Methods of identifying genetic variants
AssigneesThe University of Sydney, The Sydney Children's Hospitals Network (Randwick and Westmead)
InventorsSandra Cooper, Himanshu Joshi
Life of this patent
Estimating the term…
Abstract
The present invention relates to identification of an abnormal splice site. Provided are methods of identifying an abnormal splice site. Methods of classifying the risk of abnormal splicing of a splice site are also provided. Databases for use in the methods provided herein are also disclosed.
Claims26
A method of identifying an abnormal splice site in a sample splice site from a subject, said method comprising
- (a) obtaining a first sample splice site sequence comprised in the sample splice site from the subject;
- and
- (b) determining the frequency at which the sequence occurs in a reference genome, expressed as a Native Intron Frequency of the first sample splice site sequence (NIFvar-1);
- wherein a NIFvar-1 of 0 (zero) indicates that the sample splice site is abnormal.
7-9. (canceled)
A method of identifying an abnormal splice site in a sample splice site from a subject, said method comprising:
- (a) obtaining a first sample splice site sequence comprised in the sample splice from the subject;
- (b) determining a measure of Native Intron Frequency of the first pc splice site sequence (NIFvar-1);
- (c) determining a Percentile (NIFvar 1) of the first sample splice site sequence and determining a Percentile (NIFref 1) of the first reference splice site sequence;
- (d) determining a measure of Native Intron Frequency of a first reference splice site sequence (NIFref-1);
- wherein the first reference splice site sequence and the first sample splice site sequence originate from the same corresponding region of a gene;
- (e) calculating a lower bound and an upper bound for Percentile (NIFvar-1) and calculating a lower bound and an upper bound for Percentile (NIFref-1);
- (f) determining a range of NIF-shift by comparing the lower and upper bounds for NIFvar-1 with the lower and upper bounds for NIFref-1 calculated in (e);
- (f) identifying unique variant(s) in the CSP database that create the identical nucleotide sequence of one or more sample splice sites from the subject (var-x):
- wherein the identical sample splice sites identified in other subjects in the CSP database localise to a different splice site at a different exon-intron junction to the sample splice site in the test subject;
- (g) repeating steps (b-f) to calculate the NIF-shift for all non-identical, consecutive nucleotide sequences of the sample splice site in the CSP database identified in (f)
- (h) determining a clinical classification associated with each identical var-x nucleotide sequence in the sample splice site identified in the CSP database in (g);
- (i) determining the risk of abnormal splicing or likelihood of maintaining splicing for the sample splice site in the subject by assessing the clinical classification determined in step (h) of each identical var-x nucleotide sequence in a sample splice site in the CSP database.
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32-45. (canceled)
A method of providing a risk of abnormal splicing of a sample splice site from a subject, said method comprising:
- obtaining a first sample splice site sequence comprised in the sample splice site froth the subject;
- generating a first abnormal splicing factor based on a measure of Native Intron Frequency (NIF) of the sample splice site (NIFvar-1) and a measure of NIF of a first reference splice site (NIFref-1);
- generating a second abnormal splicing factor by comparing the sample splice site sequence to pre-classified data wherein the pre-classified data includes splice site sequences which have been classified as an abnormal splice site or a benign variant splice site;
- generating a third abnormal splicing factor based on pre-classified splice site sequences having a similar NIFvaf-1 and a similar corresponding NIFref-1;
- and
- generating a risk of abnormal splicing of the sample splice site by evaluating the first, second, and third abnormal splice factors.
-55. (canceled)
Dependencies are inferred from the claim text.