Table 2.
BNA primer, padlock probe and detection probe nucleotide sequences.
| Transcript variant | Exon targets (probe) | Nucleotide sequences (5′→3′) | ||
|---|---|---|---|---|
| BNA primer | Padlock probe | Detection probe | ||
| METexon7-8wt | Exon 7-8 (MET7,8) | CAGCCATAGGACC GTATTTCGGCGA |
GATCCTGTAATAACAAGTATGTGACATACTGACAAAGTAGCCGTG ACTATCGACTTGACCAGTTAGCAAAACAGTACATTCTCCTATGTG |
Cy5-AGTAGCCGTGACTATCGACT |
| METΔ7-8 | Exon 6-9 fusion (MET6–9) |
GGGCTGGGGTATA ACATTCAAGAAT |
TGTGTCAAACAGTATTCTTGGTGACATACTGACACCTCAATGCACA TGTTTGGCTCCTGACCAGTTAGCAAGTGAGAGCACGATGAATAC |
TexRd-XN-CCTCAATGCACATGTTTGGCTCC |
| METexon14wt | Exon 14 (MET14) |
CACTTCGGGCACTT ACAAGCCTATC |
CACTCCTCATTTGGATAGGCGTGACATACTGACAAAGTAGCCGTG ACTATCGACTTGACCAGTTAGCAAACGCTACGATGCAAGAGTACA |
Cy5-AGTAGCCGTGACTATCGACT |
| METΔ14 | Exon 13-15 fusion (MET13–15) |
TCGGCATGAACCG TTCTGAGATGAA |
ATCAGTTTCCTAATTCATCTGTGACATACTGACACCTCAATGCACAT GTTTGGCTCCTGACCAGTTAGCAAAAGAGAAAGCAAATTAAAG |
TexRd-XN-CCTCAATGCACATGTTTGGCTCC |
| EGFRwt | Exon 2-3 (EGFR2,3) |
AGGGCAATGAGGA CATAACCAGCCA |
ACCATCCAGGAGGTGGCTGGGTGACATACTGACAAAGTAGCCGT GACTATCGACTTGACCAGTTAGCAAAATGATCTTTCCTTCTTAAAG |
Cy5-AGTAGCCGTGACTATCGACT |
| EGFRvIII | Exon 1-8 fusion (EGFR1–8) |
CTCGGACGCACGAGCCGTGATCTGT |
GTAATTATGTGGTGACAGATGTGACATATGAAACCTCAATGCTGCTGC TGTACTAC TGACCAGTTAGCAGGCTCTGGAGGAAAAGAAAG |
TexRd-XN-CCTCAATGCTGCTGCTGTACTAC |
BNA primer Bridged Nucleic Acids are depicted in bold. Padlock probe target-specific sequences are depicted in italic. Detection probe complementary sequences in the padlock probe are coloured bold italic (wild-type) or italic underline (mutant).