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Projeto de investigação
European multidisciplinary ALS network identification to cure motor neuron degeneration
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A blinded international study on the reliability of genetic testing for GGGGCC-repeat expansions in C9orf72 reveals marked differences in results among 14 laboratories
Publication . Akimoto, Chizuru; Volk, Alexander E.; van Blitterswijk, Marka; Van den Broeck, Marleen; Leblond, Claire S.; Lumbroso, Serge; Camu, William; Neitzel, Birgit; Onodera, Osamu; van Rheenen, Wouter; Pinto, Susana; Weber, Markus; Smith, Bradley; Proven, Melanie; Talbot, Kevin; Keagle, Pamela; Chesi, Alessandra; Ratti, Antonia; van der Zee, Julie; Alstermark, Helena; Birve, Anna; Calini, Daniela; Nordin, Angelica; Tradowsky, Daniela C.; Just, Walter; Daoud, Hussein; Angerbauer, Sabrina; DeJesus-Hernandez, Mariely; Konno, Takuya; Lloyd-Jani, Anjali; Carvalho, Mamede; Mouzat, Kevin; Landers, John E.; Veldink, Jan H.; Silani, Vincenzo; Gitler, Aaron D.; Shaw, Christopher E.; Rouleau, Guy A; van den Berg, Leonard H.; Van Broeckhoven, Christine; Rademakers, Rosa; Andersen, Peter M.; Kubisch, Christian
Background: The GGGGCC-repeat expansion in C9orf72 is the most frequent mutation found in patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Most of the studies on C9orf72 have relied on repeat-primed PCR (RP-PCR) methods for detection of the expansions. To investigate the inherent limitations of this technique, we compared methods and results of 14 laboratories.
Methods: The 14 laboratories genotyped DNA from 78 individuals (diagnosed with ALS or FTD) in a blinded fashion. Eleven laboratories used a combination of amplicon-length analysis and RP-PCR, whereas three laboratories used RP-PCR alone; Southern blotting techniques were used as a reference.
Results: Using PCR-based techniques, 5 of the 14 laboratories got results in full accordance with the Southern blotting results. Only 50 of the 78 DNA samples got the same genotype result in all 14 laboratories. There was a high degree of false positive and false negative results, and at least one sample could not be genotyped at all in 9 of the 14 laboratories. The mean sensitivity of a combination of amplicon-length analysis and RP-PCR was 95.0% (73.9-100%), and the mean specificity was 98.0% (87.5-100%). Overall, a sensitivity and specificity of more than 95% was observed in only seven laboratories.
Conclusions: Because of the wide range seen in genotyping results, we recommend using a combination of amplicon-length analysis and RP-PCR as a minimum in a research setting. We propose that Southern blotting techniques should be the gold standard, and be made obligatory in a clinical diagnostic setting.
Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
Publication . Hop, Paul J.; Zwamborn, Ramona A. J.; Hannon, Eilis; Shireby, Gemma L.; Nabais, Marta F.; Walker, Emma M.; van Rheenen, Wouter; van Vugt, Joke J. F. A.; Dekker, Annelot M.; Westeneng, Henk-Jan; Tazelaar, Gijs H. P.; Slagboom, P. Eline; Beekman, Marian; Deelen, Joris; van Heemst, Diana; Veldink, Jan H.; van den Berg, Leonard H.; van Duijn, Cornelia M.; Hofman, Bert A.; Isaacs, Aaron; Uitterlinden, Andre G.; van Eijk, Kristel R.; van Meurs, Joyce; Jhamai, P. Mila; Verbiest, Michael; Suchiman, H. Eka D.; Verkerk, Marijn; van der Breggen, Ruud; van Rooij, Jeroen; Lakenberg, Nico; Mei, Hailiang; van Iterson, Maarten; Moisse, Matthieu; van Galen, Michiel; Bot, Jan; Zhernakova, Dasha V.; Jansen, Rick; van ‘t Hof, Peter; Deelen, Patrick; Nooren, Irene; t Hoen, Peter A. C.; Heijmans, Bastiaan T.; Moed, Matthijs; Baird, Denis; Franke, Lude; Vermaat, Martijn; Zhernakova, Dasha V.; Luijk, Rene; Jan Bonder, Marc; van Iterson, Maarten; Deelen, Patrick; van Dijk, Freerk; van Galen, Michiel; Arindrarto, Wibowo; Al Khleifat, Ahmad; Kielbasa, Szymon M.; Swertz, Morris A.; van Zwet, Erik W.; Jansen, Rick; t Hoen, Peter A. C.; Heijmans, Bastiaan T.; Al-Chalabi, Ammar; Wray, Naomi R.; Bensimon, Gilbert; Hardiman, Orla; Iacoangeli, Alfredo; Chio, Adriano; Veldink, Jan H.; Smith, George Davey; Mill, Jonathan; Ticozzi, Nicola; Ratti, Antonia; Cooper-Knock, Jonathan; Morrison, Karen E.; Shaw, Pamela J.; Basak, A. Nazli; Chiò, Adriano; Calvo, Andrea; Moglia, Cristina; Canosa, Antonio; Brunetti, Maura; Grassano, Maurizio; Gotkine, Marc; Lerner, Yossef; Zabari, Michal; Vourc’h, Patrick; Corcia, Philippe; Couratier, Philippe; Mora Pardina, Jesus S.; Salas, Teresa; Dion, Patrick; Ross, Jay P.; Henderson, Robert D.; Mathers, Susan; McCombe, Pamela A.; Needham, Merrilee; Nicholson, Garth; Rowe, Dominic B.; Pamphlett, Roger; Mather, Karen A.; Sachdev, Perminder S.; Furlong, Sarah; Garton, Fleur C.; Henders, Anjali K.; Lin, Tian; Ngo, Shyuan T.; Steyn, Frederik J.; Wallace, Leanne; Williams, Kelly L.; Neto, Miguel Mitne; Cauchi, Ruben J.; Blair, Ian P.; Kiernan, Matthew C.; Drory, Vivian; Povedano, Monica; Carvalho, Mamede; Pinto, Susana; Weber, Markus; Rouleau, Guy A.; Silani, Vincenzo; Landers, John E.; Shaw, Christopher E.; Andersen, Peter M.; McRae, Allan F.; van Es, Michael A.; Pasterkamp, R. Jeroen; Wray, Naomi R.; McLaughlin, Russell L.; Hardiman, Orla; Kenna, Kevin P.; Tsai, Ellen; Runz, Heiko; Al-Chalabi, Ammar; van den Berg, Leonard H.; Van Damme, Philip; Mill, Jonathan; Veldink, Jan H.; Heijmans, Bastiaan T.; t Hoen, Peter A. C.; van Meurs, Joyce; Jansen, Rick; Franke, Lude; Boomsma, Dorret I.; Pool, Rene; van Dongen, Jenny; Hottenga, Joukje J.; van Greevenbroek, Marleen M. J.; Stehouwer, Coen D.A.; van der Kallen, Carla J.H.; Schalkwijk, Casper G.; Wijmenga, Cisca; Franke, Lude; Zhernakova, Sasha; Tigchelaar, Ettje F.
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis
Publication . Al Khleifat, Ahmad; Iacoangeli, Alfredo; van Vugt, Joke J. F. A.; Bowles, Harry; Moisse, Matthieu; Zwamborn, Ramona A. J.; van der Spek, Rick A. A.; Shatunov, Aleksey; Cooper-Knock, Johnathan; Topp, Simon; Byrne, Ross; Gellera, Cinzia; López, Victoria; Jones, Ashley R.; Opie-Martin, Sarah; Vural, Atay; Campos, Yolanda; van Rheenen, Wouter; Kenna, Brendan; Van Eijk, Kristel R.; Kenna, Kevin; Weber, Markus; Smith, Bradley; Fogh, Isabella; Silani, Vincenzo; Morrison, Karen E.; Dobson, Richard; van Es, Michael A.; McLaughlin, Russell L.; Vourc’h, Patrick; Chio, Adriano; Corcia, Philippe; Carvalho, Mamede; Gotkine, Marc; Panades, Monica P.; Mora, Jesus S.; Shaw, Pamela J.; Landers, John E.; Glass, Jonathan D.; Shaw, Christopher E.; Basak, Nazli; Hardiman, Orla; Robberecht, Wim; Van Damme, Philip; van den Berg, Leonard H.; Veldink, Jan H.; Al-Chalabi, Ammar
There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.
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Entidade financiadora
European Commission
Programa de financiamento
FP7
Número da atribuição
259867