Harvard College

Readcoor, LLC

Other

Richard C Terry

George M Church

Evan R Daugharthy

Je-Hyuk Lee

Frederic Vigneault

Benjamin W Pruitt

Francois Vigneault

Jehyuk Lee

Sriram Kosuri

Michele A Busby

Brian M Turczyk

Di Zhang

François Vigneault

Methods of selectively sequencing amplicons in a biological sample are provided.

Method of selectively sequencing amplicons in a biological sample

The present disclosure provides methods and systems for analyzing a biological sample from a subject, comprising using probes to identify and determine the location of different genetic sequences.

Methods and systems for spatial mapping of genetic variants

The present disclosure provides methods and systems for generating and using indices in a synthetic three-dimensional (3D) matrix within a biological sample (e.g., a cell or a tissue sample). The present disclosure provides a method for processing or analyzing a nucleic acid molecule having a three-dimensional (3D) spatial position in a cell or cell derivative can comprise: (a) using a transposase to insert a nucleic acid index sequence into the nucleic acid molecule to generate an indexed nucleic acid molecule comprising the nucleic acid index sequence; (b) detecting the nucleic acid index sequence of the indexed nucleic acid molecule to identify the 3D spatial position; (c) subsequent to (b), removing the indexed nucleic acid molecule or derivative thereof from the 3D spatial position; and (d) identifying a sequence of the indexed nucleic acid molecule or derivative thereof removed from the 3D spatial position in (c).

Three-dimensional spatial molecular indexing

Methods of volumetric imaging of a three-dimensional matrix of nucleic acids within a cell is provided. An automated apparatus for sequencing and volumetric imaging of a three-dimensional matrix of nucleic acids is provided.

Method and apparatus for volumetric imaging

A method of sequencing nucleic acids is provided using DNA origami as a barcode for a nucleic acid probe.

Spatial sequencing of nucleic acids using DNA origami probes

The present disclosure provides methods that combine RNA fluorescent in situ sequencing (FISSEQ) with other molecular detection modalities, forming an integrated panomic detection platform. In various embodiments, the present disclosure provides systems and methods to prepare a biological sample to preserve the spatial relationships of biomolecules of interest within the biological sample for FISSEQ detection.

Methods of combining the detection of biomolecules into a single assay using fluorescent in situ sequencing

A method of sequencing nucleic acids is provided using sequencing by ligation and/or sequencing by hybridization.

Sequencing by structure assembly

Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Method for generating a three-dimensional nucleic acid containing matrix

The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

Methods and systems for sample processing or analysis

Method and apparatus for volumetric imaging of a three-dimensional nucleic acid containing matrix

Compositions and methods for analyte detection

The present disclosure provides a number of targeted nucleic acid FISSEQ library construction methods. Targeted FISSEQ can exhibit several benefits, such as enhanced sensitivity and/or shorter assay time in the detection, identification, quantification, and/or determining the nucleotide sequence of the target species, relative to 'random' or 'whole-omic' detection via FISSEQ.

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Carlisle, MA, United States of America

Richard C Terry