Patent ID: 8460866

Claim:
A method for the high throughput detection of a plurality of target nucleotide sequences in one or more samples, comprising the steps of: (a) providing for the plurality of target nucleotide sequences, a set of first probes and a set of second probes, wherein the probes in the set of first probes comprises a target specific section at its 3′ end and a first tag section that is non-complementary to the target nucleotide sequence and comprises a first primer binding sequence, wherein the probes in the set of second probes comprises a second target specific section at its 5′ end and a second tag section that is non-complementary to the target nucleotide sequence and comprises a second primer binding sequence, wherein the first or second tag section, or both, contain (s) an identifier sequence that is located between the respective first or second primer binding sequence and the respective first or second target specific section, (b) for each of the target sequences, allowing the first and second target specific section of the respective first probes and second probes to hybridize to the target sequence, (c) ligating the first and second probes when the respective target specific sections of the probes are hybridized to essentially adjacent sections on the target sequence to provide ligated probes of same or very similar length, (d) optionally, amplifying the ligated probes with a first and a second primer to provide amplicons, (e) subjecting the ligated probes or amplicons to high throughput sequencing to determine at least part of the nucleotide sequence, at least including the identifier sequence(s), of the ligated probes or the amplicons, (f) identifying the presence of the target nucleotide sequence in the sample by determination of the presence or absence of the identifier sequence in the nucleotide sequence of step (e) wherein the identifier does not contain 2 or more identical consecutive bases and/or wherein for two or more samples or for two or more locus/allele combinations, the corresponding identifiers mutually all differ by at least two nucleotides.