Deep reads on repeat expansion loci
Send blood, saliva, tissue or cell-line DNA. For every sample you receive per-molecule repeat distributions and a genotype report, to compare against your own method on the same DNA. Research use only.
How the reads are made
The DNA is prepared so that the fragment carrying the repeat falls in a size band that no other part of the genome occupies. That band is kept, and the molecules in it are read on a nanopore flow cell. Nothing is amplified by PCR at any step, so the distribution of reads is the distribution of molecules in your sample. Repeat count, tract sequence, methylation and allele phase (which of the two alleles a read comes from) are called for every read.
Read levels
| Level | Deliverable | Target reads per sample | Input DNA | Report output |
|---|---|---|---|---|
| Genotype | Detection and class (normal, intermediate, expanded) with both allele sizes | 20 on-target reads, at least 5 from the expanded allele | 2 to 10 µg | Both alleles called; expansion present or absent at 95 percent confidence in samples that meet specification |
| Deep | Central size with a confidence interval, progenitor allele estimate, full somatic distribution | 200 on-target reads, at least 50 from the expanded allele | 10 µg or more | Per-molecule histogram, median, interquartile range, 10th-to-90th-percentile width, progenitor allele estimate |
Throughput
| Measure | Value | Basis |
|---|---|---|
| Samples per flow cell | 12 to 25 | Six PromethION runs in 2026, with blood, saliva, tissue and cell-line samples run together |
| Loci on one flow cell | Up to four | The same runs |
| On-target molecules per flow cell | 1,000 to 2,600 | 12 to 25 libraries; runs of 16 to 72 hours |
| Deepest single donor on one flow cell | 1,900 on-target molecules, 700 of them spanning the expanded allele | A two-donor, 72-hour run |
| Cost per sample | Set by the number of samples in the run | One flow cell serves a whole cohort; its cost stays the same as samples are added, up to the 96-sample limit of the barcoding kit |
What you receive for each sample
- A report with the bioinformatics relevant to the locus: a per-read table (length, quality, interruptions, methylation) and the on-target alignments.
- The genotype call and, at the deep level, the per-molecule distribution with its summary statistics and progenitor allele estimate.
- TP-PCR and STR data on request, run alongside the sequencing.
- Raw signal data on request.
Loci
DMPK (myotonic dystrophy type 1, DM1) and TCF4 (Fuchs endothelial corneal dystrophy, FECD) run now, along with a mouse Dmpk locus on the same chemistry. Other repeat loci and repetitive regions are set up for each locus and sample type: tell us the locus and the sample type, and we will tell you what a first run returns.
Collaboration slots, Q4 2026
We are filling our analysis queue with collaborator sample sets. Send up to 18 samples at 10 µg each and receive per-molecule repeat distributions and a genotype report on every one. Both one-time projects and standing engagements are available.
In development
A genomic baseline for each subject, in one dataset: a short-read genome covering the repeat-instability modifier genes and the DMPK flanking haplotype; the long-read repeat profile; and deep-allele metrics (progenitor allele estimate with an interval, mosaic width, instability index), all read against a curated base of published DM1 evidence. We are seeking cohorts for its first build.
Contact Steven Oldenburg, PhD: [email protected] · Leominster, MA