The present invention relates to a high-throughput method of screening splicing variants of target genes as drug targets or for characterisation of their biological functions. The disclosure provides a method for the screening of splicing variants, comprising: (a) providing a first antisense oligonucleotide capable of inducing a first splice event on the target gene to express a first splicing variant, and a second antisense oligonucleotide capable of inducing a second splice event on the target gene to express a second splicing variant; (b) hybridising the first and second antisense oligonucleotides to a pre-mRNA of the target gene; and (c) characterising the effect of the splice event. In one embodiment, the first antisense oligonucleotide switches the splice event that expresses the second splicing variant towards one that expresses the first splicing variant, while the second antisense oligonucleotide switches the splice event that expresses the first splicing variant towards one that expresses the second splicing variant.

The present invention relates to a high-throughput method of screening splicing variants of target genes as drug targets or for characterisation of their biological functions. The disclosure provides a method for the screening of splicing variants, comprising: (a) providing a first antisense oligonucleotide capable of inducing a first splice event on the target gene to express a first splicing variant, and a second antisense oligonucleotide capable of inducing a second splice event on the target gene to express a second splicing variant; (b) hybridising the first and second antisense oligonucleotides to a pre-mRNA of the target gene; and (c) characterising the effect of the splice event. In one embodiment, the first antisense oligonucleotide switches the splice event that expresses the second splicing variant towards one that expresses the first splicing variant, while the second antisense oligonucleotide switches the splice event that expresses the first splicing variant towards one that expresses the second splicing variant.

Described herein are methods and kits for detecting the presence or absence of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5 portion of a target gene relative to the 3 region of the target gene. The average expression of the 5 portion of the target gene is compared with the average expression of the 3 portion of the target gene to determine an intragenic differential expression (IDE). The IDE can then be used to determine if a dysregulation or a particular disease (or susceptibility to a disease) is present or absent in a subject or sample.

Described herein are methods and kits for detecting the presence or absence of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5 portion of a target gene relative to the 3 region of the target gene. The average expression of the 5 portion of the target gene is compared with the average expression of the 3 portion of the target gene to determine an intragenic differential expression (IDE). The IDE can then be used to determine if a dysregulation or a particular disease (or susceptibility to a disease) is present or absent in a subject or sample.

The present invention discloses a method for non-invasively detecting EGFR gene mutations in subjects, comprising the following steps: designing primers according to EGFR gene exons; extracting plasma DNAs in subjects; connecting the extracted plasma DNAs with tagging linkers; PCR pre-amplifying the tagging linkers connected plasma DNAs; cyclising the pre-amplified DNAs to obtain cyclised DNAs; PCR amplifying the cyclised DNAs using the designed primers; and high throughput sequencing the PCR amplified product and analyzing the EGFR gene mutations. The present invention also discloses a corresponding kit.

The present invention discloses a method for non-invasively detecting EGFR gene mutations in subjects, comprising the following steps: designing primers according to EGFR gene exons; extracting plasma DNAs in subjects; connecting the extracted plasma DNAs with tagging linkers; PCR pre-amplifying the tagging linkers connected plasma DNAs; cyclising the pre-amplified DNAs to obtain cyclised DNAs; PCR amplifying the cyclised DNAs using the designed primers; and high throughput sequencing the PCR amplified product and analyzing the EGFR gene mutations. The present invention also discloses a corresponding kit.

The present disclosure provides a computer-implemented method for determining a set of preferences, comprising: for an unspliced sequence of the one or more unspliced sequences, identifying (i) an anchor splice site comprising a location in the unspliced sequence, and (ii) a plurality of candidate complementary splice sites (n) corresponding to the anchor splice site, wherein each of the plurality of candidate complementary splice sites comprises a location in the unspliced sequence. A splice site feature vector for each of the plurality of candidate complementary splice sites and the anchor splice site may be calculated. Each of the splice site feature vectors may comprise one or more features determined based at least in part on one or more nucleotides in the unspliced sequence. A set of preferences p.sub.1, p.sub.2, . . . , p.sub.n corresponding to each of the plurality of candidate complementary splice sites may be calculated and outputted using the splice site feature vectors.

The present disclosure provides a computer-implemented method for determining a set of preferences, comprising: for an unspliced sequence of the one or more unspliced sequences, identifying (i) an anchor splice site comprising a location in the unspliced sequence, and (ii) a plurality of candidate complementary splice sites (n) corresponding to the anchor splice site, wherein each of the plurality of candidate complementary splice sites comprises a location in the unspliced sequence. A splice site feature vector for each of the plurality of candidate complementary splice sites and the anchor splice site may be calculated. Each of the splice site feature vectors may comprise one or more features determined based at least in part on one or more nucleotides in the unspliced sequence. A set of preferences p.sub.1, p.sub.2, . . . , p.sub.n corresponding to each of the plurality of candidate complementary splice sites may be calculated and outputted using the splice site feature vectors.

Embodiments of the invention provide methods of creating clinical models for different forms of metastatic cancer. The methods may include obtaining samples from subjects with metastatic cancer, determining an allelic status of one or more markers in the samples (e.g., creating a molecular profile of the subject's cancer), and using model organisms with subject-derived xenografts for treatment selection.

Embodiments of the invention provide methods of creating clinical models for different forms of metastatic cancer. The methods may include obtaining samples from subjects with metastatic cancer, determining an allelic status of one or more markers in the samples (e.g., creating a molecular profile of the subject's cancer), and using model organisms with subject-derived xenografts for treatment selection.