The Project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public

Abstract

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive fatal neurodegenerative disease affecting 1 in 350 people. The aim of Project MinE is to elucidate the pathophysiology of ALS through whole-genome sequencing at least 15,000 ALS patients and 7,500 controls at 30Xcoverage. Here, we present the Project MinE data browser (databrowser.projectmine.com), a unique and intuitive one-stop, open-access server that provides detailed information on genetic variation analyzed in a new and still growing set of 4,366 ALS cases and 1,832 matched controls.Through its visual components and interactive design, the browser specifically aims to be a resource to those without a biostatistics background and allow clinicians and preclinical researchers to integrate Project MinE data into their own research. The browser allows users to query a transcript and immediately access a unique combination of detailed (meta)data, annotations and association statistics that would otherwise require analytic expertise and visits to scattered resources.

Revisiting the complex architecture of ALS in Turkey: Expanding genotypes, shared phenotypes, molecular networks, and a public variant database

“…Analysis of exonic variants in the WES (n = 127) and WGS (n = 623) data revealed the presence of pathogenic gene variants in 74 cases, out of which, 19 were previously published by our group (Tables 2 and 3; Akçimen et al, 2019;Özoğuz et al, 2015;Tunca et al, 2018). Variant information and clinical features of the cases solved are compiled in Table 3 and in Appendix (Table A4) an earlier onset at 38 years on average (Table 3).…”

“…Venn diagram is drawn according to the disease-gene associations obtained from the literature (Akçimen et al, 2019;Al-Saif, Al-Mohanna, & Bohlega, 2011;Annesi et al, 2005;Brenner et al, 2018;Chen et al, 2004;Cirulli et al, 2015;Cottenie et al, 2014;Daoud et al, 2012;Deschauer et al, 2012;Frasquet, Va, & Sevilla, 2017;Greenway et al, 2006;Grohmann et al, 2001;Hermosura et al, 2005;Hughes et al, 2001;Ishiura et al, 2012;Iskender et al, 2015;Kimonis, Fulchiero, Vesa, & Watts, 2008;Maruyama et al, 2010;Maystadt et al, 2007;Nalini, Pandraud, Mok, & Houlden, 2013;H. P. Nguyen, Van Broeckhoven, & van der Zee, 2018;Stoll et al, 2016;Sumner et al, 2013;Synofzik et al, 2016;Takahashi et al, 2013;Tunca et al, 2018;Velilla et al, 2019;Yang et al, 2001). ALS, amyotrophic lateral sclerosis; AO, age of onset e22 | (Fogel et al, 2014;Fogel, Satya-Murti, & Cohen, 2016;Trujillano et al, 2017).…”

“…, and FUS). In recent years, many studies showed that the frequency of ALS patients carrying more than one variant is higher than expected by chance, providing evidence that ALS may result from multiple rare variants with additive effects on disease development and presentation, for example, age of disease onset, progression and severity (van Blitterswijk et al, 2012).…”