Rigel Pharmaceuticals, Incorporated

Illumina Corporation

Other

Element Biosciences, Inc.

Ryan Kelley

Rajinder Paul Singh

Kin Tso

Hui Li

Yong Li

Thilo J Heckrodt

Yan Chen

Rose Yen

Darren J McMurtrie

Vanessa Taylor

Jack Maung

Sacha Holland

Esteban Masuda

Matthew Duncton

Rao Kolluri

Salvador Alvarez

Eric Hans Vermaas

Gordon Bean

Donald G Payan

Jing Zhang

Tatjana Singer

Johann Felix Wilhelm Schlesinger

John S Vieceli

Junhua Zhao

William Light

Jocelyne Bruand

Johann Felix Schlesinger

Konrad Scheffler

Darren Mcmurtrie

Chih Lee

The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

Single-stranded splint strands and methods of use

Disclosed embodiments concern interleukin receptor associated kinases (IRAK) inhibitors, such as oxazole compounds, and compositions comprising such inhibitors. Also disclosed are methods of making and using the compounds and compositions. The disclosed compounds and/or compositions may be used to treat or prevent an IRAK-associated disease or condition.

IRAK inhibitors and method for making and using

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

Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.

Nucleic acid indexing techniques

The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.

Universal short adapters for indexing of polynucleotide samples

Optimal index sequences for multiplex massively parallel sequencing

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

Provided are methods, systems, and computer products for genotyping polyploid organisms, as well as diploid organisms. The provided methods use an allele-intensity model to generate cluster definitions. The allele-intensity model relates allele counts of different genotypes to signal intensities generated by the genotyping platform. The model also includes a capability to update cluster positions obtained from a maximum likelihood model using a Bayesian method.

Genotyping polyploid loci

Disclosed embodiments concern novel interleukin receptor associated kinases (IRAK) inhibitors and compositions comprising such inhibitors. Also disclosed are methods of making and using the compounds and compositions. The disclosed compounds and/or compositions may be used to treat or prevent an IRAK-associated disease or condition.

Pyrazole compounds and methods for making and using the compounds

Pyrazole compounds and method for making and using the compounds

Growing community of inventors

Pacifica, CA, United States of America

Ryan Kelley