Biospyder Technologies, Inc.

Htg Molecular Diagnostics, Inc.

John Wayne Cancer Institute

Selectide Corporation

High Throughput Genomics, Inc.

Bruce Seligmann

Joanne M Yeakley

Peter J Shepard

Matt Rounseville

Joel McComb

Ihab Botros

Mark W Schwartz

Anthony Stevens

John W Luecke

Tom Vasicek

Bj Kerns

Milos Babic

Krishna Maddula

Chris Cox

Dave S B Hoon

Hui Wang

Michal Lebl

Richard M Kris

Stephen Felder

Viktor Krchnak

John Luecke

Debrah Thompson

Christy Lee Trejo

Zhenquiang Lu

Christopher Roberts

Debra A Gordon

Elliot Imler

B J Kerns

Matthew Rounseville

Justin Brown

Dave Sb Hoon

Dave SB Hoon

Ralph Martel

Mark Schwartz

Methods for designing oligonucleotide probes for detecting and profiling expression products at transcriptome scale.

Profiling expression at transcriptome scale

Barcoded ligation assay products from individual samples.

Method of nucleic acid sequence detection

Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences.

Attenuators

Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Methods of detecting gene fusions

Expression profiling of FFPE sample areas smaller than 2 mmwith single-cell sensitivity, correlated with tissue microenvironment morphology and neoplastic grade. An automated digital molecular pathology instrument for integrated imaging, immunohistochemical assessment, and processing samples for sequence detection assays. Software for instrument and sample control and analysis.

Focal gene expression profiling of stained FFPE tissues with spatial correlation to morphology

Oligonucleotides for detecting and profiling expression products at transcriptome scale.

Ligation assays in liquid phase for detecting nucleic acid sequences.

Ligation assays in liquid phase

Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes, and detecting the fusion probe after nuclease treatment. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes, and detecting these probes after nuclease treatment. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Ligation assays for detecting and profiling expression products at transcriptome scale.

Disclosed herein are methods for detecting presence of a nucleotide variant in a target nucleic acid utilizing a nuclease protection assay. The methods include contacting a sample with at least two probes, wherein the first probe is complementary to the wild-type (non-variant) nucleotide(s) at the nucleotide variant position(s) in the target nucleic acid and the second probe is complementary to the variant nucleotide(s) at the nucleotide variant position(s) in the target nucleic acid, under conditions sufficient for the probes to hybridize to the target nucleic acid, producing a mixture of hybridized and unhybridized nucleic acids. The mixture is contacted with a nuclease specific for single-stranded nucleic acid molecules under conditions sufficient to remove unhybridized nucleic acid molecules (or unhybridized portions of nucleic acid molecules). The presence of the at least two probes is then detected, thereby detecting the presence of the variant and/or non-variant target nucleic acid in the sample.

Nuclease protection methods for detection of nucleotide variants

Disclosed are methods for determining whether a melanocyte-containing sample (such as a nevus or other pigmented lesion) is benign or a primary melanoma. These methods can include detecting (at the molecular level, e.g., mRNA, miRNA, or protein) the expression of at least two disclosed genes in a biological sample obtained from a subject. Also provided are arrays and kits that can be used with the methods.

Molecular malignancy in melanocytic lesions

Disclosed herein are methods of co-detecting presence of target messenger RNA (mRNA) and small non-coding RNA (for example, miRNA) in a sample. The disclosed methods can be used to simultaneously detect mRNA and small non-coding RNA in a single assay (for example in the same reaction or the same well of a multi-well assay). The methods can include contacting a sample with a plurality of nuclease protection probes (NPPs) including at least one probe which specifically binds to a target mRNA and at least one probe which specifically binds to a target small non-coding RNA, contacting the sample with a nuclease specific for single-stranded nucleic acids, and detecting the NPP, for example on a microarray.

Methods of co-detecting MRNA and small non-coding RNA

The present disclosure provides an improvement to quantitative Nuclease Protection Assay (qNPA) and quantitative Nuclease Protection Sequencing (qNPS) methods. The disclosed methods use nuclease protection probes (NPPs) that include 5'-end and/or 3-end flanking sequences, which provide a universal hybridization and/or amplification sequence. The disclosed methods can be used to sequence or detect target nucleic acid molecules, such as those present in fixed or insoluble samples.

Growing community of inventors

Tucson, AZ, United States of America

Bruce Seligmann