Rapid and Inexpensive Screening of Genomic Copy Number Variations Using a Novel Quantitative Fluorescent PCR Method

Table 1

List of MQF-PCR primers.

Syndrome/region	Primer name	Genomic locations (GRCh37); fragment size	Sequence (5^′→3^′)
WAGR [6]; ~244 kb downstream from WT1	WAGR-MQF-F	chr11:32166342-32166440; 118 bp	AGAATGCAGTGAYACAAAGG^a
	WAGR-MQF-R	chr17:53032677-53032764; 107 bp	GGAGGTAGGTAAATCAATCA^b
Smith-Magenis/Potocki-Lupski [7]; ~9 kb upstream from TOM1L2	SMS-MQF-F	chr17:17884450-17884584; 155 bp	TACATTAGAAAAAGAGAGCTGG^a
	SMS-MQF-R	chr1:100679142-100679278; 157 bp	CATCATCCTGTTCCCCTTTG^b
Xp22.3 [8]; KAL1	Xp22-MQF-F	chrX:8572701-8572822; 136 bp	GAGACCACTGAGGGTAACT^a
	Xp22-MQF-R	chr11:114279747-114279863; 142 bp	AATTTTGAGCATCCTGAAA^b
Langer-Giedion [9]; ~63 kb downstream from UTP23	LGS-MQF-F	chr8:117842056-117842177; 142 bp	AGCAATGGCCATTCCTTAGA^a
	LGS-MQF-R	chr4:174188668-174188791; 144 bp	CCATGCAGCACCCYTCAT^b
Greig cephalopolysyndactyly [10]; GLI3	GCS-MQF-F	chr7:42088115-42088183; 93 bp	TGCWGAGATCATGGAGAGC^a
	GCS-MQF-R	chr2:121708925-121708996; 89 bp	TACRTKAAYCCCYACATGGA^b
Miller-Dieker [11]; CRK	MDS-MQF-F	chr17:1340129-1340311; 208 bp	TGATTCTCAGGCAGGAGGA^a
	MDS-MQF-R	chr17:6962293-6962479; 211 bp	CGACGTAAGGRACTGGAATC^b
Saethre-Chotzen [12]; ~46 kb downstream from TWIST1	SCS-MQF-F	chr7:19108525-19108628; 124 bp	TGGATATTTGTGYTAYTTCCTT^a
	SCS-MQF-R	chr1:195731420-195731527; 128 bp	TGCATACTMCACAATTAATTRTGTG^b

aUniversal M13-40 extension (5^′-GTTTTCCCAGTCACGAC-3^′) was added to the 5^′ end of the primer for cost-efficient fluorescent labeling of amplicons [13].
bA PIG-tail extension (5^′-GTTTCTT-3^′) was added to the 5^′ end of the primer to promote complete adenylation of the 3^′ end of the forward strand [13].