Abstract: Methods are provided for analyzing one or more genetic samples, comprising procuring one or more genetic samples comprising genetic material from one or more individuals and sequencing the genetic material using non-targeted, ultra-low coverage sequencing to obtain genetic information for individual associated with the one or more genetic samples. Personal and genetic information associated with the individuals is stored in a database for retrieval and manipulation.
Type:
Grant
Filed:
August 10, 2017
Date of Patent:
September 21, 2021
Assignee:
NEW YORK GENOME CENTER
Inventors:
Joseph K. Pickrell, Tomaz Berisa, Suma Jaini, Brian Houck-Loomis, Kaja Wasik
Abstract: Described are methods comprises transducing a mammalian cell with one or more virus vectors. Each vector comprises a nucleic acid sequence encoding a Cpf1 (also known as Cas12a) protein and an optional selectable marker in operative association with an RNA pol II promoter which controls expression thereof; and a CRISPR RNA (crRNA) array comprising at least two spacers in operative association with an RNA pol III promoter. Each spacer encodes an RNA guide which hybridizes to a unique sequence located 3? from a T-rich protospacer-adjacent motif (PAM) in a genomic region of interest. The method further comprises culturing the transduced cells, thereby providing a plurality of cultured cell cultures, each cell culture comprising said deletion. Additionally, described are compositions used in methods as well as libraries generated by the methods. Such compositions comprise libraries of transduced cell cultures, viral vectors, nucleic acid sequences, CRISPR RNA spacers, and RNA guides, as described herein.
Type:
Application
Filed:
March 2, 2020
Publication date:
July 2, 2020
Applicants:
NEW YORK GENOME CENTER, INC., NEW YORK UNIVERSITY
Abstract: Embodiments disclosed herein provide methods, including computer-implemented methods, for designing guide sequence which may be incorporated into custom, large scale guide sequence libraries. The methods require only a list of target genes as input and utilize on target and off target scores to generate an optimal set of guide sequences for a set of target genes. In certain embodiments, the methods may also utilize multi-tissue RNA-sequencing data and/or protein annotation to design targets to genes that are highly expressed and/or contain a functional protein domain. The invention further comprises guide libraries, cells comprising said guide libraries. Computer-implemented embodiments further improve computer system function by reducing excessive user wait time through the use of data structures that reduce search from linear to logarithmic time.
Type:
Application
Filed:
July 6, 2018
Publication date:
June 25, 2020
Applicants:
THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE, THE NEW YORK GENOME CENTER, NEW YORK UNIVERSITY
Inventors:
Neville Sanjana, Feng Zhang, Joshua A. Meier