Maturing platforms for targeted cell and gene-based therapies offer hope for treating over 8,000 rare genetic diseases. These therapies target the root causes of genetic diseases at the RNA or DNA level. While commercial incentives have supported treatments for prevalent rare genetic diseases, the rarest conditions, affecting less than 1:1,000,000 individuals, often lack development support. To address this gap, researchers are exploring individualized therapies tailored to a patient's unique genetic pathology, necessitating specialized trial designs and clinical outcome measures. A new framework has been proposed to address the challenges associated with N-of-1 trials, offering a structured approach to evaluating these highly personalized treatments.
Addressing Challenges in N-of-1 Trial Design
N-of-1 trials for individualized, genetically targeted therapies require careful consideration of factors common to all clinical trials. These include understanding the patient's genotype and phenotype, the drug's mechanism of action and tissue distribution, relevant treatment goals, and realistic expectations. However, N-of-1 trials also present unique challenges, particularly in assessing clinical efficacy. The framework emphasizes the need for specialized approaches to trial design and clinical outcome measures to rigorously evaluate these therapies.
Clinical Outcome Assessments (COAs) in Ultra-Rare Diseases
Many rare diseases lack pre-established, disease-relevant clinical outcome assessments (COAs). Formal development of such measures may be impossible due to the small number of patients, symptom heterogeneity, limited natural history characterization, and global patient distribution. N-of-1 trials can adapt principles from the FDA's Patient-Focused Drug Development (PFDD) Guidance documents for selecting COAs. COAs should reflect the patient's lived experience and current condition. While traditional trials use focus groups to determine COA appropriateness, N-of-1 trials focus on individual patient symptoms. Qualitative interviews can ensure a comprehensive disease concept model, identifying main impairment areas and representing each patient's experience. Identifying COAs to capture symptoms allows structured data collection to begin before intervention. Clinical investigators treating patients with ultra-rare diseases need a deep understanding of disease pathophysiology and unmet treatment needs to identify appropriate outcome measures for safety and efficacy.
Defining Meaningful Change in Individualized Treatments
Clinical trials for individualized drugs face the challenge of defining meaningful change. Traditionally, this is captured via the trial’s minimal clinically important difference (MCID)—the smallest response considered clinically impactful. With sufficient patient data, statistical methods can establish a standardized MCID. However, this is challenging in current individualized N-of-1 trials involving ultra-rare diseases where such data is lacking. Even if a standardized MCID exists, its applicability may be limited by clinical heterogeneity, as an individualized drug may only target a small subset of patients with a specific mutation.
While a standard statistical approach to MCID determination is not possible in an N-of-1 trial, diligent collection of individualized ‘natural history data’ prior to treatment may allow for determination of test-retest and longitudinal stability of measures with longer baseline data collection providing more data points. One method of MCID determination outlined by the PFDD Guidance document four is to use hypothetical scenarios measured within a particular set of COAs to understand a group of patients assessment of meaningfulness through qualitative interviews. This could be a useful method for determining an “a priori” categorization of what a meaningful outcome would be for an individual patient prior to initiating an N-of-1 trial.
A Multi-faceted Approach to N-of-1 Trial Design
The suggested strategy involves subdividing N-of-1 trial design into markers of target engagement, clinical biomarkers, and outcome assessments. These should reliably measure function, development, and behavior relevant and individualized to the patient and underlying disease. Assessments should be informed by toxicity profiles for the investigational agent. Objective and quantitative clinical assessments are valuable, but qualitative tools remain imperative for capturing clinical impacts and tracking meaningfulness to the patient in terms of disease morbidity and quality of life.
Safety Considerations
Safety outcome measures for N-of-1 trials must match potential toxicity modes associated with the therapeutic. This includes toxicity profiles of the specific investigational agent and known or suspected class effects associated with the therapeutic modality. For example, typical safety-related clinical biomarkers for intrathecal ASO trials may include CSF sampling, surveillance neuroimaging, blood testing, and urinalysis. The appropriateness of safety assessments for a particular therapeutic class is expected to evolve as more is learned about the safety profile from traditional clinical trials and N-of-1 trials.
Clinical Outcome Measures for CNS Disorders
For central nervous system disorders, relevant clinical outcome measures may include seizure logs, electroencephalograms (EEGs), electromyography/nerve conduction studies (EMG/NCVs), qualitative and/or quantitative volumetric neuroimaging, MR spectroscopy, quantitative sensory testing, neurodevelopmental assessments, and other structured neurologic rating scales. Wearable biometric sensors capable of capturing longitudinal data relevant to symptoms such as motor strength, coordination, sleep, or seizures are of particular interest. Validated devices may prove preferable when assessing an individual with significant cognitive impairment or developmental delays as they acquire data passively and do not depend upon patient understanding or cooperation with testing, such as inertial sensors for ataxic gait measurement.
The Role of Biomarkers
Ideally, an interventional trial would incorporate measurement of fluid and tissue biomarkers that demonstrate target engagement of the investigational drug. However, these do not exist and are not feasible for the majority of N-of-1 trials. This is unsurprising given the rarity of the conditions studied in these trials, combined with the fact that currently, most N-of-1 trials target the CNS where tissue sampling is not possible. Nonetheless, other fluid and tissue biomarkers may provide helpful guidance to investigators managing patients enrolled in N-of-1 trials when available. For neurodegenerative diseases, plasma or CSF neurofilament levels may correlate with rates of neuronal injury, potentially informing clinical decision making. In addition, electrophysiologic biomarkers on EEG or EMG/NCV studies, if identified, may provide an objective metric of disease course and progression as it relates to the biological underpinnings of the genetic disease. Ideally, a reliable and informative biomarker can serve in a predictive and/or prognostic capacity.
Future Statistical and Regulatory Considerations
Statistical analyses are challenging given the nature of individualized interventions, but structured approaches have been developed in other fields like oncology. Various statistical methods are available for analyzing individual data from N-of-1 trials and other single-case designs. The clinical design considerations outlined here may serve as a first step towards meeting this challenge for rare genetic disease, paving the way towards the development of master clinical protocols to allow data sharing and aggregation of signals for meta-analyses across multiple N-of-1 interventions. The current regulatory landscape allows for the development of individualized investigational drugs for ultra-rare diseases via the submission of N-of-1 research INDs. Incorporating the clinical trial design principles discussed here will support the rigorous clinical science necessary to meet approval standards.
