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Table 1 Primer and probe sequences

From: High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments

Gene

Detection

Oligonucleotide

Sequence 5′ to 3′

Amplicon length (bp)

Annealing temperature (°C)

ITGA4

Promotor methylation

Forward

TAGTTCGTTGGCGTCGGATAC

90

60

Reverse

TACCCCAAAATTACACGAAATACG

Probe

GGGGCGTTTTTTTTCGTTGGTTAATCG

MSC

Promotor methylation

Forward

GGTTGGTTTTTAGTTATATCGTTTATTTGC

89

62

Reverse

TACCAAATTCACTAAATACACGTAACCG

Probe

CGATCCTCCTACAACAA (MGB*)

EYA4

Promotor methylation

Forward

TTTTTTTTAAGGTAGCGATAATTTTAC

104

60

Reverse

CAAATACGAAACTACCGACAACG

Probe

ACGCACGCTCCGAC (MGB*)

GRIA4

Promotor methylation

Forward

TGTTTATCGGAGCGTTTTAGTTTTTC

120

60

Reverse

AATCGATCCCTCTACGAACCG

Probe

CGTTTCGGAGTTAGTTTGGTGTTAGGTTTTTTTTTTT

ACTB

Bisulphite conversion

Forward

AACCAATAAAACCTACTCCTCCCTTAA

133

62

Reverse

TGGTGATGGAGGAGGTTTAGTAAGT

Probe

ACCACCACCCAACACACAATAACAAACACA

TP53

R273C VAF

Forward

CTCTGTGCGCCGGTCTCT

62

56

Reverse

TGGGACGGAACAGCTTTGA

Probe-WT

AGGCACAAACACGCAC

Probe-Mut

AGGCACAAACACACA

  1. CpG dinucleotides are bold and underlined
  2. *MGB minor groove binder, bp base pairs