Citations 3
Comparison of mRNA Splicing Assay Protocols across Multiple Laboratories: Recommendations for Best Practice in Standardized Clinical Testing
Whiley, Phillip J , Hoya, Miguel de la , Thomassen, Mads , Becker, Alexandra, Pedersen, Inge Søkilde , Montagna, Marco , Menéndez, Mireia , Quiles, Francisco, Gutiérrez‐Enríquez, Sara , Leeneer, Kim De , Tenés, Anna, Montalban, Gemma , Tserpelis, Demis, Yoshimatsu, Toshio F. , Tirapo, Carole, Raponi, Michela , Caldés, Trinidad , Blanco, Ana , Guidugli, Lucia, Garibay, Gorka Ruíz de , Wong, Ming, Tancredi, Mariella, Fachal, Laura , Ding, Yuan Chun , Kruse, Torben A., Lattimore, Vanessa , Kwong, Ava , Chan, Tsun Leung , Colombo, Mara , Vecchi, Giovanni De, Caligo, Maria A. , Baralle, Diana , Lázaro, Conxi , Radice, Paolo , Southey, Melissa C. , Houdayer, Claude , Fackenthal, Jim, Hansen, Thomas van Overeem , Vega, Ana , Dı́ez, Orland , Blok, Rien, Claes, Kathleen , Wappenschmidt, Barbara , Walker, Logan C. , Spurdle, Amanda B. , Brown, Melissa A. , Brandão, Rita D. , Santamariña, Marta , Couch, Fergus J. , Neuhausen, Susan L. , Caligo, Maria A , Spurdle, Amanda B , Vega, Ana , de la Hoya, Miguel , Diez, Orland , Gutiérrez-Enríquez, Sara , Radice, Paolo , Claes, Kathleen B M , Southey, Melissa C , Lazaro, Conxi , Montagna, Marco , Ruiz de Garibay, Gorka , Montalban, Gemma , De Leeneer, Kim , Hansen, Thomas van Overeem , Kwong, Ava , Fachal, Laura
Clinical Chemistry | November 8, 2013 | Volume: 60 | Issue: 2 | Pages: 341-352
Abstract BACKGROUND Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting. METHODS We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2) gene variants known to alter splicing (BRCA1: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and BRCA2: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design. RESULTS PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with BRCA1, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., BRCA2 c.8632+1G>A Δ19,20 and BRCA1 c.135-1G>T Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., BRCA2 c.426-12_8delGTTTT ins18bp). CONCLUSIONS We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.
Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers
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Human Molecular Genetics | September 3, 2011 | Volume: 20 | Issue: 23 | Pages: 4732-4747
Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers
Antoniou, Antonis C. , Sinilnikova, Olga M., Soucy, Penny, McGuffog, Lesley, Healey, Sue, Peterlongo, Paolo , Manoukian, Siranoush , Peissel, Bernard , Zaffaroni, Daniela , Cattaneo, Elisa , Barile, Monica, Pensotti, Valeria , Pasini, Barbara , Dolcetti, Riccardo , Giannini, Giuseppe , Putignano, Anna Laura , Varesco, Liliana , Radice, Paolo , Mai, Phuong L., Greene, Mark H. , Andrulis, Irene L. , Glendon, Gord , Özçelik, Hilmi, Thomassen, Mads , Gerdes, Anne‐Marie , Kruse, Torben A., Jensen, Uffe Birk , Crüger, Dorthe Gylling, Caligo, Maria A. , Laitman, Yael , Milgrom, Roni, Friedman, Eitan , Loman, Niklas, Harbst, Katja , Lindblom, Annika , Arver, Brita, Ehrencrona, Hans , Melin, Beatrice , SWE-BRCA, Nathanson, Katherine L. , Rebbeck, Timothy R., Jakubowska, Anna , Lubiński, Jan , Huzarski, Tomasz , Byrski, Tomasz , Cybulski, Cezary, Górski, Bohdan , Osório, Ana , Hamann, Ute, Hogervorst, Frans B.L., Rookus, Matti A. , Hooning, Maartje J. , Nelen, Marcel , Luijt, Rob B. van der , Os, Theo A.M. van, Meijers‐Heijboer, Hanne , Gómez, E. , HEBON, Peock, Susan, Cook, Margaret , Frost, Debra, Platte, Radka, Leyland, Jean, Evans, D. Gareth , Lalloo, Fiona, Eeles, Rosalind A. , Izatt, Louise , Adlard, Julian , Davidson, Rosemarie, Eccles, Diana , Ong, Kai-Ren, Douglas, Fiona, Paterson, Joan, Miedzybrodzka, Zosia , EMBRACE, Buecher, Bruno , Belotti, Muriel, Tirapo, Carole, Mazoyer, Sylvie , Barjhoux, Laure, Lasset, Christine , Leroux, Dominique, Faivre, Laurence, Bronner, Myriam , Prieur, Fabienne, Noguès, Catherine , Rouleau, Étienne , Coupier, Isabelle, Frénay, Marc, Collaborators, CEMO Study, Daly, Mary B., Terry, Mary Beth , John, Esther M. , Yassin, Yosuf, Miron, Alexander, Goldgar, David E., Registry, Breast Cancer Family, Singer, Christian F., Tea, Muy‐Kheng, Pfeiler, Georg , Dressler, Anne Catharina, Hansen, Thomas van Overeem , Jønson, Lars, Ejlertsen, Bent , Barkardóttir, Rósa B. , Kirchhoff, Tomas , Offit, Kenneth, Piedmonte, Marion, Rodriguez, Gustavo C. , Small, Laurie, Boggess, John F., Blank, Stephanie V. , Basil, Jack, Montagna, Marco , Tognazzo, Silvia , Imyanitov, Evgeny , Janavičius, Ramūnas , Lázaro, Conxi , Blanco, Ignacio , Sucheston, Lara, Walsh, Christine , Oláh, Edith , Bozsik, Anikó , Teo, Soo‐Hwang , Seldon, Joyce, Beattie, Mary, Rensburg, Elizabeth J. van , Sluiter, Michelle D., Dı́ez, Orland , Schmutzler, Rita K., Wappenschmidt, Barbara , Engel, Christoph , Meindl, Alfons , Ruehl, I., Varon-Mateeva, Raymonda, Kast, Karin, Deißler, Helmut , Niederacher, Dieter , Arnold, Norbert , Gadzicki, Dorothea, Schönbuchner, Ines, Caldes, Trinidad, Hoya, Miguel de la , Nevanlinna, Heli , Aittomäki, Kristiina, Dumont, Martine , Chiquette, Jocelyne , Chen, Xiaoqing, Beesley, Jonathan, Spurdle, Amanda B. , investigators, kConFab, Ding, Yuan Chun , Fredericksen, Zachary, Simard, Jacques , Easton, Douglas F. , Chenevix‐Trench, Georgia , CIMBA, on behalf of, Sutter, Christian , Vasen, Hans F. A. , Durocher, Francine , Rahman, Nazneen , Karlsson, Per , Nordling, Margareta , Olsson, Håkan , Hoogerbrugge, Nicoline , Waisfisz, Quinten , Barton, David , Tobias, Edward S. , Jacobs, Chris , Ellis, Ian O. , Castro, Elena , Lucassen, Anneke , Gladieff, Laurence , Thorne, Heather , Stenmark‐Askmalm, Marie , Faivre, Laurence , Kartsonaki, Christiana , Lee, Andrew , Mai, Phuong L., Kaufman, Bella , Paluch–Shimon, Shani , SWE-BRCA, Domchek, Susan M. , Gronwald, Jacek , Cajal, Teresa Ramón y , Fostira, Florentia , Andrés, Raquel , Benı́tez, Javier , Asperen, Christi J. van , Devilee, Peter , HEBON, Cook, Jackie A , Kennedy, Michael John , EMBRACE, Godwin, Andrew K. , Stoppa‐Lyonnet, Dominique , Pujol, Pascal , Collaborators, CEMO Study, Hopper, John L. , Buys, Saundra S. , Registry, Breast Cancer Family, Singer, Christian F. , Azodi, Masoud , Toland, Amanda Ewart , Agata, Simona , Pharoah, Paul D.P. , Karlan, Beth Y. , Meindl, Alfons , Caldes, Trinidad, Tischkowitz, Marc D. , Chen, Xiaoqing, investigators, kConFab, Neuhausen, Susan L. , Wang, Xianshu , Pankratz, V. Shane , Couch, Fergus J. , CIMBA, on behalf of, Nevanlinna, H , Caligo, Maria A , Peterlongo, Paolo , Spurdle, Amanda B , Teo, Soo H , van Rensburg, Elizabeth J , Eccles, Diana , de la Hoya, Miguel , Diez, Orland , Radice, Paolo , Adlard, Julian , Arnold, Norbert , Eeles, Rosalind A , Ehrencrona, Hans , Evans, D Gareth , John, Esther M , van der Luijt, Rob B , Jakubowska, Anna , Nathanson, Katherine L , Bozsik, Aniko , Engel, Christoph , Lazaro, Conxi , Montagna, Marco , Simard, Jacques , Chenevix-Trench, Georgia , Huzarski, Tomasz , Faivre, Laurence , Gómez-García, Encarna B , Hansen, Thomas van Overeem , Pasini, Barbara , Manoukian, Siranoush , Lubinski, Jan , Terry, Mary Beth , Lindblom, Annika , Ellis, Ian
Human Molecular Genetics | May 19, 2011 | Volume: 20 | Issue: 16 | Pages: 3304-3321