{"id":"https://openalex.org/W4414346382","doi":"https://doi.org/10.1093/bioinformatics/btaf522","title":"qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics","display_name":"qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics","publication_year":2025,"publication_date":"2025-09-01","ids":{"openalex":"https://openalex.org/W4414346382","doi":"https://doi.org/10.1093/bioinformatics/btaf522","pmid":"https://pubmed.ncbi.nlm.nih.gov/40973027"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf522/64302279/btaf522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf522/64302279/btaf522.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100408614","display_name":"Xiang Liu","orcid":"https://orcid.org/0000-0002-7081-3694"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiang Liu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,"],"raw_orcid":"https://orcid.org/0000-0002-7081-3694","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032821174","display_name":"Yi-Han Tang","orcid":"https://orcid.org/0009-0006-2248-1978"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi-Han Tang","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080781659","display_name":"James S. Blachly","orcid":"https://orcid.org/0000-0002-4275-5562"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Blachly","raw_affiliation_strings":["The Ohio State University Comprehensive Cancer Center , Columbus, OH 43210,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Ohio State University Comprehensive Cancer Center , Columbus, OH 43210,","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019007552","display_name":"Stephen B. Edge","orcid":"https://orcid.org/0000-0002-3285-6191"},"institutions":[{"id":"https://openalex.org/I1292894508","display_name":"Roswell Park Comprehensive Cancer Center","ror":"https://ror.org/0499dwk57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1292894508"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Edge","raw_affiliation_strings":["Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,","institution_ids":["https://openalex.org/I1292894508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072219874","display_name":"Yasminka A. Jakubek","orcid":"https://orcid.org/0000-0003-1427-1015"},"institutions":[{"id":"https://openalex.org/I2802239656","display_name":"Markey Cancer Center","ror":"https://ror.org/01dhvva97","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285210727","https://openalex.org/I2802239656"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yasminka A Jakubek","raw_affiliation_strings":["University of Kentucky Markey Cancer Center , Lexington, KY 40536,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Kentucky Markey Cancer Center , Lexington, KY 40536,","institution_ids":["https://openalex.org/I2802239656"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036784999","display_name":"Martin D. McCarter","orcid":"https://orcid.org/0000-0001-8174-1713"},"institutions":[{"id":"https://openalex.org/I4210134151","display_name":"University of Colorado Cancer Center","ror":"https://ror.org/04cqn7d42","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210134151"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin McCarter","raw_affiliation_strings":["University of Colorado Cancer Center , Aurora, CO 80045,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado Cancer Center , Aurora, CO 80045,","institution_ids":["https://openalex.org/I4210134151","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090621600","display_name":"Abdul Rafeh Naqash","orcid":"https://orcid.org/0000-0001-7622-720X"},"institutions":[{"id":"https://openalex.org/I4210131712","display_name":"Oklahoma State University Oklahoma City","ror":"https://ror.org/03y1zyv86","country_code":"US","type":"education","lineage":["https://openalex.org/I4210131712"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abdul Rafeh Naqash","raw_affiliation_strings":["University of Oklahoma Stephenson Cancer Center , Oklahoma City, OK 73104,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Oklahoma Stephenson Cancer Center , Oklahoma City, OK 73104,","institution_ids":["https://openalex.org/I4210131712"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053326285","display_name":"Kenneth G. Nepple","orcid":"https://orcid.org/0000-0001-8100-4190"},"institutions":[{"id":"https://openalex.org/I126307644","display_name":"University of Iowa","ror":"https://ror.org/036jqmy94","country_code":"US","type":"education","lineage":["https://openalex.org/I126307644"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kenneth G Nepple","raw_affiliation_strings":["University of Iowa Holden Comprehensive Cancer Center , Iowa City, IA 52242,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Iowa Holden Comprehensive Cancer Center , Iowa City, IA 52242,","institution_ids":["https://openalex.org/I126307644"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005874695","display_name":"Afaf E.G. Osman","orcid":"https://orcid.org/0000-0002-3688-4683"},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Afaf Osman","raw_affiliation_strings":["University of Utah Huntsman Cancer Institute , Salt Lake City, UT 84112,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah Huntsman Cancer Institute , Salt Lake City, UT 84112,","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081272862","display_name":"Matthew J. Reilley","orcid":"https://orcid.org/0000-0002-4725-0459"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew J Reilley","raw_affiliation_strings":["University of Virginia Comprehensive Cancer Center , Charlottesville, VA 22903,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Virginia Comprehensive Cancer Center , Charlottesville, VA 22903,","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007869493","display_name":"Gregory Riedlinger","orcid":"https://orcid.org/0000-0001-5690-7777"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory Riedlinger","raw_affiliation_strings":["Rutgers Cancer Institute , New Brunswick, NJ 08901,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rutgers Cancer Institute , New Brunswick, NJ 08901,","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030046985","display_name":"Bodour Salhia","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bodour Salhia","raw_affiliation_strings":["Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90089,","University of Southern California Norris Comprehensive Cancer Center, , Los Angeles, CA 90089,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90089,","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"University of Southern California Norris Comprehensive Cancer Center, , Los Angeles, CA 90089,","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009816526","display_name":"Bryan P. Schneider","orcid":"https://orcid.org/0000-0003-1868-7739"},"institutions":[{"id":"https://openalex.org/I1283055418","display_name":"Indiana University Health","ror":"https://ror.org/01aaptx40","country_code":"US","type":"funder","lineage":["https://openalex.org/I1283055418","https://openalex.org/I4388446366","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210108039","display_name":"Indiana Cancer Consortium","ror":"https://ror.org/01m417e54","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210108039"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryan P Schneider","raw_affiliation_strings":["Indiana University Simon Comprehensive Cancer Center , Indianapolis, IN 46202,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University Simon Comprehensive Cancer Center , Indianapolis, IN 46202,","institution_ids":["https://openalex.org/I1283055418","https://openalex.org/I4210108039","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014595154","display_name":"Craig D. Shriver","orcid":"https://orcid.org/0000-0001-8993-5811"},"institutions":[{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Craig Shriver","raw_affiliation_strings":["Murtha Cancer Center , Bethesda, MD 20814,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Murtha Cancer Center , Bethesda, MD 20814,","institution_ids":["https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057234924","display_name":"Michelle L. Churchman","orcid":"https://orcid.org/0000-0002-6560-1056"},"institutions":[{"id":"https://openalex.org/I4210100254","display_name":"Clinical Insights","ror":"https://ror.org/0168sna55","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210100254"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle L Churchman","raw_affiliation_strings":["Aster Insights , Hudson, FL 34667,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aster Insights , Hudson, FL 34667,","institution_ids":["https://openalex.org/I4210100254"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020439533","display_name":"Robert J. Rounbehler","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100254","display_name":"Clinical Insights","ror":"https://ror.org/0168sna55","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210100254"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J Rounbehler","raw_affiliation_strings":["Aster Insights , Hudson, FL 34667,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aster Insights , Hudson, FL 34667,","institution_ids":["https://openalex.org/I4210100254"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049848426","display_name":"Jamie K. Teer","orcid":"https://orcid.org/0000-0003-4513-0282"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie K Teer","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,"],"raw_orcid":"https://orcid.org/0000-0003-4513-0282","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090831668","display_name":"Nancy Gillis","orcid":"https://orcid.org/0000-0002-7744-8490"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nancy Gillis","raw_affiliation_strings":["Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","H. Lee Moffitt Cancer Center and Research Institute Department of Cancer Epidemiology, , Tampa, FL 33612,"],"raw_orcid":"https://orcid.org/0000-0002-7744-8490","affiliations":[{"raw_affiliation_string":"Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"H. Lee Moffitt Cancer Center and Research Institute Department of Cancer Epidemiology, , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049382437","display_name":"Mingxiang Teng","orcid":"https://orcid.org/0000-0002-8536-8941"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mingxiang Teng","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,"],"raw_orcid":"https://orcid.org/0000-0002-8536-8941","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]},{"raw_affiliation_string":"H. Lee Moffitt Cancer Center and Research Institute Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","institution_ids":["https://openalex.org/I3019308854"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":18,"corresponding_author_ids":["https://openalex.org/A5049382437","https://openalex.org/A5090831668"],"corresponding_institution_ids":["https://openalex.org/I3019308854"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.30097533,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10309","display_name":"Acute Myeloid Leukemia Research","score":0.4397999942302704,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10309","display_name":"Acute Myeloid Leukemia Research","score":0.4397999942302704,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.31200000643730164,"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/T10950","display_name":"Acute Lymphoblastic Leukemia research","score":0.0364999994635582,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"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/r-package","display_name":"R package","score":0.7416999936103821},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4643999934196472},{"id":"https://openalex.org/keywords/haematopoiesis","display_name":"Haematopoiesis","score":0.42149999737739563},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.33309999108314514},{"id":"https://openalex.org/keywords/hematopoietic-cell","display_name":"Hematopoietic cell","score":0.2786000072956085}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7416999936103821},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5884000062942505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5343999862670898},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4643999934196472},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4375999867916107},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4343999922275543},{"id":"https://openalex.org/C109159458","wikidata":"https://www.wikidata.org/wiki/Q919283","display_name":"Haematopoiesis","level":3,"score":0.42149999737739563},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.33309999108314514},{"id":"https://openalex.org/C2993713153","wikidata":"https://www.wikidata.org/wiki/Q211709","display_name":"Hematopoietic cell","level":4,"score":0.2786000072956085},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2678999900817871},{"id":"https://openalex.org/C2993967602","wikidata":"https://www.wikidata.org/wiki/Q5532932","display_name":"Genetic variants","level":4,"score":0.26100000739097595}],"mesh":[{"descriptor_ui":"D000082182","descriptor_name":"Clonal Hematopoiesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000082182","descriptor_name":"Clonal Hematopoiesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000082182","descriptor_name":"Clonal Hematopoiesis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf522/64302279/btaf522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40973027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40973027","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:scholarworks.indianapolis.iu.edu:1805/51533","is_oa":true,"landing_page_url":"https://hdl.handle.net/1805/51533","pdf_url":"https://scholarworks.indianapolis.iu.edu/bitstreams/1d4540ce-1ebd-4e9b-9f3f-2c8956230f58/download","source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"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":"PMC","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:11275308","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12466928","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12466928","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12466928/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf522/64302279/btaf522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2801361321","display_name":null,"funder_award_id":"R35GM155298","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G362094","display_name":null,"funder_award_id":"P30CA076292","funder_id":"https://openalex.org/F4320311073","funder_display_name":"Moffitt Cancer Center"},{"id":"https://openalex.org/G4534256652","display_name":null,"funder_award_id":"R01 CA268973","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4551976579","display_name":null,"funder_award_id":"CA076292","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G634390504","display_name":null,"funder_award_id":"P30 CA076292","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8135003176","display_name":null,"funder_award_id":"CA076292","funder_id":"https://openalex.org/F4320311073","funder_display_name":"Moffitt Cancer Center"}],"funders":[{"id":"https://openalex.org/F4320311073","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414346382.pdf","grobid_xml":"https://content.openalex.org/works/W4414346382.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1973234126","https://openalex.org/W1984068087","https://openalex.org/W1985823023","https://openalex.org/W1992826811","https://openalex.org/W2119180969","https://openalex.org/W2126816979","https://openalex.org/W2149858388","https://openalex.org/W2511116391","https://openalex.org/W2558446569","https://openalex.org/W2745259295","https://openalex.org/W2807173852","https://openalex.org/W2898789672","https://openalex.org/W2899732591","https://openalex.org/W2971157762","https://openalex.org/W3029661147","https://openalex.org/W3205011643","https://openalex.org/W4220875894","https://openalex.org/W4225270734","https://openalex.org/W4391135865","https://openalex.org/W4392886184","https://openalex.org/W4395466186","https://openalex.org/W4406328064"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Clonal":[1],"hematopoiesis":[2],"(CH)":[3],"is":[4,114],"a":[5,46],"molecular":[6],"biomarker":[7],"associated":[8],"with":[9,19,78],"various":[10,67],"adverse":[11],"outcomes":[12],"in":[13],"both":[14],"healthy":[15],"individuals":[16],"and":[17,59,79,84,120],"those":[18],"underlying":[20],"conditions,":[21],"including":[22,70],"cancer.":[23],"Detecting":[24],"CH":[25,61,101],"usually":[26],"involves":[27],"genomic":[28],"sequencing":[29,72],"of":[30,75],"individual":[31],"blood":[32],"samples":[33],"followed":[34],"by":[35],"robust":[36],"bioinformatics":[37,47],"data":[38,68,106],"filtering.":[39],"We":[40,63,89],"report":[41],"an":[42],"R":[43,112],"package,":[44],"qcCHIP,":[45],"pipeline":[48],"that":[49,91],"implements":[50],"permutation-based":[51],"parameter":[52],"optimization":[53],"to":[54,95,99],"guide":[55],"quality":[56],"control":[57],"filtering":[58],"cohort-specific":[60,105],"identification.":[62],"benchmark":[64],"qcCHIP":[65,92,111],"under":[66],"settings,":[69],"different":[71,86],"depths,":[73],"ranges":[74],"cohort":[76],"sizes,":[77],"without":[80],"normal-tumor":[81],"paired":[82],"samples,":[83],"across":[85],"cancer":[87],"types.":[88],"show":[90],"allows":[93],"users":[94],"customize":[96],"analysis":[97],"needs":[98],"generate":[100],"calls":[102],"based":[103],"on":[104],"characteristics.":[107],"AVAILABILITY":[108],"AND":[109],"IMPLEMENTATION:":[110],"package":[113],"freely":[115],"accessible":[116],"at":[117],"GitHub":[118],"https://github.com/tenglab/qcCHIP":[119],"DOI:":[121],"10.5281/zenodo.16421861.":[122]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
