Repetitive Element Aneuploidy Sequencing Systems (REAL-SeqS)

Unmet Need
Aneuploidies are chromosomal alterations that are present in the majority of cancers and associated with numerous genetic disorders. Consequently, the detection of aneuploidy in clinical samples has important applications in prenatal testing and cancer diagnostics. The current, noninvasive methods for detecting aneuploidy in clinical samples rely upon next generation sequencing (NGS) protocols, such as whole-genome or whole-exome sequencing. However, these approaches are expensive and may not provide the depth of coverage needed to identify aneuploidy when low amounts of cell-free DNA are available. Consequently, improved methods of detecting aneuploidy would have numerous applications in diagnostics and forensics.

Technology Overview
JHU researchers have developed a rapid and sensitive genome sequencing method to identify aneuploidy in plasma samples. This test, called Real-SeqS, is an amplicon-based protocol that requires only a single primer pair to detect aneuploidy. This NGS protocol is advantageous compared to existing methods because it requires small volumes of clinical samples and provides a higher depth of coverage. The inventors paired this method with the use of a robust algorithm that they have developed specifically for amplicon-based aneuploidy detection. The inventors characterized the performance of this assay on a test cohort of 1155 healthy (euploid) and 809 cancer plasma samples. The cancer plasma samples included patients with breast, colorectal, esophageal, liver, lung, ovarian, pancreatic, and stomach cancers in stages I, II, and III. The inventors were able to detect aneuploidy in 23% of the plasma samples from cancer patients.

Stage of Development
The inventors have validated the Real-SeqS method using a test cohort of healthy (euploid) and cancer patient samples.
 

Category(s):