A simple way to evaluate self-designed probes for tumor specific Multiplex Ligation-dependent Probe Amplification (MLPA)

Table 1 The set of synthetic oligonucleotide probes used in the MLPA assay.

Probe name	Location	Length (bp)	Left probe hybridizing sequence	Right probe hybridizing sequence
ARX	Xp21.3	83	CGAATGCCGGGCTGATGAAAG	CTGGGTGTCGGAACACTGCC
AFAP1L1a	5q33.1	90	CCTACACTAACACATGATGAAAACC	TCAATATGTCCTCAGGTGGTACC
ACTR1A	10q24.32	102	GGATGAGTTAATTCACACAGCTTTG	TCAGAGCCCTCATGCAGCCTCTTGTAAGCAGATAG
AFAP1L1b	5q33.1	114	GAGACAAGACCTGATCATCTGATCACACTT	GTGCCAACTTGATTCATATTGGGCATTACTAACAACCCCTGG
CFL2	14q13.2	132	ctgacCGTGCTGCCATATCACTAAAATAGGCTTGCCAAGG	CAGGTGAGGTGTATGAATGCTCAAGCCTCACAGAACTGCAATCAAGTGCC
P1	1q25.3	106	gctaCTCCAGAGCAAATAAGCATGG	ACCTCAAGAATGAATTGATGTACCAGTTGGAgactgact
P2	1q25.3	122	CAAGAAGACCAGGTCAACTGCAAAACTGGT	CTCTAAGGCCCATAGGATCTTTGAGGAGTTTGTGGATGTGCAGGCTCCAC
P3	1q25.3	127	gactgactgactCCGTAAATGAACGTATGCTGAACATG	ATCCGTCAGATCTCTAGACCCTCAGCTgactgactgactgactgact
Fr. 14	1q25.3	101	GAGGACGTGAACCAGGACCGTAAGGA	CATGAGCCAGAGCAGTGGTAGCGAGGATGGAGG
Fr. 31	1q25.3	107	TGGGCAGATTCCTTTGATGTGCTTC	TCTCTCATAAGTGTAAGTAGAATTCAGGTCGTATCATGAC
Fr. 32	1q25.3	119	gactGACCTGCGTTCTTGATTTTGACTCAGCG	TTGTTACTAAGTAGTTGGGTGGTCTTGACAGAAACTCgactgact

Upper case correspond to the left and right hybridizing sequence of each probe, whereas lower case correspond to the stuffer sequences used to increase the size of the probe; underlined probes concern the reference probes analyzed in this study.

ISSN: 1756-0500