It is well established that cancers are caused by the accumulation of genomic and epigenomic alterations.
However, molecular changes occuring in the early stages of cancer development or in precursor lesions remain to be
poorly understood.The employment of molecular characterization of tumors prior to therapy has opened the door for
personalized therapy of individual patients. Such genetic alterations that are utilized to predict response to therapy
are considered predictive biomarkers. The development of high throughput technologies lead to the establishment
of a relatively new field of cancer genomics. These genome-wide approaches are increasingly more important in
cancer diagnostic, prognosis, and treatment. Here we briefly discuss cancer transcriptome, cancer genome and
epigenome analyses approches and their clinical utility. Gene expression patterns in tumors (cancer transcriptome)
are analyzed by expression microarrays who can serve as a diagnostic tool which facilitates distinguishing different
cancer subtypes. Another high throughput technology that may revolutionize personalized cancer therapy, lead to
the development of new genetic diagnostic tests and biomarkers is next generation sequencing (NGS). NGS has
an ability to fully sequence large number of genes in a single test and simultaneously detect deletions, insertions,
copy number alterations, translocations and exome-wide base substitutions in cancer-related genes. NGS methods
analyses DNA methylation, detection of modified histones, mapping of transcription factor occupancy, and epigenetic
regulators. DNA diagnosis often trumps clinical diagnosis in oncology. This will cause the shift toward testing minute
amounts of DNA and specimens including needle biopsies, circulating tumor cells, and ciruclating cell-free DNA
are likely to become clinically relevant. Thus, as NGS enters clinical testing it will impact clinical decisions and
cancer outcomes. Finally, improved understanding of cancer biology will lead to further development of targeted
therapies and the use of combinations of targeted approaches simultaneously, increasing treatment effectiveness
and supporting highly individualized patient care.

Objective: To investigate the clinical relevance of scoring Kaposi’s sarcoma herpes virus (KSHV) expression by Human Herpes Virus-8 (HHV-8) latency-associated nuclear antigen 1 (LANA 1) in the early (early patch and plaque) and late (nodular) stages. Methods: We applied a combined intensity weighted histoscore and a categorized score to 235 early patch, plaque and nodular stages, and compared our results with published data. Results: The mean individual scores were significantly lower in the early patch stage compared to the plaque and nodular stages. There was no significant difference in the mean individual scores between the plaque and nodular stage. There was a wide overlap in distribution of histoscore between the three stages. Conclusion: Since treatment modalities are not based on the histological stage nor on the histoscore, KSHV histoscoring appears not to be a useful biomarker of the severity of the disease.

Background: Human Papilloma virus (HPV) infection is strongly related to cervical cancer and its precursors,
but the natural history of HPV infection in men is still unknown. In this field, more information is needed for preventive
strategies, especially in view of the role that men would play in transmitting the virus to their female sexual partners.
Male HPV infection is frequently subclinical and cytologic changes distinctive of viral infection have low frequency.
Moreover, currently there is no FDA-approved molecular test to detect HPV in men.
The goals of this prospective study were to assess a reliable method to collect cells from penis, to investigate
the prevalence of HPV infection in asymptomatic male partners of women affected by cervical abnormalities, and to
evaluate HPV-types concordance between sexual partners.
Methods: 217 asymptomatic men, who were sexual partners of women with cervical lesions, were enrolled.
Exfoliated cells from different penile areas were both cytologically and molecularly evaluated to detect HPV infection
and viral oncogenic expression.
Results: Cytologic signs of penile HPV infection were founded in 13.8% of the cases. No inadequate samples
have been found at β-globin analysis. 62.7% of men and 78.8% of female partners were found to be HPV-positive.
Concordant HPV status has been achieved in 50% of the cases. 32% of the couple, where both partners tested
positive, harboured the same HPV genotype(s). HPV oncogenic expression did not correlate with the grade of
infection status in men.
Conclusions: Our data would suggest the high level of reliability and the high rate of adequacy reached by
sampling multiple penile areas. HPV infection demonstrated more prevalent in asymptomatic male partner of women
with cervical lesions. Molecular testing on penile brushing would represent the more accurate tool to diagnose HPV
infection, in view to limit the spread of the virus within the couple.

Nasopharyngeal carcinoma (NPC) is a unique tumour which is endemic in Southern China including Hong Kong. While the treatment results for early disease are encouraging, patients with advanced cancer are uniformly associated with poor prognosis. Epstein-Barr virus (EBV), the first virus related to the development of human malignancy, plays an important role in the carcinogenesis of the disease. Over the past decades, researchers have been trying to identify EBV associated biomarkers which allows early diagnosis as well as accurate monitoring of treatment response. With the development of real time quantitative polymerase chain reaction, plasma EBV DNA has been studied with much enthusiasms for its potential role in the management of patients with NPC. Since then, numerous reports have been published regarding the applications of plasma EBV-DNA for early diagnosis, monitoring of treatment response after radiotherapy or surgery, and as a prognosticator predicting oncological results after curative therapy for primary disease or palliative treatments for patients with recurrent/metastatic cancer. On-going studies are performed to investigate its potential use in the screening of at-risk populations in the endemic geographic regions. In the future, it may allow pre-treatment risk stratification for individual patients, so that personalization of treatment protocols can be achieved with potentially better oncological outcome.

Throughout the past decade, the neutral and alkaline comet assays, which lyses cells with high salt in the
absence of proteolysis, have been the most widely used methods to observe single- or double-strand breaks (SSB,
DSB) in a single nucleus. These methods evaluate the degree of DNA damage based on the amount of granular
fragments discharged from the origin, the so-called “comet tail,” but not of long chain DNA fibers. Meanwhile, a novel,
single-cell pulsed-field gel electrophoresis (SCPFGE) method, which digested cells with trypsin, observed a different
course of DNA fragmentation: first, a few large fibrous fragments were derived from a bundle of long chain fibers,
then the cleavages were advanced until finally almost all the DNA was shredded to granular fragments. Some nuclear
DNA binding components were tolerant for high salt and high alkalinity, but were degraded by trypsin digestion. A
lack of trypsin digestion causes false negative results in both SCPFGE and comet assays. Also, most DNA fibers
were still fixed with components, and the comet tail did not reflect a total amount of granular fragments, but rather
those that released components. Repair of DSB is intrinsically difficult as compared to other DNA lesions, and the
critical threshold is extremely low.DNA fibers that have already been shredded to numerous granular fragments may
be irreparable as a result.
Although 100 - 300 mmol/L NaOH was commonly used in the alkaline comet assay, the naked DNA fibers
persisted in 10 mmol/L NaOH after trypsin digestion, but were shredded to granular fragments by 30 mmol/L. Neogenesis
of the granular fragments by high pH did not clarify the mechanism of such a result; that is, it was unknown
whether it was due to dissociation of hydrogen bonds, strand breaks through alkaline labile sites, artifactual DSB,
or a combination of actions. Optimum conditions for the comet assay need to be defined to achieve quantitative
measurements.
DNA instability analyses by means SCPFGE is likely to serve as a fundamental step in single-cell genomics
to determine the competence of the cell population provided for DNA amplification methods and is likely to play an
important role in ensuring the safety of clinical regenerative medicine.

This study is to develop and validate a real-time quantitative PCR (rt-QPCR) assay for rapid quantitation
of microcystin-producing Microcystis using unprocessed surface water samples collected from Alberta lakes.
Microcystin synthetase gene E (mcyE) was targeted for microcystin-producing Microcystis and 16S rRNA was used
to measure blooming level of total cyanobacteria. The assay was optimized and validated with 20 reference samples
collected in 2011. The limit of detection (LOD) of rt-QPCR was 50 copies/ml for both mcyE and 16S rRNA. An
excellent precision was observed in 24 replicates [coefficient of variation (cv)=1.12% for 1.0E+05 and = 0.79% for
1.0E+03 copies]. The rt-QPCR assay was applied for detection of mcyE in 527 water samples collected from 45
lakes during the open-water season of 2012 in Alberta and 369 samples were mcyE positive. Microcystin-producing
Microcystis was detected in 41 out of the 45 lakes in which, relatively high copy numbers of mcyE (≥ 1.0E+05 copies/
ml) were determined in 9 lakes. Cyanobacteria were present in all 45 lakes determined by 16S rRNA. The rt-QPCR
assay developed with specific target to mcyE is sensitive, specific and robust for rapid detection and differentiation
of toxic Microcystis from non-toxic cyanobacteria in surface water.