AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

Kathleen C Keough; Svetlana Lyalina; Michael P Olvera; Sean Whalen; Bruce R Conklin; Katherine S Pollard

doi:10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

Genome Biol. 2019 Aug 15;20(1):167. doi: 10.1186/s13059-019-1783-3.

Authors

Kathleen C Keough^{1

2}, Svetlana Lyalina^{2

3}, Michael P Olvera², Sean Whalen², Bruce R Conklin^{4

5}, Katherine S Pollard^{6

7

8}

Affiliations

¹ Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA.
² Gladstone Institutes, San Francisco, CA, USA.
³ Bioinformatics Graduate Program, University of California, San Francisco, CA, USA.
⁴ Gladstone Institutes, San Francisco, CA, USA. bconklin@gladstone.ucsf.edu.
⁵ Departments of Biostatistics, Medicine, Ophthalmology and Pharmacology, University of California, San Francisco, CA, USA. bconklin@gladstone.ucsf.edu.
⁶ Gladstone Institutes, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu.
⁷ Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu.
⁸ Chan Zuckerberg Biohub, San Francisco, California, USA. katherine.pollard@gladstone.ucsf.edu.

Abstract

The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is an open-source software that incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing 1 or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer .

Keywords: CRISPR; Computational biology; Genome editing; Genome surgery; Genomics; sgRNA design.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Alleles*
Base Sequence
CRISPR-Associated Proteins / metabolism
Humans
Polymorphism, Genetic
RNA, Guide, CRISPR-Cas Systems / genetics*
Software*

Substances

CRISPR-Associated Proteins
RNA, Guide, CRISPR-Cas Systems

Abstract

Publication types

MeSH terms

Substances

Grants and funding