Enrichment by fragment size
3X-TGT uses standard enzymes to cut DNA into fragments, then selects a size range that enriches the target repeat while removing more than 90 percent of the genome. Nanopore sequencing reads each retained molecule end to end, measuring repeat length, sequence and native methylation, with allele assignment where informative variants are present. No amplification is required. How 3X-TGT works.
DMPK (myotonic dystrophy type 1) and TCF4 (Fuchs endothelial corneal dystrophy) are available now. Additional repeat loci and repetitive regions are developed individually using genome-wide enrichment modeling. Send us your target locus and sample type to learn what an initial run can deliver.
Read 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 |
Services and prices
| Service | Price | Included |
|---|---|---|
| 3X-TGT Genotype | $395 per sample | 40 on-target reads: both alleles sized, the expanded allele detected and classed, sequence and methylation on every read |
| 3X-TGT Profile | $795 per sample | 200 on-target reads: the distribution of the expanded allele, its interruptions and the methylation phased to each allele |
| 3X-TGT Deep | $1,495 per sample | 500 on-target reads: the Profile plus a progenitor allele estimate and an instability index |
| Whole genome, long read | $2,495 per sample | 30x genome on one flow cell: small and structural variants, methylation and a report on 46 disease repeat loci |
| Whole genome, adaptive | $995 per sample | 30x coverage of the repetitive regions of the genome, aligned to T2T, including the 46 disease repeat loci; the rest of the genome at 2x |
| TP-PCR and STR screen | $350 per sample | Capillary repeat-primed PCR and STR sizing of both alleles, from 100 ng |
| Long-range PCR sequencing | $250 per sample | One locus from 20 to 100 ng, amplicons read end to end; $150 for each further locus. PCR sizing |
| Long-range PCR panel, 10 loci | $795 per sample | The ten-locus repeat panel from 100 ng |
| Small-pool PCR by sequencing | $1,495 per sample | Progenitor allele, instability index and single-molecule distribution from 200 ng |
| DNA extraction at 3X | $50 blood or saliva; $110 tissue, cells or mouse tail | Magnetic-bead extraction for blood and saliva; high-molecular-weight extraction for tissue, cultured cells and mouse tail |
Research use only. Prices in US dollars. Read levels, locus prices and the whole-genome options are on the Pricing page.
Deliverables
| Deliverable | Contents |
|---|---|
| Locus report | The bioinformatics relevant to the locus: a data workbook (length, sequence, interruptions and methylation of every molecule) and the on-target alignments |
| Genotype call | The call for the sample; at the Profile and Deep levels, also the per-molecule distribution with its summary statistics; at the Deep level, the progenitor allele estimate |
| Raw signal data | On request |
Example deliverables from two DM1 samples: example report (PDF) and data workbook (XLSX, 5 MB).
Collaborations
For complex projects, 3X assigns an internal team to work with the research group. 3X also collaborates on grants and contracts, including SBIR and STTR subcontracts, and in other collaborative formats.
Contact Steven Oldenburg, PhD: [email protected] · Leominster, MA