Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Gergely Ivády, László Madar, Erika Dzsudzsák, Katalin Koczok, J. Kappelmayer, Veronika Krulisova, Milan Macek, Attila Horváth, I. Balogh

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

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. 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. 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.

Original languageEnglish
Article number158
JournalBMC Genomics
Volume19
Issue number1
DOIs
Publication statusPublished - Jan 1 2018

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Plasmids
Semiconductors
Cystic Fibrosis
Genes
Uncertainty
Exons
Genotype
Ions
Technology
Costs and Cost Analysis
Equipment and Supplies
DNA

Keywords

  • Cystic fibrosis
  • Homopolymer detection
  • Pyrosequencing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. / Ivády, Gergely; Madar, László; Dzsudzsák, Erika; Koczok, Katalin; Kappelmayer, J.; Krulisova, Veronika; Macek, Milan; Horváth, Attila; Balogh, I.

In: BMC Genomics, Vol. 19, No. 1, 158, 01.01.2018.

Research output: Contribution to journalArticle

Ivády, Gergely ; Madar, László ; Dzsudzsák, Erika ; Koczok, Katalin ; Kappelmayer, J. ; Krulisova, Veronika ; Macek, Milan ; Horváth, Attila ; Balogh, I. / Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. In: BMC Genomics. 2018 ; Vol. 19, No. 1.
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AU - Koczok, Katalin

AU - Kappelmayer, J.

AU - Krulisova, Veronika

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AB - 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. 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. 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.

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