Enrichment by fragment size
Each design uses a tailored enzyme cocktail to cut around the target, placing it within a defined fragment size range. Size selection retains these fragments while removing more than 90 percent of the genome. The window refers to the reference (wild-type) sequence; on an expanded allele, up to about 6,000 repeat units beyond the base fragment can be measured.
Human targets are available for design and pricing. Model organisms and engineered cell lines require a reference sequence and target coordinates. Targets beyond DMPK and TCF4 are checked at the bench on the first order before results are released, with no setup charge.
Native DNA and methylation
Amplification-free nanopore sequencing reads native DNA, measuring sequence and CpG methylation together. Heterozygous variants assign reads to each allele, providing allele-specific methylation.
Target classes
| Target | Measured on each molecule |
|---|---|
| Repeat expansion locus | Length of the whole repeat, its interruptions and the methylation on either side. |
| Promoter or CpG island | Methylation at every CpG in the window, without bisulfite conversion. |
| Imprinted locus | Methylation on each chromosome copy, assigned by the heterozygous variants in the same read. |
| Structural variant or breakpoint | The junction, read through on single molecules. |
| Insertion or edit site | The inserted sequence, its copy number on the molecule and the host sequence on both sides. |
| Other regions | Any window of 3,000 to 6,000 bases with a valid design against the reference. |
Read levels and prices
The price per sample follows the number of on-target reads requested. The figures below are for DMPK. Other targets are priced from their own design, because the enrichment sets how many samples share a flow cell; designs and prices for each disease repeat locus in the standard catalog are on the Pricing page. Volume pricing applies from 10 samples.
| Level | On-target reads | Measurement | Per sample | Per target read |
|---|---|---|---|---|
| Genotype | 40 | Both alleles called and sized, with methylation across the window | $395 | $9.88 |
| Profile | 200 | Length distribution across molecules, interruptions, and methylation phased to each allele | $795 | $3.98 |
| Deep | 500 | Subpopulations of about 1 percent of molecules or more | $1,495 | $2.99 |
Deliverables
| Deliverable | Contents |
|---|---|
| Alignments | The on-target BAM, with methylation tags, against the requested reference build. |
| Report | A PDF summary of the result for the target: the allele sizes or sequence found, the number of on-target reads behind each result, and the read-length and methylation statistics for the window. |
| Data workbook | An Excel workbook with a summary of the read statistics, the repeat map of every molecule aligned on each end of the tract with its flanking sequence, and the methylation at every CpG on every molecule. |
| Raw signal | The POD5 signal data on request. |
Example deliverables from two DM1 samples: example report (PDF) and data workbook (XLSX, 5 MB).
Samples and quotes
Accepted samples are extracted DNA, blood, saliva, tissue and cell lines. Input is 3 µg at the Genotype level, 5 µg at the Profile level and 15 µg at the Deep level. A quote needs the coordinates of the window, the reference build, the sample type and the number of samples. We will reply with the design summary, the predicted reads per flow cell and the price at each read level. DNA quality, materials and shipping are on the Sample requirements page.
3X Genetics operates a CLIA-registered laboratory (CLIA ID 22D2345868). Massachusetts clinical laboratory license pending. This service is for research use and is not reported for patient care.