title: Detection of somatic mutations in EGFR and KRAS genes in formalin-fixed paraffin-embedded specimens from Non-Small Cell Lung Cancer Patients

authors: Law, Tania Alice

subjects: EGFR

abstract: Non-small-cell lung cancer (NSCLC) accounts for 80% of lung cancer and has a 5 year survival rate of just 15%. Recently, tyrosine kinase inhibitors (TKIs) have been found to give dramatic therapeutic benefit to some patients increasing both their overall survival and quality of life compared with the more traditional and aggressive platinum-based chemotherapy. Subsequently, it was shown that EGFR and KRAS mutations act as biomarkers in predicting of patient response or lack thereof, respectively to TKIs.

As such, the establishment of a clinically relevant assay for the detection of EGFR and KRAS mutations would contribute to personalised treatment of NSCLC patients to ultimately improve patient outcomes. However, there are many limitations and obstacles that limit the sensitivity of current protocols to detect these biomarkers, including the inherent heterogeneous nature of NSCLC tumours and the poor quality of genomic DNA due to biopsies being stored formalin-fixed, paraffin-embedded (FFPE) specimens.
This study investigated the use of mineral oil to produce a high yield of quality DNA from FFPE NSCLC specimens. Additionally, significant optimisation experiments were carried out to find the optimum conditions for efficient amplification during PCR thermocycling using DNA derived from these FFPE specimens. Subsequently, the use of standard PCR, Co-amplification at lower denaturation temperature (COLD) PCR, restriction digest-mediated mutant enrichment PCR, single-stranded conformation polymorphism (SSCP) and DNA melt curve analysis were investigated as EGFR and KRAS mutation detection protocols in NSCLC FFPE specimens.
Significantly, this study found that the use of mineral oil contributed to the extraction of a high yield of quality genomic DNA from the FFPE specimens and the use of a high fidelity DNA polymerase enzyme and a PCR buffer with a high magnesium concentration were required to produce amplifiable products from the FFPE specimens. Subsequently, it was found that both SSCP and DNA melt curve analysis could detect putative mutations in EGFR exon 21 and 19.

Given that SSCP and DNA melt curve analysis could detect mutations in the NSCLC FFPE specimens, these mutation detection protocols were shown to be more sensitive than direct sequencing. However, further work is required to establish a clinical relevant mutation detection protocol for the routine detection of EGFR and KRAS mutations in FFPE NSCLC specimens.

text: Detection of somatic mutations in EGFR and KRAS genes in formalin-fixed paraffin-embedded specimens from Non-Small Cell Lung Cancer Patients Non-small-cell lung cancer (NSCLC) accounts for 80% of lung cancer and has a 5 year survival rate of just 15%. Recently, tyrosine kinase inhibitors (TKIs) have been found to give dramatic therapeutic benefit to some patients increasing both their overall survival and quality of life compared with the more traditional and aggressive platinum-based chemotherapy. Subsequently, it was shown that EGFR and KRAS mutations act as biomarkers in predicting of patient response or lack thereof, respectively to TKIs.

As such, the establishment of a clinically relevant assay for the detection of EGFR and KRAS mutations would contribute to personalised treatment of NSCLC patients to ultimately improve patient outcomes. However, there are many limitations and obstacles that limit the sensitivity of current protocols to detect these biomarkers, including the inherent heterogeneous nature of NSCLC tumours and the poor quality of genomic DNA due to biopsies being stored formalin-fixed, paraffin-embedded (FFPE) specimens.
This study investigated the use of mineral oil to produce a high yield of quality DNA from FFPE NSCLC specimens. Additionally, significant optimisation experiments were carried out to find the optimum conditions for efficient amplification during PCR thermocycling using DNA derived from these FFPE specimens. Subsequently, the use of standard PCR, Co-amplification at lower denaturation temperature (COLD) PCR, restriction digest-mediated mutant enrichment PCR, single-stranded conformation polymorphism (SSCP) and DNA melt curve analysis were investigated as EGFR and KRAS mutation detection protocols in NSCLC FFPE specimens.
Significantly, this study found that the use of mineral oil contributed to the extraction of a high yield of quality genomic DNA from the FFPE specimens and the use of a high fidelity DNA polymerase enzyme and a PCR buffer with a high magnesium concentration were required to produce amplifiable products from the FFPE specimens. Subsequently, it was found that both SSCP and DNA melt curve analysis could detect putative mutations in EGFR exon 21 and 19.

Given that SSCP and DNA melt curve analysis could detect mutations in the NSCLC FFPE specimens, these mutation detection protocols were shown to be more sensitive than direct sequencing. However, further work is required to establish a clinical relevant mutation detection protocol for the routine detection of EGFR and KRAS mutations in FFPE NSCLC specimens.

year: 2012

title: The Man from the Future: Traces of Masculinity and Modernity from Hamilton in the 1960s.

authors: Rule, Jeffrey Bryan

subjects: modernity

abstract: This research offers a reading of the considerable change to the landscapes of cities, masculinities and bodies that occurred after the Second World War. With an emphasis on visual sources and methods, I consider how a distinctly modern post-war identity emerged out of the interaction between Hamilton's newly (re)built cityscape, human bodies and their gendered identities. 
In the 1960s, rapid urban growth in Hamilton produced a large number of buildings designed in the Modernist style. This concrete language rendered public structures, and the city at large, as distinctly 'Modern' and progressive. The existence of these buildings was essential to Hamilton's transition from a rural town to an urban centre. Meanwhile, the 1964 Centennial served as a convenient narrative of progress to (re)create the city as Modern while remaining youthful and vibrant. Images of the past and the future were regularly and publicly invoked. Colonial Pioneers and Men from the Future were rhetorically exhumed and conceived in order to (re)construct Hamilton.
Material and discursive spaces of the cityscape were inhabited by images of a 'citified' Modern Man: the fabled Businessman and his derivatives. Images of masculine bodies offer an insight into constructions of gendered identity. Their 'suited' and impervious bodily boundaries reflect the rigid confines of 1960s masculinities and the firm geometric designs of Modernist buildings. Analysis of advertisements and photographs reveal bodily performances that maintain this identity while establishing an urban and masculine corporeality. A number of 'other' identities were excluded by dominant urban masculinity and offer areas for future research.

text: The Man from the Future: Traces of Masculinity and Modernity from Hamilton in the 1960s. This research offers a reading of the considerable change to the landscapes of cities, masculinities and bodies that occurred after the Second World War. With an emphasis on visual sources and methods, I consider how a distinctly modern post-war identity emerged out of the interaction between Hamilton's newly (re)built cityscape, human bodies and their gendered identities. 
In the 1960s, rapid urban growth in Hamilton produced a large number of buildings designed in the Modernist style. This concrete language rendered public structures, and the city at large, as distinctly 'Modern' and progressive. The existence of these buildings was essential to Hamilton's transition from a rural town to an urban centre. Meanwhile, the 1964 Centennial served as a convenient narrative of progress to (re)create the city as Modern while remaining youthful and vibrant. Images of the past and the future were regularly and publicly invoked. Colonial Pioneers and Men from the Future were rhetorically exhumed and conceived in order to (re)construct Hamilton.
Material and discursive spaces of the cityscape were inhabited by images of a 'citified' Modern Man: the fabled Businessman and his derivatives. Images of masculine bodies offer an insight into constructions of gendered identity. Their 'suited' and impervious bodily boundaries reflect the rigid confines of 1960s masculinities and the firm geometric designs of Modernist buildings. Analysis of advertisements and photographs reveal bodily performances that maintain this identity while establishing an urban and masculine corporeality. A number of 'other' identities were excluded by dominant urban masculinity and offer areas for future research.

year: 2007

title: Dreaming Ourselves and Aspirations into Places of Higher Education

authors: Nikora, Linda Waimarie

subjects: Maori

abstract: Dreams and aspirations are at the core of what higher education is about.  Students and scholars alike, the world over, are engaged in the realization of dreams that bring forth new opportunities, new ways of seeing and being and of changing the world. Many Maori students dream of making a difference and see the pursuit of higher education as a way to bring their dreams into reality. Often their dreams reflect family and community aspirations bringing with it a significant burden of responsibility and obligation.  And for Maori academics and researchers like me, my dreams are not too different to those of my own students except that where students pursue a pathway towards becoming relevant, academics are challenged to remain so. In this chapter, I will share some of my/our hopes and experiences and how Maori went about dreaming ourselves into the staff make up, curriculum and research activities in the School of Psychology at the University of Waikato.

text: Dreaming Ourselves and Aspirations into Places of Higher Education Dreams and aspirations are at the core of what higher education is about.  Students and scholars alike, the world over, are engaged in the realization of dreams that bring forth new opportunities, new ways of seeing and being and of changing the world. Many Maori students dream of making a difference and see the pursuit of higher education as a way to bring their dreams into reality. Often their dreams reflect family and community aspirations bringing with it a significant burden of responsibility and obligation.  And for Maori academics and researchers like me, my dreams are not too different to those of my own students except that where students pursue a pathway towards becoming relevant, academics are challenged to remain so. In this chapter, I will share some of my/our hopes and experiences and how Maori went about dreaming ourselves into the staff make up, curriculum and research activities in the School of Psychology at the University of Waikato.

year: 2013