{"id":"https://openalex.org/W2781853897","doi":"https://doi.org/10.1186/s12859-017-1991-3","title":"Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform","display_name":"Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform","publication_year":2018,"publication_date":"2018-01-04","ids":{"openalex":"https://openalex.org/W2781853897","doi":"https://doi.org/10.1186/s12859-017-1991-3","mag":"2781853897","pmid":"https://pubmed.ncbi.nlm.nih.gov/29301485"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1991-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1991-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1991-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1991-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084043229","display_name":"Aditya Deshpande","orcid":"https://orcid.org/0000-0002-4463-2697"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aditya Deshpande","raw_affiliation_strings":["Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","University of Texas School of Public Health, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"University of Texas School of Public Health, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112904398","display_name":"Wenhua Lang","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenhua Lang","raw_affiliation_strings":["Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035441075","display_name":"Tina L. McDowell","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tina McDowell","raw_affiliation_strings":["Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020119624","display_name":"Smruthy Sivakumar","orcid":"https://orcid.org/0000-0001-7790-5615"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Smruthy Sivakumar","raw_affiliation_strings":["Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062057879","display_name":"Jiexin Zhang","orcid":"https://orcid.org/0000-0001-9526-6730"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiexin Zhang","raw_affiliation_strings":["Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100378658","display_name":"Jing Wang","orcid":"https://orcid.org/0000-0003-1614-9662"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Wang","raw_affiliation_strings":["Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109216248","display_name":"F. Anthony San Lucas","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Anthony San Lucas","raw_affiliation_strings":["Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052675604","display_name":"Jerry Fowler","orcid":"https://orcid.org/0000-0002-6173-9031"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jerry Fowler","raw_affiliation_strings":["Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049321069","display_name":"Humam Kadara","orcid":"https://orcid.org/0000-0003-2976-9115"},"institutions":[{"id":"https://openalex.org/I98635879","display_name":"American University of Beirut","ror":"https://ror.org/04pznsd21","country_code":"LB","type":"education","lineage":["https://openalex.org/I98635879"]}],"countries":["LB"],"is_corresponding":true,"raw_author_name":"Humam Kadara","raw_affiliation_strings":["Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. hk94@aub.edu.lb","Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. hk94@aub.edu.lb","institution_ids":["https://openalex.org/I98635879"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon","institution_ids":["https://openalex.org/I98635879"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054223849","display_name":"Paul Scheet","orcid":"https://orcid.org/0000-0002-5173-7497"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I66218314","display_name":"Houston Graduate School of Theology","ror":"https://ror.org/035khbv71","country_code":"US","type":"education","lineage":["https://openalex.org/I66218314"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paul Scheet","raw_affiliation_strings":["Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. pscheet@alum.wustl.edu","University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA. pscheet@alum.wustl.edu","University of Texas School of Public Health, Houston, TX, USA. pscheet@alum.wustl.edu","University of Texas School of Public Health, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. pscheet@alum.wustl.edu","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA. pscheet@alum.wustl.edu","institution_ids":["https://openalex.org/I66218314"]},{"raw_affiliation_string":"University of Texas School of Public Health, Houston, TX, USA. pscheet@alum.wustl.edu","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"University of Texas School of Public Health, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049321069","https://openalex.org/A5054223849"],"corresponding_institution_ids":["https://openalex.org/I1343551460","https://openalex.org/I66218314","https://openalex.org/I919571938","https://openalex.org/I98635879"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.2334,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.75045379,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.6567000150680542,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.6567000150680542,"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":0.3160000145435333,"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/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.005499999970197678,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ion-semiconductor-sequencing","display_name":"Ion semiconductor sequencing","score":0.7012789249420166},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5488208532333374},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4600612223148346},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4365481734275818},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42064958810806274},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4046664535999298},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32229912281036377},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.305627703666687}],"concepts":[{"id":"https://openalex.org/C164928082","wikidata":"https://www.wikidata.org/wiki/Q6063435","display_name":"Ion semiconductor sequencing","level":4,"score":0.7012789249420166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5488208532333374},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4600612223148346},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4365481734275818},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42064958810806274},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4046664535999298},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32229912281036377},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.305627703666687},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000473","qualifier_name":"pathology","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1991-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1991-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1991-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29301485","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29301485","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5753459","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5753459","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:7d8bd67ef3354177b42a64157d1a7b2a","is_oa":true,"landing_page_url":"https://doaj.org/article/7d8bd67ef3354177b42a64157d1a7b2a","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,"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":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-10 (2018)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1991-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1991-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1991-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/1","score":0.46000000834465027,"display_name":"No poverty"}],"awards":[{"id":"https://openalex.org/G111615301","display_name":null,"funder_award_id":"P30 CA-016672","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1299990199","display_name":"Cancer Center Support Grant","funder_award_id":"3p30ca016672-48s2","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1947306073","display_name":null,"funder_award_id":"R01HG005859","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2581177976","display_name":"Elucidating the evolution of the premalignant airway genome in space and time","funder_award_id":"RP150079","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G3530808682","display_name":"Statistical Methods for Population Genomics and \"Next-gen\" Sequencing Data","funder_award_id":"5r01hg005859-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4276892241","display_name":null,"funder_award_id":"P30CA016672","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G4465965092","display_name":null,"funder_award_id":"R01HG005859","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4985569203","display_name":null,"funder_award_id":"R01CA205608","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8138165303","display_name":null,"funder_award_id":"P30CA016677","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2781853897.pdf","grobid_xml":"https://content.openalex.org/works/W2781853897.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1577822803","https://openalex.org/W1848939527","https://openalex.org/W1965856472","https://openalex.org/W1987754412","https://openalex.org/W1988929438","https://openalex.org/W2009720434","https://openalex.org/W2042386784","https://openalex.org/W2044433401","https://openalex.org/W2051380427","https://openalex.org/W2061939373","https://openalex.org/W2062375641","https://openalex.org/W2062497242","https://openalex.org/W2064676287","https://openalex.org/W2071066517","https://openalex.org/W2087008771","https://openalex.org/W2096791516","https://openalex.org/W2106181723","https://openalex.org/W2111867681","https://openalex.org/W2117131162","https://openalex.org/W2118143563","https://openalex.org/W2120048439","https://openalex.org/W2127832858","https://openalex.org/W2128945836","https://openalex.org/W2129337972","https://openalex.org/W2129802084","https://openalex.org/W2136549416","https://openalex.org/W2138601221","https://openalex.org/W2141637710","https://openalex.org/W2155943701","https://openalex.org/W2164418361","https://openalex.org/W2180435523","https://openalex.org/W2180481128","https://openalex.org/W2225287204","https://openalex.org/W2275877493","https://openalex.org/W2467417577","https://openalex.org/W2524082038","https://openalex.org/W2761678850","https://openalex.org/W2981018396"],"related_works":["https://openalex.org/W3031743318","https://openalex.org/W2091383172","https://openalex.org/W2076392095","https://openalex.org/W2293843125","https://openalex.org/W1821627046","https://openalex.org/W2120048439","https://openalex.org/W2225706572","https://openalex.org/W4281696866","https://openalex.org/W2210202376","https://openalex.org/W2041048994"],"abstract_inverted_index":{"BACKGROUND:":[0],"'Next-generation'":[1],"(NGS)":[2],"sequencing":[3,40],"has":[4,44],"wide":[5],"application":[6],"in":[7,16,28,83,150,161,216,243],"medical":[8],"genetics,":[9],"including":[10],"the":[11,63,78,145,153,180,183,189,223,228],"detection":[12],"of":[13,69,136,144,155,197,202],"somatic":[14],"variation":[15],"cancer.":[17],"The":[18],"Ion":[19,113,184,193,220],"Torrent-based":[20],"(IONT)":[21],"platform":[22],"is":[23],"among":[24,227],"NGS":[25],"technologies":[26],"employed":[27],"clinical,":[29],"research":[30,67],"and":[31,66,88,96,115,142,149,239],"diagnostic":[32,65],"settings.":[33],"However,":[34],"identifying":[35],"mutations":[36],"from":[37,77,93,98,210],"IONT":[38,247],"deep":[39,248],"with":[41],"high":[42],"confidence":[43],"remained":[45],"a":[46,56,116],"challenge.":[47],"We":[48,107],"compared":[49],"various":[50],"computational":[51],"variant-calling":[52],"methods":[53,146],"to":[54,236],"derive":[55],"variant":[57,158,244],"identification":[58],"pipeline":[59],"that":[60,164],"may":[61],"improve":[62],"molecular":[64],"utility":[68],"IONT.":[70],"RESULTS:":[71],"Using":[72],"IONT,":[73],"we":[74,119],"surveyed":[75],"variants":[76,139,171,204],"409-gene":[79],"Comprehensive":[80],"Cancer":[81],"Panel":[82],"whole-section":[84],"tumors,":[85],"intra-tumoral":[86],"biopsies":[87],"matched":[89],"normal":[90],"samples":[91],"obtained":[92],"frozen":[94],"tissues":[95],"blood":[97],"four":[99],"early-stage":[100],"non-small":[101],"cell":[102],"lung":[103],"cancer":[104],"(NSCLC)":[105],"patients.":[106],"used":[108],"MuTect,":[109],"Varscan2,":[110],"IONT's":[111],"proprietary":[112],"Reporter,":[114],"simple":[117],"subtraction":[118],"called":[120,138],"\"Poor":[121],"Man's":[122],"Caller.\"":[123],"Together":[124],"these":[125],"produced":[126],"calls":[127,159],"at":[128],"637":[129],"loci":[130],"across":[131],"all":[132,198],"samples.":[133],"Visual":[134],"validation":[135],"434":[137],"was":[140],"performed,":[141],"performance":[143,226],"assessed":[147],"individually":[148],"combination.":[151],"Of":[152],"subset":[154],"inspected":[156],"putative":[157],"(n=223)":[160],"genomic":[162],"regions":[163],"were":[165,173,205],"not":[166],"intronic":[167],"or":[168],"intergenic,":[169],"68":[170],"(30%)":[172],"deemed":[174],"valid":[175],"after":[176],"visual":[177],"inspection.":[178],"Among":[179],"individual":[181,229],"methods,":[182],"Reporter":[185,194,221],"method":[186],"offered":[187,213,222],"perhaps":[188],"most":[190,224],"reasonable":[191],"tradeoffs.":[192],"captured":[195],"83%":[196],"discovered":[199],"variants;":[200],"50%":[201],"its":[203],"visually":[206],"validated.":[207],"Aggregating":[208],"results":[209],"multiple":[211],"packages":[212],"varied":[214],"improvements":[215],"performance.":[217],"CONCLUSIONS:":[218],"Overall,":[219],"attractive":[225],"callers.":[230],"This":[231],"study":[232],"suggests":[233],"combined":[234],"strategies":[235],"maximize":[237],"sensitivity":[238],"positive":[240],"predictive":[241],"value":[242],"calling":[245],"using":[246],"sequencing.":[249]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
