Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients
The development of next-generation sequencing (NGS) technologies has a great impact in the human variation detection given their high-throughput. These techniques are particularly helpful for the evaluation of the genetic background in disorders of complex genetic etiology such as Hirschsprung disea...
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| Veröffentlicht in: | BMC medical genetics 2015-10, Vol.16 (1), p.89-89, Article 89 |
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| container_title | BMC medical genetics |
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| creator | Luzón-Toro, Berta Espino-Paisán, Laura Fernández, Raquel Ma Martín-Sánchez, Marta Antiñolo, Guillermo Borrego, Salud |
| description | The development of next-generation sequencing (NGS) technologies has a great impact in the human variation detection given their high-throughput. These techniques are particularly helpful for the evaluation of the genetic background in disorders of complex genetic etiology such as Hirschsprung disease (HSCR). The purpose of this study was the design of a panel of HSCR associated genes as a rapid and efficient tool to perform genetic screening in a series of patients.
We have performed NGS-based targeted sequencing (454-GS Junior) using a panel containing 26 associated or candidate genes for HSCR in a group of 11 selected HSCR patients.
The average percentage of covered bases was of 97%, the 91.4% of the targeted bases were covered with depth above 20X and the mean coverage was 422X. In addition, we have found a total of 13 new coding variants and 11 new variants within regulatory regions among our patients. These outcomes allowed us to re-evaluate the genetic component associated to HSCR in these patients.
Our validated NGS panel constitutes an optimum method for the identification of new variants in our patients. This approach could be used for a fast, reliable and more thorough genetic screening in future series of patients. |
| doi_str_mv | 10.1186/s12881-015-0235-5 |
| format | Article |
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We have performed NGS-based targeted sequencing (454-GS Junior) using a panel containing 26 associated or candidate genes for HSCR in a group of 11 selected HSCR patients.
The average percentage of covered bases was of 97%, the 91.4% of the targeted bases were covered with depth above 20X and the mean coverage was 422X. In addition, we have found a total of 13 new coding variants and 11 new variants within regulatory regions among our patients. These outcomes allowed us to re-evaluate the genetic component associated to HSCR in these patients.
Our validated NGS panel constitutes an optimum method for the identification of new variants in our patients. This approach could be used for a fast, reliable and more thorough genetic screening in future series of patients.</description><identifier>ISSN: 1471-2350</identifier><identifier>EISSN: 1471-2350</identifier><identifier>DOI: 10.1186/s12881-015-0235-5</identifier><identifier>PMID: 26437850</identifier><language>eng</language><publisher>England: BioMed Central</publisher><subject>Base Sequence ; Computational Biology ; Design ; Female ; Gene Library ; Genes ; Genetic testing ; Genetic Testing - methods ; High-Throughput Nucleotide Sequencing - methods ; Hirschsprung Disease - genetics ; Hirschsprung Disease - pathology ; Humans ; Male ; Molecular Sequence Data ; Mutation ; Phenotype ; Sensitivity and Specificity ; Spain</subject><ispartof>BMC medical genetics, 2015-10, Vol.16 (1), p.89-89, Article 89</ispartof><rights>Copyright BioMed Central 2015</rights><rights>Luzón-Toro et al. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c427t-d39054e2610c6e7491795a86be37af2174ec3694070bb0ccd96f40cd568c3f13</citedby><cites>FETCH-LOGICAL-c427t-d39054e2610c6e7491795a86be37af2174ec3694070bb0ccd96f40cd568c3f13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595130/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595130/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26437850$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Luzón-Toro, Berta</creatorcontrib><creatorcontrib>Espino-Paisán, Laura</creatorcontrib><creatorcontrib>Fernández, Raquel Ma</creatorcontrib><creatorcontrib>Martín-Sánchez, Marta</creatorcontrib><creatorcontrib>Antiñolo, Guillermo</creatorcontrib><creatorcontrib>Borrego, Salud</creatorcontrib><title>Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients</title><title>BMC medical genetics</title><addtitle>BMC Med Genet</addtitle><description>The development of next-generation sequencing (NGS) technologies has a great impact in the human variation detection given their high-throughput. These techniques are particularly helpful for the evaluation of the genetic background in disorders of complex genetic etiology such as Hirschsprung disease (HSCR). The purpose of this study was the design of a panel of HSCR associated genes as a rapid and efficient tool to perform genetic screening in a series of patients.
We have performed NGS-based targeted sequencing (454-GS Junior) using a panel containing 26 associated or candidate genes for HSCR in a group of 11 selected HSCR patients.
The average percentage of covered bases was of 97%, the 91.4% of the targeted bases were covered with depth above 20X and the mean coverage was 422X. In addition, we have found a total of 13 new coding variants and 11 new variants within regulatory regions among our patients. These outcomes allowed us to re-evaluate the genetic component associated to HSCR in these patients.
Our validated NGS panel constitutes an optimum method for the identification of new variants in our patients. This approach could be used for a fast, reliable and more thorough genetic screening in future series of patients.</description><subject>Base Sequence</subject><subject>Computational Biology</subject><subject>Design</subject><subject>Female</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genetic testing</subject><subject>Genetic Testing - methods</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Hirschsprung Disease - genetics</subject><subject>Hirschsprung Disease - pathology</subject><subject>Humans</subject><subject>Male</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Phenotype</subject><subject>Sensitivity and Specificity</subject><subject>Spain</subject><issn>1471-2350</issn><issn>1471-2350</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</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>eNpdkU1vFDEMhkeoiJbCD-CCIvXCJZBMviYXJLQCilTBpfcok3FmU2aTJclU9MRfJ8uWqnCyrbx-HPvtuleUvKV0kO8K7YeBYkIFJj0TWDzpzihXFLeCnDzKT7vnpdwQQtXA2LPutJecqUGQs-7XV_hZ8QwRsq0hRTzaAhOqNs9QW1LgxwrRhTgjW5CNCLwPLkCsqKa0IJ8yqltApa7THUr-T3HA1eDQaN33Oac1TihEdBlycduyz2uD7du0BikvuqfeLgVe3sfz7vrTx-vNJb769vnL5sMVdrxXFU9ME8Ghl5Q4CYprqrSwgxyBKet7qjg4JjUniowjcW7S0nPiJiEHxzxl5937I3a_jjuYXBud7WL2OexsvjPJBvPvSwxbM6dbw4UWlJEGeHMPyKldpFSzC8XBstgIaS2GKqq1kr2QTXrxn_QmrTm27ZpKaUWasG8qelS5nErJ4B8-Q4k5uGuO7prmrjm4a0Tref14i4eOv3ay3wMQoog</recordid><startdate>20151005</startdate><enddate>20151005</enddate><creator>Luzón-Toro, Berta</creator><creator>Espino-Paisán, Laura</creator><creator>Fernández, Raquel Ma</creator><creator>Martín-Sánchez, Marta</creator><creator>Antiñolo, Guillermo</creator><creator>Borrego, Salud</creator><general>BioMed Central</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>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20151005</creationdate><title>Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients</title><author>Luzón-Toro, Berta ; 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These techniques are particularly helpful for the evaluation of the genetic background in disorders of complex genetic etiology such as Hirschsprung disease (HSCR). The purpose of this study was the design of a panel of HSCR associated genes as a rapid and efficient tool to perform genetic screening in a series of patients.
We have performed NGS-based targeted sequencing (454-GS Junior) using a panel containing 26 associated or candidate genes for HSCR in a group of 11 selected HSCR patients.
The average percentage of covered bases was of 97%, the 91.4% of the targeted bases were covered with depth above 20X and the mean coverage was 422X. In addition, we have found a total of 13 new coding variants and 11 new variants within regulatory regions among our patients. These outcomes allowed us to re-evaluate the genetic component associated to HSCR in these patients.
Our validated NGS panel constitutes an optimum method for the identification of new variants in our patients. This approach could be used for a fast, reliable and more thorough genetic screening in future series of patients.</abstract><cop>England</cop><pub>BioMed Central</pub><pmid>26437850</pmid><doi>10.1186/s12881-015-0235-5</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central Open Access; Springer Nature OA Free Journals; PubMed Central |
| subjects | Base Sequence Computational Biology Design Female Gene Library Genes Genetic testing Genetic Testing - methods High-Throughput Nucleotide Sequencing - methods Hirschsprung Disease - genetics Hirschsprung Disease - pathology Humans Male Molecular Sequence Data Mutation Phenotype Sensitivity and Specificity Spain |
| title | Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients |
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