NEWS: HealthLumen launches AlleleAtlas, a tool for estimating the prevalence of rare genetic diseases 

HealthLumen has today announced the launch of AlleleAtlas, the genetic variant prevalence projection tool. 

Rare diseases are individually rare, yet collectively common – estimated to impact over 400 million individuals around the globe. Despite this, accurately estimating the prevalence of many rare diseases, if not perhaps the majority of them, is challenging.   

Traditional methodologies to obtain these estimates rely on reported patient numbers gathered from literature reviews, data registries, surveillance programs, and rare disease specialists. However, due to the phenotypic and genetic complexity of rare diseases, many individuals living with these conditions may be misdiagnosed or not diagnosed at all and, consequently, patient population size estimates established according to traditional methodologies can be subject to inaccuracies.  

AlleleAtlas is a free tool that enables accurate estimates of the number of individuals carrying causal alleles for rare genetic diseases to be generated at the population level. 

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How does it work? 

• The tool uses data from the gnomAD genetic database to determine the frequency of rare genetic variants per 100,000 individuals – by ancestry and sex 

• National population data (currently for the USA and UK) is then applied to estimate allele frequency within the current and future population  

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The tool has been developed to bring a valuable resource to the rare disease community, including those engaged in rare disease research and therapeutics in the pharmaceutical, biotech and research spaces, and for patient advocacy organisations aiming to raise awareness. Robust prevalence estimates can help to inform decision-making at each stage of the drug development lifecycle to help bring therapies to rare disease patients faster. 

AlleleAtlas is intended as a starting point for estimating the prevalence of rare genetic diseases, with the following considerations to be taken into account: 

• The carrier and affected population estimates provided do not account for variant-specific penetrance or more granular demographic breakdowns (such as age and the distribution of ancestry groups by age group) within the countries included in the tool.  

• AlleleAtlas can be used to estimate the allele frequency of any genetic variant or combination of variants within the same gene that pass quality control in the version of gnomAD selected for use within the tool.  

• gnomAD is not always representative of whole populations and certain alleles may be under or overrepresented in the dataset. In particular, causal alleles for rare genetic diseases may be underrepresented due to healthy volunteer bias among contributing datasets (such as UK Biobank in gnomAD version 4), the removal of samples suffering from documented pediatric or severe disease in addition to the removal of their first-degree relatives, and underrepresentation of certain ancestry groups within gnomAD.  

As such, AlleleAtlas is best suited to the study of adult-onset autosomal recessive diseases, as affected probands and unaffected carriers of such conditions are more likely to be included within gnomAD.  

For a guide on how to use AlleleAtlas, please consult our user video below:

This tool is still undergoing development and we welcome feedback from users – please contact info@healthlumen.com with any feedback or suggestions for additional features. 

To further your insights into the prevalence of your rare disease interest, book in a call with us today to discuss a full epidemiological report. 

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