A Superior Method for Designing Padlock Probes for Targeted Genomic Sequencing
Increased number of targetable genomic regions for padlock probe sequencing, More efficient and unbiased capture of genomic regions, and Reduced cost of sequencing to obtain target coverage.
Efficient padlock probe design for targeted high throughput genomic and epigenomic sequencing,SNP genotyping, mutation discovery, quantification of allele-specific gene expression, analysis of DNA methylation profiles, anddiagnosis, detection, and monitoring of the presence of any organism.
UCSD researchers have developed a method to generate efficient padlock probes, an automation-compatible library-free protocol that dramatically reduces sample preparation cost and time, and an efficient bioinformatics pipeline to accurately obtain both methylation levels and genotypes in a targeted high-throughput sequencing experiment. The method designs large numbers of highly effective, low-bias padlock probe molecules using a computational algorithm for probe efficiency prediction. This method is implemented in a software program that accepts as input a complete genome and a tabular list of specific regions of interest, along with several customizable probe properties (such as desired target length, desired binding arm length, and desired DNA melting temperature). It uses this information in a backpropagation neural network-derived equation to predict probe efficiency based on many probe characteristics. The software outputs the optimal set of probes to obtain maximum coverage of a desired set of genomic regions in a high-throughput sequencing experiment. It also adds a customized linker sequence to each probe molecule, allowing easy usage in modern high-throughput sequencers. The probe design software can additionally perform an in silico bisulfite conversion prior to probe design in order to generate an optimal set of probes for targeted bisulfite sequencing; both methylation levels and genotypes can then be simultaneously quantified. An additional feature allows the probe design software to output the most efficient padlock probe molecules for specific unique regions of a genome, allowing for efficient multiplex detection of organisms.
Inventor: ZHANG, Kun | GORE, Athurva
Priority Number: WO2012149171A1
IPC Current: C12Q000168 | C12N001500 | G01N003350
Assignee Applicant: The Regents of the University of California
Title: DESIGNING PADLOCK PROBES FOR TARGETED GENOMIC SEQUENCING | CONCEPTION DE SONDES CADENAS POUR EFFECTUER UN SÉQUENÇAGE GÉNOMIQUE CIBLÉ
Usefulness: DESIGNING PADLOCK PROBES FOR TARGETED GENOMIC SEQUENCING | CONCEPTION DE SONDES CADENAS POUR EFFECTUER UN SÉQUENÇAGE GÉNOMIQUE CIBLÉ
Summary: The method is useful for designing probes or primers for sequencing target nucleic acid molecule (claimed).
Novelty: Designing probes or primers for sequencing target nucleic acid molecule, comprises selecting inputs associated with efficiency of probe or primer, selecting target nucleic acid sequence, and generating library of probe or primer sequences
Biomedical
DNA/Gene Engineering
20140357497
State Of Development The software incorporating the invention method has been used to design a variety of genomic and epigenomic probes for Homo sapiens, Mus musculus and Drosophila melanogaster. Brief Description A sophisticated and robust algorithm, with intuitive web and user friendly interface, designs primers that work “out of the box” amid genomic complexity. Related Materials Tech ID/UC Case 22411/2011-310-0 Related Cases 2011-310-0
USA
