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Next-Generation Sequencing Diagnostics

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The utilization of next-generation sequencing (NGS) in genetic diagnosis allows for rapid, parallel, and cost-efficient analysis of disease-relevant genes and completes the range of services offered by our laboratory. In our routine diagnostic testing we now employ not only analysis of individual genes using Sanger sequencing, but additionally simultaneous analysis of multiple genes via our Multi-Gene Panels using the latest NGS technologies. We ensure these methods meet our high diagnostic standards both in terms of quality of data and interpretation of sequence variants.

Various levels of diagnostic standards are available depending on clinical information (see Diagnostic NGS Quality Types A to C and Guidelines for diagnostic next generation sequencing (EuroGentest). Detailed information can be found here.

NGS Analysis

  • Enrichment of specific genomic regions with Agilent SureSelectTM or Illumina TruSightTM kits followed by parallel "paired-end" sequencing on the MiSeq or NextSeq 500 IlluminaRAnalyzer.
  • All coding exons plus exon/intron borders (+/- 5 bp) are tested for point mutations and small insertions/deletions (to approx. 50 bp).
  • Individual test reports include detailed interpretation of all identified variants made by an experienced team of biomedical experts and clinical geneticists. Information on the regions analyzed and their coverage as well as data regarding the quality of analysis are also included.

Diagnostic Quality Criteria for NGS Analysis

Our NGS analyses must meet the following quality criteria:

  • An average sequence quality (Phred or Q Score) of over 30 per sequence cycle (corresponds to a detection accuracy of 99.9%).
  • A sequence depth of over 20 sequences per base pair in at least 98% of all analyzed regions. No definitive statement can be made regarding regions with coverage of fewer sequences per base pair.
  • Furthermore, our NGS panels are validated by current NGS diagnostic guidelines1 and ensure enough sensitivity and specificity for accurate “variant calling.”
  • According to clinical criteria, various categories of next-generation sequencing (NGS) diagnostics are available (NGS Types A-C)2.
  • Parallel to NGS analysis, the genotype of every patient is determined based on 12 polymorphic markers in order to exclude contamination and/or sample mix-up in the course of NGS testing.

Limitations

  • Intronic regions (> +/- 5 bp from exonic borders) are not analyzed, thus regulatory mutations in these regions cannot be detected by this analysis.
  • For techincal reasons larger genomic deletions or duplications (>50 bp) and structural rearrangements (transversions, inversions) cannot be reliably detected at this time. Depending on clinical details of a patient, an additional gene dosage analysis may be necessary (e.g., MLPA, array-CGH).
  • Repeat expansions in individual genes (e.g., HTT, FMR1, FXN, and DMPK) are not detected.
  • The analysis of genes with known pseudogenes or homologous regions is possible only for a limited number of genes (e.g., CHEK2 and PMS2).

 

References:

1 Recommendations according to "Guidelines for diagnostic next generation sequencing" (EuroGentest, 2014) and "ACMG clinical laboratory standards for next-generation sequencing" (Genetics in Medicine, 2013, 15:733-747).

2 The analysis of BRCA1, BRCA2, Duchenne / Becker-Kiener Muscular Dystrophy ID 20.00 and Hereditary Nonpolyposis Colon Cancer / Lynch Syndrome ID 99.00 multi-gene panels are assigned special quality criteria. A sequence depth of more than 20 sequences per base pair for 100% of analyzed regions is required, followed by MLPA to detect larger insertions/deletions.