Product capabilities FAQ for the TruPath Genome assay

Can TruPath Genome be integrated with Illumina 5-Base? (ie, get proximal reads as well as methylation information?)

There is no methylation/5-Base support for TruPath Genome.

Can TruPath Genome replace Trios? In Phasing, can it be identified if the variant comes from mother or father?

• TruPath Genome can phase from a single genome. The datasheet and technical note demonstrate such performance.

• Parents must be sequenced to determine things like de novo parent-of-origin assignment, etc.

Can this technology detect uniparental disomy (UPD**)?**

UPD has not been specifically tested for TruPath. Uniparental isodisomy (two identical haplotypes from the same parent) would be detected as ROH (runs of homozygosity) for a whole chromosome for the proband only. Uniparental heterodisomy would look normal for proband only. Both cases would need at least one parent to deduce the parental origin; Illumina does not offer a caller to do this currently.

Is there resolution of mosaicism with this technology?

Mosaicism is in scope for future DRAGEN releases supporting TruPath, but performance for mosaic variant detection has not been assessed at this time.

For Fragile X, is this technology capable of doing everything that long reads can? TruPath can accurately estimate Fragile X repeat expansion lengths of any size and distinguish between intermediate mutations, permutations, and full mutations. In this sense, it is similar to what long reads are capable of. TruPath differs from long reads in that it does not read contiguous repeat expansion sequence, but estimates repeat length using enhanced repeat read recovery and other informatic advances. Those advances will continue to improve performance in future DRAGEN releases.

For any feedback or questions regarding this article (Illumina Knowledge Article #10165), contact Illumina Technical Support [e-mail].