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Settling the score: variant prioritization and Mendelian disease

Key Points

  • Exome and genome sequencing reveal thousands to millions of genetic variants in a typical individual. A fundamental challenge in human genetics is isolating the small subset (typically one or two) of variants that cause a Mendelian disease phenotype. This Review describes the computational approaches used to prioritize variants in Mendelian disease.

  • A multitude of tools prioritize variants on the basis of biochemical, evolutionary, allele segregation and population frequency characteristics in an attempt to prioritize the list of potential causative variants. The strategies and caveats associated with these tools are outlined in this Review.

  • Burden tests take prioritization to the next level by aggregating the variants observed at a given locus to calculate a burden score for the gene. Most burden testing software tools also evaluate potentially damaging genotypes in the context of other genotypes observed at the same locus in a control population.

  • Variant interpretation is the process of drawing direct connections from individual variants to disease phenotypes, and this process is central to both clinical reporting of results and incidental findings, as well as research endeavours that include variant discovery and return of results.

  • Variant prioritization and interpretation are especially challenging for non-coding variants, structural variants and synonymous exonic variants. Furthermore, increasingly complex reference genomes introduce new demands for variant discovery tools. Each of these challenges drive increasingly sophisticated software solutions.

Abstract

When investigating Mendelian disease using exome or genome sequencing, distinguishing disease-causing genetic variants from the multitude of candidate variants is a complex, multidimensional task. Many prioritization tools and online interpretation resources exist, and professional organizations have offered clinical guidelines for review and return of prioritization results. In this Review, we describe the strengths and weaknesses of widely used computational approaches, explain their roles in the diagnostic and discovery process and discuss how they can inform (and misinform) expert reviewers. We place variant prioritization in the wider context of gene prioritization, burden testing and genotype–phenotype association, and we discuss opportunities and challenges introduced by whole-genome sequencing.

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Figure 1: A demonstration of the multiple possible effects of a single variant across transcripts and genes.
Figure 2: Population stratification and regional constraint within a gene are critical to variant interpretation.
Figure 3: Phenotypes are described across a spectrum of granularity, and different terminologies are used to define these features.

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Acknowledgements

The authors thank J. Chong for insightful discussions about the challenges of rare disease research at the University of Washington Center for Mendelian Genomics Workshop. This Review was supported by US National Institute of Health awards to A.Q. (NIH R01HG006693, NIH U24CA209999), K.E (NIH U41HG006834 (subcontract), NIH U01HG007437 (subcontract), NIH R01HG008628) and M.Y. (NIH R01GM104390, NIH UM1HL128711, NIH U01HL131698 and NSF IOS-1561337).

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Correspondence to Mark Yandell.

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A.Q. is a co-founder of Base2 Genomics, LLC. M.Y. is on the Scientific Advisory Board of Fabric Genomics.

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Glossary

Mendelian disorders

Diseases or conditions that result from mutation at a genomic locus and are inherited according to Mendel's laws.

Variant prioritization

The process of ranking the variants observed in an individual genome on the basis of factors such as the predicted consequence of each variant and the observed frequency in a population.

Population allele frequencies

The proportion of chromosomes within a population that carry a particular change at a given locus.

Gene prioritization

The process of associating a gene with a disease phenotype; this strategy is often used during variant prioritization.

Burden testing

A gene prioritization approach that scores, ranks and prioritizes genes based on genotypes rather than on single variants. The observed (or for some methods, the theoretical) distribution of burden scores within the wider population is often used to rank a proband's genotype score. Many burden tests can also incorporate adjunct information into their calculations such as phylogenetic conservation, mode of inheritance and variant frequency data. Unlike variant prioritization tools, burden tests require access to genotype data for their calculations.

Decision support frameworks

Interactive, dynamic tools to guide medical decision-making by displaying and integrating patient data.

Nonsense-mediated decay

(NMD). A conserved eukaryotic pathway, the role of which is to detect and eliminate the translation of mRNAs that have premature stop codons.

Variant of uncertain significance

(VUS). Also known as variant of unknown significance. The canonical definition of a VUS is a variant in a disease-associated gene, the specific effect of which is unknown or uncertain. More generally, VUS can also be applied to variants in genes that lack direct disease association but are plausible given the biological function of the resulting protein.

Controlled vocabularies

Sets of agreed upon terms and definitions.

Exome

Generally, the portion of the genome that is translated into proteins.

Population stratification

The difference in allele frequencies across subpopulations.

Balancing selection

Under balancing selection, multiple alleles exist in a population when natural selection favours heterozygous genotypes.

Disease prevalence

The number of cases of a disease that are present in a population at a given point in time.

Purifying selection

Under purifying selection, deleterious alleles are selectively removed from a population.

Functional variants

Variants that alter gene function or expression.

Probands

The proband is the initial person of study in a genetics investigation. In the case of a family trio, the proband is usually the affected child.

De novo variant

A spontaneous mutation in a proband that is missing from the parents.

Phase

For a single variant, phase involves the determination of the parental chromosome on which a variant allele exists. When a proband and both parents have been sequenced, this can be directly determined for 'informative sites' where the allele transmission is unambiguous (for example, the proband is heterozygous A/G, the father is homozygous A/A, and the mother heterozygous A/G; in this case the G allele was clearly transmitted from the mother). More generally, phasing refers to the assignment of alleles from multiple variant sites to parental haplotypes.

Population genotype frequency

The proportion of individuals with a particular genotype at a given locus.

Incidental findings

In whole-exome sequencing (WES) or whole-genome sequencing (WGS), pathogenic and likely pathogenic variants in genes that are not relevant to the initial reason for sequencing may be found and reported back to the patient. These variants may relate to rare disease, disease risk, pharmacogenetic response, and status relating to prenatal screening.

Return of results

The process of returning findings from a research study, or incidental findings from a genetic test, back to the participant or patient.

Compound heterozygous inheritance

The situation in which a proband receives a damaging but different allele in the same gene, from each parent. Both copies of the gene are affected.

Topologically associating domains

(TADs). TADs are genomic regions in which loci have a higher probability of physical interaction.

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Eilbeck, K., Quinlan, A. & Yandell, M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet 18, 599–612 (2017). https://doi.org/10.1038/nrg.2017.52

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