{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T13:49:51Z","timestamp":1762004991542,"version":"3.37.3"},"reference-count":22,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2018,3,5]],"date-time":"2018-03-05T00:00:00Z","timestamp":1520208000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01HD032652"],"award-info":[{"award-number":["P01HD032652"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Clinical Genetics"],"published-print":{"date-parts":[[2018,5]]},"abstract":"<jats:p>Lysosomal storage diseases (LSDs) are a group of genetic disorders, resulting from deficiencies of lysosomal enzyme. Genotype\u2010phenotype correlation is essential for timely and proper treatment allocation. Recently, by integrating prediction outcomes of 7 bioinformatics tools, we developed a SAAMP algorithm to predict the impact of individual amino\u2010acid substitution. To optimize this approach, we evaluated the performance of these bioinformatics tools in a broad array of genes. PolyPhen and PROVEAN had the best performances, while SNP&amp;GOs, PANTHER and I\u2010Mutant had the worst performances. Therefore, SAAMP 2.0 was developed by excluding 3 tools with worst performance, yielding a sensitivity of 94% and a specificity of 90%. To generalize the guideline to proteins without known structures, we built the three\u2010dimensional model of iduronate\u20102\u2010sulfatase by homology modeling. Further, we investigated the phenotype severity of known disease\u2010causing mutations of the <jats:italic>GLB1<\/jats:italic> gene, which lead to 2 LSDs (GM1 gangliosidosis and Morquio disease type B). Based on the previous literature and structural analysis, we associated these mutations with disease subtypes and proposed a theory to explain the complicated genotype\u2010phenotype correlation. Collectively, an updated guideline for phenotype prediction with SAAMP 2.0 was proposed, which will provide essential information for early diagnosis and proper treatment allocation, and they may be generalized to many monogenic diseases.<\/jats:p>","DOI":"10.1111\/cge.13226","type":"journal-article","created":{"date-parts":[[2018,2,3]],"date-time":"2018-02-03T02:32:43Z","timestamp":1517625163000},"page":"1008-1014","source":"Crossref","is-referenced-by-count":8,"title":["SAAMP 2.0: An algorithm to predict genotype\u2010phenotype correlation of lysosomal storage diseases"],"prefix":"10.1111","volume":"93","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7743-5649","authenticated-orcid":false,"given":"L.","family":"Ou","sequence":"first","affiliation":[{"name":"Department of Pediatrics Gene Therapy Center  Minneapolis Minnesota, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.J.","family":"Przybilla","sequence":"additional","affiliation":[{"name":"Department of Genetics, Cell Biology and Development University of Minnesota  Minneapolis Minnesota"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C.B.","family":"Whitley","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Gene Therapy Center  Minneapolis Minnesota, USA"},{"name":"Department of Genetics, Cell Biology and Development University of Minnesota  Minneapolis Minnesota"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2018,3,5]]},"reference":[{"volume-title":"Fabry Disease: Perspectives from 5 Years of FOS","year":"2006","author":"Fuller M","key":"e_1_2_7_2_1"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.281.3.249"},{"key":"e_1_2_7_4_1","first-page":"3421","volume-title":"The Metabolic and Molecular Bases of Inherited Disease","author":"Neufeld EF","year":"2001"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00431-011-1644-x"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpeds.2013.01.031"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13023-017-0678-1"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3213"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0925-4439(99)00075-7"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M113.529529"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.293795"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku340"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163964"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10038-005-0266-4"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10545-006-0440-7"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.9128"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1042\/BJ20040739"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddl171"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2004.11.010"},{"volume-title":"SourceGeneReviews\u00ae [Internet]","year":"1993","author":"Regier DS","key":"e_1_2_7_20_1"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/0009-8981(82)90199-1"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2011.03.018"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.9475"}],"container-title":["Clinical Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fcge.13226","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/cge.13226","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,24]],"date-time":"2023-09-24T15:11:55Z","timestamp":1695568315000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/cge.13226"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3,5]]},"references-count":22,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2018,5]]}},"alternative-id":["10.1111\/cge.13226"],"URL":"https:\/\/doi.org\/10.1111\/cge.13226","archive":["Portico"],"relation":{},"ISSN":["0009-9163","1399-0004"],"issn-type":[{"type":"print","value":"0009-9163"},{"type":"electronic","value":"1399-0004"}],"subject":[],"published":{"date-parts":[[2018,3,5]]}}}