{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:20:55Z","timestamp":1740144055143,"version":"3.37.3"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T00:00:00Z","timestamp":1564704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31801098","91746113","31501062"],"award-info":[{"award-number":["31801098","91746113","31501062"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Projects of Education Department of Heilongjiang Province","award":["1254G041","12511273"],"award-info":[{"award-number":["1254G041","12511273"]}]},{"name":"Research Project of Health Department of Heilongjiang Province","award":["2011-249"],"award-info":[{"award-number":["2011-249"]}]},{"DOI":"10.13039\/501100010845","name":"Harbin Science and Technology Bureau","doi-asserted-by":"publisher","award":["RC2013QN004112"],"award-info":[{"award-number":["RC2013QN004112"]}],"id":[{"id":"10.13039\/501100010845","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundamental Research Funds for the Provincial Universities","award":["2017JCZX50"],"award-info":[{"award-number":["2017JCZX50"]}]},{"name":"Internal Fund Project of Eye Hospital of Wenzhou Medical University","award":["YJGG20181001"],"award-info":[{"award-number":["YJGG20181001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The recent extensive application of next-generation sequencing has led to the rapid accumulation of multiple types of data for functional DNA elements. With the advent of precision medicine, the fine-mapping of risk loci based on these elements has become of paramount importance. In this study, we obtained the human reference genome (GRCh38) and the main DNA sequence elements, including protein-coding genes, miRNAs, lncRNAs and single nucleotide polymorphism flanking sequences, from different repositories. We then realigned these elements to identify their exact locations on the genome. Overall, 5%\u201320% of all sequence element locations deviated among databases, on the scale of kilobase-pair to megabase-pair. These deviations even affected the selection of genome-wide association study risk-associated genes. Our results implied that the location information for functional DNA elements may deviate among public databases. Researchers should take care when using cross-database sources and should perform pilot sequence alignments before element location-based studies.<\/jats:p>","DOI":"10.1093\/bib\/bbz073","type":"journal-article","created":{"date-parts":[[2019,6,1]],"date-time":"2019-06-01T19:12:55Z","timestamp":1559416375000},"page":"1293-1301","source":"Crossref","is-referenced-by-count":5,"title":["Location deviations of DNA functional elements affected SNP mapping in the published databases and references"],"prefix":"10.1093","volume":"21","author":[{"given":"Hewei","family":"Zheng","sequence":"first","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Xueying","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6649-649X","authenticated-orcid":false,"given":"Hong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P R China"}]},{"given":"Yu","family":"Ding","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Xiaoyan","family":"Lu","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Guosi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Jiaxin","family":"Yang","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Lianzong","family":"Wang","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Haotian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Yu","family":"Bai","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Jing","family":"Li","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Jingqi","family":"Wu","sequence":"additional","affiliation":[{"name":"Harbin Medical University and Wenzhou Medical University"}]},{"given":"Yongshuai","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P. R. China"}]},{"given":"Liangde","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, and Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, P. R. China"}]}],"member":"286","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"2020080709265496300_ref1","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","article-title":"The impact of next-generation sequencing technology on genetics","volume":"24","author":"Mardis","year":"2008","journal-title":"Trends Genet"},{"key":"2020080709265496300_ref2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/501261a","article-title":"The genome jigsaw","volume":"501","author":"sequencing","year":"2013","journal-title":"Nature"},{"key":"2020080709265496300_ref3","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/526029a","article-title":"Human Genome Project: twenty-five years of big biology","volume":"526","author":"Green","year":"2015","journal-title":"Nature"},{"key":"2020080709265496300_ref4","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1016\/j.omtn.2018.06.007","article-title":"Recurrence-associated long non-coding RNA signature for determining the risk of recurrence in patients with colon cancer","volume":"12","author":"Zhou","year":"2018","journal-title":"Mol Ther Nucleic Acids"},{"key":"2020080709265496300_ref5","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1126\/science.298.5595.941a","article-title":"Human genome. HapMap launched with pledges of $100 million","volume":"298","author":"Couzin","year":"2002","journal-title":"Science"},{"key":"2020080709265496300_ref6","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nature02168","article-title":"The International HapMap Project","volume":"426","author":"International HapMap C","year":"2003","journal-title":"Nature"},{"key":"2020080709265496300_ref7","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/nbt0308-256b","article-title":"1000 Genomes Project","volume":"26","author":"Siva","year":"2008","journal-title":"Nat Biotechnol"},{"key":"2020080709265496300_ref8","doi-asserted-by":"crossref","first-page":"2322, 2325","DOI":"10.1001\/jama.2012.88674","article-title":"1000 Genomes Project finds substantial genetic variation among populations","volume":"308","author":"Kuehn","year":"2012","journal-title":"JAMA"},{"key":"2020080709265496300_ref9","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2013.01.027","article-title":"GWAS meets TCGA to illuminate mechanisms of cancer predisposition","volume":"152","author":"Kim","year":"2013","journal-title":"Cell"},{"key":"2020080709265496300_ref10","article-title":"Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer's disease","author":"Zhou","year":"2018","journal-title":"Brief Bioinform"},{"key":"2020080709265496300_ref11","first-page":"A68","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"Tomczak","year":"2015","journal-title":"Contemp Oncol (Pozn)"},{"key":"2020080709265496300_ref12","article-title":"Evaluation of drug efficacy based on the spatial position comparison of drug-target interaction centers","author":"Ding","year":"2019","journal-title":"Brief Bioinform"},{"key":"2020080709265496300_ref13","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0968-0004(99)01400-0","article-title":"Nucleotide sequence databases: a gold mine for biologists","volume":"24","author":"Pandey","year":"1999","journal-title":"Trends Biochem Sci"},{"key":"2020080709265496300_ref14","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.tig.2014.12.002","article-title":"Accounting for uncertainty in DNA sequencing data","volume":"31","author":"O'Rawe","year":"2015","journal-title":"Trends Genet"},{"issue":"Suppl","key":"2020080709265496300_ref15","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1093\/nar\/20.suppl.2065","article-title":"GenBank","volume":"20","author":"Burks","year":"1992","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref16","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature","volume":"34","author":"Griffiths-Jones","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref17","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"Consortium EP","year":"2004","journal-title":"Science"},{"key":"2020080709265496300_ref18","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1093\/nar\/28.1.352","article-title":"dbSNP: a database of single nucleotide polymorphisms","volume":"28","author":"Smigielski","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref19","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/nar\/30.1.38","article-title":"The Ensembl genome database project","volume":"30","author":"Hubbard","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref20","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1093\/nar\/gkg129","article-title":"The UCSC Genome Browser Database","volume":"31","author":"Karolchik","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref21","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1186\/gb-2005-6-3-312","article-title":"Large-scale discovery and validation of functional elements in the human genome","volume":"6","author":"Bernstein","year":"2005","journal-title":"Genome Biol"},{"key":"2020080709265496300_ref22","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/cgt.2016.5","article-title":"Integrative analysis of microRNA and mRNA expression profiles in non-small-cell lung cancer","volume":"23","author":"Yang","year":"2016","journal-title":"Cancer Gene Ther"},{"key":"2020080709265496300_ref23","doi-asserted-by":"crossref","first-page":"4825","DOI":"10.1038\/onc.2012.493","article-title":"Inhibition of the Nrf2 transcription factor by the alkaloid trigonelline renders pancreatic cancer cells more susceptible to apoptosis through decreased proteasomal gene expression and proteasome activity","volume":"32","author":"Arlt","year":"2013","journal-title":"Oncogene"},{"key":"2020080709265496300_ref24","doi-asserted-by":"crossref","first-page":"56383","DOI":"10.18632\/oncotarget.10891","article-title":"Construction and analysis of dysregulated lncRNA-associated ceRNA network identified novel lncRNA biomarkers for early diagnosis of human pancreatic cancer","volume":"7","author":"Zhou","year":"2016","journal-title":"Oncotarget"},{"key":"2020080709265496300_ref25","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1158\/0008-5472.CAN-11-1682","article-title":"Mitochondrial DNA sequence variation and risk of pancreatic cancer","volume":"72","author":"Lam","year":"2012","journal-title":"Cancer Res"},{"key":"2020080709265496300_ref26","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1126\/science.349.6255.1433","article-title":"NIH opens precision medicine study to nation","volume":"349","author":"Kaiser","year":"2015","journal-title":"Science"},{"key":"2020080709265496300_ref27","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nature15816","article-title":"Building the foundation for genomics in precision medicine","volume":"526","author":"Aronson","year":"2015","journal-title":"Nature"},{"key":"2020080709265496300_ref28","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bby102","article-title":"Landscape of SNPs-mediated lncRNA structural variations and their implication in human complex diseases","author":"Wang","year":"2018","journal-title":"Brief Bioinform"},{"key":"2020080709265496300_ref29","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/j.bbrc.2017.02.100","article-title":"Insight into HOTAIR structural features and functions as landing pads for transcription regulation proteins","volume":"485","author":"Wang","year":"2017","journal-title":"Biochem Biophys Res Commun"},{"key":"2020080709265496300_ref30","doi-asserted-by":"crossref","DOI":"10.3390\/ijms18122659","article-title":"LncRNA structural characteristics in epigenetic regulation","volume":"18","author":"Wang","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2020080709265496300_ref31","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ygeno.2017.01.005","article-title":"Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis","volume":"109","author":"Guo","year":"2017","journal-title":"Genomics"},{"key":"2020080709265496300_ref32","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.1860604","article-title":"An overview of Ensembl","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2020080709265496300_ref33","first-page":"17","article-title":"Aligning short sequencing reads with Bowtie","volume":"11","author":"Langmead","year":"2010","journal-title":"Curr Protoc Bioinformatics"},{"key":"2020080709265496300_ref34","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2020080709265496300_ref35","doi-asserted-by":"crossref","first-page":"D975","DOI":"10.1093\/nar\/gkt1211","article-title":"NCBI's database of Genotypes and Phenotypes: dbGaP","volume":"42","author":"Tryka","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref36","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1093\/nar\/gkw245","article-title":"Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer","volume":"44","author":"Mazza","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2020080709265496300_ref37","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0206632","article-title":"Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association","volume":"13","author":"Vossen","year":"2018","journal-title":"PLoS One"},{"key":"2020080709265496300_ref38","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.schres.2014.05.038","article-title":"Resequencing and association study of the NFKB activating protein-like gene (NKAPL) in schizophrenia","volume":"157","author":"Chen","year":"2014","journal-title":"Schizophr Res"},{"key":"2020080709265496300_ref39","doi-asserted-by":"crossref","first-page":"R126","DOI":"10.1186\/gb-2010-11-12-r126","article-title":"ArchAlign: coordinate-free chromatin alignment reveals novel architectures","volume":"11","author":"Lai","year":"2010","journal-title":"Genome Biol"},{"key":"2020080709265496300_ref40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0167742","article-title":"Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study","volume":"12","author":"Vries","year":"2017","journal-title":"PLoS One"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/4\/1293\/33583608\/bbz073.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/4\/1293\/33583608\/bbz073.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,7]],"date-time":"2020-08-07T13:42:03Z","timestamp":1596807723000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/21\/4\/1293\/5539362"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,2]]},"references-count":40,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,8,2]]},"published-print":{"date-parts":[[2020,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbz073","relation":{},"ISSN":["1477-4054"],"issn-type":[{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2019,8,2]]}}}