blanco, A, Bluemcke, B, Bonache, S, Bonanni, B, Borg, A, Bortesi, B, Brunet, J, Bruzzone, C, Bucksch, K, Cagnoli, G, Caldes, T, Caliebe, A, Caligo, MA, Calvello, M, Capone, GL, Caputo, SM, Carnevali, I, Carrasco, E, Caux-Moncoutier, V, Cavalli, P, Cini, G, Clarke, EM, Concolino, P, Cops, EJ, Cortesi, L, Couch, FJ, Darder, E, de la Hoya, M, Dean, M, Debatin, I, Del Valle, J, Delnatte, C, Derive, N, Diez, O, Ditsch, N, Domchek, SM, Dutrannoy, V, Eccles, DM, Ehrencrona, H, Enders, U, Evans, DG, Farra, C, Faust, U, Felbor, U, Feroce, I, Fine, M, Foulkes, WD, Galvao, HC, Gambino, G, Gehrig, A, Gensini, F, Gerdes, A-M, Germani, A, Giesecke, J, Gismondi, V, Gomez, C, Garcia, EBG, Gonzalez, S, Grau, E, Grill, S, Gross, E, Guerrieri-Gonzaga, A, Guillaud-Bataille, M, Gutierrez-Enriquez, S, Haaf, T, Hackmann, K, Hansen, TV, Harris, M, Hauke, J, Heinrich, T, Hellebrand, H, Herold, KN, Honisch, E, Horvath, J, Houdayer, C, Huebbel, V, Iglesias, S, Izquierdo, A, James, PA, Janssen, LA, Jeschke, U, Kaulfuss, S, Keupp, K, Kiechle, M, Koelbl, A, Krieger, S, Kruse, TA, Kvist, A, Lalloo, F, Larsen, M, Lattimore, VL, Lautrup, C, Ledig, S, Leinert, E, Lewis, AL, Lim, J, Loeffler, M, Lopez-Fernandez, A, Lucci-Cordisco, E, Maass, N, Manoukian, S, Marabelli, M, Matricardi, L, Meindl, A, Michelli, RD, Moghadasi, S, Moles-Fernandez, A, Montagna, M, Montalban, G, Monteiro, AN, Montes, E, Mori, L, Moserle, L, Mueller, CR, Mundhenke, C, Naldi, N, Nathanson, KL, Navarro, M, Nevanlinna, H, Nichols, CB, Niederacher, D, Nielsen, HR, Ong, K-R, Pachter, N, Palmero, E, Papi, L, Pedersen, IS, Peissel, B, Perez-Segura, P, Pfeifer, K, Pineda, M, Pohl-Rescigno, E, Poplawski, NK, Porfirio, B, Quante, AS, Ramser, J, Reis, RM, Revillion, F, Rhiem, K, Riboli, B, Ritter, J, Rivera, D, Rofes, P, Rump, A, Salinas, M, Sanchez de Abajo, AM, Schmidt, G, Schoenwiese, U, Seggewiss, J, Solanes, A, Steinemann, D, Stiller, M, Stoppa-Lyonnet, D, Sullivan, KJ, Susman, R, Sutter, C, Tavtigian, S, Teo, SH, Teule, A, Thomassen, M, Tibiletti, MG, Tischkowitz, M, Tognazzo, S, Toland, AE, Tornero, E, Torngren, T, Torres-Esquius, S, Toss, A, Trainer, AH, Tucker, KM, van Asperen, CJ, van Mackelenbergh, MT, Varesco, L, Vargas-Parra, G, Varon, R, Vega, A, Velasco, A, Vesper, A-S, Viel, A, Vreeswijk, MPG, Wagner, SA, Waha, A, Walker, LC, Walters, RJ, Wang-Gohrke, S, Weber, BHF, Weichert, W, Wieland, K, Wiesmueller, L, Witzel, I, Woeckel, A, Woodward, ER, Zachariae, S, Zampiga, V, Zeder-Goss, C, Lazaro, C, De Nicolo, A, Radice, P, Engel, C, Schmutzler, RK, Goldgar, DE, Spurdle, AB, Parsons, MT, Tudini, E, Li, H, Hahnen, E, Wappenschmidt, B, Feliubadalo, L, Aalfs, CM, Agata, S, Aittomaki, K, Alducci, E, Concepcion Alonso-Cerezo, M, Arnold, N, Auber, B, Austin, R, Azzollini, J, Balmana, J, Barbieri, E, Bartram, CR, Blanco, A, Bluemcke, B, Bonache, S, Bonanni, B, Borg, A, Bortesi, B, Brunet, J, Bruzzone, C, Bucksch, K, Cagnoli, G, Caldes, T, Caliebe, A, Caligo, MA, Calvello, M, Capone, GL, Caputo, SM, Carnevali, I, Carrasco, E, Caux-Moncoutier, V, Cavalli, P, Cini, G, Clarke, EM, Concolino, P, Cops, EJ, Cortesi, L, Couch, FJ, Darder, E, de la Hoya, M, Dean, M, Debatin, I, Del Valle, J, Delnatte, C, Derive, N, Diez, O, Ditsch, N, Domchek, SM, Dutrannoy, V, Eccles, DM, Ehrencrona, H, Enders, U, Evans, DG, Farra, C, Faust, U, Felbor, U, Feroce, I, Fine, M, Foulkes, WD, Galvao, HC, Gambino, G, Gehrig, A, Gensini, F, Gerdes, A-M, Germani, A, Giesecke, J, Gismondi, V, Gomez, C, Garcia, EBG, Gonzalez, S, Grau, E, Grill, S, Gross, E, Guerrieri-Gonzaga, A, Guillaud-Bataille, M, Gutierrez-Enriquez, S, Haaf, T, Hackmann, K, Hansen, TV, Harris, M, Hauke, J, Heinrich, T, Hellebrand, H, Herold, KN, Honisch, E, Horvath, J, Houdayer, C, Huebbel, V, Iglesias, S, Izquierdo, A, James, PA, Janssen, LA, Jeschke, U, Kaulfuss, S, Keupp, K, Kiechle, M, Koelbl, A, Krieger, S, Kruse, TA, Kvist, A, Lalloo, F, Larsen, M, Lattimore, VL, Lautrup, C, Ledig, S, Leinert, E, Lewis, AL, Lim, J, Loeffler, M, Lopez-Fernandez, A, Lucci-Cordisco, E, Maass, N, Manoukian, S, Marabelli, M, Matricardi, L, Meindl, A, Michelli, RD, Moghadasi, S, Moles-Fernandez, A, Montagna, M, Montalban, G, Monteiro, AN, Montes, E, Mori, L, Moserle, L, Mueller, CR, Mundhenke, C, Naldi, N, Nathanson, KL, Navarro, M, Nevanlinna, H, Nichols, CB, Niederacher, D, Nielsen, HR, Ong, K-R, Pachter, N, Palmero, E, Papi, L, Pedersen, IS, Peissel, B, Perez-Segura, P, Pfeifer, K, Pineda, M, Pohl-Rescigno, E, Poplawski, NK, Porfirio, B, Quante, AS, Ramser, J, Reis, RM, Revillion, F, Rhiem, K, Riboli, B, Ritter, J, Rivera, D, Rofes, P, Rump, A, Salinas, M, Sanchez de Abajo, AM, Schmidt, G, Schoenwiese, U, Seggewiss, J, Solanes, A, Steinemann, D, Stiller, M, Stoppa-Lyonnet, D, Sullivan, KJ, Susman, R, Sutter, C, Tavtigian, S, Teo, SH, Teule, A, Thomassen, M, Tibiletti, MG, Tischkowitz, M, Tognazzo, S, Toland, AE, Tornero, E, Torngren, T, Torres-Esquius, S, Toss, A, Trainer, AH, Tucker, KM, van Asperen, CJ, van Mackelenbergh, MT, Varesco, L, Vargas-Parra, G, Varon, R, Vega, A, Velasco, A, Vesper, A-S, Viel, A, Vreeswijk, MPG, Wagner, SA, Waha, A, Walker, LC, Walters, RJ, Wang-Gohrke, S, Weber, BHF, Weichert, W, Wieland, K, Wiesmueller, L, Witzel, I, Woeckel, A, Woodward, ER, Zachariae, S, Zampiga, V, Zeder-Goss, C, Lazaro, C, De Nicolo, A, Radice, P, Engel, C, Schmutzler, RK, Goldgar, DE, and Spurdle, AB

Abstract

The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.

Published
2019

87. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Author

Parsons, M. T., Tudini, E., Li, H., Hahnen, E., Wappenschmidt, B., Feliubadalo, L., Aalfs, C. M., Agata, S., Aittomaki, K., Alducci, E., Alonso-Cerezo, M. C., Arnold, N., Auber, B., Austin, R., Azzollini, J., Balmana, J., Barbieri, E., Bartram, C. R., Blanco, A., Blumcke, B., Bonache, S., Bonanni, B., Borg, A., Bortesi, B., Brunet, J., Bruzzone, C., Bucksch, K., Cagnoli, G., Caldes, T., Caliebe, A., Caligo, M. A., Calvello, M., Capone, G. L., Caputo, S. M., Carnevali, I., Carrasco, E., Caux-Moncoutier, V., Cavalli, P., Cini, G., Clarke, E. M., Concolino, Paola, Cops, E. J., Cortesi, L., Couch, F. J., Darder, E., de la Hoya, M., Dean, M., Debatin, I., Del Valle, J., Delnatte, C., Derive, N., Diez, O., Ditsch, N., Domchek, S. M., Dutrannoy, V., Eccles, D. M., Ehrencrona, H., Enders, U., Evans, D. G., Farra, C., Faust, U., Felbor, U., Feroce, I., Fine, M., Foulkes, W. D., Galvao, H. C. R., Gambino, G., Gehrig, A., Gensini, F., Gerdes, A. -M., Germani, A., Giesecke, J., Gismondi, V., Gomez, C., Gomez Garcia, E. B., Gonzalez, S., Grau, E., Grill, S., Gross, E., Guerrieri-Gonzaga, A., Guillaud-Bataille, M., Gutierrez-Enriquez, S., Haaf, T., Hackmann, K., Hansen, T. V. O., Harris, M., Hauke, J., Heinrich, T., Hellebrand, H., Herold, K. N., Honisch, E., Horvath, J., Houdayer, C., Hubbel, V., Iglesias, S., Izquierdo, A., James, P. A., Janssen, L. A. M., Jeschke, U., Kaulfuss, S., Keupp, K., Kiechle, M., Kolbl, A., Krieger, S., Kruse, T. A., Kvist, A., Lalloo, F., Larsen, M., Lattimore, V. L., Lautrup, C., Ledig, S., Leinert, E., Lewis, A. L., Lim, J., Loeffler, M., Lopez-Fernandez, A., Lucci Cordisco, Emanuela, Maass, N., Manoukian, S., Marabelli, M., Matricardi, L., Meindl, A., Michelli, R. D., Moghadasi, S., Moles-Fernandez, A., Montagna, M., Montalban, G., Monteiro, A. N., Montes, E., Mori, L., Moserle, L., Muller, C. R., Mundhenke, C., Naldi, N., Nathanson, K. L., Navarro, M., Nevanlinna, H., Nichols, C. B., Niederacher, D., Nielsen, H. R., Ong, K. -R., Pachter, N., Palmero, E. I., Papi, L., Pedersen, I. S., Peissel, B., Perez-Segura, P., Pfeifer, K., Pineda, M., Pohl-Rescigno, E., Poplawski, N. K., Porfirio, B., Quante, A. S., Ramser, J., Reis, R. M., Revillion, F., Rhiem, K., Riboli, B., Ritter, J., Rivera, D., Rofes, P., Rump, A., Salinas, M., Sanchez de Abajo, A. M., Schmidt, G., Schoenwiese, U., Seggewiss, J., Solanes, A., Steinemann, D., Stiller, M., Stoppa-Lyonnet, D., Sullivan, K. J., Susman, R., Sutter, C., Tavtigian, S. V., Teo, S. H., Teule, A., Thomassen, M., Tibiletti, M. G., Tischkowitz, M., Tognazzo, S., Toland, A. E., Tornero, E., Torngren, T., Torres-Esquius, S., Toss, A., Trainer, A. H., Tucker, K. M., van Asperen, C. J., van Mackelenbergh, M. T., Varesco, L., Vargas-Parra, G., Varon, R., Vega, A., Velasco, A., Vesper, A. -S., Viel, A., Vreeswijk, M. P. G., Wagner, S. A., Waha, A., Walker, L. C., Walters, R. J., Wang-Gohrke, S., Weber, B. H. F., Weichert, W., Wieland, K., Wiesmuller, L., Witzel, I., Wockel, A., Woodward, E. R., Zachariae, S., Zampiga, V., Zeder-Goss, C., Investigators, K., Lazaro, C., De Nicolo, A., Radice, P., Engel, C., Schmutzler, R. K., Goldgar, D. E., Spurdle, A. B., Concolino P., Lucci Cordisco E. (ORCID:0000-0002-6279-7604), Parsons, M. T., Tudini, E., Li, H., Hahnen, E., Wappenschmidt, B., Feliubadalo, L., Aalfs, C. M., Agata, S., Aittomaki, K., Alducci, E., Alonso-Cerezo, M. C., Arnold, N., Auber, B., Austin, R., Azzollini, J., Balmana, J., Barbieri, E., Bartram, C. R., Blanco, A., Blumcke, B., Bonache, S., Bonanni, B., Borg, A., Bortesi, B., Brunet, J., Bruzzone, C., Bucksch, K., Cagnoli, G., Caldes, T., Caliebe, A., Caligo, M. A., Calvello, M., Capone, G. L., Caputo, S. M., Carnevali, I., Carrasco, E., Caux-Moncoutier, V., Cavalli, P., Cini, G., Clarke, E. M., Concolino, Paola, Cops, E. J., Cortesi, L., Couch, F. J., Darder, E., de la Hoya, M., Dean, M., Debatin, I., Del Valle, J., Delnatte, C., Derive, N., Diez, O., Ditsch, N., Domchek, S. M., Dutrannoy, V., Eccles, D. M., Ehrencrona, H., Enders, U., Evans, D. G., Farra, C., Faust, U., Felbor, U., Feroce, I., Fine, M., Foulkes, W. D., Galvao, H. C. R., Gambino, G., Gehrig, A., Gensini, F., Gerdes, A. -M., Germani, A., Giesecke, J., Gismondi, V., Gomez, C., Gomez Garcia, E. B., Gonzalez, S., Grau, E., Grill, S., Gross, E., Guerrieri-Gonzaga, A., Guillaud-Bataille, M., Gutierrez-Enriquez, S., Haaf, T., Hackmann, K., Hansen, T. V. O., Harris, M., Hauke, J., Heinrich, T., Hellebrand, H., Herold, K. N., Honisch, E., Horvath, J., Houdayer, C., Hubbel, V., Iglesias, S., Izquierdo, A., James, P. A., Janssen, L. A. M., Jeschke, U., Kaulfuss, S., Keupp, K., Kiechle, M., Kolbl, A., Krieger, S., Kruse, T. A., Kvist, A., Lalloo, F., Larsen, M., Lattimore, V. L., Lautrup, C., Ledig, S., Leinert, E., Lewis, A. L., Lim, J., Loeffler, M., Lopez-Fernandez, A., Lucci Cordisco, Emanuela, Maass, N., Manoukian, S., Marabelli, M., Matricardi, L., Meindl, A., Michelli, R. D., Moghadasi, S., Moles-Fernandez, A., Montagna, M., Montalban, G., Monteiro, A. N., Montes, E., Mori, L., Moserle, L., Muller, C. R., Mundhenke, C., Naldi, N., Nathanson, K. L., Navarro, M., Nevanlinna, H., Nichols, C. B., Niederacher, D., Nielsen, H. R., Ong, K. -R., Pachter, N., Palmero, E. I., Papi, L., Pedersen, I. S., Peissel, B., Perez-Segura, P., Pfeifer, K., Pineda, M., Pohl-Rescigno, E., Poplawski, N. K., Porfirio, B., Quante, A. S., Ramser, J., Reis, R. M., Revillion, F., Rhiem, K., Riboli, B., Ritter, J., Rivera, D., Rofes, P., Rump, A., Salinas, M., Sanchez de Abajo, A. M., Schmidt, G., Schoenwiese, U., Seggewiss, J., Solanes, A., Steinemann, D., Stiller, M., Stoppa-Lyonnet, D., Sullivan, K. J., Susman, R., Sutter, C., Tavtigian, S. V., Teo, S. H., Teule, A., Thomassen, M., Tibiletti, M. G., Tischkowitz, M., Tognazzo, S., Toland, A. E., Tornero, E., Torngren, T., Torres-Esquius, S., Toss, A., Trainer, A. H., Tucker, K. M., van Asperen, C. J., van Mackelenbergh, M. T., Varesco, L., Vargas-Parra, G., Varon, R., Vega, A., Velasco, A., Vesper, A. -S., Viel, A., Vreeswijk, M. P. G., Wagner, S. A., Waha, A., Walker, L. C., Walters, R. J., Wang-Gohrke, S., Weber, B. H. F., Weichert, W., Wieland, K., Wiesmuller, L., Witzel, I., Wockel, A., Woodward, E. R., Zachariae, S., Zampiga, V., Zeder-Goss, C., Investigators, K., Lazaro, C., De Nicolo, A., Radice, P., Engel, C., Schmutzler, R. K., Goldgar, D. E., Spurdle, A. B., Concolino P., and Lucci Cordisco E. (ORCID:0000-0002-6279-7604)

Abstract

The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.

Published
2019

93. Anthelmintic activity of Stevia multiaristata extract against Echinococcus granulosus sensu stricto.

Author

Albani, C. M., Borgo, J., Fabbri, J., Pensel, P., Fasciani, L., Elso, O., Papademetrio, D., Grasso, D., Paladini, A., Beer, M. F., Farias, N. E., Elissondo, N., Gambino, G., Zoppi, J., Sülsen, V., and Elissondo, M. C.

Subjects
ECHINOCOCCUS granulosus, LEISHMANIASIS, ESSENTIAL oils, STEVIA, DITERPENES
Abstract

Keywords: Anti-parasitic treatment; cystic echinococcosis; phytotherapy; plant extract EN Anti-parasitic treatment cystic echinococcosis phytotherapy plant extract 519 528 10 03/29/22 20220401 NES 220401 Introduction Cystic echinococcosis (CE) is a worldwide zoonotic disease caused by the larval stage of the parasite I Echinococcus granulosus sensu lato i ( I s.l. i ) which provokes long-term infections in humans and animals, being a serious public health problem (Pavletic I et al i ., 2017). Based on the World Health Organization Informal Working Group on Echinococcosis (WHO-IWGE) classification of cyst stages by imaging-based techniques, four treatment options have been suggested: percutaneous-aspiration-injection and re-aspiration (PAIR), surgery, anti-parasitic therapy with benzimidazoles (BZM) and a watch-and-wait approach for inactive cysts (Siles-Lucas I et al i ., 2018). For I in vitro i studies involving Huh7 cells, the I S. multiaristata i extract (10 mg) was sequentially resuspended in 20 I i L of DMSO, 40 I i L of ethanol 96% and finally, 40 I i L of deionized water, giving a solution of 100 mg mL SP -1 sp . We found that the I S. multiaristata i extract caused both an I in vitro i effect on protoscoleces and cysts and also an I in vivo i therapeutic effect. [Extracted from the article]

Published
2022
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96. Validation and harmonization of diagnostic methods for the detection of Grapevine Pinot gris virus (GPGV)

Author

Gentili, A., Angelini, E., Babini, A.R., Bertazzon, N., Bianchi, G.L., Botti, S., Calvi, M., Cardoni, M., Casati, P., Cosmi, T., Gambino, G., Gualandri, V., Kubaa, R.A., Malossini, U., Martini, M., Mason, M., Raiola, A., Ratti, C., Saldarelli, P., Silletti, M.R., Tarquini, G., and Faggioli, F.

Subjects
diagnostic protocols, real-time RT-PCR, Settore AGR/12 - PATOLOGIA VEGETALE, Grapevine virus
Abstract

Grapevine pinot gris virus (GPGV) has been originally found in Northern Italy associated to symptoms of stunting, chlorotic mottling and leaf deformations in grapevine plants. Successively, its presence has been reported in many countries even on asymptomatic plants. The study of this virus with regard to its biological and molecular characterization, its etiological role and spread by Eryophid mites vectors Colomerus vitis, the symptoms on different grapevine varieties cannot disregard the use of reliable, robust and validated diagnostic methods to implement possible prevention strategies. To this aim, a test performance study (TPS) was carried out to evaluate, harmonize and validate four diagnostic protocols used in the detection of GPGV in symptomatic and asymptomatic grapevine material. Specifically, two end point RT-PCR (Glasa et.al. 2014 - protocol 1; Saldarelli et al. 2015 - protocol 2) and two real time RT-PCR (Bianchi et al. 2015 - protocol 3; Ratti personal communication 2015- protocol 4) protocols have been compared. Obtained performance data from the four molecular protocols are reported and evaluated in the present Abstract. Both diagnostic methods, (end point and real time RT-PCR) were proven to be highly effective, although analytical sensitivity was more efficient for real time protocols, as expected. No statistically significant differences were observed for the other validation parameters. Moreover, all protocols gave satisfactory results even if six samples with low virus concentration were selected to stress the tests. Despite the large number of laboratories that performed the TPS and the different instruments and extraction methods (Nitrogen or different mechanic grinding system), no statistically significant differences were observed in the analytical specificity using the non target samples infected by other viruses than GPGV. All protocols showed good accuracy and robustness as proven using a large number of samples in a high number of laboratories. In conclusion, harmonized and validated reference protocols for the diagnosis of GPGV are, for the first time, available.

Published
2018

97. A viral suppressor modulates the plant immune response early in infection by regulating miRNA activity

Author

Pertermann R., Tamilarasan S., Gursinsky T., Gambino G., Schuck J., Weinholdt C., Lilie H., Grosse I., Golbik R., Pantaleo V., and Behrens S.E.

Subjects
RISC, RNA interference, RNA replication, RNA silencing, RNA-protein interactions, VSR, antiviral, immune evasion, miRNA, plant viruses, plus-strand RNA virus, siRNA
Abstract

Many viral suppressors (VSRs) counteract antiviral RNA silencing, a central component of the plant's immune response by sequestration of virus-derived antiviral small interfering RNAs (siRNAs). Here, we addressed how VSRs affect the activities of cellular microRNAs (miRNAs) during a viral infection by characterizing the interactions of two unrelated VSRs, the Tombusvirus p19 and the Cucumovirus 2b, with miRNA 162 (miR162), miR168, and miR403. These miRNAs regulate the expression of the important silencing factors Dicer-like protein 1 (DCL1) and Argonaute proteins 1 and 2 (AGO1 and AGO2), respectively. Interestingly, while the two VSRs showed similar binding profiles, the miRNAs were bound with significantly different affinities, for example, with the affinity of miR162 greatly exceeding that of miR168. In vitro silencing experiments revealed that p19 and 2b affect miRNA-mediated silencing of the DCL1, AGO1, and AGO2 mRNAs in strict accordance with the VSR's miRNA-binding profiles. In Tombusvirus-infected plants, the miRNA-binding behavior of p19 closely corresponded to that in vitro Most importantly, in contrast to controls with a ?p19 virus, infections with wild-type (wt) virus led to changes of the levels of the miRNA-targeted mRNAs, and these changes correlated with the miRNA-binding preferences of p19. This was observed exclusively in the early stage of infection when viral genomes are proposed to be susceptible to silencing and viral siRNA (vsiRNA) concentrations are low. Accordingly, our study suggests that differential binding of miRNAs by VSRs is a widespread viral mechanism to coordinately modulate cellular gene expression and the antiviral immune response during infection initiation.IMPORTANCE Plant viruses manipulate their hosts in various ways. Viral suppressor proteins (VSRs) interfere with the plant's immune response by sequestering small, antivirally acting vsiRNAs, which are processed from viral RNAs during the plant's RNA-silencing response. Here, we examined the effects of VSRs on cellular microRNAs (miRNAs), which show a high degree of similarity with vsiRNAs. Binding experiments with two unrelated VSRs and three important regulatory miRNAs revealed that the proteins exhibit similar miRNA-binding profiles but bind different miRNAs at considerably different affinities. Most interestingly, experiments in plants showed that in the early infection phase, the Tombusvirus VSR p19 modulates the activity of these miRNAs on their target mRNAs very differently and that this differential regulation strictly correlates with the binding affinities of p19 for the respective miRNAs. Our data suggest that VSRs may specifically control plant gene expression and the early immune response by differential sequestration of miRNAs.

Published
2018

98. Transcriptional reprogramming and epigenomic landscape dynamics during grapevine somatic embryogenesis process

Author

Dal Santo S., Amato A., Pagliarani C., Del Fabbro C., Pezzotti M., Gambino G., De Paoli E., and Perrone I.

Subjects
fungi, transcriptional variation, somatic embryogenesis, grapevine
Abstract

"Somatic embryogenesis (SE), a morphogenic process that takes advantage of the regenerative potential of plants to replicate whole plants starting from somatic explants, can be a source of variation with potential applications in plant breeding. It is one of the most suitable tools to apply functional genomics studies and genetic improvement in plants. However, beyond a few pioneering works mainly focused on model plants, the molecular characterization of SE mechanisms is still elusive, especially for woody species. In grapevine, this process is affected by many factors such as explant type, culture conditions and, most importantly, genotype. Many cultivars, in fact, have shown recalcitrance to tissue culture and transformation, and very low SE competence. Thus, the understanding of SE competence behind the regenerative aptitude is fundamental to the widespread application of the so-called "next-generation breeding techniques", such as cisgenesis and genome editing, in grapevine. Here, we explored genetic and epigenetic features of the SE process in grapevine by investigating the behavior of two genotypes showing opposite SE competence. Embryogenic tissues were induced from immature stamens excised from field-collected flower clusters of Sangiovese (highly competent for embryogenesis) and Cabernet Sauvignon (poorly competent for embryogenesis). A multilayered approach was used to profile mRNA, smallRNAs and methylated DNA with high-throughput sequencing technologies in the initial explants, on undifferentiated calli induced after 40 days of culture, and in embryogenic and non-embryogenic calli after 3 months of culture. A comprehensive comparison of transcriptomes of the different types of calli with the grapevine gene expression atlas revealed that, in grapevine, the dedifferentiation to the callus formation during the embryogenesis process occurs via a 'berry' developmental pathway. This is dissimilar from that shown in Arabidopsis, in which dedifferentiated calli are more similar to the tip of a root meristem. Interestingly, a Gene Ontology (GO) analysis revealed that secondary metabolism and gene expression regulation/epigenetics are the enriched functional categories of genes differentially down- and up-regulated in embryogenic vs non-embryogenic calli, respectively. These results prompted us to define the epigenetic landscape dynamics during SE in grapevine, revealing a significant increase in DNA methylation, especially in intergenic regions, in the embryogenic calli tissues. Finally, we proposed potential key regulators of SE in different genotypes that could represent putative targets of next-generation breeding techniques in grapevine."

Published
2018

99. Interactive responses of Vitis vinifera L. plants infected by Grapevine virus B (GVB) in field conditions leads to ameliorate berry secondary metabolism

Author

Chitarra W., Cuozzo D., Ferrandino A., Secchi F., Palmano S., Perrone I., Boccacci P., Pagliarani C., Gribaudo I., Mannini F., and Gambino G.

Subjects
Plant-virus interaction, sugar signaling, fungi, food and beverages, gas exchange, anthocyanins, grapevine
Abstract

A plant virus infection results from a complex molecular and physiological interplay with the host. In light of this, the impact of the phloem-limited virus Grapevine virus B (GVB) on the Vitis vinifera L. wine-red cultivar 'Albarossa' was analyzed in field conditions. This study was carried out during two growth seasons, by combining agronomical, molecular, biochemical and ecophysiological approaches. The obtained data showed that GVB did not induce macroscopic symptoms on 'Albarossa', but it rather affected the ecophysiological performances of vines in terms of assimilation rates, particularly at the end of the season, without compromising yield and vigor. Moreover, in GVB-infected plants, the soluble carbohydrate accumulation in leaves and expression profiles of sugar- and photosynthetic-related genes seemed to activate defense responses similar to those observed in plants infected by phytoplasmas, although with lesser extent. In addition, GVB presence induces an activation of secondary metabolism positively affecting anthocyanin profiles in berry. In particular, total anthocyanins and their acetylated forms have been accumulated in GVB-infected berries at high levels according also to the up-regulation of some important biosynthetic genes. All together, these results can contribute both to improve current understanding of the multifaceted grapevine-virus interaction in response to environmental condition and to support future approaches of sustainable viticulture.

Published
2018

100. Transcriptional response of different Vitis vinifera 'Nebbiolo' clones involves molecular signals regulating berry development in coordination with stress defence mechanisms

Author

Pagliarani C., Boccacci P., Chitarra W., Cosentino E., Sandri M., Perrone I., Mori A., Cuozzo D., Nerva L., Rossato M., Zuccolotto P., Pezzotti M., Delledonne M., Mannini F., Gribaudo I., and Gambino G.

Subjects
fungi, food and beverages, Grapevine, genotype x environment interaction, berry
Abstract

"Many research works have unveiled how grapevine cultivars respond to environmental conditions; however, the molecular mechanisms underlying the interplay between clones (vegetatively propagated lines of selected mother plants) and environment need to be elucidated. This study was aimed to explore the complexity of the clone x environment interaction by investigating changes controlled by clone, vineyard or developmental stage. The transcriptome of berries collected over ripening in different vineyards from three 'Nebbiolo' clones was analyzed by integrating RNA-seq data with analysis of candidate genes, quantification of secondary metabolites and agronomical parameters. Transcripts associated to sugar transport and anthocyanin biosynthesis were differently modulated among clones, while genes involved in secondary metabolism and defence, such as stilbene synthase genes, were affected by vineyard, consistently with stilbenoid accumulation. This attests that clone-specific responses exert a role in shaping agronomic performances of a grape variety in different environments, thus providing indications for orienting viticultural practices in light of both cultivation area and clone choice."

Published
2018

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