Fusion transcript detection methods and fusion transcripts identified thereby
AssigneeSplicingcodes.Com
InventorsDegen ZHUO, Xiaoyan YANG
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Abstract
This present disclosure generally relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure provides a computerized method for detecting fusion transcripts from RNA-seq data and provides the fusion transcripts identified thereby in human cancers. Compositions and methods for identifying the fusion transcripts are also provided.
Claims21
A method of detecting alternatively spliced transcripts or fusion transcripts in at least one RNA sequence obtained from biochemical analysis of a biological sample from a species or from a database, comprising the steps of:
- (a) providing a computer for data identification, aligning, and comparison purposes, wherein the computer has access to predetermined genome data of said species, comprising data of predetermined genomic nucleotide sequences, predetermined splicing junctions, predetermined exons, predetermined introns, and annotated genes;
- (b) generating a splicing code table using the predetermined genome data, the splicing code table comprising ordered E5 keys, I5 keys, E3 keys and I3 keys, wherein the E5 keys, the I5 keys, the E3 keys and the I3 keys are subsequences of predetermined 5′ exonic (E5), 5′ intronic (I5), 3′ exonic (E3), and 3′ intronic (I3) splicing sequences for each of the predetermined splicing junctions respectively;
- (c) aligning the at least one RNA sequence with each of the E5 keys and each of the E3 keys in the splicing code table;
- and
- (d) determining that the at least one RNA sequence is an alternatively spliced transcriptif:
- the at least one RNA sequence contains a first subsequence substantially identical to an E5 key of a first splicing junction and a second subsequence substantially identical to an E3 key of a second splicing junction of the same gene;
- or
- the at least RNA sequence contains a subsequence substantially identical to an E5 key of an annotated gene, but an immediate downstream sequence of said subsequence is mapped to an intron region of the same annotated gene;
- or
- the at least one RNA sequence contains a subsequence substantially identical to an E3 key of a splicing junction, but an immediate upstream sequence of said subsequence is mapped to an intron region of the same annotated gene;
- or determining that the at least one RNA sequence is a fusion transcriptif:
- the at least one RNA sequence contains a subsequence substantially identical to an E5 key of a first annotated gene, and an immediate downstream sequence of said subsequence is substantially identical to an E3 key of a second annotated gene;
- or
- the at least RNA sequence contains a subsequence substantially identical to an E5 key of a first annotated gene, and an immediate downstream sequence of said subsequence is mapped to a second annotated gene;
- or
- the at least one RNA sequence contains a subsequence substantially identical to an E3 key of a first annotated gene, and an immediate upstream sequence of said subsequence is mapped to a second annotated gene.
A method of characterizing at least one RNA sequence read in a transcriptome dataset, obtained from a transcriptome sequencing of a biological sample, for fusion transcripts, the method comprising the steps of:
- (a) providing a computer for data identification, aligning, comparison and computation purposes, wherein:
- the computer has access to the transcriptome dataset, the transcriptome dataset comprising data of genome-wide RNA sequence reads and counts thereof and;
- and
- the computer has access to a predetermined fusion transcript table, the predetermined fusion transcript table comprising data of predetermined E5-E3 keys, wherein:
- each of the predetermined E5-E3 keys corresponds to junction sequence of a predetermined fusion transcript, comprising an E5 key and an E3 key, wherein:
- the E5 key corresponds to a 5′-end subsequence of the predetermined fusion transcript and is mapped to a first annotated gene;
- the E3 key corresponds to a 3′-end subsequence of the predetermined fusion transcript and is mapped to a second annotated gene;
- and
- the E5 key and the E3 key is connected at a junction of the predetermined fusion transcript;
- (b) aligning the at least one RNA sequence read with each of the E5-E3 keys in the predetermined fusion transcript table;
- (c) determining that the at least one RNA sequence read is mapped to a predetermined fusion transcript if the at least one RNA sequence read contains a subsequence substantially identical to an E5-E3 key in the predetermined fusion transcript table.
A set of isolated, cloned recombinant or synthetic polynucleotides, comprising at least one polynucleotide, wherein:
- each of the at least one polynucleotide encodes a fusion transcript, the fusion transcript comprising a 5′ portion from a first gene and a 3′ portion from a second gene, wherein:
- the 5′ portion from the first gene and the 3′ portion from the second gene is connected at a junction;
- the junction has a flanking sequence, comprising a sequence selected from the group of nucleotide sequences as set forth in SEQ ID NOs:
- 1-258,853, or from complementary sequences thereof.
Dependencies are inferred from the claim text.