Long Reads, Short Time: Feasibility of Prenatal Sample Karyotyping by Nanopore Genome Sequencing
Cost-wise, the full process has a reagent price of about 500 Euros (US$547)/ sample, lower than the cost of conventional karyotype plus arrayCGH assay [about 800 Euros (US$874)/sample]. [...]ONT has the potential to become a standard approach for prenatal diagnosis. Niccolò Bartalucci2 Simone Romagn...
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| Veröffentlicht in: | Clinical chemistry (Baltimore, Md.) Md.), 2019-12, Vol.65 (12), p.1605-1608 |
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| container_title | Clinical chemistry (Baltimore, Md.) |
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| creator | Bartalucci, Niccolò Romagnoli, Simone Contini, Elisa Marseglia, Giuseppina Magi, Alberto Guglielmelli, Paola Pelo, Elisabetta Vannucchi, Alessandro M |
| description | Cost-wise, the full process has a reagent price of about 500 Euros (US$547)/ sample, lower than the cost of conventional karyotype plus arrayCGH assay [about 800 Euros (US$874)/sample]. [...]ONT has the potential to become a standard approach for prenatal diagnosis. Niccolò Bartalucci2 Simone Romagnoli2,3 Elisa Contini2 Giuseppina Marseglia4 Alberto Magi5 Paola Guglielmelli2 Elisabetta Pelo4 Alessandro M. Vannucchi2 2 Department of Experimental and Clinical Medicine, CRIMM, University of Florence, Florence, Italy 3 Department of Medical Biotechnologlies, University of Siena Siena, Italy 4 Department of Laboratory Diagnosis, Genetic Diagnosis Service Careggi Teaching Hospital Florence, Italy 5 Department of Information Engineering, University of Florence Florence, Italy "Address correspondence to this author at: Viale Pieraccini 6 Florence 50139 Italy Fax+39-055-7947688 e-mail amvannucchi@unifi.it Previously published online at DOI: 10.1373/clinchem.2019.310805 1 Nonstandard abbreviations: CVS, chorionic villus sampling; ONT, Oxford Nanopore Technologies sequencing technology; gDNA, genomic DNA; CNA, copy number alteration; VAF, variant allele frequency; CGH, comparative genomic hybridization. |
| doi_str_mv | 10.1373/clinchem.2019.310805 |
| format | Article |
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Vannucchi2 2 Department of Experimental and Clinical Medicine, CRIMM, University of Florence, Florence, Italy 3 Department of Medical Biotechnologlies, University of Siena Siena, Italy 4 Department of Laboratory Diagnosis, Genetic Diagnosis Service Careggi Teaching Hospital Florence, Italy 5 Department of Information Engineering, University of Florence Florence, Italy "Address correspondence to this author at: Viale Pieraccini 6 Florence 50139 Italy Fax+39-055-7947688 e-mail amvannucchi@unifi.it Previously published online at DOI: 10.1373/clinchem.2019.310805 1 Nonstandard abbreviations: CVS, chorionic villus sampling; ONT, Oxford Nanopore Technologies sequencing technology; gDNA, genomic DNA; CNA, copy number alteration; VAF, variant allele frequency; CGH, comparative genomic hybridization.</description><identifier>ISSN: 0009-9147</identifier><identifier>EISSN: 1530-8561</identifier><identifier>DOI: 10.1373/clinchem.2019.310805</identifier><identifier>PMID: 31645339</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Abbreviations ; Bioinformatics ; Biotechnology ; Chorionic Villi Sampling - methods ; Chromosomes ; Clinching ; Clinical medicine ; Copy number ; Deoxyribonucleic acid ; Diagnosis ; DNA ; DNA sequencing ; Facsimile communication ; Feasibility Studies ; Female ; Gene frequency ; Genetic screening ; Genome - genetics ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Hybridization ; Information engineering ; Investigations ; Karyotypes ; Karyotyping - methods ; Male ; Nanopores ; Porosity ; Prenatal diagnosis ; Prenatal Diagnosis - methods ; Reagents ; Sequence Analysis, DNA - methods ; Villus</subject><ispartof>Clinical chemistry (Baltimore, Md.), 2019-12, Vol.65 (12), p.1605-1608</ispartof><rights>Copyright American Association for Clinical Chemistry Dec 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c432t-3bf52e4bb87a543115ae27d674d791fdd43132a0cd1691e16a76fe7fa478e1453</citedby><cites>FETCH-LOGICAL-c432t-3bf52e4bb87a543115ae27d674d791fdd43132a0cd1691e16a76fe7fa478e1453</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,778,782,27911,27912</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31645339$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bartalucci, Niccolò</creatorcontrib><creatorcontrib>Romagnoli, Simone</creatorcontrib><creatorcontrib>Contini, Elisa</creatorcontrib><creatorcontrib>Marseglia, Giuseppina</creatorcontrib><creatorcontrib>Magi, Alberto</creatorcontrib><creatorcontrib>Guglielmelli, Paola</creatorcontrib><creatorcontrib>Pelo, Elisabetta</creatorcontrib><creatorcontrib>Vannucchi, Alessandro M</creatorcontrib><title>Long Reads, Short Time: Feasibility of Prenatal Sample Karyotyping by Nanopore Genome Sequencing</title><title>Clinical chemistry (Baltimore, Md.)</title><addtitle>Clin Chem</addtitle><description>Cost-wise, the full process has a reagent price of about 500 Euros (US$547)/ sample, lower than the cost of conventional karyotype plus arrayCGH assay [about 800 Euros (US$874)/sample]. 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Vannucchi2 2 Department of Experimental and Clinical Medicine, CRIMM, University of Florence, Florence, Italy 3 Department of Medical Biotechnologlies, University of Siena Siena, Italy 4 Department of Laboratory Diagnosis, Genetic Diagnosis Service Careggi Teaching Hospital Florence, Italy 5 Department of Information Engineering, University of Florence Florence, Italy "Address correspondence to this author at: Viale Pieraccini 6 Florence 50139 Italy Fax+39-055-7947688 e-mail amvannucchi@unifi.it Previously published online at DOI: 10.1373/clinchem.2019.310805 1 Nonstandard abbreviations: CVS, chorionic villus sampling; ONT, Oxford Nanopore Technologies sequencing technology; gDNA, genomic DNA; CNA, copy number alteration; VAF, variant allele frequency; CGH, comparative genomic hybridization.</description><subject>Abbreviations</subject><subject>Bioinformatics</subject><subject>Biotechnology</subject><subject>Chorionic Villi Sampling - methods</subject><subject>Chromosomes</subject><subject>Clinching</subject><subject>Clinical medicine</subject><subject>Copy number</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Facsimile communication</subject><subject>Feasibility Studies</subject><subject>Female</subject><subject>Gene frequency</subject><subject>Genetic screening</subject><subject>Genome - genetics</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Hybridization</subject><subject>Information engineering</subject><subject>Investigations</subject><subject>Karyotypes</subject><subject>Karyotyping - methods</subject><subject>Male</subject><subject>Nanopores</subject><subject>Porosity</subject><subject>Prenatal diagnosis</subject><subject>Prenatal Diagnosis - methods</subject><subject>Reagents</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Villus</subject><issn>0009-9147</issn><issn>1530-8561</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkTFPwzAQhS0EoqXwDxCyxMJAii-O44QNVbQgKkC0zMFJLjRVEgc7GfrvcdWWgck6-3t3fvcIuQQ2Bi75XVaVTbbCeuwziMccWMTEERmC4MyLRAjHZMgYi70YAjkgZ9auXRnIKDwlAw5hIDiPh-Rrrptv-oEqt7d0sdKmo8uyxns6RWXLtKzKbkN1Qd8NNqpTFV2ouq2Qviiz0d2mLZ063dBX1ehWG6QzbHSNdIE_PTaZez0nJ4WqLF7szxH5nD4uJ0_e_G32PHmYe1nA_c7jaSF8DNI0kkoEHEAo9GUeyiCXMRR57u64r1iWQxgDQqhkWKAslHOE4MyMyM2ub2u0m227pC5thlWlGtS9TXzOIuH7UcQdev0PXeveNO53juJMyFDAlgp2VGa0tQaLpDVl7WwnwJJtAskhgWSbQLJLwMmu9s37tMb8T3RYOf8FyOyCuw</recordid><startdate>20191201</startdate><enddate>20191201</enddate><creator>Bartalucci, Niccolò</creator><creator>Romagnoli, Simone</creator><creator>Contini, Elisa</creator><creator>Marseglia, Giuseppina</creator><creator>Magi, Alberto</creator><creator>Guglielmelli, Paola</creator><creator>Pelo, Elisabetta</creator><creator>Vannucchi, Alessandro M</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>4U-</scope><scope>7QO</scope><scope>7RV</scope><scope>7TM</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>NAPCQ</scope><scope>P64</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>S0X</scope><scope>7X8</scope></search><sort><creationdate>20191201</creationdate><title>Long Reads, Short Time: Feasibility of Prenatal Sample Karyotyping by Nanopore Genome Sequencing</title><author>Bartalucci, Niccolò ; Romagnoli, Simone ; Contini, Elisa ; Marseglia, Giuseppina ; Magi, Alberto ; Guglielmelli, Paola ; Pelo, Elisabetta ; Vannucchi, Alessandro M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c432t-3bf52e4bb87a543115ae27d674d791fdd43132a0cd1691e16a76fe7fa478e1453</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Abbreviations</topic><topic>Bioinformatics</topic><topic>Biotechnology</topic><topic>Chorionic Villi Sampling - 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Academic</collection><jtitle>Clinical chemistry (Baltimore, Md.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bartalucci, Niccolò</au><au>Romagnoli, Simone</au><au>Contini, Elisa</au><au>Marseglia, Giuseppina</au><au>Magi, Alberto</au><au>Guglielmelli, Paola</au><au>Pelo, Elisabetta</au><au>Vannucchi, Alessandro M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Long Reads, Short Time: Feasibility of Prenatal Sample Karyotyping by Nanopore Genome Sequencing</atitle><jtitle>Clinical chemistry (Baltimore, Md.)</jtitle><addtitle>Clin Chem</addtitle><date>2019-12-01</date><risdate>2019</risdate><volume>65</volume><issue>12</issue><spage>1605</spage><epage>1608</epage><pages>1605-1608</pages><issn>0009-9147</issn><eissn>1530-8561</eissn><abstract>Cost-wise, the full process has a reagent price of about 500 Euros (US$547)/ sample, lower than the cost of conventional karyotype plus arrayCGH assay [about 800 Euros (US$874)/sample]. [...]ONT has the potential to become a standard approach for prenatal diagnosis. Niccolò Bartalucci2 Simone Romagnoli2,3 Elisa Contini2 Giuseppina Marseglia4 Alberto Magi5 Paola Guglielmelli2 Elisabetta Pelo4 Alessandro M. Vannucchi2 2 Department of Experimental and Clinical Medicine, CRIMM, University of Florence, Florence, Italy 3 Department of Medical Biotechnologlies, University of Siena Siena, Italy 4 Department of Laboratory Diagnosis, Genetic Diagnosis Service Careggi Teaching Hospital Florence, Italy 5 Department of Information Engineering, University of Florence Florence, Italy "Address correspondence to this author at: Viale Pieraccini 6 Florence 50139 Italy Fax+39-055-7947688 e-mail amvannucchi@unifi.it Previously published online at DOI: 10.1373/clinchem.2019.310805 1 Nonstandard abbreviations: CVS, chorionic villus sampling; ONT, Oxford Nanopore Technologies sequencing technology; gDNA, genomic DNA; CNA, copy number alteration; VAF, variant allele frequency; CGH, comparative genomic hybridization.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31645339</pmid><doi>10.1373/clinchem.2019.310805</doi><tpages>4</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Abbreviations Bioinformatics Biotechnology Chorionic Villi Sampling - methods Chromosomes Clinching Clinical medicine Copy number Deoxyribonucleic acid Diagnosis DNA DNA sequencing Facsimile communication Feasibility Studies Female Gene frequency Genetic screening Genome - genetics Genomes High-Throughput Nucleotide Sequencing - methods Humans Hybridization Information engineering Investigations Karyotypes Karyotyping - methods Male Nanopores Porosity Prenatal diagnosis Prenatal Diagnosis - methods Reagents Sequence Analysis, DNA - methods Villus |
| title | Long Reads, Short Time: Feasibility of Prenatal Sample Karyotyping by Nanopore Genome Sequencing |
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