{"id":"https://openalex.org/W4394960952","doi":"https://doi.org/10.1142/s0219720024500094","title":"A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations","display_name":"A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations","publication_year":2024,"publication_date":"2024-04-19","ids":{"openalex":"https://openalex.org/W4394960952","doi":"https://doi.org/10.1142/s0219720024500094","pmid":"https://pubmed.ncbi.nlm.nih.gov/39030667"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720024500094","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720024500094","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5074024326","display_name":"Rituparna Sinha","orcid":"https://orcid.org/0000-0002-5742-8468"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Rituparna Sinha","raw_affiliation_strings":["Information Technology, Heritage Institute of Technology, Anandapur Kolkata, West Bengal, India"],"raw_orcid":"https://orcid.org/0000-0002-5742-8468","affiliations":[{"raw_affiliation_string":"Information Technology, Heritage Institute of Technology, Anandapur Kolkata, West Bengal, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037279956","display_name":"Rajat Kumar Pal","orcid":"https://orcid.org/0000-0001-9838-6500"},"institutions":[{"id":"https://openalex.org/I106542073","display_name":"University of Calcutta","ror":"https://ror.org/01e7v7w47","country_code":"IN","type":"education","lineage":["https://openalex.org/I106542073"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajat Kumar Pal","raw_affiliation_strings":["Computer Science and Engineering Department, University of Calcutta, Kolkata, India"],"raw_orcid":"https://orcid.org/0000-0001-9838-6500","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department, University of Calcutta, Kolkata, India","institution_ids":["https://openalex.org/I106542073"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000655826","display_name":"Rajat K. De","orcid":"https://orcid.org/0000-0001-6080-1131"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajat Kumar De","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India"],"raw_orcid":"https://orcid.org/0000-0001-6080-1131","affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India","institution_ids":["https://openalex.org/I6498739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074024326"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05398874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"03","first_page":"2450009","last_page":"2450009"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9950000047683716,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9950000047683716,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9944999814033508,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.632729709148407},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5912948846817017},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4791116714477539},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43928876519203186},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4166480600833893},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3820565640926361}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.632729709148407},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5912948846817017},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4791116714477539},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43928876519203186},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4166480600833893},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3820565640926361}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"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":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720024500094","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720024500094","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:39030667","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39030667","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1885678170","https://openalex.org/W1988650678","https://openalex.org/W2012151892","https://openalex.org/W2018604728","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2097160089","https://openalex.org/W2117608012","https://openalex.org/W2118526609","https://openalex.org/W2127230663","https://openalex.org/W2130077037","https://openalex.org/W2137779717","https://openalex.org/W2152036878","https://openalex.org/W2167722550","https://openalex.org/W2616754551","https://openalex.org/W2734616888","https://openalex.org/W2748971311","https://openalex.org/W2790245822","https://openalex.org/W2796391389","https://openalex.org/W2892132701","https://openalex.org/W2921762809","https://openalex.org/W2970472078","https://openalex.org/W3003473637","https://openalex.org/W3035033158","https://openalex.org/W3125141729","https://openalex.org/W4224127506","https://openalex.org/W4293054794"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"A":[0],"turning":[1],"point":[2],"in":[3,37,43,57,107,181,199],"cancer":[4],"research":[5],"is":[6,175,192,236],"the":[7,17,26,32,49,67,72,97,118,122,131,145,154,163,189,214,221,227,233],"introduction":[8],"of":[9,34,69,71,99,109,114,125,162,177,188,195,229],"massively":[10],"parallel":[11],"sequencing":[12],"technology":[13],"which":[14,46],"greatly":[15],"reduced":[16],"cost":[18],"and":[19,30,102,134,144,191,217,241],"time":[20],"for":[21,28],"genome":[22],"sequencing.":[23],"This":[24,84],"enhanced":[25],"scope":[27],"detecting":[29,196],"analyzing":[31],"role":[33],"structural":[35],"alterations":[36],"cancer.":[38],"However,":[39],"certain":[40],"bias":[41,81,105,253],"exists":[42],"NGS-based":[44],"approaches,":[45],"badly":[47],"affects":[48],"CNV":[50,58,74,255],"identification":[51],"process.":[52],"Moreover,":[53],"DNA":[54,100,128,164,200],"repeats":[55,101,165],"existing":[56,73,106,198],"regions":[59,108],"need":[60],"special":[61],"attention":[62],"as":[63,183,185,248],"they":[64],"will":[65],"degrade":[66],"performance":[68],"majority":[70],"detection":[75,256],"tools,":[76],"even":[77],"after":[78],"applying":[79],"generalized":[80],"correction":[82,254],"method.":[83],"motivated":[85],"this":[86],"work,":[87],"where":[88,117,232],"a":[89,149,168,206],"novel":[90,150],"method":[91,112,174],"has":[92,242],"been":[93],"designed":[94],"to":[95,152,158],"address":[96],"issue":[98],"thereby":[103],"mappability":[104],"CNV.":[110],"The":[111,142,172,203],"consists":[113],"three":[115],"phases,":[116],"first":[119],"phase":[120,147],"computes":[121],"alignment":[123],"information":[124],"uniquely":[126],"mapped":[127,156],"reads,":[129],"considering":[130],"base":[132,135],"quality":[133],"mismatch":[136],"parameters":[137],"at":[138],"nucleotide":[139],"level":[140],"precision.":[141],"second":[143],"third":[146],"use":[148],"approach":[151],"allocate":[153],"non-uniquely":[155],"reads":[157],"an":[159],"optimal":[160],"region":[161,187],"based":[166],"on":[167,218],"probabilistic":[169],"membership":[170],"model.":[171],"proposed":[173],"capable":[176,194],"identifying":[178],"CNVs":[179,197],"present":[180],"coding,":[182],"well":[184],"non-coding":[186],"DNA,":[190],"also":[193,237],"repeat":[201],"regions.":[202],"methodology":[204],"achieves":[205],"sensitivity":[207],"greater":[208,238],"than":[209,239],"[Formula:":[210],"see":[211],"text]":[212],"during":[213],"performed":[215],"simulations,":[216],"real":[219],"data,":[220],"detected":[222],"variants":[223],"are":[224],"validated":[225],"with":[226,250],"database":[228],"genomic":[230],"variants,":[231],"percentage":[234],"overlap":[235],"95%,":[240],"achieved":[243],"much":[244],"better":[245],"breakpoint":[246],"prediction,":[247],"compared":[249],"other":[251],"popular":[252],"methods.":[257]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}