Qiaamp dna ffpe tissue purification kit

The extraction of the genomic DNA from the samples was performed using the QIAamp DNA FFPE Tissue Purification Kit (QIAGEN®) according to the extraction protocol suggested by the manufacturer.
The Nested PCR reactions were performed by using primers PGMY09 and PGMY11 for the first round, and primers GP + 5 and GP + 6 for the second round [26 (link), 28 ].
After denaturation, the material was applied to a nylon strip containing immobilized probes for two different concentrations of β-globin, 19 HPV genotypes with high oncogenic risk (16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 69, 73 and 82) and 18 types of HPV with low oncogenic risk (6, 11, 40, 42, 54, 55, 61, 62, 64, 67, 70, 71, 72, 81, 83, 84, IS39 and CP6108).

The samples were reviewed by the pathologist, and blocks with tumor representativeness (over 50% of the total area of the fragment) were selected. After microtomy, sections suffered a process of deparaffinization. The sections were stored at 4°C, awaiting DNA extraction.
The extraction of the genomic DNA from the samples was performed using the QIAamp DNA FFPE Tissue Purification Kit (QIAGEN®) according to the extraction protocol suggested by the manufacturer.
The Nested PCR reactions were performed by using primers PGMY09 and PGMY11 for the first round, and primers GP + 5 and GP + 6 for the second round [9 (link)].
The sequencing reactions were performed in the Laboratory of Genetics of the National Cancer Institute (INCA) with ET Dye Terminator Cycle Sequencing kit (GE Healthcare, UK) according to the manufacturer’s suggested protocol.

The extraction of the genomic DNA from the samples was performed using the QIAamp DNA FFPE Tissue Purification Kit (QIAGEN®) according to manufacturer protocols.
The Nested PCR reactions were performed by using primers PGMY09 and PGMY11 for the first round, and primers GP + 5 and GP + 6 for the second round [12 (link)] (Table 1).
Table 1

Primer sequences used for PCR reaction to identify HPV DNA

Primer	Sequence 5′ - 3′
PGMY11	PGMY11-A	GCA CAG GGA CAT AAC AAT GG
	PGMY11-B	GCG CAG GGC CAT AAT AAT GG
	PGMY11-C	GCA CAG GGA CAT AAT AAT GG
	PGMY11-D	GCC CAG GGC CAC AAC AAT GG
	PGMY11-E	GCT CAG GGT TTA AAC AAT GG
PGMY09	PGMY09-F	CGT CCC AAA GGA AAC TGA TC
	PGMY09-G	CGA CCT AAA GGA AAC TGA TC
	PGMY09-H	CGT CCA AAA GGA AAC TGA TC
	PGMY09-Ia	G CCA AGG GGA AAC TGA TC
	PGMY09-J	CGT CCC AAA GGA TAC TGA TC
	PGMY09-K	CGT CCA AGG GGA TAC TGA TC
	PGMY09-L	CGA CCT AAA GGG AAT TGA TC
	PGMY09-M	CGA CCT AGT GGA AAT TGA TC
	PGMY09-N	CGA CCA AGG GGA TAT TGA TC
	PGMY09-Pa	G CCC AAC GGA AAC TGA TC
	PGMY09-Q	CGA CCC AAG GGA AAC TGG TC
	PGMY09-R	CGT CCT AAA GGA AAC TGG TC
	HMB01b	GCG ACC CAA TGC AAA TTG GT
GP + 5/6	GP + 5	TTT GTT ACT GTG GTA GAT ACT AC
	GP + 6	GAA AAA TAA ACT GTA AAT CAT ATT C