Methods and systems for detecting genetic variants

What is this patent about?

’306 is related to the field of genetic analysis and molecular diagnostics, specifically focusing on the detection of rare genetic variants and copy number variations in cell-free DNA (cfDNA) samples. The technology addresses the challenges of accurately quantifying DNA fragments in heterogeneous populations, such as those found in liquid biopsies for cancer monitoring, where the signal-to-noise ratio is often extremely low.

The underlying idea behind ’306 is that standard sequencing often fails to capture every molecule in a sample, leading to an underestimation of genetic material that can skew diagnostic results. By using duplex tags to differently label the Watson and Crick strands of double-stranded DNA, the system can track which original molecules were fully recovered as pairs, which were only partially recovered as singlets, and—crucially—statistically infer the number of molecules that were entirely missed during the process.

The claims of ’306 focus on a method for processing cfDNA by tagging molecules with duplex tags containing molecular barcodes, where the number of barcode combinations is specifically calibrated to the expected number of duplicate molecules mapping to the same genomic coordinates. The independent claims cover the amplification and sequencing of these tagged fragments, followed by a redundancy reduction process that sorts sequence reads into families of paired and unpaired strands to identify distinct original parent molecules.

In practice, the invention works by attaching specialized adapters to both ends of DNA fragments before amplification. These adapters allow the bioinformatic pipeline to group progeny reads back to their original source molecule and distinguish between true biological mutations and errors introduced by the polymerase or sequencer. By identifying whether a variant appears on both complementary strands of a single DNA duplex, the system achieves a much higher level of confidence in calling rare somatic mutations.

This approach differs from prior methods by moving beyond simple unique identification to a more sophisticated model of recovery. While traditional barcoding helps eliminate PCR duplicates, this invention uses the relationship between paired and unpaired reads to correct for sampling bias and 'unseen' molecules. This statistical correction allows for a more precise determination of copy number variation and the detection of rare DNA at concentrations below 1% with a specificity greater than 99.9%.