Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics

Nicole Hoppman-Chaney, Lisa M. Peterson, Eric W Klee, Sumit Middha, Laura K. Courteau, Matthew J. Ferber

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

BACKGROUND: Next-generation DNA sequencing (NGS) techniques have the potential to revolutionize molecular diagnostics; however, a thorough evaluation of these technologies is necessary to ensure their performance meets or exceeds that of current clinical sequencing methods. METHODS: We evaluated the NimbleGen Sequence Capture 385K Human Custom Arrays for enrichment of 22 genes. We sequenced each sample on both the Roche 454 Genome Sequencer FLX (GS-FLX) and the Illumina Genome Analyzer II (GAII) to compare platform performance. RESULTS: Although the sequence capture method allowed us to rapidly develop a large number of sequencing assays, we encountered difficulty enriching G+C-rich regions. Although a high proportion of reads consistently mapped outside of the targeted regions, >80% of targeted bases for the GAII and >30% of bases for the GS-FLX were covered by a read depth of ≥20, and >90% of bases for the GAII and >80% of bases for the GS-FLX were covered by a read depth of ≥5. We observed discrepancies among sequence variants identified by the different platforms. CONCLUSIONS: Although oligonucleotide arrays are quick and easy to develop, some problematic regions may evade capture, necessitating sequential redesigning for complete optimization. Neither sequencing technology was able to detect every variant identified by Sanger sequencing because of well-known draw-backs of the NGS technologies. The rapidly decreasing error rates and costs of these technologies, however, coupled with advancing bioinformatic capabilities, make them an attractive option for molecular diagnostics in the very near future.

Original languageEnglish (US)
Pages (from-to)1297-1306
Number of pages10
JournalClinical Chemistry
Volume56
Issue number8
DOIs
StatePublished - Aug 2010

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Molecular Pathology
Oligonucleotides
Genes
Genome
Technology
DNA Sequence Analysis
Oligonucleotide Array Sequence Analysis
Computational Biology
DNA
Bioinformatics
Assays
Costs and Cost Analysis
Costs

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics. / Hoppman-Chaney, Nicole; Peterson, Lisa M.; Klee, Eric W; Middha, Sumit; Courteau, Laura K.; Ferber, Matthew J.

In: Clinical Chemistry, Vol. 56, No. 8, 08.2010, p. 1297-1306.

Research output: Contribution to journalArticle

Hoppman-Chaney, Nicole ; Peterson, Lisa M. ; Klee, Eric W ; Middha, Sumit ; Courteau, Laura K. ; Ferber, Matthew J. / Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics. In: Clinical Chemistry. 2010 ; Vol. 56, No. 8. pp. 1297-1306.
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