Distinguish genes from pseudogenes

High-fidelity enrichment allows detailed characterisation of large DNA fragments

Xdrop™ enrichment for long-read sequencing overcomes ambiguity caused by pseudogenes and structural variants

  • Capture sequence differences down to a single nucleotide within a single heterogenous sample

  • Distinguish genes from highly homologous and close-proximity pseudogenes

  • Take advantage of accurate long reads to de novo assemble complex contigs

Background

The presence of highly homologous pseudogenes in close proximity of a target gene complicates accurate detection and sequencing. This is the case with CYP2D6, a gene that impacts patient response to approximately 25% of all clinically used drugs. Common hybridization-based enrichment tools fail to distinguish CYP2D6 from its highly similar pseudogenes CYP2D7 and CYP2D8. 

With the Indirect Sequencing Capture of Xdrop™, you get the single-molecule resolution needed to not only tease apart genes versus pseudogenes, but also to correctly call SNP variants within a single sample. Plus, the enrichment fidelity facilitates de novo assembly to resolve structural variation.

The granularity to distinguish genes from pseudogenes

CYP2D6 has a number of alleles that determine how quickly a patient metabolizes a drug. Accurate characterization of these alleles, like calling single-nucleotide variants in a single sample, can be complicated by the co-enrichment of the pseudogenes CYP2D7 and CYP2D8. That co-enrichment happens with hybridization methods. As a result, short sequencing reads end up being randomly assigned to gene and pseudogenes. That doesn’t happen with the Xdrop™ workflow.

Read.coverage RoT100 CYP2DX plot

A simple workflow for high-fidelity insights

The Indirect Sequence Capture of Xdrop™ enriches individual DNA fragments in a very simple workflow. The outcome is a high-fidelity sequencing library that enables the detailed characterization of a wide stretch of the genome. For example, alleles of CYP2D6 within a single sample (see inset of graph) can be accurately called and de novo assembly reveals details of structural variation. Download our Application Note to see the outcome of our de novo assembly of a 100 kb region around CYP2D6 [link to App Note].

coverage zoom(2)

Do you want to know more? 

With single-molecule resolution and  a simple workflow, Xdrop™ accurately resolves structural and sequence complexity - big and small - that confounds sequencing analysis. Work without limitations.