Illumina Corporation

Johann Felix Wilhelm Schlesinger

Ryan Kelley

Michael D Ruehle

Rami Mehio

Jocelyne Bruand

Viraj Deshpande

Sean Truong

John Cooper Roddey

Konrad Scheffler

Severine Catreux

Methods, systems, and apparatuses, including computer programs for identifying a gene fusion in a biological sample are disclosed. The method can include actions of obtaining first data that represents a plurality of aligned reads, identifying a plurality of fusion candidates included within the obtained first data, filtering the plurality of fusion candidates to determine a filtered set of fusion candidates, for each particular fusion candidate of the filtered set of fusion candidates: generating, by one or more computers, input data for input to a machine learning model that includes extracted feature data that to represents the particular fusion candidate, providing the generated input data as an input to the machine learning model that has been trained to generate output data representing a likelihood that a fusion candidate is a valid gene fusion, and determining whether the particular fusion candidate corresponds to a valid gone fusion based on the output data.

Rapid detection of gene fusions

Computer methods and systems for quantifying a nucleic acid sample comprising nucleic acid of one or more contributors to: receive nucleic acid sequence reads obtained from the nucleic acid sample and mapped to alleles at polymorphism loci; determine, using the nucleic acid sequence reads, allele counts for each of the alleles at the polymorphism loci; use a probabilistic mixture model that applies a probabilistic mixture model to the allele counts, and that uses probability distributions to model the allele counts at the polymorphism loci; quantify, using the probabilistic mixture model, one or more fractions of nucleic acid of the one or more contributors in the nucleic acid sample; determine a probability that a specific contributor among the one or more contributors has a specific genotype; and call, based on the posterior probability, that the nucleic acid sample includes nucleic acid from the specific contributor.

Methods for accurate computational decomposition of DNA mixtures from contributors of unknown genotypes

Disclosed herein are systems and methods for multiplex primer design and selection. In one example, a system includes non-transitory memory configured to store executable instructions; and a hardware processor programmed by the executable instructions to receive a plurality of target gene sequences and determine a set of primers for each target gene sequence based on a penalty score associated with the set of primers, wherein the penalty score is based on a non-linear combination of a primer-level penalty score and a set-level penalty score.

Systems and methods for multiplex PCR primer selection

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San Diego, CA, United States of America

Johann Felix Wilhelm Schlesinger