Core Research Flashcards
Tissue bank
a collection of human tissue or other biological material, stored for potential research use beyond the life of a specific project with ethical approval
What is a HTA license (consent) required for?
any “scheduled purpose” involving removal, storage and use of human tissue, from the living or decease
- anatomical examination
- storage/use for public display
- research in connection with disorders of human body
- post mortem examinations, including removal and storage of tissue
Conditions where license/consent not required?
- tissue that is stored and used for NHS REC approved specified research projects (anonymised) (unspecified requires lisence)
- Storing organs for less than 24 hours prior to transplantation
Generic consent?
Broad consent given eg. donation to a tissue bank for storage/use for unspecified research bank
Proteome definition
the entire set of proteins expressed by a cell, tissue or organism
Central Dogma
an explanation of the FLOW of generic information within a biological system “DNA makes mRNA and mRNA makes protein”
miRNA
short, non coding RNA molecules that act as negative regulators of gene expression, by inhibiting mRNA translation or promoting mRNA degradation
Evidence Based Medicine
the conscientious, explicit, and judicious use of current best evidence in making decisions about the care of individual patients
Bias
any influence that acts to make observed results non-representative of the true effect of therapy
Placebo effect
a response to a medical intervention that results from the act of carrying out the intervention itself, rather that from the specific treatment mechanism
Microsatellites
repetitive segments of DNA scattered throughout the genome in non coding regions. Used as markers of linkage analysis because of their naturally occurring high variability in repeat number between individuals
GWAS
OBSERVATIONAL study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait - determine what AREAS of the genome contribute to disease
Epigenetics
the study of heritable changes in gene EXPRESSION that do not involve changes to the underlying DNA sequence
Intervention
a set of planned actions that are designed to bring about desired changes (outcomes) in defined beneficiaries in order to address a health or social problem
Bradford Hill Criteria
group of principles that are used to establish epidemiological evidence of a causal relationship between a presumed cause and an observed effect
Bias
Any systematic error (in the research methodology) in an epidemiological study that results in an incorrect estimate of the association between exposure and risk of disease
Confounding
Possibility that an observed association is due to the effects of differences between the study groups (other than the exposure under investigation), that could affect the risk of developing the outcome being studied
Sanger Sequencing
To determine the DNA sequence of a shorter sequence of DNA (900 bp). Uses chemically altered, dyed ‘dideoxy’ bases to terminate newly synthesised DNA fragments at specific bases. The fragments are then separated by gel electrophoresis, and the modified didNTP bases can be detected as each one emits a light of a specific wavelength
Illumina Sequencing
Involves cleaving the DNA sample into short fragments, then cluster generator by ligating longer fragments to ‘adaptors’ and annealing to a slide using the adaptors.
Bridge PCR
Slide flooded with modified dNTPs (contain terminator) and DNA polymerase
Image taken of the slide at each read location - fluorescent signal which means that a picture of the DNA is built up base by base
NGS: sequencing reactions are constructed simultaneously on a large no of DNA fragments on a solid surface, fast and cheap
PCR
Used to amplify a specific fragment of DNA for analysis
- Denaturation -> separate strands
- Annealing -> cool so primers bind to complementary sequences
- Extension -> raise reaction temp so taq polymerase extends primers, creating new strands
- doubles each cycle 1,2,4,8*
Adv: speed, simplicity, low cost, can amplify a really small fragment, used in qt RT PCR, immunohistochemistry etc, don’t need to know DNA sequence
Disadv: primer can attach to wrong part if sequence appears more than once, doesn’t allow for localisation
Pre-clinical trial drug development
safety pharmacology, preliminary toxicological testing, pharmacokinetic testing, chemical + pharmaceutical development
drug discovery: natural sources, study of metabolites, molecular design, new disease insight
Phase 1 trial
initial administration of drug into humans 20-50 people, healthy volunteers determine tolerability of dose range Single ascending dose (SAD): PK Multiple ascending dose (MAD): PK, PD
NOAEL
MABEL
use lowest estimated dose with a safety margin, cautious increases in dose - steep dose response curve
drug administration: continuous monitoring, best clinical practice, preform in specialist clinical trials unit, prepared for adverse consequences, stringent stop criteria
Phase 2a trial
50-500 people (patients)
to test drug effectiveness
continuing safety evaluations
Phase 2b trial
assessment of dose ranging and dosing intervals - how well the drug works at the prescribed dose
Phase 3 trial
RTC - multi centre, multi country
assessment of efficacy and safety in comparison to gold standard
3a: before marketing approval, info for insert/labelling
3b: after regulatory submission but before marketing approval
Phase 4 trial
evaluate drug safety in a real world setting
LT safety surveillance designed to detect rare or long term adverse effects in a larger population/over a longer time (2 years or more)
Positivist
QUANT
methods of natural sciences eg. hypothesis testing are appropriate for the study of social phenomena
quantifiable observations that lead to statistical analysis
the world is independent of and unaffected by the researcher
understanding of phenomena must be measured and supported by evidence
allows generalisability of results to different populations
Interpretivism
QUAL
a social phenomenon may have multiple interpretations rather than a truth that can be determined by a process of measurement
the researcher and the social world impact on each other
understanding humans/events/attitudes in social context
interviews and observations
Qualitative research
research that helps the researcher gain an understanding into how or why various social phenomena occur, through observations and interviews. gain deeper understanding of perceptions, understanding and experiences, how individuals/groups behave and how interactions shape relationships
Quantitative research
the systematic, empirical investigation of observable phenomena, with the statistical/mathematical/numerical analysis of data in order to carry out hypothesis testing and to develop mathematical models/theories. Results are generalisable to larger populations
Purposive
Non probability where participants are selected based on pre-selected criteria set by the research q
Adv: investigate sociodemographic groups, participants are experienced in area of research
Dis: risk of researcher bias - subjectivity
Convenience
non probability where people are sampled due to their availability to the researcher - geographical proximity or known contacts
Adv: least time consuming and expensive, useful in exploration stage of research or in pilot data collection
Dis: sampling bias, non representative, low external validity, can’t generalise
Snowballing
non probability where researcher asks initial subject to identify another potential subject who meets the criteria
Adv: useful in rare/difficult to access/engage populations eg. drug users/sex workers
Dis: subject to bias of first participant (community bias), lack of definite knowledge about whether sample is relevant to the target population
Theoretical
the process of coding and analysing data, then selecting additional sample elements on the basis of their potential for confirming or disconfirming emerging theories
adv: provides structure to data collection, provides deeper understanding to something that is only initially partially understood
dis: complex, req time and money, skill
Epidemiology
the study of the distribution and determinants of health related states or events in specific populations, and the application of this to control health problems
the science and practice which describes and explains disease patterns in populations
Cross sectional study
involves data collection from a population or representative subset at a specific point in time - point prevalence and period prevalence
Cohort study
longitudinal study that samples a cohort (group of people that share a defining characteristic), and preforms cross sections at intervals through time
Case control study
observational study where two existing groups differing in outcome are identified and compared on the basis of a causal attribute
cases vs controls
Bias
any systematic error in an epidemiological study that results in an incorrect estimate of the association between exposure and risk of disease
Confounding
possibility that an observed association is due to the effects of differences between the study groups (other than the exposure under investigation), that could affect the risk of developing the outcome being studied
must be a risk factor for the outcome, associated with the exposure but not on the causal pathway between exposure and disease
In situ hybridisation
uses a probe (labelled cDNA, RNA or normal probe) to localise a specific RNA sequence in a tissue (in situ)
cDNA Library
cloned cDNA fra gments inserted into host cells, which constitute a portion of the transcriptome of an organism - a collection of only the genes that are encoded into proteins (transcribed)
cDNA sequences can be incorporated into bacterial plasmids, transfected into bacteria, where the resultant colonies can be picked and sequenced
intons, upstream/downstream
Northern Blot
detecting specific RNA molecules in a mixture of RNA
separated using gel electrophoresis, transferred to a membrane, radioactive labelled probes (complementary_, x ray film to identify and expression, biodistribution
toxic chemicals, newer techniques do the same thing but higher sensitivity
Gene expression microarrays
microscopic DNA fragments attached to a solid surface - can measure expression of large no of genes simultaneously or genotype multiple regions
reverse transcriptase to get cDNA (fluro)
complementary probe on microarray plate - attach
laser scanner
compare and control labelled two different colours - expression determined by measuring intensity ratio
qRT-PCR
monitors the amplification of a specific molecule (cDNA/RNA) during PCR in real time, in order to determine it’s abundance
relative or absolute quantification
BCA (bicinchoninic acid) Assay
for determining the amount of protein in a solution
total protein concentration is exhibited by a colour change in proportion to the amount of protein
ELISA
enzyme linked immunosorbent assay
Chromatin
the complex of DNA packaged within histone proteins into nucleosomes
SNP
Variation in a single allele in a DNA sequence among individuals, could lead to variations in the AA sequence
eg. haemochromatosis
