Systems and methods to detect rare mutations and copy number variation

What is this patent about?

'678 is related to the field of non-invasive cancer diagnostics, specifically methods for detecting rare genetic mutations and copy number variations in cell-free DNA (cfDNA) found in bodily fluids. This field addresses the need for early cancer detection and monitoring, which can significantly improve treatment outcomes. Traditional methods often require invasive biopsies, while this invention aims to provide a less invasive alternative.

The underlying idea behind '678 is to improve the sensitivity and accuracy of detecting cancer-related genetic alterations in cfDNA by using molecular barcodes to track and correct for errors introduced during the sequencing process. By tagging individual cfDNA molecules with barcodes before amplification and sequencing, the method allows for the identification and removal of PCR duplicates and sequencing errors, leading to a more accurate representation of the original cfDNA population.

The claims of '678 focus on a method for detecting the presence or absence of somatic genetic variants in a sample of cfDNA. The method involves tagging cfDNA molecules with molecular barcodes, amplifying the tagged molecules, sequencing the amplified products, and then detecting somatic genetic variants such as single nucleotide variants (SNVs), copy number variations (CNVs), insertions or deletions (indels), or gene fusions from the sequencing reads. A key aspect is the use of a limited set of barcodes, resulting in multiple tagged parent polynucleotides sharing the same barcode combination.

In practice, the method begins with extracting cfDNA from a patient's bodily fluid. These cfDNA fragments are then tagged at both ends with molecular barcodes from a set of 2 to 1,000 different barcodes. The barcoded fragments are amplified using PCR, and the resulting amplified DNA is sequenced using a next-generation sequencing platform. The sequencing data is then analyzed to identify somatic genetic variants indicative of cancer. The use of molecular barcodes allows for the identification and removal of PCR duplicates and sequencing errors, improving the accuracy of variant detection.

This approach differentiates itself from prior methods by using a limited set of molecular barcodes, which simplifies the barcoding process and reduces the cost of reagents. While multiple cfDNA fragments may share the same barcode combination, the method still allows for accurate variant detection by leveraging the high throughput of next-generation sequencing and sophisticated bioinformatics algorithms to distinguish true variants from errors. This enables the detection of rare mutations and copy number variations with high sensitivity and specificity, even in samples with low tumor burden.