Baylor College of Medicine

The Broad Institute, Inc.

Olga Dudchenko

Eric Lander

Erez Lieberman Aiden

Elena Stamenova

Suhas Rao

Arina Omer

Maxim Massenkoff

Sanjit Singh Batra

Sarah Nyquist

Neva Durand

Anthony Tzen

Melanie Pham

Erez Lieberman-Aiden

Per Aspera Adastra

Aviva Aiden

Christopher Lui

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

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.

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

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Houston, TX, United States of America

Olga Dudchenko