{"id":"https://openalex.org/W2472617162","doi":"https://doi.org/10.1093/bioinformatics/btw381","title":"Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes","display_name":"Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes","publication_year":2016,"publication_date":"2016-06-26","ids":{"openalex":"https://openalex.org/W2472617162","doi":"https://doi.org/10.1093/bioinformatics/btw381","mag":"2472617162","pmid":"https://pubmed.ncbi.nlm.nih.gov/27354691"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw381","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw381","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090490484","display_name":"Jacob Shujui Hsu","orcid":"https://orcid.org/0000-0001-7358-5343"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jacob Shujui Hsu","raw_affiliation_strings":["1 Department of Psychiatry"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Psychiatry","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110622634","display_name":"Johnny S. H. Kwan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Johnny S.H. Kwan","raw_affiliation_strings":["1 Department of Psychiatry"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Psychiatry","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102916235","display_name":"Zhicheng Pan","orcid":"https://orcid.org/0000-0002-3977-5722"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhicheng Pan","raw_affiliation_strings":["1 Department of Psychiatry"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Psychiatry","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113715488","display_name":"Mar\u00eda-Merc\u00e9 Garc\u00eda-Barcel\u00f3","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maria-Merc\u00e8 Garcia-Barcelo","raw_affiliation_strings":["2 Department of Surgery"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Surgery","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018516395","display_name":"Pak C. Sham","orcid":"https://orcid.org/0000-0002-2533-7270"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Pak Chung Sham","raw_affiliation_strings":["1 Department of Psychiatry","3 Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Psychiatry","institution_ids":[]},{"raw_affiliation_string":"3 Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040633212","display_name":"Miaoxin Li","orcid":"https://orcid.org/0000-0002-4733-0109"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Miaoxin Li","raw_affiliation_strings":["1 Department of Psychiatry","3 Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Psychiatry","institution_ids":[]},{"raw_affiliation_string":"3 Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5040633212"],"corresponding_institution_ids":["https://openalex.org/I889458895"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3664,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.83983185,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"20","first_page":"3065","last_page":"3071"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.7767661809921265},{"id":"https://openalex.org/keywords/haploinsufficiency","display_name":"Haploinsufficiency","score":0.7617112398147583},{"id":"https://openalex.org/keywords/mendelian-inheritance","display_name":"Mendelian inheritance","score":0.680463433265686},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6801472902297974},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6662919521331787},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.602916955947876},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5809235572814941},{"id":"https://openalex.org/keywords/inheritance","display_name":"Inheritance (genetic algorithm)","score":0.5452947020530701},{"id":"https://openalex.org/keywords/omim-online-mendelian-inheritance-in-man","display_name":"OMIM : Online Mendelian Inheritance in Man","score":0.5218945145606995},{"id":"https://openalex.org/keywords/candidate-gene","display_name":"Candidate gene","score":0.41546106338500977},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3944084644317627},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.350747287273407},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.206354558467865}],"concepts":[{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7767661809921265},{"id":"https://openalex.org/C68838962","wikidata":"https://www.wikidata.org/wiki/Q852654","display_name":"Haploinsufficiency","level":4,"score":0.7617112398147583},{"id":"https://openalex.org/C175783326","wikidata":"https://www.wikidata.org/wiki/Q185055","display_name":"Mendelian inheritance","level":3,"score":0.680463433265686},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6801472902297974},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6662919521331787},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.602916955947876},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5809235572814941},{"id":"https://openalex.org/C2780902518","wikidata":"https://www.wikidata.org/wiki/Q6033780","display_name":"Inheritance (genetic algorithm)","level":3,"score":0.5452947020530701},{"id":"https://openalex.org/C191791410","wikidata":"https://www.wikidata.org/wiki/Q241953","display_name":"OMIM : Online Mendelian Inheritance in Man","level":4,"score":0.5218945145606995},{"id":"https://openalex.org/C69991583","wikidata":"https://www.wikidata.org/wiki/Q1423575","display_name":"Candidate gene","level":3,"score":0.41546106338500977},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3944084644317627},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.350747287273407},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.206354558467865}],"mesh":[{"descriptor_ui":"D005799","descriptor_name":"Genes, Dominant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005799","descriptor_name":"Genes, Dominant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005799","descriptor_name":"Genes, Dominant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005808","descriptor_name":"Genes, Recessive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005808","descriptor_name":"Genes, Recessive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005808","descriptor_name":"Genes, Recessive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw381","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw381","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27354691","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27354691","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/20/3065","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/20/3065","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W152918045","https://openalex.org/W1527414495","https://openalex.org/W1556094842","https://openalex.org/W1925054293","https://openalex.org/W1964426200","https://openalex.org/W1967151948","https://openalex.org/W1970413157","https://openalex.org/W1970927316","https://openalex.org/W1981215030","https://openalex.org/W1987158791","https://openalex.org/W2002655468","https://openalex.org/W2009720434","https://openalex.org/W2046499002","https://openalex.org/W2046829538","https://openalex.org/W2051315170","https://openalex.org/W2058536769","https://openalex.org/W2059145105","https://openalex.org/W2080310417","https://openalex.org/W2080779026","https://openalex.org/W2086072858","https://openalex.org/W2086877638","https://openalex.org/W2089335658","https://openalex.org/W2095521407","https://openalex.org/W2096791516","https://openalex.org/W2106588029","https://openalex.org/W2107420626","https://openalex.org/W2111326065","https://openalex.org/W2114029728","https://openalex.org/W2118246164","https://openalex.org/W2123724865","https://openalex.org/W2132297623","https://openalex.org/W2132654573","https://openalex.org/W2138014988","https://openalex.org/W2140653951","https://openalex.org/W2141307855","https://openalex.org/W2143238378","https://openalex.org/W2143417375","https://openalex.org/W2143602768","https://openalex.org/W2145187337","https://openalex.org/W2155845523","https://openalex.org/W2156830367","https://openalex.org/W2159386098","https://openalex.org/W2160995259","https://openalex.org/W2161978970","https://openalex.org/W2171777347","https://openalex.org/W2234270799","https://openalex.org/W2255312347","https://openalex.org/W2885727518","https://openalex.org/W4210767115","https://openalex.org/W6689894798"],"related_works":["https://openalex.org/W3033608749","https://openalex.org/W2472617162","https://openalex.org/W2751412613","https://openalex.org/W4306874640","https://openalex.org/W4238113154","https://openalex.org/W4292359978","https://openalex.org/W2198170080","https://openalex.org/W2155445544","https://openalex.org/W2942567521","https://openalex.org/W1506618449"],"abstract_inverted_index":{"MOTIVATION:":[0],"Exome":[1],"sequencing":[2,31],"studies":[3],"have":[4,112,129,233],"facilitated":[5],"the":[6,17,63,75,123,153,174],"detection":[7],"of":[8,19,26,62,77],"causal":[9,21],"genetic":[10],"variants":[11,116],"in":[12,28,193,242],"yet-unsolved":[13],"Mendelian":[14,58,78,89,126,149],"diseases.":[15],"However,":[16],"identification":[18],"disease":[20,79,90,127,228],"genes":[22,46,80,91,111,128,147,226],"among":[23],"a":[24,136,140],"list":[25],"candidates":[27],"an":[29],"exome":[30],"study":[32,223],"is":[33,40,240,249],"still":[34],"not":[35],"fully":[36,68],"settled,":[37],"and":[38,101,117,132,179,217,246],"it":[39],"often":[41],"difficult":[42],"to":[43,152,160,173,232],"prioritize":[44],"candidate":[45,146],"for":[47,56,144,148],"follow-up":[48],"studies.":[49],"The":[50,85,197],"inheritance":[51,83,96,154,175,182,229],"mode":[52,97,176],"provides":[53],"crucial":[54],"information":[55],"understanding":[57],"diseases,":[59],"but":[60],"none":[61],"existing":[64],"gene":[65,164],"prioritization":[66,201],"tools":[67],"utilize":[69],"this":[70],"information.":[71],"RESULTS:":[72],"We":[73],"examined":[74],"characteristics":[76],"under":[81,189],"different":[82],"modes.":[84],"results":[86],"suggest":[87],"that":[88,225],"with":[92],"autosomal":[93,108],"dominant":[94],"(AD)":[95],"are":[98,258],"more":[99,114],"haploinsufficiency":[100],"de":[102],"novo":[103],"mutation":[104],"sensitive,":[105],"whereas":[106],"those":[107],"recessive":[109],"(AR)":[110],"significantly":[113],"non-synonymous":[115,131],"regulatory":[118],"transcript":[119],"isoforms.":[120],"In":[121],"addition,":[122],"X-linked":[124],"(XL)":[125],"fewer":[130],"synonymous":[133],"variants.":[134],"As":[135],"result,":[137],"we":[138],"derived":[139],"new":[141],"scoring":[142,157],"system":[143,158],"prioritizing":[145],"diseases":[150],"according":[151,172],"mode.":[155,195],"Our":[156],"assigned":[159],"each":[161],"annotated":[162],"protein-coding":[163],"(N":[165],"=":[166,191],"18":[167],"859)":[168],"three":[169],"pathogenic":[170],"scores":[171],"(AD,":[177],"AR":[178],"XL).":[180],"This":[181,221],"mode-specific":[183],"framework":[184],"achieved":[185],"higher":[186],"accuracy":[187],"(area":[188],"curve":[190],"0.84)":[192],"XL":[194],"CONCLUSION:":[196],"inheritance-mode":[198],"specific":[199],"pathogenicity":[200],"(ISPP)":[202],"outperformed":[203],"other":[204],"well-known":[205],"methods":[206],"including":[207],"Haploinsufficiency,":[208],"Recessive,":[209],"Network":[210],"centrality,":[211],"Genic":[212],"Intolerance,":[213],"Gene":[214,218],"Damage":[215],"Index":[216],"Constraint":[219],"scores.":[220],"systematic":[222],"suggests":[224],"manifesting":[227],"modes":[230],"tend":[231],"unique":[234],"characteristics.":[235],"AVAILABILITY":[236],"AND":[237],"IMPLEMENTATION:":[238],"ISPP":[239],"included":[241],"KGGSeq":[243],"v1.0":[244],"(http://grass.cgs.hku.hk/limx/kggseq/),":[245],"source":[247],"code":[248],"available":[250,259],"from":[251],"(https://github.com/jacobhsu35/ISPP.git).":[252],"CONTACT:":[253],"mxli@hku.hkSupplementary":[254],"information:":[255],"Supplementary":[256],"data":[257],"at":[260],"Bioinformatics":[261],"online.":[262]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":4}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}