Genotypic and phenotypic analysis of 173 patients with extremely rare pathogenic mutations who applied for experimental antisense oligonucleotide treatment
Authors: Crooke Stanley T. , Cole Tracy , Carroll Jeffrey B. , Gleeson Joseph G. , Mignon Laurence , Douville Julie , Chung Wendy , Bain Jennifer , Berry-Kravis Elizabeth , Leung Nelson , Watt Andy , Powers Berit , Tekendo-Ngongang Cedrik , Kmoch Stanislav , Vyletal Petr , Glass Sarah 
Published: August 2024

Recent advances in “omics” technologies allow for the identification of an increasing number of individuals with diseases caused by nano-rare mutations. These difficult-to-diagnose individuals are uniquely disadvantaged and pose significant challenges to healthcare systems and society. Despite having diseases caused by actionable single gene mutations, in many cases, there is no commercial path for treatments for such small patient populations. We have defined nano-rare mutations as, mutations with a known worldwide prevalence <30. Since antisense oligonucleotide (ASO) technology has proven to be suited to address the needs of a portion of these patients, the n-Lorem Foundation is establishing an industrialized approach that couples detailed genotypic and phenotypic data to the immediate potential for ASO therapy. In this manuscript we have leveraged our experience in assessing the causality of nano-rare genetic variants and associated proximal molecular pathological events to attempt a correlation between detailed genetic data with patient specific phenotypic observations in 173 nano-rare individuals from diverse age groups evaluated for experimental ASO therapy. We found that the time required to achieve a molecular diagnosis varies from 1 month to 36 years, with the mean and median times from symptom onset to diagnosis estimated to be 4.32 years and 2 years, respectively. Amongst submitted cases there is a significant bias toward neurological diseases, with diverse genes and functional families involved and a marked preponderance of mutations in ion channel genes. The variability in phenotypic expression associated with nano-rare variants in genes such asGNAO1, H3F3A, GBE1, UBTF,orPACS1clearly supports previous observations that phenotypes associated with same variants in the same gene can vary. We also observe that different, but functionally equivalent variants can result in both similar (e.g.,TARDBP) and different phenotypes (e.g.,GNAO1). Despite the relatively small size of the patient population investigated, this first compilation of its kind allows a variety of insights into the genotype and phenotype relationships in nano-rare conditions. Moreover, we show that our unique patient population presents a remarkable opportunity to apply “modern omics” approaches to begin to understand the various homeostatic, compensatory, and secondary effects of these genetic variants on the networks that result in expression of their unique phenotypes.

To provide a more detailed description of the processes involved to provide a personalized antisense medicine, we have included nonclinical and clinical data on three exemplary patients who display disease in three different organs, the CNS, the eye and the kidney and are treated with ASOs of different designs. In contrast to traditional drug development, each patient presents unique genomic, ASO design, clinical treatment and management and evaluation challenges.