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The future of next generation sequencing?
A web focus from European Journal of Human Genetics and Oncogene
Next generation sequencing is rapidly pervading all areas of Human genetics: improving speed, precision, and last but not least breadth of diagnostics; opening up new avenues of screening; are screening and testing still different or is there a confluence? In parallel, it profoundly affects basic biology discovery by unravelling mutation mechanisms and causes and consequences in gene regulation and what goes wrong in genetic disease and cancer. Besides many insights, the data deluge also brings questions: on how to handle this, internally and towards the patients; the role of geneticists in the process; how - and if - to integrate direct to consumer services; how to maintain a proper public-private balance to allow therapy development but avoid undue restrictions in data access.
Follow the contributions to this debate in European Journal of Human Genetics and Oncogene
From European Journal of Human Genetics
DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia FREE
Ryan KC Yuen, Maria S Peñaherrera, Peter von Dadelszen, Deborah E McFadden and Wendy P Robinson
Eur J Hum Genet 18: 1006-1012; advance online publication, May 5, 2010; doi:10.1038/ejhg.2010.63
The causality of de novo copy number variants is overestimated FREE
Joris R Vermeesch, Irina Balikova, Connie Schrander-Stumpel, Jean-Pierre Fryns and Koenraad Devriendt
Eur J Hum Genet 19: 1112-1113; advance online publication, May 18, 2011; doi:10.1038/ejhg.2011.83
The GENCODE exome: sequencing the complete human exome EJHGOpen
Alison J Coffey, Felix Kokocinski, Maria S Calafato, Carol E Scott, Priit Palta, Eleanor Drury, Christopher J Joyce, Emily M LeProust, Jen Harrow, Sarah Hunt, Anna-Elina Lehesjoki, Daniel J Turner, Tim J Hubbard and Aarno Palotie
Eur J Hum Genet 19: 827-831; advance online publication, March 2, 2011; doi:10.1038/ejhg.2011.28
Disease gene identification strategies for exome sequencing FREE
Christian Gilissen, Alexander Hoischen, Han G Brunner and Joris A Veltman
Eur J Hum Genet 20: 490-497; advance online publication, January 18, 2012; doi:10.1038/ejhg.2011.258
Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes FREE
Lídia Feliubadaló, Adriana Lopez-Doriga, Ester Castellsagué, Jesús del Valle, Mireia Menéndez, Eva Tornero, Eva Montes, Raquel Cuesta, Carolina Gómez, Olga Campos, Marta Pineda, Sara González, Victor Moreno, Joan Brunet, Ignacio Blanco, Eduard Serra, Gabriel Capellá and Conxi Lázaro
Eur J Hum Genet advance online publication, December 19, 2012; doi:10.1038/ejhg.2012.270
Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease FREE
Morag E Shanks, Susan M Downes, Richard R Copley, Stefano Lise, John Broxholme, Karl AZ Hudspith, Alexandra Kwasniewska, Wayne IL Davies, Mark W Hankins, Emily R Packham, Penny Clouston, Anneke Seller, Andrew OM Wilkie, Jenny C Taylor, Jiannis Ragoussis and Andrea H Németh
Eur J Hum Genet 21: 274-280; advance online publication, September 12, 2012; doi:10.1038/ejhg.2012.172
Advances in Alport syndrome diagnosis using next-generation sequencing FREE
Rosangela Artuso, Chiara Fallerini, Laura Dosa, Francesca Scionti, Maurizio Clementi, Guido Garosi, Laura Massella, Maria Carmela Epistolato, Roberta Mancini, Francesca Mari, Ilaria Longo, Francesca Ariani, Alessandra Renieri and Mirella Bruttini
Eur J Hum Genet 20: 50-57; advance online publication, September 7, 2011; doi:10.1038/ejhg.2011.164
An urgent need for a change in policy revealed by a study on prenatal testing for Duchenne muscular dystrophy EJHGOpen
Apollonia T J M Helderman-van den Enden, Kamlesh Madan, Martijn H Breuning, Annemieke H van der Hout, Egbert Bakker, Christine E M de Die-Smulders and Hendrika B Ginjaar
Eur J Hum Genet 21: 21-26; advance online publication, June 6, 2012; doi:10.1038/ejhg.2012.101
Sex chromosome trisomies in Europe: prevalence, prenatal detection and outcome of pregnancy FREE
Patricia Anne Boyd, Maria Loane, Ester Garne, Babak Khoshnood and Helen Dolk a EUROCAT working group
Eur J Hum Genet 19: 231-234; advance online publication, August 25, 2010; doi:10.1038/ejhg.2010.148
Non-invasive prenatal testing for single gene disorders: exploring the ethics FREE
Zuzana Deans, Melissa Hill, Lyn S Chitty and Celine Lewis
Eur J Hum Genet advance online publication, November 28, 2012; doi:10.1038/ejhg.2012.250
Rapid aneuploidy detection or karyotyping? Ethical reflection FREE
Antina de Jong, Wybo J Dondorp, Daniëlle RM Timmermans, Jan MM van Lith and Guido MWR de Wert
Eur J Hum Genet 19: 1020-1025; advance online publication, June 1, 2011; doi:10.1038/ejhg.2011.82
Twenty-year trends in the prevalence of Down syndrome and other trisomies in Europe: impact of maternal age and prenatal screening FREE
Maria Loane, Joan K Morris, Marie-Claude Addor, Larraitz Arriola, Judith Budd, Berenice Doray, Ester Garne, Miriam Gatt, Martin Haeusler, Babak Khoshnood, Kari Klungsøyr Melve, Anna Latos-Bielenska, Bob McDonnell, Carmel Mullaney, Mary O'Mahony, Annette Queißer-Wahrendorf, Judith Rankin, Anke Rissmann, Catherine Rounding, Joaquin Salvador, David Tucker, Diana Wellesley, Lyubov Yevtushok and Helen Dolk
Eur J Hum Genet 21: 27-33; advance online publication, June 20, 2012; doi:10.1038/ejhg.2012.94
Genome-wide linkage analysis is a powerful prenatal diagnostic tool in families with unknown genetic defects FREE
Maria Arélin, Bernt Schulze, Bertram Müller-Myhsok, Denise Horn, Alexander Diers, Birgit Uhlenberg, Peter Nürnberg, Gudrun Nürnberg, Christian Becker, Stefan Mundlos, Tom H Lindner, Karl Sperling and Katrin Hoffmann
Eur J Hum Genet 21: 367-372; advance online publication, October 3, 2012; doi:10.1038/ejhg.2012.198
Genetic testing and common disorders in a public health framework FREE
Carla G van El and Martina C Cornel
Eur J Hum Genet 19: 377-381; advance online publication, January 26, 2011; doi:10.1038/ejhg.2010.176
Genetic testing and common disorders in a public health framework: how to assess relevance and possibilities FREE
Frauke Becker, Carla G van El, Dolores Ibarreta, Eleni Zika, Stuart Hogarth, Pascal Borry, Anne Cambon-Thomsen, Jean Jacques Cassiman, Gerry Evers-Kiebooms, Shirley Hodgson, A Cécile J W Janssens, Helena Kaariainen, Michael Krawczak, Ulf Kristoffersson, Jan Lubinski, Christine Patch, Victor B Penchaszadeh, Andrew Read, Wolf Rogowski, Jorge Sequeiros, Lisbeth Tranebjaerg, Irene M van Langen, Helen Wallace, Ron Zimmern, Jörg Schmidtke and Martina C Cornel
Eur J Hum Genet 19: S6-S44; doi:10.1038/ejhg.2010.249
Not so simple: a quasi-experimental study of how researchers adjudicate genetic research results FREE
Robin Zoe Hayeems, Fiona Alice Miller, Li Li and Jessica Peace Bytautas
Eur J Hum Genet 19: 740-747; advance online publication, March 16, 2011; doi:10.1038/ejhg.2011.34
Strengthening the reporting of genetic risk prediction studies: the GRIPS statement EJHGOpen
A Cecile JW Janssens, John PA Ioannidis, Cornelia M van Duijn, Julian Little and Muin J Khoury for the GRIPS Group
Eur J Hum Genet 19: 833-836; advance online publication, March 16, 2011; doi:10.1038/ejhg.2011.25
Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration EJHGOpen
A Cecile JW Janssens, John PA Ioannidis, Sara Bedrosian, Paolo Boffetta, Siobhan M Dolan, Nicole Dowling, Isabel Fortier, Andrew N Freedman, Jeremy M Grimshaw, Jeffrey Gulcher, Marta Gwinn, Mark A Hlatky, Holly Janes, Peter Kraft, Stephanie Melillo, Christopher J O'Donnell, Michael J Pencina, David Ransohoff, Sheri D Schully, Daniela Seminara, Deborah M Winn, Caroline F Wright, Cornelia M van Duijn, Julian Little and Muin J Khoury
Eur J Hum Genet 19: ; advance online publication, March 16, 2011; doi:10.1038/ejhg.2011.27
Impact of gene patents on diagnostic testing: a new patent landscaping method applied to spinocerebellar ataxia FREE
Nele Berthels, Gert Matthijs and Geertrui Van Overwalle
Eur J Hum Genet 19: 1114-1121; advance online publication, August 3, 2011; doi:10.1038/ejhg.2011.109
The next controversy in genetic testing: clinical data as trade secrets? EJHGOpen
Robert Cook-Deegan, John M Conley, James P Evans and Daniel Vorhaus
Eur J Hum Genet 21: 585-588; advance online publication, November 14, 2012; doi:10.1038/ejhg.2012.217
Are the kids really all right? Direct-to-consumer genetic testing in children: are company policies clashing with professional norms? FREE
Heidi Carmen Howard, Denise Avard and Pascal Borry
Eur J Hum Genet 19: 1122-1126; advance online publication, June 1, 2011; doi:10.1038/ejhg.2011.94
Motivators for participation in a whole-genome sequencing study: implications for translational genomics research FREE
Flavia M Facio, Stephanie Brooks, Johanna Loewenstein, Susannah Green, Leslie G Biesecker and Barbara B Biesecker
Eur J Hum Genet 19: 1213-1217; advance online publication, July 6, 2011; doi:10.1038/ejhg.2011.123
Limits of DTC
Direct-to-consumer genetic testing services: what are the medical benefits? FREE
Thierry Frebourg
Eur J Hum Genet 20: 483; advance online publication, January 4, 2012; doi:10.1038/ejhg.2011.229
Reply to Ross' commentary: Reproductive benefit through newborn screening: preferences, policy and ethics FREE
Yvonne Bombard and Fiona A Miller
Eur J Hum Genet 20: 486-487; advance online publication, February 29, 2012; doi:10.1038/ejhg.2012.25
Disease gene identification strategies for exome sequencing FREE
Christian Gilissen, Alexander Hoischen, Han G Brunner and Joris A Veltman
Eur J Hum Genet 20: 490-497; advance online publication, January 18, 2012; doi:10.1038/ejhg.2011.258
Direct-to-consumer genomic testing: systematic review of the literature on user perspectives FREE
Lesley Goldsmith, Leigh Jackson, Anita O'Connor and Heather Skirton
Eur J Hum Genet 20: 811-816; advance online publication, February 15, 2012; doi:10.1038/ejhg.2012.18
An exploration of genetic health professionals' experience with direct-to-consumer genetic testing in their clinical practice FREE
Gemma R Brett, Sylvia A Metcalfe, David J Amor and Jane L Halliday
Eur J Hum Genet 20: 825-830; advance online publication, February 8, 2012; doi:10.1038/ejhg.2012.13
The changing landscape of genetic testing and its impact on clinical and laboratory services and research in Europe FREE
Ros Hastings, Guido de Wert, Brian Fowler, Michael Krawczak, Eric Vermeulen, Egbert Bakker, Pascal Borry, Wybo Dondorp, Niels Nijsingh, David Barton, Jörg Schmidtke, Carla G van El, Joris Vermeesch, Yrrah Stol, Heidi Carmen Howard and Martina C Cornel
Eur J Hum Genet 20: 911-916; advance online publication, March 28, 2012; doi:10.1038/ejhg.2012.56
Quality assurance practices in Europe: a survey of molecular genetic testing laboratories FREE
Sarah Berwouts, Katrina Fanning, Michael A Morris, David E Barton and Elisabeth Dequeker
Eur J Hum Genet 20: 1118-1126; advance online publication, June 27, 2012; doi:10.1038/ejhg.2012.125
Quality issues in genetic testing
Can (should) molecular diagnostic labs improve the quality of their services? FREE
Jean-Jacques Cassiman
Eur J Hum Genet 20: 1103-1104; advance online publication, June 27, 2012; doi:10.1038/ejhg.2012.126
From Oncogene
Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett’s esophagus
M M Streppel, S Lata, M DelaBastide, E A Montgomery, J S Wang, M I Canto, A M Macgregor-Das, S Pai, F H M Morsink, G J Offerhaus, E Antoniou, A Maitra and W R McCombie
Oncogene advance online publication, January 14, 2013; doi:10.1038/onc.2012.586
CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute FREE
G Zoppoli, S Solier, W C Reinhold, H Liu, J W Connelly Jr, A Monks, R H Shoemaker, O D Abaan, S R Davis, P S Meltzer, J H Doroshow and Y Pommier
Oncogene 31: 403-418; advance online publication, July 18, 2011; doi:10.1038/onc.2011.283
CpG island shore methylation regulates caveolin-1 expression in breast cancer Open
X Rao, J Evans, H Chae, J Pilrose, S Kim, P Yan, R-L Huang, H-C Lai, H Lin, Y Liu, D Miller, J-K Rhee, Y-W Huang, F Gu, J W Gray, TH-M Huang and K P Nephew
Oncogene advance online publication, November 5, 2012; doi:10.1038/onc.2012.474
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