Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization

Abstract

Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast amount of variations in a cost-efficient manner. However, there still are inconsistencies and debates about how to process and analyse this 'big data'.To accurately extract clinically relevant information from genomics data, choosing appropriate tools, knowing how to best utilize them and interpreting the results correctly is crucial. This chapter reviews state-of-the-art bioinformatics approaches in clinically relevant genomic variant detection. Best practices of reads-to-variant discovery workflows for germline and somatic short genomic variants are presented along with the most commonly utilized tools for each step. Additionally, methods for detecting structural variations are overviewed. Finally, approaches and current guidelines for clinical interpretation of genomic variants are discussed. As emphasized in this chapter, data processing and variant discovery steps are relatively wellunderstood. The differences in prioritization algorithms on the other hand can be perplexing, thus creating a bottleneck during interpretation. This review aims to shed light on the pros and cons of these differences to help experts give more informed decisions.

Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data

“…Highlighting the importance of our study, we reinforce the monitoring of genetic diversity and in silico genetic stability testing as part of the vaccine manufacturing process to ensure the safety of all vaccine lots administered to the population. However, existing pipelines that analyse viral NGS samples do not accurately extract genetic diversity royalsocietypublishing.org/journal/rsfs Interface Focus 11: 20200063 information when dealing with viral vaccine samples due to the lack of specific parameters [22,38], use of inappropriate tools [19,23,36], and not performing quasispecies reconstruction [15,35,37,38]. This often leads to false results and affects negatively the sensitivity and specificity metrics.…”

“…The limitations of Sanger sequencing may be overcome by next-generation sequencing (NGS), which generates the required depth of coverage for the analysis of the variants in viral populations within a sample. It allows for high-throughput detection of a vast amount of SNPs and their co-occurrences in a genome [ 19 ].…”

“…Detection of genetic diversity from raw sequencing data is a multistep task and can be executed using numerous tools and resources. To accurately extract relevant information from NGS data it is crucial to choose reliable tools, fine-tune them and correctly interpret their results [ 19 ]. Previous studies have used NGS directly on viral vaccine stocks [ 15 , 20 , 21 ] and applied different methods to infer genetic diversity.…”

Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies

“…• First, if a patient with a diagnosed NCP and harboring a SV is encountered, it is essential to map the SV breakpoints with base-pair resolution. For this purpose, different methods and tools can be used (Zhao et al, 2013;Ugur Sezerman et al, 2019), such as BreakDancer (Chen et al, 2009), an algorithm for high-resolution mapping of genomic structural variation. • Then, the functional genomic data (e.g., cell type-specific gene-expression levels, epigenetic profiles, cranial NCCs, and craniofacial embryonic tissue enhancer maps, etc.)…”

“…First, if a patient with a diagnosed NCP and harboring a SV is encountered, it is essential to map the SV breakpoints with base-pair resolution. For this purpose, different methods and tools can be used ( Zhao et al, 2013 ; Ugur Sezerman et al, 2019 ), such as BreakDancer ( Chen et al, 2009 ), an algorithm for high-resolution mapping of genomic structural variation.…”