Inivata Ltd.

Matthew Edward Smith

Samuel Woodhouse

Tim Forshew

Vincent Plagnol

Stefanie Viola Lensing

Karen Howarth

Michael Epstein

Andrew Lawson

Provided herein is a method for the analysis of minimal residual disease, the method comprising obtaining multiple pairs of primers, performing a targeted multiplex amplification using the multiple pairs of primers to produce amplicons, sequencing the amplicons or an amplification product thereof, thereby generating sequence reads, calculating a score based on the minority of sequences containing identified sequence variations, and using the calculated score to determine the presence or absence of minimal residual disease in the patient.

Method for the analysis of minimal residual disease

The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.

Computational method for detecting fusion events

A method for the analysis of minimal residual disease is provided. In some embodiments, the method comprises obtaining multiple pairs of primers designed to amplify sequences that contain a plurality of sequence variations that have been previously identified in a patient's tumor. Amplicons are then obtained through a targeted multiplex amplification that amplifies those sequences from cell-free DNA isolated from a plasma sample. The amplicons are sequenced and two or more of the sequence variations are detected from sequence reads, wherein the detecting comprises comparing a quantity of sequence reads containing a sequence variation against a threshold value. A score is then calculated for the patient sample based on the combined allele frequencies of the detected two or more sequence variations, wherein the score indicates the presence of minimal residual disease.

Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).

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Cambridge, United Kingdom

Matthew Edward Smith