{"id":"https://openalex.org/W2104644553","doi":"https://doi.org/10.1101/gr.171701","title":"Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization","display_name":"Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization","publication_year":2001,"publication_date":"2001-06-01","ids":{"openalex":"https://openalex.org/W2104644553","doi":"https://doi.org/10.1101/gr.171701","mag":"2104644553","pmid":"https://pubmed.ncbi.nlm.nih.gov/11381034","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/311125"},"language":"en","primary_location":{"id":"doi:10.1101/gr.171701","doi":"https://doi.org/10.1101/gr.171701","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.171701","pdf_url":"https://genome.cshlp.org/content/11/6/1086.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://genome.cshlp.org/content/11/6/1086.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010680275","display_name":"Peter K. Rogan","orcid":"https://orcid.org/0000-0003-2070-5254","observed_orcids":["https://orcid.org/0000-0003-2070-5254"]},"institutions":[{"id":"https://openalex.org/I1328594524","display_name":"Children's Mercy Hospital","ror":"https://ror.org/04zfmcq84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328594524"]},{"id":"https://openalex.org/I75421653","display_name":"University of Missouri\u2013Kansas City","ror":"https://ror.org/01w0d5g70","country_code":"US","type":"education","lineage":["https://openalex.org/I75421653"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter K. Rogan","raw_affiliation_strings":["Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA. progan@cmh.edu","Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA. progan@cmh.edu","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]},{"raw_affiliation_string":"Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090723703","display_name":"Patricia M. Cazcarro","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1328594524","display_name":"Children's Mercy Hospital","ror":"https://ror.org/04zfmcq84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328594524"]},{"id":"https://openalex.org/I75421653","display_name":"University of Missouri\u2013Kansas City","ror":"https://ror.org/01w0d5g70","country_code":"US","type":"education","lineage":["https://openalex.org/I75421653"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patricia M. Cazcarro","raw_affiliation_strings":["Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014952448","display_name":"Joan H.M. Knoll","orcid":"https://orcid.org/0000-0001-6691-1710","observed_orcids":["https://orcid.org/0000-0001-6691-1710"]},"institutions":[{"id":"https://openalex.org/I1328594524","display_name":"Children's Mercy Hospital","ror":"https://ror.org/04zfmcq84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328594524"]},{"id":"https://openalex.org/I75421653","display_name":"University of Missouri\u2013Kansas City","ror":"https://ror.org/01w0d5g70","country_code":"US","type":"education","lineage":["https://openalex.org/I75421653"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joan H.M. Knoll","raw_affiliation_strings":["Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and Clinics, University of Missouri-Kansas City\n                           School of Medicine, Kansas City, Missouri 64108","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"6","first_page":"1086","last_page":"1094"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9955999851226807,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.002300000051036477,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fluorescence-in-situ-hybridization","display_name":"fluorescence in situ hybridization","score":0.9200000166893005},{"id":"https://openalex.org/keywords/chromosomal-rearrangements","display_name":"chromosomal rearrangements","score":0.7760000228881836},{"id":"https://openalex.org/keywords/probe-design","display_name":"probe design","score":0.6119999885559082},{"id":"https://openalex.org/keywords/long-pcr","display_name":"long PCR","score":0.5320000052452087},{"id":"https://openalex.org/keywords/repetitive-dna","display_name":"repetitive DNA","score":0.6499999761581421},{"id":"https://openalex.org/keywords/magel2","display_name":"MAGEL2","score":0.9559999704360962},{"id":"https://openalex.org/keywords/hira","display_name":"HIRA","score":0.984000027179718},{"id":"https://openalex.org/keywords/chromosome-1p36","display_name":"chromosome 1p36","score":0.9580000042915344},{"id":"https://openalex.org/keywords/chromosome-22q11-2","display_name":"chromosome 22q11.2","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8126755952835083},{"id":"https://openalex.org/C70278784","wikidata":"https://www.wikidata.org/wiki/Q574427","display_name":"Metaphase","level":4,"score":0.7175900936126709},{"id":"https://openalex.org/C2777542201","wikidata":"https://www.wikidata.org/wiki/Q1336182","display_name":"Fluorescence in situ hybridization","level":4,"score":0.6785942912101746},{"id":"https://openalex.org/C130197536","wikidata":"https://www.wikidata.org/wiki/Q418436","display_name":"Hybridization probe","level":3,"score":0.6735687851905823},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.5862182378768921},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.5595514178276062},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5097276568412781},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4722955524921417},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.47176840901374817},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4701048731803894},{"id":"https://openalex.org/C182901222","wikidata":"https://www.wikidata.org/wiki/Q419061","display_name":"Bacterial artificial chromosome","level":4,"score":0.4633982479572296},{"id":"https://openalex.org/C169802333","wikidata":"https://www.wikidata.org/wiki/Q424473","display_name":"Repeated sequence","level":4,"score":0.4612705707550049},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.4326384663581848},{"id":"https://openalex.org/C40767141","wikidata":"https://www.wikidata.org/wiki/Q285697","display_name":"Recombinant DNA","level":3,"score":0.4259055554866791},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.36469823122024536},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27763038873672485}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002891","descriptor_name":"Chromosomes, Human, Pair 21","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002892","descriptor_name":"Chromosomes, Human, Pair 22","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":"D009693","descriptor_name":"Nucleic Acid Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":true},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","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":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1101/gr.171701","doi":"https://doi.org/10.1101/gr.171701","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.171701","pdf_url":"https://genome.cshlp.org/content/11/6/1086.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:311125","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/311125","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,"listed_in":[],"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":"Genome Res","raw_type":"Text"},{"id":"pmid:11381034","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11381034","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,"listed_in":[],"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":"Genome research","raw_type":"Comparative Study"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.714.8617","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.714.8617","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://cytognomix.org/scFISH/genomeresearch11_1086.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1101/gr.171701","doi":"https://doi.org/10.1101/gr.171701","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.171701","pdf_url":"https://genome.cshlp.org/content/11/6/1086.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310169","display_name":"University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690"},{"id":"https://openalex.org/F4320310179","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83"},{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2104644553.pdf","grobid_xml":"https://content.openalex.org/works/W2104644553.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W29320742","https://openalex.org/W1233117074","https://openalex.org/W1919421741","https://openalex.org/W2021243296","https://openalex.org/W2025847893","https://openalex.org/W2033049603","https://openalex.org/W2033860372","https://openalex.org/W2043882061","https://openalex.org/W2044914133","https://openalex.org/W2052241801","https://openalex.org/W2055043387","https://openalex.org/W2062956770","https://openalex.org/W2071398217","https://openalex.org/W2074681588","https://openalex.org/W2082650750","https://openalex.org/W2085358347","https://openalex.org/W2103951922","https://openalex.org/W2115602625","https://openalex.org/W2116302199","https://openalex.org/W2128831915","https://openalex.org/W2130158853","https://openalex.org/W2166516745","https://openalex.org/W2205616920","https://openalex.org/W2397044371","https://openalex.org/W2614575602","https://openalex.org/W2949977409","https://openalex.org/W4415309844","https://openalex.org/W6628187006","https://openalex.org/W6677212175","https://openalex.org/W6844625789"],"related_works":["https://openalex.org/W2137102564","https://openalex.org/W7097319040","https://openalex.org/W2105733616","https://openalex.org/W4388311142","https://openalex.org/W1980856922","https://openalex.org/W2140901938","https://openalex.org/W7100728620","https://openalex.org/W1576217091","https://openalex.org/W251446049","https://openalex.org/W2417243885"],"abstract_inverted_index":{"Chromosomal":[0],"rearrangements":[1],"are":[2,22,58,94,123,195],"frequently":[3],"monitored":[4],"by":[5,47,60,134,197],"fluorescence":[6],"in":[7,70,169],"situ":[8],"hybridization":[9,92,116],"(FISH)":[10],"using":[11],"large,":[12],"recombinant":[13,135],"DNA":[14,81,89,136],"probes":[15,33,44,57,86,102,109,122,141,224],"consisting":[16],"of":[17,51,108,176,185,190,200],"contiguous":[18],"genomic":[19,54,127],"intervals":[20,189],"that":[21,100,213],"often":[23],"distant":[24],"from":[25,35,110,126],"disease":[26],"loci.":[27],"We":[28,138],"developed":[29,139],"smaller,":[30],"targeted,":[31],"single-copy":[32,41,140],"directly":[34,125],"the":[36,111,173],"human":[37,73],"genome":[38],"sequence.":[39],"These":[40],"FISH":[42],"(scFISH)":[43],"were":[45],"designed":[46],"computational":[48],"sequence":[49],"analysis":[50],"approximately":[52],"100-kb":[53],"sequences.":[55,90],"ScFISH":[56,121],"produced":[59,124],"long":[61],"PCR,":[62],"then":[63],"purified,":[64],"labeled,":[65],"and":[66,129,152,202,208],"hybridized":[67],"individually":[68],"or":[69,76,193],"combination":[71],"to":[72,96],"chromosomes.":[74,120],"Preannealing":[75],"blocking":[77],"with":[78,222],"unlabeled,":[79],"repetitive":[80,88],"is":[82],"unnecessary,":[83],"as":[84],"scFISH":[85,177,223],"lack":[87],"The":[91,162],"results":[93],"analogous":[95],"conventional":[97],"FISH,":[98],"except":[99],"shorter":[101],"can":[103],"be":[104,220],"readily":[105],"visualized.":[106],"Combinations":[107],"same":[112],"region":[113],"gave":[114],"single":[115],"signals":[117],"on":[118,205,216],"metaphase":[119,217],"DNA,":[128],"thus":[130],"more":[131],"quickly":[132],"than":[133,229],"techniques.":[137],"for":[142,160,178],"three":[143],"chromosomal":[144,183],"regions-the":[145],"CDC2L1":[146],"(chromosome":[147,150,154],"1p36),":[148],"MAGEL2":[149],"15q11.2),":[151],"HIRA":[153],"22q11.2)":[155],"genes-and":[156],"show":[157],"their":[158],"utility":[159,175],"FISH.":[161],"smallest":[163],"probe":[164],"tested":[165],"was":[166],"2290":[167],"bp":[168],"length.":[170],"To":[171],"assess":[172],"potential":[174],"high-resolution":[179],"analysis,":[180],"we":[181],"determined":[182],"distributions":[184],"such":[186],"probes.":[187],"Single-copy":[188],"this":[191],"length":[192],"greater":[194,228],"separated":[196],"an":[198],"average":[199],"29.2":[201],"22.3":[203],"kb":[204],"chromosomes":[206,218],"21":[207],"22,":[209],"respectively.":[210],"This":[211],"indicates":[212],"abnormalities":[214],"seen":[215],"could":[219],"characterized":[221],"at":[225],"a":[226],"resolution":[227],"previously":[230],"possible.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":10},{"year":2021,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
