Systems and methods to detect rare mutations and copy number variation

What is this patent about?

’880 is related to the field of molecular biology and medical diagnostics, specifically focusing on the detection of rare genetic alterations in cell-free polynucleotides. The technology addresses the challenge of identifying low-frequency mutations and copy number variations within bodily fluids, such as blood or plasma, where disease-derived genetic material is often obscured by a vast majority of healthy germline DNA.

The underlying idea behind ’880 is to improve the sensitivity and specificity of liquid biopsies by maximizing the conversion of original sample molecules into a sequenceable library and using molecular tagging to filter out noise. By attaching identifiers to both ends of individual DNA fragments at high efficiency, the system can track progeny molecules back to their original parent strands, allowing the software to distinguish between true somatic mutations and errors introduced during PCR amplification or the sequencing process itself.

The claims of ’880 focus on a method for identifying somatic genetic variants by tagging at least 20% of a cell-free DNA population with molecular barcodes. This process specifically requires attaching these barcodes to both ends of the DNA molecules using a significant molar excess of tags—at least 10-fold—to ensure high-efficiency labeling, followed by determining the sequences of the parent polynucleotides based on the barcode information to identify variants against a reference.

In practice, the invention works by utilizing a high-diversity library preparation that ensures a large proportion of the extracted fragments are successfully tagged and sequenced. This high conversion efficiency is critical because, in early-stage disease, only a handful of mutated molecules may exist in a standard blood draw. By collapsing multiple sequencing reads into a single consensus sequence based on the barcodes, the system effectively eliminates the 'background noise' of sequencing artifacts that typically plague conventional next-generation sequencing.

This approach differs from prior methods by moving away from simple average measurements of pooled samples toward a digital sequencing framework that tracks individual molecules. While traditional workflows often lose the majority of starting material during preparation or fail to distinguish rare variants from 1-2% baseline sequencing errors, the ’880 method uses molecular barcodes and high-ratio tagging to achieve a sensitivity threshold as low as 0.1%, enabling the detection of residual disease or early-stage cancer that would otherwise be invisible.