Comparative Assessment of DNA Extraction Techniques From Formalin-Fixed, Paraffin-Embedded Tumor Specimens and Their Impact on Downstream Analysis

OBJECTIVES

Good-quality nucleic acid extraction from formalin-fixed, paraffin-embedded (FFPE) specimens remains a challenge in molecular-oncopathology practice. This study evaluates the efficacy of an in-house developed FFPE extraction buffer compared with other commercially available kits.

METHODS

Eighty FFPE specimens processed in different surgical pathology laboratories formed the study sample. DNA extraction was performed using three commercial kits and the in-house developed FFPE extraction buffer. DNA yield was quantified by a NanoDrop spectrophotometer and Qubit Fluorometer, and its purity was measured by the 260/280-nm ratio. A fragment analyzer system was used for accurate sizing of DNA fragments of FFPE DNA. The downstream effects of all extraction methods were evaluated by polymerase chain reaction (PCR) and Sanger sequencing.

RESULTS

In comparison with the commercial kits, the in-house buffer yielded higher DNA quantity and quality number (P < .0001). In addition, DNA integrity and fragment size were preserved in a significantly greater number of samples isolated with the in-house buffer (P < .05). The target PCR amplification rate with the in-house buffer extracted samples was also significantly higher, with 98% of the samples showing interpretable sequencing results.

CONCLUSIONS

The in-house developed FFPE extraction buffer performed superior to other methods in terms of suitability for downstream applications, time, cost-efficiency, and ease of performance.

Evidence for the presence of high risk human papillomavirus in retinoblastoma tissue from nonfamilial retinoblastoma in developing countries

BACKGROUND

The prevalence of human papillomavirus (HPV) infection in India is high. HPV infection is known to cause cervical cancer and has also been implicated in the pathogenesis of retinoblastoma (RB), a common intraocular malignant tumor of childhood which can be familial or sporadic. Despite the high incidence of RB in India, its familial form is rare. Hence this study was undertaken to investigate whether high-risk HPV types 16 and 18 are involved in the development of RB.

METHODS

Formalin fixed paraffin embedded RB tissues (n = 76) including prospective cases with corresponding maternal cervical smears (n = 10) were analyzed for the presence of HPV DNA sequences. Expression of the cell cycle regulatory proteins viz; p105, p107, p30, p16, E2F-1, E2F-4, and MiB-1 was studied by immunohistochemistry (IHC) (n = 34).

RESULTS

A total of 53 out of 76 (69.7%) cases were positive for HPV, of these 3 cases were positive for HPV-16, 23 for HPV-18, and 27 for both HPV-16 and -18. Of the prospective cases (n = 10) studied, five cases along with the corresponding maternal cervical cytology smear had identical HPV status. HPV-16 positive tumors were classified as well differentiated (P = 0.013). Nuclear expression of pRB2/p130 showed significant association with HPV-16 infection (P = 0.04) or dual infection of HPV-16/-18 (P = 0.02).

CONCLUSIONS

Our study lends support to the hypothesis that infection of HPV-16/-18 may play an important role in the development of nonfamilial form of RB in children in India.