Assessment of Disease‐Associated Sequence Variants and Considerations for Functional Validation using Mouse Models

Abstract

Whole‐exome and whole‐genome sequencing approaches are rapidly becoming mainstream tools accessible to both basic researchers and clinical teams. Likewise, technological advances in genome editing, such as the CRISPR/Cas system, are poised to revolutionise model system research, making it more feasible to create animal models that truly recapitulate the human condition. However, procedures for identifying disease‐associated sequence variants are still far from robust and there are many biological variables that need to be considered when attempting to functionally validate disease‐associated variants. In this article, we highlight the many limitations and issues that should be considered at different stages throughout this process – from the filtering of sequencing data to the selection of variants, and from the selection of the model organism to the appropriate means of phenotyping.

Key Concepts

  • Researchers must appreciate the limitations of exome sequencing when considering candidate gene variants.
  • Researchers using sequencing services should ensure they receive the original BAM files of their sequencing data.
  • Common bioinformatic algorithms used to process sequencing data are predictive tools only.
  • Bioinformatic tools should not be used in isolation or their outputs taken as proof of disease causation of a variant.
  • Gene expression in a tissue consistent with that affected in patients can be used to help prioritise candidate genes but is not evidence for causation.
  • Demonstration of a functional impact of a given variant in an in vitro assay is useful but does not necessarily mean it is responsible for the disease of interest.
  • Genetic background of the mouse strain(s) can significantly influence the phenotypic presentation.
  • Researchers using animal models should consider the composition of animal chow when modelling a disease with considerable phenotypic variability.

Keywords: mouse model; CRISPR; exome sequencing; SNP; genetic background

Figure 1. Variables that can impact success in identifying disease‐associated variants. (a) Overview of the methodology to generate a list of possible disease‐associated gene variants. Many inputs of data and knowledge, as well as assumptions, help create and prioritise a ‘manageable’ list of variants to be considered. None of these data or knowledge inputs is proof of causation of any given variant but, collectively, they provide evidence to support a role of the selected gene. Demonstration of a functional impact of the actual variant, and that this impact on function gives rise to the condition, is necessary. RVIS, residual variation intolerance score; GERP, Genomic Evolutionary Rate Profiling; CADD, Combined Annotation‐Dependent Depletion. (b) The detail and thoroughness of the clinical phenotyping (i.e. the strictness of the criteria and the objectivity of the phenotyping) can often be inversely correlated with the level of genetic heterogeneity expected in the cohort. (c) Schematic representation of the volume of exome variants ‘lost’ in the process of exome sequencing. When no clear candidate gene is found in exome studies, recheck your data (BAM files). The technical limitations of many exome sequencing platforms and the bioinformatics thresholds for data cleanup may be responsible: as many as 10–20% of actual variants (red asterisk) are excluded by current procedures.
Figure 2. Considerations for the functional validation of potential disease‐associated variants using mouse models. (a) Multiple factors should be considered when seeking to functionally validate variants using the mouse as the model system. All these factors can influence the phenotypic presentation of disease in mice and thus the interpretation of the variant being causal. (b) If creating a new mouse model, a number of genetic modification strategies should be considered. The choice will depend on many factors, including the predicted functional impact of the variant to be assessed, the tissue distribution of expression and the mode of inheritance expected. Each approach has pros and cons of which investigators should be aware and control for as necessary when assessing phenotypes. HR, homologous recombination; CRISPR, clustered regularly interspaced short palindromic repeats; Cas, CRISPR‐associated; TALEN, transcription‐activator‐like effector nuclease; KO, knockout; SNP, single nucleotide polymorphism.
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Cox, Timothy C, and Cox, Liza L(Aug 2016) Assessment of Disease‐Associated Sequence Variants and Considerations for Functional Validation using Mouse Models. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0026656]