Universal Spike-Ins for ctDNA Assays


Researchers at TGen have developed a method for validating patient-specific oligonucleotides using spike-in sequences. This method involves introducing spike-in oligo sequences to cosynthesized synthesis-control oligonucleotides and patient-specific oligonucleotides. Reading out the counts of spike-in sequences determines the dose-response characteristics of the synthesis-control oligonucleotides, which act as proxies for those of the patient-specific oligo in the assay, and thus provide a quality control check for the batch synthesis of the patient-specific oligonucleotides.


Clinical applications of patient-specific genome analysis such as single-gene or multi-gene panels are currently limited by the cost and complexity of validating the analytic performance of patient-specific oligonucleotides. Current procedures for validating assays are not practical for validating patient-specific oligonucleotides, as they require each test be run a large number of times to establish the assay’s analytic performance characteristics. Such testing greatly increases the cost of using patient-specific oligonucleotides and introduces a significant time delay in being able to use the patient-specific tests.


A spike-in validation method overcomes the commercial and practical limitations in using multiple patient-specific oligonucleotides by greatly reducing the cost and complexity of validating their analytic performance. This results in a cheap, sensitive, accurate, and widely applicable diagnostic tool for detecting patient-specific genetic anomalies. For example, liquid biopsies of cancer patients require a sensitive and accurate system for detecting circulating tumor DNA (ctDNA). Once the patient’s specific somatic ctDNA mutations have been identified, patient-specific oligonucleotides can be used to target those ctDNA to monitor disease progression or treatment efficacy. Thus the patient’s whole genome or exome need only be sequenced once, and the cost of subsequent sample analysis is significantly reduced.


Patent Information:
For Information, Contact:
Katie Bray
Intellectual Property Counsel
The Translational Genomics Research Institute
Tim Mcdaniel
Muhammed Murtaza