{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T01:13:52Z","timestamp":1788484432542,"version":"build-2803163510"},"reference-count":52,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2019,1,13]],"date-time":"2019-01-13T00:00:00Z","timestamp":1547337600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000864","name":"Michael J. Fox Foundation for Parkinson's Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molec Gen &amp; Gen Med"],"published-print":{"date-parts":[[2019,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Mutations in\n                      <jats:italic>GBA<\/jats:italic>\n                      cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous.\n                      <jats:italic>GBA<\/jats:italic>\n                      analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing\n                      <jats:italic>GBA<\/jats:italic>\n                      using long reads.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We sequenced\n                      <jats:italic>GBA<\/jats:italic>\n                      on the Oxford Nanopore MinION as an 8.9\u00a0kb amplicon from 102 individuals, including patients with Parkinson's and Gaucher diseases. We used NanoOK for quality metrics, NGMLR to align data (after comparing with GraphMap), Nanopolish and Sniffles to call variants, and WhatsHap for phasing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We detected all known missense mutations in these samples, including the common p.N409S (N370S) and p.L483P (L444P) in multiple samples, and nine rarer ones, as well as a splicing and a truncating mutation, and intronic SNPs. We demonstrated the ability to phase mutations, confirm compound heterozygosity, and assign haplotypes. We also detected two known risk variants in some Parkinson's patients. Rare false positives were easily identified and filtered, with the Nanopolish quality score adjusted for the number of reads a very robust discriminator. In two individuals carrying a recombinant allele, we were able to detect and fully define it in one carrier, where it included a 55\u2010base pair deletion, but not in another one, suggesting a limitation of the PCR enrichment method. Missense mutations were detected at the correct zygosity, except for the case where the RecNciI one was missed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantages of phasing and intronic analysis. It can be used as an efficient research tool, but additional work is required to exclude all recombinants.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/mgg3.564","type":"journal-article","created":{"date-parts":[[2019,1,14]],"date-time":"2019-01-14T01:18:51Z","timestamp":1547428731000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":83,"title":["Evaluation of the detection of\n                    <i>GBA<\/i>\n                    missense mutations and other variants using the Oxford Nanopore MinION"],"prefix":"10.1002","volume":"7","author":[{"given":"Melissa","family":"Leija\u2010Salazar","sequence":"first","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fritz J.","family":"Sedlazeck","sequence":"additional","affiliation":[{"name":"Human Genome Sequencing Center Baylor College of Medicine Houston Texas"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Toffoli","sequence":"additional","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Mullin","sequence":"additional","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"},{"name":"Institute of Translational and Stratified Medicine Plymouth University Peninsula School of Medicine  Plymouth UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katya","family":"Mokretar","sequence":"additional","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Athanasopoulou","sequence":"additional","affiliation":[{"name":"Department of Molecular Neuroscience, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aimee","family":"Donald","sequence":"additional","affiliation":[{"name":"Department of Paediatrics Royal Manchester Children\u2019s Hospital Manchester UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reena","family":"Sharma","sequence":"additional","affiliation":[{"name":"The Mark Holland Metabolic Unit, Salford Royal Foundation NHS Trust Salford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derralynn","family":"Hughes","sequence":"additional","affiliation":[{"name":"Institute of Immunity and Transplantation Lysosomal Storage Disorders Unit, Royal Free Hospital London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony H.V.","family":"Schapira","sequence":"additional","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6423-6539","authenticated-orcid":false,"given":"Christos","family":"Proukakis","sequence":"additional","affiliation":[{"name":"Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of Neurology University College London London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,1,13]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/ene.13395"},{"issue":"9","key":"e_1_2_7_3_1","first-page":"2648","article-title":"Glucocerebrosidase activity in Parkinson\u2019s disease with and without GBA mutations. 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