Life Technologies Corporation

Singular Genomics Systems, Inc.

Timothy Looney

Eli N Glezer

Geoffrey Lowman

Lifeng Lin

Abrehet Abdu

Fiona Hyland

Asha Kamat

Elizabeth Linch

Lauren Miller

Daan Witters

Martin Maria Fabani

Sabrina Shore

Ryan Shultzaberger

Provided herein are methods including alternating series of sequencing cycles and dark extension cycles allowing longer read lengths and addressing disadvantages of traditional nucleic acid sequencing protocols.

Dark cycle sequencing

The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

Methods for context based compression of genomic data for immuno-oncology biomarkers

The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire using genomic DNA from a biological sample. In one aspect, target-specific primer panels provide for the effective amplification of sequences of T cell receptor and/or B cell receptor chains with improved sequencing accuracy and resolution over the repertoire. Nucleic acid sequences of variable regions associated with the immune cell receptor are determined to effectively portray clonal diversity of a biological sample and/or differences associated with the immune cell repertoire of a biological sample.

Compositions and methods for immune repertoire sequencing

Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided.

Linked paired strand sequencing

Methods for long read sequencing

The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, methods provide for determining convergence of T cell receptor and/or B cell receptor repertoires in samples prior to a treatment and predicting a subjects response to the treatment based on the measured convergence frequency. In another aspect, methods provide for an immune receptor haplotype group and predicting a subjects potential or predisposition to be protected from or vulnerable to an adverse event following a treatment.

Immune repertoire monitoring

The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, target-specific primer panels provide for the effective amplification of sequences of T cell receptor and/or B cell receptor chains with improved sequencing accuracy and resolution over the repertoire. Variable regions associated with the immune cell receptor are resolved to effectively portray clonal diversity of a biological sample and/or differences associated with the immune cell repertoire of a biological sample.

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Austin, TX, United States of America

Timothy Looney