{"id":"https://openalex.org/W4396977092","doi":"https://doi.org/10.3390/biomedinformatics4020071","title":"IMPI: An Interface for Low-Frequency Point Mutation Identification Exemplified on Resistance Mutations in Chronic Myeloid Leukemia","display_name":"IMPI: An Interface for Low-Frequency Point Mutation Identification Exemplified on Resistance Mutations in Chronic Myeloid Leukemia","publication_year":2024,"publication_date":"2024-05-13","ids":{"openalex":"https://openalex.org/W4396977092","doi":"https://doi.org/10.3390/biomedinformatics4020071"},"language":"en","primary_location":{"id":"doi:10.3390/biomedinformatics4020071","doi":"https://doi.org/10.3390/biomedinformatics4020071","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biomedinformatics4020071","pdf_url":null,"source":{"id":"https://openalex.org/S4210213753","display_name":"BioMedInformatics","issn_l":"2673-7426","issn":["2673-7426"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioMedInformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/biomedinformatics4020071","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014814037","display_name":"Julia Vetter","orcid":"https://orcid.org/0000-0002-9169-3935","observed_orcids":["https://orcid.org/0000-0002-9169-3935"]},"institutions":[{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]},{"id":"https://openalex.org/I4210136249","display_name":"University of Applied Sciences Upper Austria","ror":"https://ror.org/03jqp6d56","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210136249"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Julia Vetter","raw_affiliation_strings":["Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria","Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Stra\u00dfe 34, 5020 Salzburg, Salzburg, Austria"],"raw_orcid":"https://orcid.org/0000-0002-9169-3935","affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210136249"]},{"raw_affiliation_string":"Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Stra\u00dfe 34, 5020 Salzburg, Salzburg, Austria","institution_ids":["https://openalex.org/I182212641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087744395","display_name":"Jonathan Burghofer","orcid":"https://orcid.org/0000-0001-6720-4671","observed_orcids":["https://orcid.org/0000-0001-6720-4671"]},"institutions":[{"id":"https://openalex.org/I4210117569","display_name":"Ordensklinikum Linz Barmherzige Schwestern","ror":"https://ror.org/028rf7391","country_code":"AT","type":"healthcare","lineage":["https://openalex.org/I4210117569"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Jonathan Burghofer","raw_affiliation_strings":["Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria"],"raw_orcid":"https://orcid.org/0000-0001-6720-4671","affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210117569"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088256245","display_name":"Theodora Malli","orcid":"https://orcid.org/0000-0003-4244-7954","observed_orcids":["https://orcid.org/0000-0003-4244-7954"]},"institutions":[{"id":"https://openalex.org/I4210117569","display_name":"Ordensklinikum Linz Barmherzige Schwestern","ror":"https://ror.org/028rf7391","country_code":"AT","type":"healthcare","lineage":["https://openalex.org/I4210117569"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Theodora Malli","raw_affiliation_strings":["Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210117569"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Anna M. Lin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136249","display_name":"University of Applied Sciences Upper Austria","ror":"https://ror.org/03jqp6d56","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210136249"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Anna M. Lin","raw_affiliation_strings":["Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210136249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022408812","display_name":"Gerald Webersinke","orcid":"https://orcid.org/0000-0001-5654-6190","observed_orcids":["https://orcid.org/0000-0001-5654-6190"]},"institutions":[{"id":"https://openalex.org/I4210117569","display_name":"Ordensklinikum Linz Barmherzige Schwestern","ror":"https://ror.org/028rf7391","country_code":"AT","type":"healthcare","lineage":["https://openalex.org/I4210117569"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Gerald Webersinke","raw_affiliation_strings":["Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria"],"raw_orcid":"https://orcid.org/0000-0001-5654-6190","affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz GmbH, Barmherzige Schwestern, Seilerst\u00e4tte 4, 4010 Linz, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210117569"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073315136","display_name":"Markus Wiederstein","orcid":"https://orcid.org/0000-0002-4750-4746","observed_orcids":["https://orcid.org/0000-0002-4750-4746"]},"institutions":[{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Markus Wiederstein","raw_affiliation_strings":["Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Stra\u00dfe 34, 5020 Salzburg, Salzburg, Austria"],"raw_orcid":"https://orcid.org/0000-0002-4750-4746","affiliations":[{"raw_affiliation_string":"Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Stra\u00dfe 34, 5020 Salzburg, Salzburg, Austria","institution_ids":["https://openalex.org/I182212641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036920760","display_name":"Stephan Winkler","orcid":"https://orcid.org/0000-0002-5196-4294","observed_orcids":["https://orcid.org/0000-0002-5196-4294"]},"institutions":[{"id":"https://openalex.org/I4210136249","display_name":"University of Applied Sciences Upper Austria","ror":"https://ror.org/03jqp6d56","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210136249"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Stephan M. Winkler","raw_affiliation_strings":["Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210136249"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023010182","display_name":"Susanne Schaller","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136249","display_name":"University of Applied Sciences Upper Austria","ror":"https://ror.org/03jqp6d56","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210136249"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Susanne Schaller","raw_affiliation_strings":["Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Upper Austria, Austria","institution_ids":["https://openalex.org/I4210136249"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014814037"],"corresponding_institution_ids":["https://openalex.org/I182212641","https://openalex.org/I4210136249"],"apc_list":{"value":1000,"currency":"CHF","value_usd":1137},"apc_paid":{"value":1000,"currency":"CHF","value_usd":1137},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"4","issue":"2","first_page":"1289","last_page":"1307"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6029999852180481,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6029999852180481,"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"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.25119999051094055,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.049300000071525574,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/point-mutation-detection","display_name":"point mutation detection","score":0.9150000214576721},{"id":"https://openalex.org/keywords/unique-molecular-identifiers","display_name":"unique molecular identifiers","score":0.9610000252723694},{"id":"https://openalex.org/keywords/bcr-abl-fusion","display_name":"BCR-ABL fusion gene","score":0.640999972820282},{"id":"https://openalex.org/keywords/chronic-myeloid-leukemia","display_name":"chronic myeloid leukemia","score":0.9900000095367432},{"id":"https://openalex.org/keywords/resistance-mutations","display_name":"resistance mutations","score":0.7879999876022339},{"id":"https://openalex.org/keywords/allele-frequency-estimation","display_name":"allele frequency estimation","score":0.7350000143051147},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"graphical user interface","score":0.7429999709129333},{"id":"https://openalex.org/keywords/low-frequency-variants","display_name":"low-frequency variants","score":0.6129999756813049}],"concepts":[{"id":"https://openalex.org/C2778729363","wikidata":"https://www.wikidata.org/wiki/Q11688946","display_name":"Myeloid leukemia","level":2,"score":0.7725293636322021},{"id":"https://openalex.org/C176944494","wikidata":"https://www.wikidata.org/wiki/Q1415380","display_name":"Point mutation","level":4,"score":0.7508853673934937},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5948719382286072},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5446670651435852},{"id":"https://openalex.org/C102306862","wikidata":"https://www.wikidata.org/wiki/Q6943735","display_name":"Mutation frequency","level":4,"score":0.5061933398246765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49052828550338745},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.44845646619796753},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.3864556550979614},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3555978834629059},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3332440257072449},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15140128135681152},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C58226133","wikidata":"https://www.wikidata.org/wiki/Q1324199","display_name":"Pulmonary surfactant","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/biomedinformatics4020071","doi":"https://doi.org/10.3390/biomedinformatics4020071","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biomedinformatics4020071","pdf_url":null,"source":{"id":"https://openalex.org/S4210213753","display_name":"BioMedInformatics","issn_l":"2673-7426","issn":["2673-7426"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioMedInformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:1cbce76317354a29a363b753513ebce2","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/1cbce76317354a29a363b753513ebce2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioMedInformatics, Vol 4, Iss 2, Pp 1289-1307 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/biomedinformatics4020071","doi":"https://doi.org/10.3390/biomedinformatics4020071","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biomedinformatics4020071","pdf_url":null,"source":{"id":"https://openalex.org/S4210213753","display_name":"BioMedInformatics","issn_l":"2673-7426","issn":["2673-7426"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioMedInformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.46810001134872437,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1527347967","https://openalex.org/W1576660662","https://openalex.org/W1964577312","https://openalex.org/W2002946752","https://openalex.org/W2041263286","https://openalex.org/W2076500257","https://openalex.org/W2079913459","https://openalex.org/W2096504879","https://openalex.org/W2099797874","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2133697722","https://openalex.org/W2143701918","https://openalex.org/W2155943701","https://openalex.org/W2170551349","https://openalex.org/W2323326409","https://openalex.org/W2398047035","https://openalex.org/W2560986453","https://openalex.org/W2590237903","https://openalex.org/W2591733518","https://openalex.org/W2727497686","https://openalex.org/W2742136635","https://openalex.org/W2766307464","https://openalex.org/W2770095154","https://openalex.org/W2810131406","https://openalex.org/W2884089970","https://openalex.org/W2895911184","https://openalex.org/W2904592340","https://openalex.org/W2952109315","https://openalex.org/W2953170162","https://openalex.org/W2996575833","https://openalex.org/W3014892303","https://openalex.org/W3015686339","https://openalex.org/W4241242326"],"related_works":["https://openalex.org/W2763347431","https://openalex.org/W3082037286","https://openalex.org/W2946766521","https://openalex.org/W3003747570","https://openalex.org/W4399296388","https://openalex.org/W4293512409","https://openalex.org/W7214259428","https://openalex.org/W4417488105","https://openalex.org/W2611802561","https://openalex.org/W4377016673"],"abstract_inverted_index":{"Background:":[0],"In":[1,138],"genomics,":[2],"highly":[3],"sensitive":[4],"point":[5],"mutation":[6,31],"detection":[7,32],"is":[8,26,118],"particularly":[9],"relevant":[10],"for":[11,43,54,90,120,170],"cancer":[12],"diagnosis":[13],"and":[14,68,77,87,94,111,128,151],"early":[15],"relapse":[16],"detection.":[17],"Next-generation":[18],"sequencing":[19,136],"combined":[20],"with":[21,48],"unique":[22],"molecular":[23],"identifiers":[24],"(UMIs)":[25],"known":[27],"to":[28,60,180],"improve":[29],"the":[30,82,146,156,162,168],"sensitivity.":[33],"Methods:":[34],"We":[35],"present":[36],"an":[37,115],"open-source":[38],"bioinformatics":[39],"framework":[40],"named":[41],"Interface":[42],"Point":[44],"Mutation":[45],"Identification":[46],"(IMPI)":[47],"a":[49,142],"graphical":[50],"user":[51],"interface":[52],"(GUI)":[53],"processing":[55],"especially":[56],"small-scale":[57],"NGS":[58,91,177],"data":[59,92],"identify":[61],"variants.":[62],"IMPI":[63,108,124,140],"ensures":[64],"detailed":[65,143],"UMI":[66,95,98,149],"analysis":[67,144],"clustering,":[69],"as":[70,72],"well":[71],"initial":[73],"raw":[74],"read":[75],"processing,":[76],"consensus":[78],"sequence":[79],"building.":[80],"Furthermore,":[81],"effects":[83],"of":[84,145,148],"custom":[85],"algorithm":[86],"parameter":[88,121,152],"settings":[89],"pre-processing":[93],"collapsing":[96],"(e.g.,":[97,183],"clustered":[99],"versus":[100],"unclustered":[101],"(raw)":[102],"reads)":[103],"can":[104],"be":[105,190],"investigated.":[106],"Additionally,":[107],"implements":[109],"optimization":[110],"quality":[112],"control":[113],"methods;":[114],"evolution":[116],"strategy":[117],"used":[119],"optimization.":[122],"Results:":[123],"was":[125],"designed,":[126],"implemented,":[127],"tested":[129],"using":[130,192],"BCR::ABL1":[131,163],"fusion":[132],"gene":[133],"kinase":[134],"domain":[135],"data.":[137],"summary,":[139],"enables":[141],"impact":[147],"clustering":[150],"setting":[153],"changes":[154],"on":[155],"measured":[157],"allele":[158],"frequencies.":[159],"Conclusions:":[160],"Regarding":[161],"data,":[164],"IMPI\u2019s":[165],"results":[166],"underlined":[167],"need":[169],"caution":[171],"while":[172],"designing":[173],"specialized":[174],"single":[175],"amplicon":[176],"approaches":[178],"due":[179],"methodical":[181],"limitations":[182],"high":[184],"PCR-mediated":[185],"recombination":[186],"rate).":[187],"This":[188],"cannot":[189],"corrected":[191],"UMIs.":[193]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2024-05-17T00:00:00"}