Cross-species nucleic acid probes
OwnerJyh-Lyh Juang, Chao Agnes Hsiung +1inventors
InventorsJyh-Lyh Juang, Chao Agnes Hsiung, Chung-Yen Lin
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Abstract
The present invention features a collection of at least four nucleic acid probes. The probes each comprises a segment, the entirety of which hybridizes under low stringency conditions to at least a first gene of a first species and a second gene of a second species, wherein the hybridizing probes correspond to different genes of the first or second species, and the first and the second genes are orthologous to each other. In some embodiments, the entirety of the segment is at least 60% (e.g., 65%, 70%, 80%, 90%, or 95%) identical to the first gene and the second gene.
Claims40
A collection comprising at least four nucleic acid probes, the probes each including a segment, the entirety of which hybridizes under low stringency conditions to at least a first gene of a first species and a second gene of a second species, wherein the hybridizing probes correspond to different genes of the first or second species, and the first and the second genes are orthologous to each other.
A method for producing a collection of probes, the method comprising:
- for each of a plurality of genes of a first species, identifying a segment that is conserved relative to an orthologous gene from a second species;
- selecting a sequence from the orthologous gene that is at least 60% identical to the conserved segment, and
- preparing a probe having the selected sequence or a reverse complement of the selected sequence, thereby producing a collection of probes.
A method for evaluating a sample, the method comprising:
- contacting a sample that comprises nucleic acids from a third species to a collection of nucleic acid probes, wherein (i) each probe comprises a segment, the entirety of which hybridizes under low stringency conditions to at least a first gene of a first species and a second gene of a second species, wherein the hybridizing probes correspond to different genes of the first or second species, and the first and the second genes are orthologous to each other, and (ii) the third species differs from both the first and the second species;
- evaluating binding of the sample to each of the probes;
- and
- for each probe that is bound, inferring the presence, in the sample, of a nucleic acid for a third gene of the third species, the third gene being an ortholog of the first and second gene.
A substrate comprising a plurality of addresses, each address comprising a nucleic acid probe, each probe comprising a segment, the entirety of which hybridizes under low stringency conditions to at least a first gene of a first species and a second gene of a second species, wherein the hybridizing probes correspond to different genes of the first or second species, and the first and the second genes are orthologous to each other.
A collection comprising at least four nucleic acid probes, the probes each including a segment, the entirety of which hybridizes under low stringency conditions to at least a first gene of a first sub-species and a second gene of a second sub-species, wherein the hybridizing probes correspond to different genes of the first or second sub-species, and the first and the second genes are orthologous to each other.
Dependencies are inferred from the claim text.