Analysis methods
View Patent ↗The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.
1. A method for identifying a novel mutation associated with a disease, the method comprising:
obtaining nucleic acid from a subject having a disease;
sequencing the nucleic acid to obtain a sequence of the nucleic acid; and
using a computer system comprising a processor coupled to a memory for:
comparing the sequence of the nucleic acid from the subject to a reference sequence, thereby determining the presence of at least one spatially ambiguous mutation in the nucleic acid;
comparing the spatially ambiguous mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations;
calculating an equivalent insertion/deletion region for the spatially ambiguous mutation;
annotating the spatially ambiguous mutation with functional information;
retrieving an extreme lower position and an extreme upper position of the equivalent insertion/deletion region for the spatially ambiguous mutation; and
choosing one of the extreme lower position and the extreme upper position of the equivalent insertion/deletion region for the spatially ambiguous mutation that is outside of a functional region, wherein said spatially ambiguous mutation is not causative of the disease.
2. The method according to claim 1 , wherein sequencing is sequencing-by-synthesis.
3. The method according to claim 2 , wherein sequencing-by-synthesis is single molecule sequencing-by-synthesis.
4. The method according to claim 1 , wherein the reference sequence is a consensus human sequence or a sequence from a non-diseased sample.
5. The method according to claim 1 , wherein prior to determining the presence of the at least one spatially ambiguous mutation in the nucleic acid, the method further comprises attaching a barcode sequence to the nucleic acid.
6. The method according to claim 1 , wherein the disease is cystic fibrosis.
7. The method according to claim 6 , wherein the subject is Hispanic.
8. A method for identifying a novel mutation associated with a disease, the method comprising:
obtaining nucleic acid from a subject having a disease;
sequencing the nucleic acid;
comparing, using a computer system comprising a processor coupled to a memory, the sequence of the nucleic acid from the subject to a reference sequence, thereby determining the presence of a spatially ambiguous mutation in the nucleic acid; and
comparing, using the computer system, the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations;
identifying, using the computer system, a contiguous block of DNA in the reference sequence representing a tandem repeat associated with the spatially ambiguous mutation;
annotating, using the computer system, the spatially ambiguous mutation with functional information;
retrieving, using the computer system, an extreme lower position and an extreme upper position of the contiguous block of DNA in the reference sequence for the spatially ambiguous mutation; and
choosing, using the computer system, one of the lower position and the upper position of the equivalent insertion/deletion region for the spatially ambiguous mutation that is outside of a functional region, wherein said spatially ambiguous mutation is not causative of the disease.
9. The method according to claim 8 , wherein sequencing is sequencing-by-synthesis.
10. The method according to claim 9 , wherein sequencing-by-synthesis is single molecule sequencing-by-synthesis.
11. The method according to claim 8 , wherein the reference sequence is a consensus human sequence or a sequence from a non-diseased sample.
12. The method according to claim 8 , wherein prior to sequencing, the method further comprises attaching a barcode sequence to the nucleic acid.
13. The method according to claim 8 , wherein the disease is cystic fibrosis.
14. The method according to claim 8 , wherein the subject is Hispanic.
15. A method for determining if a mutation is causative of a disease, the method comprising:
conducting an assay to obtain a nucleic acid sequence from a subject having a disease; and using a computer system comprising a memory coupled to a processor for:
determining the presence of a spatially ambiguous novel mutation in the sequence;
calculating an equivalent insertion/deletion region for the spatially ambiguous mutation;
annotating the mutation with appropriate functional information;
retrieving an extreme lower position and an extreme upper position of the equivalent insertion/deletion region for the mutation; and
choosing one of the extreme lower position and the extreme upper position for the spatially ambiguous mutation that is outside of a functional region, wherein said spatially ambiguous mutation is not causative of the disease.