Systems And Methods To Detect Rare Mutations And Copy Number Variation

What is this patent about?

’265 is related to the field of genetic diagnostics, specifically the detection of rare mutations and copy number variations (CNVs) in cell-free polynucleotides (cfDNA). The background context involves the increasing importance of genetic testing for early disease detection and monitoring, particularly for conditions like cancer where early intervention significantly improves outcomes. Traditional methods often struggle with the low concentration of disease-related cfDNA amidst a large background of normal cfDNA, necessitating more sensitive and accurate detection techniques.

The underlying idea behind ’265 is to improve the sensitivity and accuracy of detecting rare genetic alterations in cfDNA by employing a strategy that involves non-unique tagging of cfDNA molecules with molecular barcodes, followed by high-throughput sequencing and sophisticated bioinformatics analysis. The key inventive insight is that by using a molar excess of adapters with molecular barcodes and allowing for non-unique tagging, the method can effectively capture and analyze a larger proportion of the original cfDNA molecules, even when present at very low concentrations.

The claims of ’265 focus on methods for treating a subject having cancer, where the treatment decision is based on the presence or absence of somatic genetic variants detected in cfDNA. The detection method relies on sequencing reads generated from tagged polynucleotides derived from cfDNA molecules. A crucial aspect is the use of non-uniquely tagged polynucleotides contacted with a molar excess of adapters comprising molecular barcodes, ensuring that a significant portion of the cfDNA molecules are tagged, and that the number of different molecular barcodes is less than the number of cfDNA molecules mapping to a specific location in the genome.

In practice, the method involves extracting cfDNA from a patient's sample (e.g., blood), attaching adapters containing molecular barcodes to the cfDNA fragments, amplifying the tagged fragments, and then performing high-throughput sequencing. The resulting sequencing reads are then analyzed using bioinformatics tools to identify rare mutations and CNVs by comparing the sequence data to a reference genome. The use of molecular barcodes allows for the identification and correction of errors introduced during PCR amplification and sequencing, further enhancing the accuracy of the detection.

The differentiation from prior approaches lies in the combination of non-unique tagging with a molar excess of adapters and the subsequent bioinformatics analysis. Traditional methods often rely on unique tagging, which can be inefficient and costly, or lack the sensitivity to detect rare variants present at very low concentrations. By allowing for non-unique tagging and using a high adapter concentration , the method ensures that a larger proportion of the original cfDNA molecules are captured and analyzed, leading to improved sensitivity in detecting rare mutations and CNVs, which ultimately informs treatment decisions for cancer patients.