Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

Autor: Sarah E. Brnich, Ahmad N. Abou Tayoun, Fergus J. Couch, Garry R. Cutting, Marc S. Greenblatt, Christopher D. Heinen, Dona M. Kanavy, Xi Luo, Shannon M. McNulty, Lea M. Starita, Sean V. Tavtigian, Matt W. Wright, Steven M. Harrison, Leslie G. Biesecker, Jonathan S. Berg, On behalf of the Clinical Genome Resource Sequence Variant Interpretation Working Group

Publikováno v: Genome Medicine, Vol 12, Iss 1, Pp 1-12 (2019)

Abstract Background The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria for different types of evidence. This includes the strong evide

Externí odkaz: https://doaj.org/article/4407a9ebc41048f29d3325398d3b8d31

Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria

Autor: Vikas Pejaver, Alicia B. Byrne, Bing-Jian Feng, Kymberleigh A. Pagel, Sean D. Mooney, Rachel Karchin, Anne O’Donnell-Luria, Steven M. Harrison, Sean V. Tavtigian, Marc S. Greenblatt, Leslie G. Biesecker, Predrag Radivojac, Steven E. Brenner, Ahmad A. Tayoun, Jonathan S. Berg, Garry R. Cutting, Sian Ellard, Peter Kang, Izabela Karbassi, Jessica Mester, Tina Pesaran, Sharon E. Plon, Heidi L. Rehm, Natasha T. Strande, Scott Topper

Publikováno v: The American Journal of Human Genetics. 109:2163-2177

Recommendations from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants specify the use of computational predictors as "supporting" level of evidence for pat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::63d921f44375e47e5baccb6ef134edc1
https://doi.org/10.1016/j.ajhg.2022.10.013

Extracting seizure frequency from epilepsy clinic notes: a machine reading approach to natural language processing

Autor: Kevin Xie, Ryan S Gallagher, Erin C Conrad, Chadric O Garrick, Steven N Baldassano, John M Bernabei, Peter D Galer, Nina J Ghosn, Adam S Greenblatt, Tara Jennings, Alana Kornspun, Catherine V Kulick-Soper, Jal M Panchal, Akash R Pattnaik, Brittany H Scheid, Danmeng Wei, Micah Weitzman, Ramya Muthukrishnan, Joongwon Kim, Brian Litt, Colin A Ellis, Dan Roth

Publikováno v: Journal of the American Medical Informatics Association. 29:873-881

Objective Seizure frequency and seizure freedom are among the most important outcome measures for patients with epilepsy. In this study, we aimed to automatically extract this clinical information from unstructured text in clinical notes. If successf

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca62b82a63595b59b98e4edc41628d69
https://doi.org/10.1093/jamia/ocac018

Determining the clinical validity of hereditary colorectal cancer and polyposis susceptibility genes using the Clinical Genome Resource Clinical Validity Framework

Autor: Marc S. Greenblatt, Deborah I. Ritter, Matthew J. Ferber, Jennifer McGlaughon, Kristy Lee, Ryan J. Schmidt, Bryony A. Thompson, Bryce A. Seifert, Maegan E. Roberts, Liying Zhang, Mackenzie Trapp, Sharisse Jimenez, Sarah A. Jackson, Sharon E. Plon, Zsofia K. Stadler, Kenneth Offit

Publikováno v: Genetics in medicine : official journal of the American College of Medical Genetics

Purpose: Gene-disease associations implicated in hereditary colorectal cancer and polyposis susceptibility were evaluated using the ClinGen Clinical Validity framework. Methods: Forty-two gene-disease pairs were assessed for strength of evidence supp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::550545b14b4a91cfbee4d917685cdc82
https://doi.org/10.1038/s41436-018-0373-1

No Difference in Penetrance between Truncating and Missense/Aberrant Splicing Pathogenic Variants in MLH1 and MSH2: A Prospective Lynch Syndrome Database Study

Autor: Guy Rosner, Walter Hernán Pavicic, Claudia Perne, Carlos A. Vaccaro, Elke Holinski-Feder, Leticia Moreira, Wouter H. de Vos tot Nederveen Cappel, Stefan Aretz, Einar Andreas Rødland, Polly A. Newcomb, Karin Alvarez, Ariadna Sánchez, Lone Sunde, Wolff Schmiegel, Joan Brunet, Marc S. Greenblatt, Christina Therkildsen, Karl Heinimann, Lior H. Katz, Fiona Lalloo, Jürgen Weitz, Anna Lepistö, Rolf H. Sijmons, Maartje Nielsen, Hans F. A. Vasen, Deepak Vangala, Monika Morak, Jukka-Pekka Mecklin, Toni T. Seppälä, Sigve Nakken, Stefanie Holzapfel, Douglas Tjandra, Finlay A. Macrae, Päivi Peltomäki, Daniel D. Buchanan, Stephen N. Thibodeau, Adriana Della Valle, James Hill, Annika Lindblom, Bernardo Bonanni, Reinhard Büttner, Francisco López-Köstner, Giulia Martina Cavestro, John Burn, Emma J Crosbie, Lucio Bertario, Sanne W. ten Broeke, D. G. R. Evans, Kate Green, Verena Steinke-Lange, Eivind Hovig, Miquel Serra-Burriel, Francesc Balaguer, Kirsi Pylvänäinen, Gabriela Möslein, Revital Kariv, Thomas Hansen, Maria Grazia Tibiletti, Tamara Alejandra Piñero, Nils Rahner, Magnus von Knebel Doeberitz, Ingrid Winship, Nathan Gluck, Lars Joachim Lindberg, Christoph Engel, Mev Dominguez-Valentin, John-Paul Plazzer, Julian R. Sampson, Marta Pineda, John L. Hopper, Pablo Kalfayan, Heike Görgens, Aung Ko Win, Steven Gallinger, Loic Le Marchand, Mark A. Jenkins, Markus Loeffler, Noralane M. Lindor, Inge Bernstein, Pål Møller, Laura Renkonen-Sinisalo, Florencia Neffa, Huw Thomas, Gabriel Capellá, Jane C. Figueiredo, Miriam Mints, Patricia Esperon, Matilde Navarro, Robert Hüneburg

Publikováno v: Journal of Clinical Medicine, 10(13):2856. MDPI AG
Dipòsit Digital de la UB
Universidad de Barcelona
Journal of Clinical Medicine, Vol 10, Iss 2856, p 2856 (2021)
Dominguez-Valentin, M, Plazzer, J P, Sampson, J R, Engel, C, Aretz, S, Jenkins, M A, Sunde, L, Bernstein, I, Capella, G, Balaguer, F, Macrae, F, Winship, I M, Thomas, H, Evans, D G, Burn, J, Greenblatt, M, de Vos tot Nederveen Cappel, W H, Sijmons, R H, Nielsen, M, Bertario, L, Bonanni, B, Tibiletti, M G, Cavestro, G M, Lindblom, A, Della Valle, A, Lopez-Kostner, F, Alvarez, K, Gluck, N, Katz, L, Heinimann, K, Vaccaro, C A, Nakken, S, Hovig, E, Green, K, Lalloo, F, Hill, J, Vasen, H F A, Perne, C, Büttner, R, Görgens, H, Holinski-Feder, E, Morak, M, Holzapfel, S, Hüneburg, R, Doeberitz, M V K, Loeffler, M, Rahner, N, Weitz, J, Steinke-Lange, V, Schmiegel, W, Vangala, D, Crosbie, E J, Pineda, M, Navarro, M, Brunet, J, Moreira, L, Sánchez, A, Serra-Burriel, M, Mints, M, Kariv, R, Rosner, G, Piñero, T A, Pavicic, W H, Kalfayan, P, Ten Broeke, S W, Mecklin, J P, Pylvänäinen, K, Renkonen-Sinisalo, L, Lepistö, A, Peltomäki, P, Hopper, J L, Win, A K, Buchanan, D D, Lindor, N M, Gallinger, S, Marchand, L L, Newcomb, P A, Figueiredo, J C, Thibodeau, S N, Therkildsen, C, Hansen, T V O, Lindberg, L, Rødland, E A, Neffa, F, Esperon, P, Tjandra, D, Möslein, G, Seppälä, T T & Møller, P 2021, ' No difference in penetrance between truncating and missense/aberrant splicing pathogenic variants in mlh1 and msh2 : A prospective lynch syndrome database study ', Journal of Clinical Medicine, vol. 10, no. 13, 2856 . https://doi.org/10.3390/jcm10132856
Journal of Clinical Medicine
Dominguez-Valentin, M, Plazzer, J-P, Sampson, J R, Engel, C, Aretz, S, Jenkins, M A, Sunde, L, Bernstein, I, Capella, G, Balaguer, F, Macrae, F, Winship, I M, Thomas, H, Evans, D G, Burn, J, Greenblatt, M, de Vos Tot Nederveen Cappel, W H, Sijmons, R H, Nielsen, M, Bertario, L, Bonanni, B, Tibiletti, M G, Cavestro, G M, Lindblom, A, Valle, A D, Lopez-Kostner, F, Alvarez, K, Gluck, N, Katz, L, Heinimann, K, Vaccaro, C A, Nakken, S, Hovig, E, Green, K, Lalloo, F, Hill, J, Vasen, H F A, Perne, C, Büttner, R, Görgens, H, Holinski-Feder, E, Morak, M, Holzapfel, S, Hüneburg, R, von Knebel Doeberitz, M, Loeffler, M, Rahner, N, Weitz, J, Steinke-Lange, V, Schmiegel, W, Vangala, D, Crosbie, E J, Pineda, M, Navarro, M, Brunet, J, Moreira, L, Sánchez, A, Serra-Burriel, M, Mints, M, Kariv, R, Rosner, G, Piñero, T A, Pavicic, W H, Kalfayan, P, Broeke, S W T, Mecklin, J-P, Pylvänäinen, K, Renkonen-Sinisalo, L, Lepistö, A, Peltomäki, P, Hopper, J L, Win, A K, Buchanan, D D, Lindor, N M, Gallinger, S, Marchand, L L, Newcomb, P A, Figueiredo, J C, Thibodeau, S N, Therkildsen, C, Hansen, T V O, Lindberg, L, Rødland, E A, Neffa, F, Esperon, P, Tjandra, D, Möslein, G, Seppälä, T T & Møller, P 2021, ' No Difference in Penetrance between Truncating and Missense/Aberrant Splicing Pathogenic Variants in MLH1 and MSH2 : A Prospective Lynch Syndrome Database Study ', Journal of Clinical Medicine, vol. 10, no. 13, 2856 . https://doi.org/10.3390/jcm10132856
Evans, D G, Crosbie, E, Hill, J & et al. 2021, ' No difference in penetrance between truncating and missense/aberrant splicing pathogenic variants in MLH1 and MSH2: A Prospective Lynch Syndrome Database study ', Journal of Clinical Medicine, vol. 10, no. 13, 2856 . https://doi.org/10.3390/jcm10132856
Volume 10
Issue 13
Journal of Clinical Medicine, 10(13). MDPI

Background. Lynch syndrome is the most common genetic predisposition for hereditary cancer. Carriers of pathogenic changes in mismatch repair (MMR) genes have an increased risk of developing colorectal (CRC), endometrial, ovarian, urinary tract, pros

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76a724a577132e178f2435d01b2921fa
https://research.rug.nl/en/publications/f2566b72-3f15-4434-8fa2-7b01e2ee1c88