Detection methods based on sequencing

A probe set for analyzing a genetic locus of a target polynucleotide sequence, comprising:

• one or more first probes comprising:
• (1) a first hybridization sequence that specifically binds to the target polynucleotide sequence upstream of or including the genetic locus, and (2) a first primer sequence upstream of the first hybridization sequence, wherein the first primer sequence does not bind to the target polynucleotide sequence;
• and
• one or more second probes comprising:
• (i) a second hybridization sequence that specifically binds to the target polynucleotide sequence downstream of or starting from the genetic locus, and (ii) a second primer sequence downstream of the second hybridization sequence, wherein the second primer sequence does not bind to the target polynucleotide sequence,
• wherein:
• the extension directions of the first and second probes are the same;
• the first probe is upstream of the second probe;
• and
• the first and second probes are adjacent and, when coupled, form a sequence comprising the genetic locus, and wherein:
• a) the genetic locus comprises an insertion at the nth residue of a wild-type target polynucleotide sequence;
• and
• the one or more first probes comprise at least two first probes, one of which specifically binds to the wild-type target polynucleotide sequence until and excluding the nth residue, while the other specifically binds to the target polynucleotide sequence including and until the last residue of the inserted sequence, and the second hybridization sequence of the one or more second probes specifically binds to the target polynucleotide sequence downstream of the insertion, and the 5′ terminal nucleotide of the one or more second probes is complementary to nth residue;
• or
• the one or more second probes comprise at least two second probes, one of which specifically binds to the wild-type target polynucleotide sequence starting from the nth residue, while the other specifically binds to the target polynucleotide sequence including and from the first residue of the inserted sequence, and the first hybridization sequence of the one or more first probes specifically binds to the target polynucleotide sequence upstream of the insertion, and the 3′ terminal nucleotide of the one or more first probes is complementary to the residue immediately upstream of nth residue in the wild-type target polynucleotide;
• or
• b) the genetic locus comprises a deletion at the nth residue of a wild-type target polynucleotide sequence;
• and
• the one or more first probes comprise at least two first probes, one of which specifically binds to the wild-type target polynucleotide sequence until and excluding the nth residue, while the other specifically binds to the target polynucleotide sequence until the first residue immediately upstream of the deleted sequence, and the second hybridization sequence of the one or more second probes specifically binds to the target polynucleotide sequence downstream of the deletion, and the 5′ terminal nucleotide of the one or more second probes is complementary to nth residue;
• or
• the one or more second probes comprise at least two second probes, one of which specifically binds to the wild-type target polynucleotide sequence starting from the nth residue, while the other specifically binds to the target polynucleotide sequence including and from the first residue of the deleted sequence, and the first hybridization sequence of the one or more first probes specifically binds to the target polynucleotide sequence upstream of the deletion, and the 5′ terminal nucleotide of the one or more first probes is complementary to the residue immediately upstream of nth residue in the wild-type target polynucleotide.