The Broad Institute, Inc.

Massachusetts Institute of Technology

Harvard College

Whitehead Institute for Biomedical Research

Dana-Farber-Cancer Institute Inc.

Other

University of Massachusetts

Baylor College of Medicine

The Brigham and Women's Hospital, Inc.

The United States of America, as Represented by the Secretary, Department of Health and Human Services

The General Hospital Corporation

Rutgers, the State University of New Jersey

University of California

Johns Hopkins University

University of Pittsburgh

Eric Lander

Feng Zhang

Omar O Abudayyeh

Jonathan S Gootenberg

James Joseph Collins

Todd R Golub

Erez Lieberman Aiden

Andreas Gnirke

Job Dekker

Georgia Giannoukos

Alexandre Melnikov

Nynke Van Berkum

Chad Nusbaum

Louise Williams

Florence Fevrier Wagner

Pablo Tamayo

Julia Joung

Anna Greka

Brian T Chamberlain

Maria Alimova

Joseph Growney

Jill P Mesirov

Donna K Slonim

James S Ireland

Moran Dvela-Levitt

Valeria Padovano

Olga Dudchenko

Aviv Regev

Silvana Konermann

Le Cong

George Q Daley

Mitchell Guttman

Konstantin Severinov

Eugene Koonin

Sergey Shmakov

Yuri I Wolf

Kira S Makarova

Ekaterina Semenova

Pamela Sklar

Joel N Hirschhorn

Leonid Minakhin

Suhas Rao

Elena Stamenova

Melvin G McInnis

J Raymond DePaulo, Jr

Michele Cargill

Stacey Bolk

Alexander A Shishkin

Christine F Surka

Erez Lieberman

David Sabatini

Alexander K Shalek

Levi A Garraway

Deborah Hung

Orit Rozenblatt-Rosen

Jennifer Rubin Grandis

Jonathan S Weissman

Jellert Gaublomme

Thomas W Norman

Thomas J Hudson

Roby Bhattacharyya

Jesse Engreitz

Brian Cleary

Atray Dixit

Mark Daly

Kathy Siminovitch

John Rioux

Oren Parnas

Aaron D Tward

Jane E Staunton

Hilary A Coller

Virginia Willour

Brittany Adamson

James Potash

Jeanette J McCarthy

Steven G Rozen

David De Graaf

Angela Early

Daniel Neafsey

David M Altshuler

Neva Durand

Aviva Aiden

Arina Omer

Tim Wang

Su-Chen Huang

Sanjit Singh Batra

Erez Lieberman-Aiden

Adrian L Sanborn

Sarah Nyquist

Anthony Tzen

Maxim Massenkoff

Melanie Pham

Per Aspera Adastra

Neva C Durand

Christopher Lui

Miriam Huntley

Andrew Jewett

Ann Marie Egloff

Nicholas Stransky

Embodiments provide a method for sequencing and assembling long DNA genomes comprising generating a 3D contact map of chromatin loop structures in a target genome, the 3D contact map of chromatin loop structures defining spatial proximity relationships between genomic loci in the genome, and deriving a linear genomic nucleic acid sequence from the 3D map of chromatin loop structures.

Linear genome assembly from three dimensional genome structure

The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.

HiC: method of identifying regulatory interactions between genomic loci

The present disclosure relates to compositions and methods for the diagnosis and treatment or prevention of proteinopathies, particularly MUC1-associated kidney disease (ADTKD-MUC1 or MKD), Retinitis Pigmentosa (e.g., due to rhodopsin mutations), autosomal dominant tubulo-interstitial kidney disease due to UMOD mutation(s) (ADTKD-UMOD), and other forms of toxic proteinopathies resulting from mutant protein accumulation in the ER or other secretory pathway compartments and/or vesicles, among others. The disclosure also identifies and provides TMED9-binding agents as capable of treating or preventing proteinopathies of the secretory pathway, and further provides methods for identifying additional TMED9-binding agents.

Agents for reversing toxic proteinopathies

Provided herein includes a method for generating an error-corrected genome assembly for an organism comprising: generating a genomic contact map derived from a DNA proximity ligation assay conducted on one or more samples from the organism or a closely related species; superimposing a reference assembled genome derived from whole genome sequencing of one or more samples from the organism on top of the genomic contact map using computer software; correcting errors in the reference assembled genome through a computer user interface to obtain a corrected assembly file, wherein errors in the reference assembled genome are visualized by observing aberrant contacts in the genomic contact map; and applying the corrected assembly file to the reference assembled genome.

The embodiments disclosed herein utilized RNA targeting effectors to provide a robust CRISPR-based diagnostic with attomolar sensitivity. Embodiments disclosed herein can detect broth DNA and RNA with comparable levels of sensitivity and can differentiate targets from non-targets based on single base pair differences. Moreover, the embodiments disclosed herein can be prepared in freeze-dried format for convenient distribution and point-of-care (POC) applications. Such embodiments are useful in multiple scenarios in human health including, for example, viral detection, bacterial strain typing, sensitive genotyping, and detection of disease-associated cell free DNA.

CRISPR effector system based diagnostics for malaria detection

The disclosed invention is related to a universal strand-specific protocol for the sequencing preparation of all classes of RNA. The protocol allows for sequencing for dozens to more than thousands of samples simultaneously. Specifically, the disclosed invention is a method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification. The method includes providing samples of RNA comprising target RNA from two or more sources; labeling, at the 3' end, the RNA from the two or more sources with a first nucleic acid adaptor that comprises a nucleic acid sequence that differentiates between the RNA from the two or more sources; reverse transcribing the two or more sources to create a single stranded DNA comprising the nucleic acid sequence that differentiates between the RNA from the two or more sources; amplifying the single stranded DNA to create DNA amplification products that comprise the nucleic acid sequence that differentiates between the RNA from the two or more sources; sequencing the DNA amplification products thereby parallel sequencing target RNA from samples from multiple sources while maintaining source identification.

Massively multiplexed RNA sequencing

The application relates to methods for compositions for identifying lncRNA loci associated with target genotypes or phenotypes, including desirable plant genotypes or phenotype. The application also relates to regulatory regions and genes associated with drug resistance, such as resistance to BRAF-inhibitors. Such regulatory regions and genes form the basis for methods for identifying resistance to BRAF-inhibitors, which is useful for improving disease prognosis, treatment, and likely outcomes. The regulatory regions and genes are also suitable targets for therapy in melanoma that is resistant to BRAF-inhibitors.

Methods for identification and modification of lncRNA associated with target genotypes and phenotypes

The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

CRISPR enzymes and systems

Disclosed is an in situ method for detecting spatial proximity relationships between nucleic acid sequences, such as DNA, in a cell. The method includes: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells that leaves 5' overhanging ends; filling in the overhanging ends with at least one labeled nucleotide; joining the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having a junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; and determining the sequence at the junction of the one or more end joined nucleic acid fragments.

Method for in situ determination of nucleic acid proximity

The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Assays for massively combinatorial perturbation profiling and cellular circuit reconstruction

Chromatin 3D structure modulating agents in the context of the present invention are intended to interfere or manipulate the function of loop anchor motifs, such as CTCF motifs. In certain example embodiments, the present invention may block formation of an loop anchor or chromatin domain or induce formation of a loop anchor or chromatin domain at a targeted genomic location. For instance, a loop anchor motif can be altered, such as by mutating (including inverting) a binding motif so as to remove such a motif, or by adding new binding motifs in new locations within a loop domain, so as to reduce the size of an existing loop, so as to modify the size of an existing loop, or combinations thereof. Alternatively, the chromatin 3D structure modulating agent may bind a target region and mask a loop anchor motif, thereby preventing a loop anchor or chromatin domain from forming. The chromatin 3D structure modulating agent may bind a target region and cause a loop anchor of chromatin domain to form.

Methods and compositions for altering function and structure of chromatin loops and/or domains

The embodiments disclosed herein utilized RNA targeting effectors to provide a robust CRISPR-based diagnostic with attomolar sensitivity. Embodiments disclosed herein can detect both DNA and RNA with comparable levels of sensitivity and can differentiate targets from non-targets based on single base pair differences. Moreover, the embodiments disclosed herein can be prepared in freeze-dried format for convenient distribution and point-of-care (POC) applications. Such embodiments are useful in multiple scenarios in human health including, for example, viral detection, bacterial strain typing, sensitive genotyping, and detection of disease-associated cell free DNA.

CRISPR effector system based diagnostics

The present invention generally relates to libraries, kits, methods, applications and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof. The present invention also relates to rules for making potent single guide RNAs (sgRNAs) for use in CRISPR-Cas systems. Provided are genomic libraries and genome wide libraries, kits, methods of knocking out in parallel every gene in the genome, methods of selecting individual cell knock outs that survive under a selective pressure, methods of identifying the genetic basis of one or more medical symptoms exhibited by a patient, and methods for designing a genome-scale sgRNA library.

Functional genomics using CRISPR-Cas systems, compositions, methods, screens and applications thereof

Growing community of inventors

Cambridge, MA, United States of America

Eric Lander