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Table 2 Summary of oligonucleotides

From: Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: Pathological significance in early- and late-onset breast carcinoma

Primers

Location

Analytical purpose

Forward Primer

Reverse Primer

Size (bp)

PHF2 Ex-18

9q22.32

HD/HED

5'-ACTCCTGCCTGCAGACCAC-3'

5'-CCTGCTCTTCCTCGTAGTCG-3'

168

FANCC Ex-2

9q22.32

HD/HED

5'-TGGCTCAAGATTCAGTAGATCTTTC-3'

5'-TTTCAAGGCTTCATACATCTTCC-3'

158

PHF2 promoter

-893 to -670 region

Methylation

5'-GTGGTGTCCCAACCAGAAAC-3'

5'-GGGACCCCGAGGATAAGATA-3'

223

FANCC promoter

-319 to -144 region

Methylation

5'-TTTTACCCCGTTGACAAAGC-3'

5'-CGGTACTGCTCCAGTGTTCC-3'

175

PTCH1 promoter

-715 to -420 region

Methylation

5'-CGAGGAGCACAAGAAAGCAG-3'

5'-AGAAAGAGCCAGCGAATCC-3'

295

XPA promoter Ex.1

-126 to +56 region

Methylation

5'-AGGCGCTCTCACTCAGAAAG-3'

5'-TCCGCGGGTTGCTCTAAA-3'

182

PTCH1 Ex.*23

Intron 22–23 to Ex.23

SSCP

5'-TCTAACCCACCCTCACCCTC-3'

5'-ATTGCTAGGGCCAGAATGCC-3'

226

PTCH1 Ex.23

Ex.23 to Intron 23–24

SSCP

5'-TTCTGCCTCCGTGACTGTC-3'

5'-CTCTAGGTCCCTTGGCTGC-3'

265

PHF2 Ex. 18–19

Coding regions of exons

Q-PCR

5'-ACTCCTGCCTGCAGACCAC-3'

5'-TCGACCGGGACTTAAAGATG-3'

257

FANCC Ex. 7–8

Coding regions of exons

Q-PCR

5'-TGGAGGCTCTCCTCATCTGT-3'

5'-GCATTCGATCCTTCTCAGACA-3'

223

PTCH1 Ex. 1–2

Coding regions of exons

Q-PCR

5'-GACCGGGACTATCTGCA-3'

5'-GAGGAGGCCCACAACC-3'

186

β2 Microglobulin

15q21-q22.2

Q-PCR

5'-GTGCTCGCGCTACTCTCTCT-3'

5'-TCAATGTCGGATGGATGAAA-3'

153

β-3A-adaptin (K1*)

5q14.1

DNA cleavage control

5'-TGCCCTCTGGACTGGAACCT-3'

5'-CCTGAGCCCAGCCCAAGTC-3'

445

RARβ2 (K2**)

3p24.2

DNA integrity control

5'-AGAGTTTGATGGAGTTGGGT-3'

5'-CATTCGGTTTGGGTCAATCC-3'

229