Methods and means for identification of gene features
OwnerPeter Lonnerberg, Mats Oldin +2inventors
InventorsPeter Lonnerberg, Mats Oldin, Sten Linnarsson, Patrik Ernfors
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Abstract
Identification of gene variants, and in particular identification of differences between sequence variants that occur in a population of nucleic acid molecules, especially identification or discovery of polyA site usage, or determination of polyA site usage in a nucleic acid sample, and gene variants arising from alternative polyA sites.
Claims35
A method for determining the presence of and/or identifying a polyadenylation site or alternative polyadenylation sites within a sequence of a transcribed gene or sequences of transcribed gene variants present or potentially present in a sample, the method comprising:
- (a) generating a dataset comprising a set of signals obtained for individual gene fragments within a population of gene fragments produced from transcribed genes in the sample, wherein the signal for an individual gene fragment comprises a combination of length and partial sequence information and a magnitude component for that gene fragment, wherein the dataset contains a magnitude component of zero for combinations of length and partial sequence information determined not to be present in the population and the magnitude component of the signal for gene fragments for which the combination of length and partial sequence information is determined to be present is either qualitative to indicate presence in the population of a gene fragment with that combination or quantitative to provide an indication of the amount of individual gene fragments present in the population;
- and
- (b) assigning to gene fragments one or more gene candidates within a database by comparing signals within the dataset with the database, the database comprising data representing mRNA's with known polyA sites and/or “virtual genes”, wherein virtual genes are defined as each representing a possible polyadenylation site within an actual gene,
- (c) eliminating from results gene candidates which are each assigned to at least one signal of magnitude zero,
- (d) thereby obtaining results defining a set of one or more genes or gene variants each being a mRNA with a known polyadenylation site and/or virtual gene assigned to a signal with non-zero magnitude in the dataset, which results provide indication of actual presence of said set of one or more genes or gene variants in said sample.
A method according to any one of the preceding claims wherein signals in the dataset are compared with a database of signals determined or predicted for mRNA's with known polyA sites and/or said virtual genes, by:
- (i) listing all mRNA's with known polyA sites and/or virtual genes in the database which may correspond to a gene fragment in each of said first and second and optionally third or further populations, forming a list of mRNA's with known polyA sites and/or virtual genes possibly present for each population, and
- (ii) listing mRNA's with known polyA sites and/or virtual genes which definitely do not correspond to a gene fragment, forming a list of mRNA's with known polyA sites and/or virtual genes definitely not present for each population, then
- (iii) removing the mRNA's with known polyA sites and/or virtual genes definitely not present from the list of mRNA's with known polyA sites and/or virtual genes possibly present for each population, and
- (iv) generating a list of mRNA's with known polyA sites and/or virtual genes possibly present and mRNA molecules definitely not present by combining each list generated for each population in (iii);
- thereby identifying one or more mRNA's with known polyA sites and/or virtual genes as corresponding to mRNA actually present in the sample.
Dependencies are inferred from the claim text.