Compositions and methods for enriching populations of nucleic acids
Inventors
Blauwkamp, Timothy A. • Christians, Fred • Vilfan, Igor D. • Smith, Scott • Kertesz, Michael
Assignees
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Publication Number
US-12291739-B2
Publication Date
2025-05-06
Expiration Date
Abstract
This disclosure provides methods and compositions that are useful for enriching a particular population of nucleic acids (a “population of interest”) within a complex mixture of nucleic acids. The population of interest may make up a minor portion of a complex mixture of nucleic acids. The methods and compositions provided herein are useful for detecting, predicting, diagnosing, or monitoring a disease or disorder, particularly a disease or disorder caused by a foreign microbe or pathogen.
Core Innovation
The invention relates to enriching microbial cell-free nucleic acids from a plasma sample obtained from a mammalian host, where the plasma sample comprises cell-free nucleic acids that include mammalian host cell-free nucleic acids and microbial cell-free nucleic acids. The approach enriches the plasma sample for microbial cell-free nucleic acids by removing or physically isolating cell-free nucleic acids of one or more selected length ranges from the plasma sample.
In particular, the removing or physically isolating step enriches the plasma sample for microbial cell-free nucleic acids in length interval ranges of about 10 to about 60 base pairs, about 240 to about 280 base pairs, about 425 to about 475 base pairs, or any combination thereof. The document further describes related background depletion and enrichment strategies for cell-free samples, including self-hybridization, duplex-specific nuclease-based removal of abundant host nucleic acids, nucleosome depletion by anti-histone or nucleosome immunodepletion, and length-interval size selection to enrich non-host fragments.
The disclosed framework is extended to downstream use in sequencing workflows, including priming and capture of sequencing libraries and preferential amplification and sequencing of enriched non-host nucleic acids. The document also describes generating non-host or microbial oligonucleotide collections and using primer or bait pools for enriching pathogen nucleic acids from host background, including use of labeled probes, blocker oligonucleotides, and removal of host-bound probes.
Claims Coverage
The provided independent claim set contains 1 independent claim. It covers a method of enriching microbial cell-free nucleic acids from mammalian host plasma by length-interval removal or isolation, with specific enrichment size ranges and combinations.
Length-interval enrichment of microbial cell-free nucleic acids from mammalian plasma
A method comprising providing a plasma sample from a mammalian host comprising mammalian host cell-free nucleic acids and microbial cell-free nucleic acids, and removing or physically isolating cell-free nucleic acids of one or more length ranges from the plasma sample to enrich for microbial cell-free nucleic acids in length interval ranges of from about 10 to about 60 base pairs, from about 240 to about 280 base pairs, from about 425 to about 475 base pairs, or any combination thereof.
Claim coverage centers on length-interval removal or isolation applied to a mammalian plasma sample to enrich microbial cell-free nucleic acids in specified base-pair ranges, including optional combinations of the ranges.
Stated Advantages
Enriches the plasma sample for microbial cell-free nucleic acids in specified length interval ranges.
Documented Applications
Analyzing enriched microbial cell-free nucleic acids to generate sequence reads using next generation sequencing.
Detecting diverse pathogens from clinical samples by enriching microbial cell-free nucleic acids from host background.
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