SYSTEM AND PROCESS FOR DATA-DRIVEN DESIGN, SYNTHESIS, AND APPLICATION OF MOLECULAR PROBES

• Main Authors: Qadir, Mohammad, Zhan, Shing H, Kwok, Brian S
• Format: Patent
• Language: English; French; German
• Published: 25.12.2019
• Subjects: BEER; BIOCHEMISTRY; CHEMISTRY; COMBINATORIAL CHEMISTRY; COMPOSITIONS OR TEST PAPERS THEREFOR; COMPOSITIONS THEREOF; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES; CULTURE MEDIA; DERIVATIVES THEREOF; ENZYMOLOGY; INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICOLIBRARIES; MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS; METALLURGY; MICROBIOLOGY; MICROORGANISMS OR ENZYMES; MUTATION OR GENETIC ENGINEERING; NUCLEIC ACIDS; NUCLEOSIDES; NUCLEOTIDES; ORGANIC CHEMISTRY; PHYSICS; PROCESSES OF PREPARING SUCH COMPOSITIONS; PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS; SPIRITS; SUGARS; VINEGAR; WINE

The disclosure provides methods and systems for designing and synthesizing probes to capture a representative sample of genomic variants of a target genome from a sample. The methods include providing a multiple sequence alignment (MSA), designing a plurality of representative subsequences, and optionally synthesizing a nucleic acid probe. The designing step can comprise designating a plurality of intervals in the MSA, shifting start positions for each MSA subset, clustering the aligned subsequences within each adjusted subset, and determining a representative sequence for each reduced MSA subset. The disclosure also encompasses methods of isolating a plurality of nucleic acid variants of a targeted genomic subregion from a sample using the disclosed probe design, as well as the probe compositions themselves.