Sequence based genotyping based on oligonucleotide ligation assays

A method for detection of one or more polymorphisms in at least one target nucleotide sequence in a sample comprising:

• (a) providing for each target nucleotide sequence a first probe and a second probe,
• wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that optionally comprises a first primer binding sequence;
• wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence and that comprises an optional second primer binding sequence;
• (b) allowing the first and second target specific section of the respective first and second probe to hybridize to the target sequence;
• (c) ligating the first and second probe when the respective target specific sections of the probes are hybridized to essentially adjacent sections on the target sequence to provide ligated probes;
• (d) amplifying the ligated probes with a first and/or an optional second primer wherein the first primer comprises an identifier to provide amplicons containing an identifier;
• (e) subjecting the amplicons to a high throughput sequencing to determine at least part of the target nucleotide sequence and the identifier contained in the amplicons;
• and
• (f) identifying one or more polymorphism in the target nucleotide sequence in the sample using the identifier.

A method for detection of one or more polymorphisms in at least one target nucleotide sequence in a sample comprising:

• (a) providing for each target nucleotide sequence a first probe and a second probe,
• wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that comprises a first primer binding sequence;
• wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence and that comprises an optional second primer binding sequence;
• (b) allowing the first and second target specific section of the respective first and second probe to hybridize to the target sequence;
• (c) gap ligating the first and second probe by extension of at least one end of the first or second probe using a polymerase and a ligase in combination with single or multiple nucleotides;
• (d) amplifying the ligated probes with a first and/or an optional second primer wherein the first primer comprises an identifier to provide amplicons containing an identifier;
• (e) subjecting the amplicons to a high throughput sequencing to determine at least part of the target nucleotide sequence and the identifier contained in the amplicons;
• and
• (f) identifying one or more polymorphism in the target nucleotide sequence in the sample using the identifier.