Introduction to Bioinformatics - Part 1 Flashcards
What are two ways in which cancer can be classified?
- Type of tissue in which the cancer originates (histological type)
- the location in the body where the cancer first developed
What are 6 major categories of cancer?
Carcinoma (malignant neoplasm of epithelial origin)
Sarcoma (originates in supportive and connective tissues)
Myeloma (plasma cells of bone marrow)
Leukemia (“liquid cancers” or “blood cancers”) are cancers of the bone marrow (the site of blood cell production)
Lymphoma (develop in the glands or nodes of the lymphatic system)
Mixed Types
In breast cancer patients what is investigated?
Lymph nodes investigated
Tumours are not only composed of tumour cells, but what other cell types?
Immune cells and stromal cells
What are the four levels of cancer heterogeneity?
- Different type of cancers
- Different sites of neoplasia in a single patient
- primary tumour, metastatic lesions - Same types tumours differ amongst patients
- inter-tumour heterogeneity - Cellular and molecular heterogeneity within a single tumour
- Intra-tumour heterogeneity - composition of different cell types and different tumour clones
The molecular pathology of cancer is what?
discipline within pathology (anatomical and clinical)
the study & diagnosis of disease through the examination of molecules within organs, tissue or bodily fluids
molecular & genetic information in combination with classical pathological approaches
- to diagnosis and classify human diseases
- to inform treatment and prognosis
multidisciplinary field, including cancer bioinformatics
What is bioinformatics?
Field of study that utilises computational tools to understand biology combining biological knowledge with computational science and information technology
What is the central dogma?
Genes encoded by DNA code for proteins whose structure accounts for function depending on their environment may result in phenotype
How does diagnosis of cancers determine quantity and quality of material to work with?
Laboratory tests: blood, urine and other bodyfluids
Images: Mammogram, Ultrasound, MRI, PET scans and X-rays
Biopsy: remove a sample from a tissue.
- with surgery: excisional or incisional
- with a needle: fine needle aspiration (FNA): tissue or fluid
- with a needle: core needle biopsy – tissue
- with an endoscope, Cyto-Sponge
What are choices of the clinical sample?
- Fresh- frozen material
- Formalin-fixed paraffin-embedded (FFPE) tissue
- formalin: ~60% formal aldehyde in methanol
- a good fixation method should preserve the cell/tissue as a whole
- used for pathological diagnosis
- good availability in our tissue banks with long term follow up data
FFPE artefacts
- the DNA/RNA is fragmented and has more breaks- leading to less coverage of the genome, assembling issues
- more indels
- often an enhanced C>T bias- can preclude extracting informative patterns
What can liquid biopsies measure?
- Circulating tumour cells (CTC)
– 1 in 10-6 to 10-8 total circulating cells
2.Circulating tumour DNA (ctDNA)
– DNA released from apoptotic tumour cells
- Exosomes- DNA, RNA, proteins, metabolites, & other materials (even viruses) surrounded by a lipid membrane.
How can a breath test be used for the early detection of cancer?
Molecules called volatile organic compounds (VOCs) are released when cells in the body carry out biochemical reactions
VOCs are organic chemicals with high vapour pressure at ordinary room temperature
PAN-study: Pan-Cancer Early Detection Study (PAN)
https://clinicaltrials.gov/ct2/show/NCT03756597
ReCIVA breath collector, a breath biopsy test -developed by Owlstone Medical
- works for multiple cancer types
- paving the way for an universal breath test
- could be quickly administered by a GP
