Chapter 9 - Insertions and Deletions (Indels)

Abstract

Insertion–deletion mutations (indels) refer to insertion and/or deletion of nucleotides into genomic DNA and include events less than 1kb in length. Indels are supremely important in clinical next-generation sequencing (NGS), as they are implicated as the driving mechanism underlying many constitutional and oncologic diseases. Additionally, indels are a common mechanism of kinase activation in cancer—a feature exploited clinically by targeted therapy with kinase inhibitors. The sequencing techniques and bioinformatics tools used for NGS analysis both influence the sensitivity and specificity of indel detection. Multiple factors inherent to indels as a mutation class also complicate their detection, including indel size, sequence context, and variant annotation. This chapter provides an overview of the mechanisms that generate indels and the impact these mechanisms have on detection. The functional effects of indels are also discussed, with clinically relevant examples. Tools for predicting the functional consequences of novel indels are covered, as are their limitations in clinical interpretation. Technical factors of NGS assay design and specimen selection that impact indel detection are discussed, as are the general bioinformatics approaches to identifying indels in NGS data, including the benefits and limitations of different algorithms. Problems with developing consensus annotations for identified indels and their impact on evidence-based interpretation of identified indel variants, a major issue in clinical NGS indel testing, are reviewed. Finally, the lack of a gold-standard for indel detection and validation, and barriers to development of reference indel materials are covered.