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Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.

ABSTRACT: Genome sequencing is enabling precision medicine-tailoring treatment to the unique constellation of variants in an individual's genome. The impact of recurrent pathogenic variants is often understood, however there is a long tail of rare genetic variants that are uncharacterized. The problem of uncharacterized rare variation is especially acute when it occurs in genes of known clinical importance with functionally consequential variants and associated mechanisms. Variants of uncertain significance (VUSs) in these genes are discovered at a rate that outpaces current ability to classify them with databases of previous cases, experimental evaluation, and computational predictors. Clinicians are thus left without guidance about the significance of variants that may have actionable consequences. Computational prediction of the impact of rare genetic variation is increasingly becoming an important capability. In this paper, we review the technical and ethical challenges of interpreting the function of rare variants in two settings: inborn errors of metabolism in newborns and pharmacogenomics. We propose a framework for a genomic learning healthcare system with an initial focus on early-onset treatable disease in newborns and actionable pharmacogenomics. We argue that (1) a genomic learning healthcare system must allow for continuous collection and assessment of rare variants, (2) emerging machine learning methods will enable algorithms to predict the clinical impact of rare variants on protein function, and (3) ethical considerations must inform the construction and deployment of all rare-variation triage strategies, particularly with respect to health disparities arising from unbalanced ancestry representation.

SUBMITTER: McInnes G

PROVIDER: S-EPMC8059338 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Introduction and motivationMany health studies measure a continuous outcome and compare means between groups. Since means for biological data are often difficult to interpret clinically, it is common to dichotomise using a cut-point and present the 'percentage abnormal' alongside or in place of means. Examples include birthweight where 'abnormal' is defined as <2500 g (low birthweight), systolic blood pressure with abnormal defined as >140 mm Hg (high blood pressure) and lung function with varying definitions of the 'limit of normal'. In vulnerable populations with low means, for example, birthweight in a population of preterm babies, a given difference in means between two groups will represent a larger difference in the percentage with low birthweight than in a general population of babies where most will be full term. Thus, in general, the difference in percentage of patients with abnormal values for a given difference in means varies according to the reference population's mean value. This phenomenon leads to challenges in interpreting differences in means in vulnerable populations and in defining an outcome-specific minimal clinically important difference (MCID) in means since the proportion abnormal, which is useful in interpreting means, is not constant-it varies with the population mean. This has relevance for study power calculations and data analyses in vulnerable populations where a small observed difference in means may be difficult to interpret clinically and may be disregarded, even if associated with a relatively large difference in percentage abnormal which is clinically relevant.MethodsTo address these issues, we suggest both difference in means and difference in percentage (proportion) abnormal are considered when choosing the MCID, and that both means and percentages abnormal are reported when analysing the data.ConclusionsWe describe a distributional approach to analyse proportions classified as abnormal that avoids the usual loss of precision and power associated with dichotomisation.

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Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.

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