Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system.
Identifieur interne : 000A12 ( PubMed/Checkpoint ); précédent : 000A11; suivant : 000A13Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system.
Auteurs : Gergely Ivády [Hongrie] ; Lászl Madar [Hongrie] ; Erika Dzsudzsák [Hongrie] ; Katalin Koczok [Hongrie] ; János Kappelmayer [Hongrie] ; Veronika Krulisova [République tchèque] ; Milan Macek [République tchèque] ; Attila Horváth [Hongrie] ; István Balogh [Hongrie]Source :
- BMC genomics [ 1471-2164 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Cystic Fibrosis Transmembrane Conductance Regulator.
- genetics : Cystic Fibrosis.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Humans, Plasmids, Tandem Repeat Sequences.
Abstract
Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.
DOI: 10.1186/s12864-018-4544-x
PubMed: 29466940
Affiliations:
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pubmed:29466940Le document en format XML
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<term>Plasmids</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Tandem Repeat Sequences</term>
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<term>Mucoviscidose (génétique)</term>
<term>Plasmides</term>
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<term>Tandem Repeat Sequences</term>
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<term>Humains</term>
<term>Plasmides</term>
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<front><div type="abstract" xml:lang="en">Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.</div>
</front>
</TEI>
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<DateCompleted><Year>2018</Year>
<Month>08</Month>
<Day>30</Day>
</DateCompleted>
<DateRevised><Year>2019</Year>
<Month>12</Month>
<Day>10</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>19</Volume>
<Issue>1</Issue>
<PubDate><Year>2018</Year>
<Month>02</Month>
<Day>21</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system.</ArticleTitle>
<Pagination><MedlinePgn>158</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-018-4544-x</ELocationID>
<Abstract><AbstractText Label="BACKGROUND">Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.</AbstractText>
<AbstractText Label="RESULTS">In the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 - 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.</AbstractText>
<AbstractText Label="CONCLUSIONS">Our results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ivády</LastName>
<ForeName>Gergely</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Madar</LastName>
<ForeName>László</ForeName>
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</AffiliationInfo>
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<AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.</Affiliation>
</AffiliationInfo>
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</AffiliationInfo>
<AffiliationInfo><Affiliation>Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.</Affiliation>
</AffiliationInfo>
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</AffiliationInfo>
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</AffiliationInfo>
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</AffiliationInfo>
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<AffiliationInfo><Affiliation>Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary.</Affiliation>
</AffiliationInfo>
</Author>
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<ForeName>István</ForeName>
<Initials>I</Initials>
<AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary. balogh@med.unideb.hu.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary. balogh@med.unideb.hu.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
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<Agency>Országos Tudományos Kutatási Alapprogramok</Agency>
<Country>International</Country>
</Grant>
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<Agency>Ministry of National Economy, Hungary</Agency>
<Country>International</Country>
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<ArticleDate DateType="Electronic"><Year>2018</Year>
<Month>02</Month>
<Day>21</Day>
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<MedlineTA>BMC Genomics</MedlineTA>
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<ISSNLinking>1471-2164</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C505032">CFTR protein, human</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>126880-72-6</RegistryNumber>
<NameOfSubstance UI="D019005">Cystic Fibrosis Transmembrane Conductance Regulator</NameOfSubstance>
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