Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays

Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication machinery that results in an accumulation of genomic aberrations in the form of duplications, deletions, translocations, and other genomic alterations. Microarray methods allow for finer mapping of these aberrations than has previously been possible; however, data processing and analysis methods have not taken full advantage of this higher resolution. Attention has primarily been given to analysis on the single sample level, where multiple adjacent probes are necessarily used as replicates for the local region containing their target sequences. However, regions of concordant aberration can be short enough to be detected by only one, or very few, array elements. We describe a method called Multiple Sample Analysis for assessing the significance of concordant genomic aberrations across multiple experiments that does not require a-priori definition of aberration calls for each sample. If there are multiple samples, representing a class, then by exploiting the replication across samples our method can detect concordant aberrations at much higher resolution than can be derived from current single sample approaches. Additionally, this method provides a meaningful approach to addressing population-based questions such as determining important regions for a cancer subtype of interest or determining regions of copy number variation in a population. Multiple Sample Analysis also provides single sample aberration calls in the locations of significant concordance, producing high resolution calls per sample, in concordant regions. The approach is demonstrated on a dataset representing a challenging but important resource: breast tumors that have been formalin-fixed, paraffin-embedded, archived, and subsequently UV-laser capture microdissected and hybridized to two-channel BAC arrays using an amplification protocol. We demonstrate the accurate detection on simulated data, and on real datasets involving known regions of aberration within subtypes of breast cancer at a resolution consistent with that of the array. Similarly, we apply our method to previously published datasets, including a 250K SNP array, and verify known results as well as detect novel regions of concordant aberration. The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA

Concept riqualificazione aree facoltà architettura politecnico di Milano. supervisor: santiago quesada

(From curators) The MIAW.2/forests program ///Day 1 Salutations Alessandro Balducci, Vice Rector of the Politecnico di Milano - Gianni Scudo, Vice Dean of the School ʻArchitettura e Societàʼ - Ilaria Valente, President School ʻArchitettura e Societàʼ Master of Sciences in Architecture Course - Emilio Genovesi, Councillorship of Culture, Expo, Fashion and Design, Comune di Milano - Richard Haag, Professor Emeritus University of Washington, Seattle // Opening Lecture ʻStick-Chartsʼ by Christine Dalnoky, Atelier Christine Dalnoky (France) // Workshops opening ///Day 2 MIAW Open Lectures Morning Sessions Françoise Akinosho / Maja Leonelli - MIAW Open Lectures Afternoon Sessions Anders Berensson + Ulf Mejergren (Visiondivison) / Drew Seskunas and Brice Delarue (Zirkumflex) ///Day 3 MIAW Open Lectures Morning Sessions Marialena Nikolopoulou / Marta Bottero and Chiara DʼAlpaos - MIAW Afternoon Open Lectures Sessions Giovanni Attili / Santiago Quesada ///Day 4 MIAW Open Lectures Morning Sessions Duilio Forte (AtelierFORTE) / Andre Dekker (Observatorium) ///Day 5 MIAW.2 Final and Farewell Party at the Politecnico di Milano Leonardo Campus /// The 2011 MIAWers are:/// 1 Rachele Albini / Giada Albonico / Jacopo Biasio / Sara Caramaschi / Elisa Carraro / Desislava Dimitrova / Cristina Gatti / Elisa Gulino / Mariya Hasamova / Nina Mikhailova / Ottavia Molatore / Joao Molinar / Azadeh Moradiasr / Mohyedin Navabzadeh Navabi / Giuseppe Maria Palermo / Riccardo Somaini / Bogdan Stojanovic /// 2 Andra Elena Apostolescu / Valentina Armenti / Dana Baranes / Sofia Chicherina / Guadalupe Ciocoletto / Marina Franzi / Gulin Keskin / Somayeh Khoshdelmishamandani / Gabriella Milo / Filippo Minora / Ayca Ozbank / Priyank Dipakbhai Parmar / Elena Piazza / Nicolò Rota / Pietro Spazzini / Paolo Volpetti / Tamara Zarkovic / Maia Zheliazkova /// 3 Kalina Andreeva / Giacomo Ardesio / Giulia Cascella / Filippo Cima / Carolina Luísa De Sá E Brito / Alaleh Emami / Michele Gerli / Anna Chiara Leardini / Marina Meloni / Navid Moshfeghi / Alexandra Nita / Rohit Perla / Gabriele Tomassini /// 4 Alessia Albini / Laura Beltrami / Giuseppe Biscottini / Lorenzo Campini / Angela Charalambous / Michela Di Noia / Reza Kamyabi / Ivana Lilikj / Jacopo Marcolini / Behnam Meimandpour / Surajkumar Nandakumar / Sophia Theologou / Ofelia Vera / Marco Zanini / Alice Cristina Jola Zingales / Riccardo Zocche /// 5 Fabio Bonaventura / Mattia Bravin / Matteo Calati / Lia Crupi / Serena DʼAndrea / Maria Grubova / Ketaki Kadam / Maria Korobitsyna / Aly Mohamed Mohamed Ahmed El Sayed / Mattia Morandi / Haitham Nabil Mohamed Mousa / Ozge Noyan / Arlinda Sheqiri / Ceren Sipahioglu / Paula Stefan / Claudio Valcamonico /// 6 Alessandra D'Apolito / Chrysafina Geronta / Bernardo Gonzalez De Cossio Paez / Rajesh Gupta / Sona Keresztesová / Federico Montagna / Maria Nickolova / Parsa Pahlavan / Raluca-Mihaela Serdaru / Alexandra Shatskaya /// 7 Elena Alexandrova / Chrystalla Argyrou / Tijana Djordjevic / Gloria Ferrari / Priscilla Gazzellini / Deborah Gotti / Francesco Ernst Lupic / Giulia Marcosano / Lara Mondonico / Veronica Notaro / Savia Palate / Caterina Pilar Palumbo / Ilaria Pedrini / Andrea Perletti / Giulia Repetti / Aster Sittoni / Gulcin Tanil / Matteo Tressi / Erica Ubbiali / Ayman Wagdy Mohamed Ibrahim /// 8 Giada Bonatti / Matteo Chelazzi / Alberto DʼOspina / Serena Di Nocera / Katarzyna Dudycz / Nenad Duric / Filip Durickovic / Francesca Fabiana Fochi / Andrea Guaiti / Daniela Iallorenzi / Americo Iannazzone / Mickeal Milocco / Gabriele Motta / Andreea Onu / Patrizio Pelosi / Marta Petrov / Olga Shishova / Jue Wang /// 9 Constantina Agroti / Arezoo Akbarvand / Glykeria Anaxagorouglyka / Stefano Arrighi / Nicolò Bianchi / Giulia Borghi / Miruna-Luiza Caragheorgheopol / Daniele Cremaschi / Vedat Ali Dalokay / Matteo Gobbi / Seyedeh Golkoo Hooshmand Ziafi / Daniele Iori / Berk Kangoz / Katarzyna Krol / Georgios Kyriazis / Lorenza Manfredi / Abdulkadir Eren Ozturk / Amanda Parisi De Marchi / Isha Rathod / Negin Salamat / Marina Serratine Paul / Alessia Tosini / Maria Vassileva / Ege Yuksek /// 10 Stefan Andelkovic / Mirko Andolina / Pietro Bodria / Alessandro Danesi / Irene De Donatis / Claudia De Flumeri / Corinna Del Bianco / Joris Katkecivius / Claudia Mainardi / Federico Marcantognini / Jenni Mazzoni / Luca Menegaldo / Milena Meregalli / Emanuele Migliorosi / Sara Moriggia / Manuele Mossoni / Claudia Praderio / Filippo Tiozzo / Arianne Veloce / Francesca Zanotto MIAW.2/forestsThe 2nd Milano International Architectural Workshop of the Politecnico di Milanoʼs School of ʻArchitettura e Societàʼ programmes, playing with the metaphor of forests, aimed to generate 10 new visions to explain nowadays living and its next future in the spirit of green design, resilience, recycling, and ethical consciousness.MIAW.2 took place from September 26th to September 30th 2011 involving more than 100 students supervised by 15 international tutors working on 10 different workshop themes with the target to enrich the Politecnico di Milanoʼs Leonardo Campus environscape with light installations.This catalogue shows the MIAW.2/forests resul

Concept riqualificazione aree facolt\ue0 architettura politecnico di Milano. supervisor: santiago quesada

(From curators) The MIAW.2/forests program ///Day 1 Salutations Alessandro Balducci, Vice Rector of the Politecnico di Milano - Gianni Scudo, Vice Dean of the School \u2bbArchitettura e Societ\ue0\u2bc - Ilaria Valente, President School \u2bbArchitettura e Societ\ue0\u2bc Master of Sciences in Architecture Course - Emilio Genovesi, Councillorship of Culture, Expo, Fashion and Design, Comune di Milano - Richard Haag, Professor Emeritus University of Washington, Seattle // Opening Lecture \u2bbStick-Charts\u2bc by Christine Dalnoky, Atelier Christine Dalnoky (France) // Workshops opening ///Day 2 MIAW Open Lectures Morning Sessions Fran\ue7oise Akinosho / Maja Leonelli - MIAW Open Lectures Afternoon Sessions Anders Berensson + Ulf Mejergren (Visiondivison) / Drew Seskunas and Brice Delarue (Zirkumflex) ///Day 3 MIAW Open Lectures Morning Sessions Marialena Nikolopoulou / Marta Bottero and Chiara D\u2bcAlpaos - MIAW Afternoon Open Lectures Sessions Giovanni Attili / Santiago Quesada ///Day 4 MIAW Open Lectures Morning Sessions Duilio Forte (AtelierFORTE) / Andre Dekker (Observatorium) ///Day 5 MIAW.2 Final and Farewell Party at the Politecnico di Milano Leonardo Campus /// The 2011 MIAWers are:/// 1 Rachele Albini / Giada Albonico / Jacopo Biasio / Sara Caramaschi / Elisa Carraro / Desislava Dimitrova / Cristina Gatti / Elisa Gulino / Mariya Hasamova / Nina Mikhailova / Ottavia Molatore / Joao Molinar / Azadeh Moradiasr / Mohyedin Navabzadeh Navabi / Giuseppe Maria Palermo / Riccardo Somaini / Bogdan Stojanovic /// 2 Andra Elena Apostolescu / Valentina Armenti / Dana Baranes / Sofia Chicherina / Guadalupe Ciocoletto / Marina Franzi / Gulin Keskin / Somayeh Khoshdelmishamandani / Gabriella Milo / Filippo Minora / Ayca Ozbank / Priyank Dipakbhai Parmar / Elena Piazza / Nicol\uf2 Rota / Pietro Spazzini / Paolo Volpetti / Tamara Zarkovic / Maia Zheliazkova /// 3 Kalina Andreeva / Giacomo Ardesio / Giulia Cascella / Filippo Cima / Carolina Lu\uedsa De S\ue1 E Brito / Alaleh Emami / Michele Gerli / Anna Chiara Leardini / Marina Meloni / Navid Moshfeghi / Alexandra Nita / Rohit Perla / Gabriele Tomassini /// 4 Alessia Albini / Laura Beltrami / Giuseppe Biscottini / Lorenzo Campini / Angela Charalambous / Michela Di Noia / Reza Kamyabi / Ivana Lilikj / Jacopo Marcolini / Behnam Meimandpour / Surajkumar Nandakumar / Sophia Theologou / Ofelia Vera / Marco Zanini / Alice Cristina Jola Zingales / Riccardo Zocche /// 5 Fabio Bonaventura / Mattia Bravin / Matteo Calati / Lia Crupi / Serena D\u2bcAndrea / Maria Grubova / Ketaki Kadam / Maria Korobitsyna / Aly Mohamed Mohamed Ahmed El Sayed / Mattia Morandi / Haitham Nabil Mohamed Mousa / Ozge Noyan / Arlinda Sheqiri / Ceren Sipahioglu / Paula Stefan / Claudio Valcamonico /// 6 Alessandra D'Apolito / Chrysafina Geronta / Bernardo Gonzalez De Cossio Paez / Rajesh Gupta / Sona Keresztesov\ue1 / Federico Montagna / Maria Nickolova / Parsa Pahlavan / Raluca-Mihaela Serdaru / Alexandra Shatskaya /// 7 Elena Alexandrova / Chrystalla Argyrou / Tijana Djordjevic / Gloria Ferrari / Priscilla Gazzellini / Deborah Gotti / Francesco Ernst Lupic / Giulia Marcosano / Lara Mondonico / Veronica Notaro / Savia Palate / Caterina Pilar Palumbo / Ilaria Pedrini / Andrea Perletti / Giulia Repetti / Aster Sittoni / Gulcin Tanil / Matteo Tressi / Erica Ubbiali / Ayman Wagdy Mohamed Ibrahim /// 8 Giada Bonatti / Matteo Chelazzi / Alberto D\u2bcOspina / Serena Di Nocera / Katarzyna Dudycz / Nenad Duric / Filip Durickovic / Francesca Fabiana Fochi / Andrea Guaiti / Daniela Iallorenzi / Americo Iannazzone / Mickeal Milocco / Gabriele Motta / Andreea Onu / Patrizio Pelosi / Marta Petrov / Olga Shishova / Jue Wang /// 9 Constantina Agroti / Arezoo Akbarvand / Glykeria Anaxagorouglyka / Stefano Arrighi / Nicol\uf2 Bianchi / Giulia Borghi / Miruna-Luiza Caragheorgheopol / Daniele Cremaschi / Vedat Ali Dalokay / Matteo Gobbi / Seyedeh Golkoo Hooshmand Ziafi / Daniele Iori / Berk Kangoz / Katarzyna Krol / Georgios Kyriazis / Lorenza Manfredi / Abdulkadir Eren Ozturk / Amanda Parisi De Marchi / Isha Rathod / Negin Salamat / Marina Serratine Paul / Alessia Tosini / Maria Vassileva / Ege Yuksek /// 10 Stefan Andelkovic / Mirko Andolina / Pietro Bodria / Alessandro Danesi / Irene De Donatis / Claudia De Flumeri / Corinna Del Bianco / Joris Katkecivius / Claudia Mainardi / Federico Marcantognini / Jenni Mazzoni / Luca Menegaldo / Milena Meregalli / Emanuele Migliorosi / Sara Moriggia / Manuele Mossoni / Claudia Praderio / Filippo Tiozzo / Arianne Veloce / Francesca Zanotto MIAW.2/forestsThe 2nd Milano International Architectural Workshop of the Politecnico di Milano\u2bcs School of \u2bbArchitettura e Societ\ue0\u2bc programmes, playing with the metaphor of forests, aimed to generate 10 new visions to explain nowadays living and its next future in the spirit of green design, resilience, recycling, and ethical consciousness.MIAW.2 took place from September 26th to September 30th 2011 involving more than 100 students supervised by 15 international tutors working on 10 different workshop themes with the target to enrich the Politecnico di Milano\u2bcs Leonardo Campus environscape with light installations.This catalogue shows the MIAW.2/forests resul