Rapid Aneuploidy Detection Reading a Whole Genome's Worth of Chromosome Errors From One Test

This patent describes a fast, low-cost way to spot when a sample has the wrong number of chromosomes, a condition called aneuploidy, which is a hallmark of cancer and of conditions like Down syndrome. It comes from The Johns Hopkins University, with inventors including cancer genetics pioneers Bert Vogelstein and Kenneth Kinzler.

The Problem

Counting chromosomes accurately matters across medicine. Aneuploidy was the first genetic abnormality ever found in cancer and is present in more than 90 percent of cancers of most types, and the same chromosome counting underpins non-invasive prenatal testing for conditions such as Down syndrome. The trouble is that established ways of measuring it, from older karyotype studies to modern massively parallel sequencing, can be slow, expensive, or require large amounts of sequencing to read across the whole genome. A method that detects aneuploidy quickly and cheaply, from tiny amounts of DNA, would make these tests more practical and more widely available.

What This Invention Does

The patent provides methods and materials for evaluating sequencing data to identify a person or other mammal as having one or more chromosomal anomalies. The key idea is to use a single primer pair to amplify roughly a million short, repetitive DNA elements scattered across the genome in one reaction, rather than reading the genome broadly. Those short pieces, averaging under 100 base pairs, are then sequenced and analysed with an approach the inventors call WALDO, short for Within-Sample Aneuploidy Detection, to judge whether any chromosomes are present in abnormal numbers. Because one simple amplification step samples the whole genome at once, the test can flag aneuploidy from very small or degraded samples, which makes it suited to cancer diagnostics, liquid biopsy from blood plasma, prenatal testing, and screening of embryos.

Key Features

• Single primer pair. One pair of primers amplifies about a million repetitive elements across the whole genome in a single reaction.
• Short amplicons. The amplified pieces average under 100 base pairs, so the method works on small or fragmented DNA.
• WALDO analysis. A purpose-built method evaluates the sequencing data to detect aneuploidy within a sample.
• Many uses. It supports cancer diagnostics, prenatal testing, embryo screening, and evaluation of congenital abnormalities.
• Plasma-ready. The approach was demonstrated on more than a thousand blood plasma samples, fitting non-invasive testing.

Who Is Behind It

The applicant is The Johns Hopkins University, a leading research university in Baltimore whose Sidney Kimmel Comprehensive Cancer Center has long been central to cancer genetics. The named inventors include Bert Vogelstein, Kenneth W. Kinzler, Christopher Douville, Nickolas Papadopoulos, and Cristian Tomasetti, a group known for foundational work on the genetics of cancer and on blood-based cancer detection. The work was supported in part by the United States National Institutes of Health. This filing is a divisional application from an earlier related Australian application.

Why It Matters

A test that reads chromosome errors quickly and from tiny samples could lower the cost and broaden the reach of both cancer detection and prenatal screening. Detecting aneuploidy in blood plasma supports the growing field of liquid biopsy, where cancers are found and tracked from a simple blood draw. Protecting the methods in Australia supports the university’s research and any clinical or commercial use of the technology in the local market.

Related Concepts

• Aneuploidy – the abnormal chromosome number the test detects.
• Liquid biopsy – blood-based cancer detection that the method supports.
• Cell-free fetal DNA – the basis of non-invasive prenatal testing.
• Massive parallel sequencing – the sequencing technology the method builds on.
• Karyotype – the older way of viewing and counting chromosomes.

---

AU 2026201955 was published in the Australian Official Journal of Patents on 16 April 2026 and is open for public inspection. Patent applications represent inventions that are sought to be protected and do not necessarily reflect commercially available products.