316P Implementation of Vela Analytics to accelerate comprehensive interpretation and reporting of next-generation sequencing-based oncology testing in clinical diagnostic laboratories

Copy number variants (CNV) are a major cause of disease, with over 30,000 reported in the DECIPHER database. To use read depth data from targeted Next Generation Sequencing (NGS) panels to identify CNVs with the highest degree of sensitivity, it is necessary to account for biases inherent in the data. GC content and ambiguous mapping due to repetitive sequence elements and pseudogenes are the principal components of technical variability. In addition, the algorithms used favour the detection of multi-exon CNVs, and rely on suitably matched normal dosage samples for comparison. We developed a calling strategy that subdivides target intervals, and uses pools of historical control samples to overcome these limitations in a clinical diagnostic laboratory. We compared our enhanced strategy with an unmodified pipeline using the R software package ExomeDepth, using a cohort of 109 heterozygous CNVs (91 deletions, 18 duplications in 26 genes), including 25 single exon CNVs. The unmodified pipeline detected 104/109 CNVs, giving a sensitivity of 89.62% to 98.49% at the 95% confidence interval. The detection of all 109 CNVs by our enhanced method demonstrates 95% confidence the sensitivity is ≥96.67%, allowing NGS read depth analysis to be used for CNV detection in a clinical diagnostic setting.

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One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants

European Journal of Human Genetics ◽

10.1038/s41431-019-0515-1 ◽

2019 ◽

Vol 28 (2) ◽

pp. 202-212 ◽

Cited By ~ 2

Author(s):

Maria Weronika Gutowska-Ding ◽

Zandra C. Deans ◽

Christophe Roos ◽

Jukka Matilainen ◽

Farrah Khawaja ◽

...

Keyword(s):

Next Generation Sequencing ◽

Variant Calling ◽

Molecular Techniques ◽

Performance Criteria ◽

Next Generation ◽

Gene Target ◽

Clinical Diagnostic ◽

And Performance ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Next-generation sequencing (NGS) is replacing other molecular techniques to become the de facto gene diagnostics approach, transforming the speed of diagnosis for patients and expanding opportunities for precision medicine. Consequently, for accredited laboratories as well as those seeking accreditation, both objective measures of quality and external review of laboratory processes are required. External quality assessment (EQA), or Proficiency Testing (PT), can assess a laboratory’s service through an independent external agency, the EQA provider. The analysis of a growing number of genes and whole exome and genomes is now routine; therefore, an EQA must be delivered to enable all testing laboratories to participate. In this paper, we describe the development of a unique platform and gene target independent EQA scheme for NGS, designed to scale from current to future requirements of clinical diagnostic laboratories testing for germline and somatic variants. The EQA results from three annual rounds indicate that clinical diagnostic laboratories are providing an increasingly high-quality NGS service and variant calling abilities are improving. From an EQA provider perspective, challenges remain regarding delivery and performance criteria, as well as in analysing similar NGS approaches between cohorts with meaningful metrics, sample sourcing and data formats.

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