Trial requirements
Many DM1 drug programs in development act on the repeat or on the DNA-repair genes that drive its expansion. Such a program needs the repeat measured in every participant: the inherited length to stratify enrollment, and the somatic distribution to test whether a therapy slows expansion.
Results used to enroll participants must come from a clinical laboratory. 3X works with sponsors to plan that path under an IRB-approved protocol; clinical testing is planned for 2027.
Marker panel
| Marker | Measurement | Interpretation |
|---|---|---|
| DMPK repeat, both alleles | Repeat count on each molecule; carrier status against the standard size bands | The basis of diagnosis and carrier status |
| Progenitor allele estimate | An estimate of the length inherited at conception, from the low end of the per-molecule distribution | Predicts age at onset better than the length a standard blood test reports |
| Somatic distribution | The per-molecule spread of the expanded allele, with an instability index | Faster expansion is associated with earlier onset, independent of inherited length |
| Interruptions | Whether variant repeats interrupt the tract, how many and where, placed on each molecule | In DM1, associated with later onset and milder disease; a factor to balance across trial arms |
| Flanking CTCF sites | Methylation at the CTCF binding sites on either side of the repeat, read directly from native DNA | Changes with allele length; under study as a marker of disease severity |
| Flanking haplotype | Which of the two chromosome copies carries the expansion | Assigns each molecule to its chromosome |
| DNA-repair modifier genotypes | Published onset variants in MSH3, FAN1, MLH1, PMS2, LIG1 and related genes, from a lower-depth long-read genome | Variants in these genes shift age at onset in Huntington disease; MSH3 variants are also associated with somatic instability in DM1 |
| Genetic ancestry | Ancestry calculated from the lower-depth long-read genome | Context for interpreting the modifier genotypes |
Samples and read depth
DNA from blood, saliva, tissue and cell lines runs together on one flow cell, and no step amplifies it. Each sample is read at one of three levels.
| Level | Deliverable | Target reads per sample | Input DNA |
|---|---|---|---|
| Genotype | Detection and size class with both allele sizes, sequence and methylation | 40 on-target reads | 3 µg |
| Profile | Median and spread of the expanded allele, its interruptions and the methylation phased to each allele | 200 on-target reads, at least 30 from the expanded allele | 5 µg |
| Deep | The Profile plus a progenitor allele estimate, the full somatic distribution and an instability index | 500 on-target reads | 15 µg |
One flow cell carries 12 to 24 samples. The deep level pools fewer, because each sample takes a larger share of the reads from the flow cell.
Participant record
Each participant record combines the markers above from 3X-TGT and the lower-depth long-read genome. For a trial or registry program, 3X and the sponsor agree on the markers, read level and delivery format.
Loci and validation status
The DMPK and TCF4 assays are in analytical validation in our CLIA-registered laboratory (CLIA ID 22D2345868); Massachusetts clinical laboratory license pending. TCF4, the locus of Fuchs endothelial corneal dystrophy, runs on the same chemistry as DMPK. Other repeat loci, including HTT, FXN and C9orf72, are added one at a time, each after its enrichment design has been computed against the whole genome and checked at the bench. Research characterization is available now; clinical testing is planned for 2027, in our laboratory or through a partner CLIA laboratory.
To discuss a trial or registry program, contact Steven Oldenburg, PhD, Co-Founder and Chief Scientist: [email protected]