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Copy of Cancer research and Bioinformatics
Transcript of Copy of Cancer research and Bioinformatics
Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. While almost all cells in an organism contain the entire genome of the organism, only a small subset of those genes is expressed as messenger RNA (mRNA) at any given time, and their relative expression can be evaluated. Techniques include DNA Genechip , microarray technology or sequenced-based techniques such as serial analysis of gene expression (SAGE). Gene expression profiling has been around since the nineties but has only recently become apart of clinical cancer application research.
Current Uses-Cancer Research
Cancer is a disease characterized by uncontrolled cell growth and rapid reproduction of cells. For cancer to develop, genes regulating cell growth and differentiation must be altered; these mutations are then maintained through subsequent cell divisions and are thus present in all cancerous cells. In the context of cancer, gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression profiling often has an impact on predicting the patient’s clinical outcome.
How this works
How has gene expression profiling in Cancer treatment impacted patients?
Gene mutations result in the alteration of the gene's expression. This change in the gene expression profile can be used to work out treatments. The most recent example is the skin cancer, melanoma. If the patient's melanoma tumor has the B-raf mutation it will respond to a particular drug that effects the B-raf structure in the cell. This can lead to dramatic responses in patients who would have otherwise ran out of treatment options.
What is Gene Expression profiling?
How Does it effect Cancer treatment?
Affymetrix GeneChip System (microarray)
Affymetrix GeneChIP system is a microarray technology that can be used from genome-wide gene expression profiling and copy number analysis. The Molecular Genomics facility offers access to an Affymetrix platform including hybridisation ovens, wash stations and scanner, but no longer offers microarray service provision to researchers.
The facility also houses ancillary equipment for sample preparation and quality control including an Eppendorf epMotion robotic liquid handling system, Agilent Bioanalyzer 2100 and TapeStation, BioTek Synergy HT Microplate Reader, Covaris S2 Ultrasonicator and Life Technologies Qubit fluorometer.
Illumina HiSeq 2500 (next-generation sequencer)
The llumina HiSeq 2500 is arguably the current industry standard in next-generation sequencing; the sequencer was acquired through generous donations from Peter Mac’s donor community and Therapeutic Innovation Australia. Key applications include DNA resequencing (whole genome and targeted capture) for mutation discovery, transcriptome sequencing (RNA-seq) and epigenomics applications, such as ChIP-seq and bisulphite sequencing.
The molecular genomics facility at Peter Mac operates two major platforms; Illumina HiSeq 2500 (next-generation sequencer) and Affymetrix GeneChip System (microarray).
What does this mean?
Gene Expression Profiling ultimately gives doctors the ability to individualize treatments and target specific cancers. This development has changed the face of cancer treatments and has had many positive outcomes for many patients. As two people with the same stage of the same cancer often react differently to the same treatment, identifying the exact gene which has mutated and is causing the tumor allows a specific and accurate treatment to be applied - avoiding any unnecessary side effects related to other cancer treatments. Once doctors have identified the tumor they then determine a suitable treatment which can be either chemotherapy, surgery, radiotherapy, hormone therapy or complementary and alternative therapies used alongside conventional medicines.
In a 2001 study published in the Proceedings of the National Academy of Sciences, scientists in the field of gene expression profiling stratified the classifications and explored the clinical value of cancer subtypes. The authors separated Breast cancer ER-positive (estrogen recepter positive) tumors into two distinct groups and found that tumor classification based on gene expression was related to patient survival. The expression of 427 genes was measured for 78 cancers and seven non-malignant breast samples.The authors further found once they performed survival analyses that tumors belonging to the various groups showed significantly different outcomes when treated uniformly.
Former Director of Cancer Genomics at Peter Mac
Dr David Bowtell,
Illumina HiSeq 2500 (next-generation sequencer)
Although Professor David Bowtell of Peter Mac believes 'the future is here' , it is likely that gene expression profiling in cancer treatment will become both more accessible to the general public and available for a greater variety of cancers.