MAID 2.1-2.8 Flashcards
1
Q
OR calculation?
A
(TP/FN)/(FP/TN)
2
Q
At what EGFR is contrast CT probably a bad idea?
A
<45/30, although not absoulte
3
Q
Key danger groups for ionising radiation?
A
Children that are likely to need high lifetime dose e.g. Crohns, and pregnancy (more due to risk of breast cancer then fetal harm; V/Q more likely to harm fetus). However, if need test then get test.
4
Q
Risk with contrast MRI?
A
If using gadolinium-based contrast, can get NSF. Get fibrosis of skin, joints, eyes, lungs/heart/liver. Usually have ESRD.
5
Q
Imaging for gallstones?
A
All stones will show up on US/MRCP; non-calcified will not be seen on AXR/CT. ERCP may be needed to actually clear (MRCP is not therapeutic).
6
Q
Which infections may need radiological biopsy?
A
Thinks like discitis and osteomyelitis, as blood cultures are fairly useless and must be certain about diagnosis because antibiotics courses are prolonged
7
Q
Likelihood ratio definition?
A
The probability of a finding in those with the disease/same probability in those without disease. 1 means exactly as likely in each.
8
Q
What may interfere with analytical specificity?
A
Related molecules e.g. metabolites, matrix effects, heterophilic or antireagent antibodies
9
Q
What are heterophilic antibodies?
A
Weak antibodies against poorly defined antigens; get broad reactivity and so can interfere with assays
10
Q
Significance of high accuracy and low precision?
A
Not a systematic bias as mean is good, but total error is significant
11
Q
Use of high precision and low accuracy?
A
Can be useful if use reference ranges/diagnostic rule out for that particular assay, but has no value between assays
12
Q
Assays and tests?
A
For any test e.g. FBC a whole range of assays is available; precision and error are relevant to assays, sens and spec are intrinsic to a test (although relate to the assay)
13
Q
Principles of spectophotometry?
A
Reaction must either produce or consume a substance that absorbs light at a certain wavelength; progress affects proportion which affects absorption. Used for many common tests
14
Q
Pros and cons of spectophotometry?
A
\+ = fully automatable, fast, cheap - = affected by haemolysis/icterus/lipaemia (get interference because some breakdown products e.g. Hb have very broad absorption), not available for many analytes
15
Q
Polyclonal vs monoclonal antibody diagnostics?
A
- Polyclonal uses mixture of antibodies, isolated from animal serum, low cost, recognise multiple epitopes. High affinity (may work even if an epitope is masked) BUT have between-batch variation.
- Monoclonal uses single Ab, isolated from single cell line. High cost, recognises SINGLE epitope. Minimal batch variability and high specificity.
16
Q
Immunoassay (1): sandwich?
A
Used for large molecules e.g. peptides. Have capture Ab anchored to solid support; binds to analyte to fix it. Then add signal Ab with radiolabel, binds to different epitope on analyte. Wash away remainder; signal proportional to analyte concentration.
17
Q
Immunassay (2): competitive?
A
Used for small molecules. Capture Ab on solid support; add sample Ag and labelled version; compete with each other. Signal inversely proportional to analyte.
18
Q
When would you use sandwich versus competitive immunoassays?
A
Sandwich uses two binding sites (epitopes) per antigen; better for larger molecules e.g. proteins. Competitive only one so better for smaller.
19
Q
Pros and cons of immunoassays?
A
\+ = often automatable, wide range of analytes, fast, can be highly sensitive. - = manual for some analytes, CROSS-REACTIVITY (binding of Ab to other epitopes) can be expensive, heterophilic antibodies in sample can interfere.
20
Q
Examples of cross-reactivity in immunoassays?
A
Measuring cortisol; get significant cross-reactivity to some compounds e.g. corticosterone, very minor to prednisolone. Only matters in specific cases e.g. CAH, metyrapone therapy. The opposite is true in pseudo-Cushing’s
21
Q
How does IHC work?
A
Tend to use indirect immunostaining (amplifies signal). Add primary Ab; binds to tissue Ag. Secondary Ab added; binds to constant region of primary with one ‘arm’ and to stain complex with other ‘arm’
22
Q
Clinical applications of IHC?
A
Diagnosis of primary malignant tumours (especially when poorly differentiated), likely site of met origin, categorising malignancies, detecting molecules with prog/ther significance e.g. HER2, detection of minimal disease (small numbers of tumour cells), used alongside FNA cytology, used for semi-quantitative proliferation index
23
Q
Limitations of IHC?
A
- Epitope masking (protein cross-linking during fixation; can reverse with heat/enzymes).
- Background staining (non-specific binding of 1/2ndary Abs, or endogenous signal enzyme)
- Ab selection/performance (select carefully, validate).
- Standardisation of IHC tests is challenging (wide range of variables)
24
Q
Immunoassay microarrays?
A
(Mostly academic). Take sample, biotinylate, conjugate protein to Ab array, then add dye (binds it biotin). Allows many different protein to be detected and conc. determined at once.
25
Pros and cons of immunoassay microarrays?
```
+ = multiplex detection (100s-1000s of Ag), cost-effective compared to single, powerful technique for investigating new biomarkers/drugs
- = imprecise compared to traditional immunoassays (semi-quant), perhaps not robust enough for clinical practice, standardisation/calibration issues
```
26
Pros and cons of mass spec?
```
+ = can be highly specific/sensitive, applicable to a wide range of analytes, low cost consumables and can multiplex.
- = expensive equipment (high one-off cost), high level of expertise, standardisation. Isobaric interference/ion suppression.
```
27
What does the metabolome consist of?
Sugars, nucleotides, amino acids, lipids (lipidome).
28
Technology driving proteomics?
2D gels, mass spec, microarray immunoassays etc. 2D gels involves electophoresis of disease sample overlaid to control, then compare. MALDI-TOF mass spec. creates peptide 'fingerprint' and compares to control; allows identification of potential biomarkers.
29
Uses of metabolomics?
Biomarker discovery (finding metabolites that discriminate benign vs carcinoma e.g bile/urine/saliva), personalised medicine (test every metabolite at once for rapid diagnosis). Could be used in toxicology when testing drugs; typical metabolites of liver/renal injury could be detected early
30
Limits of "-omics"?
Huge amount of data, hard to interpret, need statistical significance to be useful clinically, multi-step process so hard to standardise, biomarker validation is extremely lengthy process.
31
Examples of when personalised cancer medicine is diagnostic?
BCR-ABL in CML, JAK2 in myeloproliferative disorders
32
Examples of when personalised cancer medicine is predictive?
EGFR in NSCLC; predicts TKI response. HER2 in CaBreast; amplification predicts reponse to Herceptin
33
Examples of when personalised cancer medicine is prognostic (different to predictive)?
TP53 in CLL = bad outcomes, BRAF in CRC = bad outcomes.
34
Examples of when personalised cancer medicine is used for disease monitoring?
BRC-ABL1 in CML used for minimal residual disease detection (as is only found in leukaemia cells i.e. not germline!
35
Type of DNA tests for very big mutations? (aneuploidy/large deletions/translocations?)
Cytogenetic e.g. karyotyping, FISH. Cytogenetics means how chromosomes relate to cell function. FISH is quicker than karotype.
36
Types of DNA tests for microdeletions?
Can used FISH again, or arrayCGH (compare labelled patient DNA to labelled reference DNA; get different colour ratios in duplications/deletions). aCGH also counts as cytogenetics
37
Two main uses of cytogenetics in children?
1. Does this child have X syndrome?
2. Does this child have an identifiable chromosome problem? (quite large scale).
e. g. Downs, Williams (large deletion found in FISH/aCGH)
38
Problems with aCGH?
If find duplications/deletions without specific linked syndromes, or find multiple changes, can be hard to ascertain clinical significance i.e. findings are often "unique".
39
Specificity of karyotyping?
Usually ~100% i.e. no child with trisomy 21 will NOT have Down's.
40
Use of single BASE sequencing?
Used to see if known family mutation is passed on, or look for specific 'driver' mutation in a tumour e.g. BRAF; will need to extract tumour DNA first. Use MALDI/TOF as different base fragments will be revealed; cheaper and easier than sequencing.
41
Use of single GENE sequencing?
Used for specific rare diseases linked to single genes e.g. Marfans, NF1, ADPKD, DMD, CF. Use next-gen sequencing.
42
Use of gene PANEL sequencing?
Specific rare disease diagnosis if multiple genes implicated (heterogeneity) e.g. familial breast cancer (~5 genes), familial HCM (30 genes). Use next-gen sequencing.
43
Use of whole EXOME sequencing?
Sequence all exons. Can add "virtual" panels. 30 megabases (30,000,000 BP). Use high-throughput DNA sequencing; aim is to find varients that alter protein sequences @ much lower cost than whole genome. Especially effective in study of rare Mendelian disease, as all genetic variants may be relevant. Aim to find the variants that are only present in very small numbers of people.
44
Whole exome vs whole genome?
Exome process good for rare Mendelian disease, because assumes that any severe causing variants are much more likely to be in protein coding sequence (1% of whole genome).
45
When is whole exome sequencing better than SNP array?
Better if variant is extremely rare; only have SNP probes for fairly common abnormalities i.e. recognised single nucleotide polymorphisms.
46
Why do you need two probes in SNP arrays?
Detects both alleles; otherwise failure would be indistinguishable form homozygosity of non-probed allele.
47
Main use of SNP arrays?
Used to map SNPs to assocations with specific diseases to determine susceptibility; involves looking for KNOWN variants rather than extremely rare mutations.
48
Whole GENOME sequencing?
All genes (introns and exons) and everything in between. Huge potential for in silico analysis, proven effectiveness in rare inherited disease. Will eventually become the standard DNA test and replace all current cytogenetics tests.
49
Applications for whole genome sequencing?
1. Establish mutation frequency for whole genomes (= ~70 per generation from parent to child). Much higher in cancer.
2. Genomic-wide associating studies
3. Diagnostic use (very rare conditions)
50
Why is the distribution of somatic mutations very uneven across the genome?
Gene-rich, early replication areas (oncogenes/TS genes) are packaged/used far more often and FAR EARLIER, which leaves them far more susceptible to damage, and explains why carcinogens preferentially affect these areas and not boring DNA!
51
Concerns with whole genome sequencing?
Reveals far more information than is probably healthy to know e.g. carrier status for AR disorders, risk factors for adult onset untreatable disease, genes assoc. with intelligence [genetic discrimination], non-paternity etc. Also still high cost, needs high computing power, very hard to interpret, tonnes of surplus, meaningless information. Worrying implications for asymptomatic children i.e. predictive testing. Also reveals information about close relatives; questions over obligations to inform them. Even if used in research, patients would by definition be identifiable from their genome.
52
Problems with interpreting whole genome data?
Everyone has 3 million changes; ~2,500 at conserved spaces (i.e. would change amino acid) from what is "normal". 20-40 likely to be damaging, 3-5 rare and causing disease. Also ~150 loss of function variants, of which 10-20 are rare and probably cause disease. Not enough data to know what that means!
53
Problems with diagnostic genetic testing (of any modality) i.e. find the mutation to confirm the diagnosis (of CRC, for example)?
Sensitivity <100%, multiple genes involved, specificity uncertain and get VUS! If do single gene etc. then can be targeted, but whole genome means added info about irrelevant data e.g. CVA.
54
Using Marfans as example of problems with diagnostic genetic testing e.g. have phenotype, and want to see if have gene?
Positive FBN1 mutation; not 100% specificity for Marfans because some (~5%) will have mutations and only arachnodactlyl for example, and some with phenotype will not have FBN1 mutation (<100% sensitivity). Some will have no mutation found, and some will have VUS. Note: analytic sensitivity and specificity is 100%.
55
Process of identifying obscure clinical syndrome with supposed genetic cause?
Do whole genome sequencing; screen at certain positions; get 1,000s of variants. Filter down with functional models, segregation studies, stochiometry to get one cause (hopefully).
56
Consequences of FBN1 mutation that are not Marfans?
Familial ectopia lentis, familial TAA, familial arachnodactyly ALONE. Not enough for diagnosis. Variable expressivity.
57
What is a polymorphism/VUS/mutation on amino acid level?
Changes sequence but not amino acid (genetic degeneracy). Not EXPECTED but not problematic. VUS might be another amino acid, similar in structure. Mutation would be polar instead of non-polar, for example, altering the protein.
58
Characteristics of VUS vs characterstics of mutations?
VUS = Limited data, unreported, present in controls, weak conservation. Mutations tend to be better researched = mutation type e.g. STOP, splice impact, functional data, absent from controls, evolutionary conservation, segregation.
59
Difference between doing predictive testing for son of father with Marfans and FBN1 mutations/VUS?
If dad has FBN1, do predictive (cord blood) and can say son will probably get Marfans (of some degree) if positive; if VUS then no point testing if passed on because information is meaningless.
60
Questions if have definite phenotype and then get VUS/no mutation?
If VUS, need detailed testing to find out if to blame. If no mutation, then consider low sensitivity, or if range is broad enough.
61
If have borderline phenotype and definite mutation?
Confirms diagnosis. If have borderline phenotype and VUS = real problem. If have normal genes then probably not Marfans.
62
If have normal phenotype and mutation?
Can be positive predictive test (e.g. BRCA if found in other relative) [useful]. If done for whole genome etc, pretty useless and worrying. If have normal phenotype and negative mutation then useful for negative predictive etc.
63
Expected ABG in major trauma?
Metabolic acidosis; hypoperfusion and high lactate, gives low pH, low HCO3, strongly negative base excess etc., CO2 low (tachypnoea). Lactate key!
64
Trauma triad of death?
Explains pathophysiology of traumatic bleeding. Hypothermia; acidosis; coagulopathy. Hypothermia leads to impaired coagulation; blood loss leads to more lactate and acidosis, which damages myocardium so more hypothermia.
65
Best imaging for finding bleeding in major trauma?
If have major trauma, do not use FAST/CXR/pelvic xray before whole body CT! Can do CXR for respiratory compromise/pelvic fracture etc, can do FAST (focused assessment with sonography for trauma) for pericardial effusion and haemoperitoneum. Can do eFAST (extended) to detect pneumothoraces.
66
Only time MRI is used in trauma
Spinal injury!
67
Pathophysiology of traumatic brain injury?
Impact, connections are torn/lacerated, get microscopic haemorrhage, then inflammation; get oedema and raised ICP causing hypoperfusion.
68
Autoregulation of cerebral blood flow?
Stays constant for large variation of MAP; cerebral arteries dilate at lower MAP to maintain flow, and constrict at higher.
69
When cerebral blood flow drops too far?
Initially get increased extraction of O2; then cells die as ion pumps fail, get lysis and swelling and raised ICP
70
Monroe-Kelly doctrine?
Brain has fixed surroundings, filled with parenchyma, blood and CSF; (haematoma) get CSF shift into spinal cord, venous blood removed; suddenly fails and get dramatic rise in pressure.
71
CPP equation and significance?
CPP=MAP-ICP; means that when ICP goes up in trauma, need ever-higher MAP to maintain flow
72
Cushing reflex?
Terminal stages of acute head injury; response to raised ICP. Get Cushing's triad of increased blood pressure, irregular breathing and bradycardia. May indicate imminent uncal herniation. Classically only systolic HTN (widened pulse pressure).
73
Mechanism of Cushing reflex?
When ICP exceeds MAP, compress arteries. ICP rise also stimulates para and symp; symp much greater initially causing HTN and tachycardia. Meanwhile, baroreceptors detect HTN and trigger vagal response, causing bradycardia. BP stays high to match ICP; combined pressure on brainstem causes abnormal ventilation. Aim is to maintain CPP until ICP drops.
74
Clinical signs of raised ICP?
1. Raised ICP. Reduced GCS, pressor (Cushing's ) response, projectile vomiting, CNVI palsies.
2. Brainstem herniation. CNIII palsy, motor posturing, lower extremity rigidity, hyperventilation.
75
Monitoring ICP?
Can insert fibreoptic intraparenchymal ICP monitor
76
Methods to control ICP?
Remove mass lesion, reduce CSF volume (drain), reduced parenchymal volume (mannitol), reduced cerebral blood volume.
77
How to reduce cerebral blood volume?
1. Arterial: sedate, ventilate, avoid fever, treat seizures.
2. Venous: head up, avoid jugular compression
Ventilation helps manage O2 and CO2 levels which can alter CBF; high CO2 causes vasodilation (bad) but too low get vasoconstriction and cerebral ischaemia (bad)
78
Managing CPP in raised ICP?
Paradoxically need to keep it reasonably high, or arteries dilate and ICP rises. But if increase CPP too much, ICP also rises.
79
When medical means are exhausted in high ICP?
Remember Monroe-Kelly; open up skull and remove haemotoma. If still high, need decompressive craniotomy and remove part of frontal bone.
80
Giving fluid in major trauma?
Never really use crystalloid; use plasma and red cells and remember to warm!
81
Red flags in ?sepsis?
HR >130, RR >25, SBP <90 (will independently give NEWS of 3). Also purpuric rash, supplemental O2, >2 lactate, V or less on AVPU.
82
What are PRRs?
Includes TLRs; key receptors on innate immune cells; bind to PAMPs to trigger innate and adaptive immune response. Primes macrophages/NK cells/dendritic cells/mast cells.
83
Difference between CTL T cells and NK cells?
CD8 T cells are specific; NK cells are not
84
IFNY in IR?
Released by NK and T cells to prime macrophages etc.
85
Function of TNFa?
Produced mainly by macrophages. Locally get inflammation, systemically get fever and shock.
86
Resting macrophages?
Sentinels, at skin/mucosa. Process debris. Express few MHC II (no point presenting dead tissue to T cells)
87
Priming macrophages?
Barrier penetrated, IFN release, macrophage reacts, upregulates MHC II and so can act as APC for T cells
88
Hyperactivating macrophages?
PRR (e.g. TLR4) recognises PAMP; increases reactive o2 molecules and lysosomes to become effective killer.
89
What generally follows PAMP/PRR interaction?
IL-1 and therefore start of acute phase response
90
What do activated macrophages secrete?
1. IL-1. Activates endothelium, activates lymphocytes, fever.
2. TNFa - activates vascular endothelium, increased vasc. permability (get cell/IgG/complement entry). Also fever, shock.
3. IL-6. Lymphocyte activation, increased antibody production and fever
Essentially activate and recruit complement and cells
91
What is upregulated along with MHC in acute inflammation on APCs?
Costimulatory molecules (second signal) e.g. CD80 and CD86.
92
NK cells?
Kill tumour and virally infected cells; secrete IFNY to activate macrophages (and activates by TNFa and IL-12 from macrophages). Non-specific.
93
Dendritic cell story?
Resting, immature, sentinel, low MHC. Stimulated by TLR or IFNy, increase B7 and MHC, phagocytose pathogen then travel to LN to kick start adaptive immunity!
94
What do dendritic cells do in LN?
Await sampling by T cell with cognate TCR, and secretes chemokines to promote monocyte (circulating macrophage) recruitment to infection. Survies ~1 week in LN.
95
How do dendritic cells influence T cell differentiation?
No infection; DC makes TGF-B and low IL-6; CD4 T cells express FoxP3 and become Tregs. In infection, DC makes high IL-6, T cell becomes TH17. Also affected by other cytokines etc. depending on type of pathogen and most useful type of T cell.
96
Why do naive B cells need T cells?
Helps them proliferate, form germinal centres and differentiate into plasma cells.
97
What happens after B cells form primary focus?
Some migrate to medullary cords and secrete antibody, others form germinal centre for somatic mutation [affinity maturation] and class switching and rapid proliferation. Die if do not retain capacity to bind Ag!
98
APC role of B cells?
Once activated, express high levels of B7 amd MHC and can present Ag to Th cells.
99
Special APC function of B cells?
BCR has high affinity for Ag, so can concentrate it for presentation to T cells at very low levels, very quickyl!
100
Intrinsic cell death?
Cessation of survival signals. Cytochrome c binds to Apaf:1, activates pro-caspase, cleavs I-CAD, CAD cleaves DNA
101
Extrinsic cell death?
FasL binds to and trimerises Fas. Clustering of death domains recruits FADD; recruits pro-caspase.
102
'Contextualised' discrimination of IS?
Context in which any antigen is encountered determines risk. Allows retention of maximal diversity of IR
103
Function of Tregs?
Suppress potentially dangerous activities of conventional Th lymphocytes
104
Two ways Tregs are formed?
1. Natural (thymic)
| 2. Induced/peripheral (induced from conventional CD4 T cells).
105
Central and peripheral tolerance?
Central is deletion in thymus of highly autoreactive T cells, peripheral is inactivation/deletion of partially autoreactive T cells (by T regs and apoptosis)
106
How can self-tolerance fail?
1. Molecular mimicry (bacterial Ag homologous to self)
2. Down-reg of reg cells (IS, IPEX)
3. Failure of central tolerance (AIRE)
4. Chronic APC stimulation (chronic bacterial inflammation)
107
What is signal transduction?
EC signal binds to cell surface receptor, alter sIC molecules, creates response, second messenger transmits signal into cell for a physiological response. Essentially EC signal to IC
108
Two examples of direct-ligand gated channels?
Nicotinic cholinergic, GABA
109
Two examples of G protein receptors?
Muscarinic ACh, adrenergic receptors
110
How do G protein coupled receptors work? (detail)
1. Hormone binds, receptor can bind to Ga (Ga/b/y and GDP together), causing conformational change and exchanging GDP for GTP)
2. Ga dissociates from Gb/y/receptor.
3. Hormone leaves receptor, Ga binds to and activates effector.
4. GTP hydrolysed, causes Ga to dissociates and reassociate with Gby (along with GDP).
Effector may be something like phospholipase C and starts PIP2 pathway.
111
PIP2 pathway?
Hormone to GPCR; Ga (patr of Gq protein) binds PLC; cleaves PIP2 to DAG and IP3; IP3 binds to ER an causes Ca2+ efflux. DAG activates PKC. DAG and IP3 are second messengers.
112
Adenylate cyclase pathway?
Hormone to GPCR, Conformation change, Ga binds to adenylate cyclase and activates it. Converts ATP to cAMP (lose 2P). These are secondary messengers, target protein kinase.
113
GPCR and renal water channels?
ADH binding to V2R (vasopressin 2 receptor) leads to aquaporin synthesis and water retention.
1. Inactivating V2R mutations gives NDI
2. Gain of function leads to NSIAD (inappropriate antidiuresis)
114
Tyrosine kinase linked receptors?
Ligand binds, receptors (inactive monomers) dimerise and are activated domers but not P'd. Then are P'd (fully activated) and can activate relay proteins for cellular response. 3 domains (EC, TM, IC).
115
EGFR family?
TKLRs. Her2 has no endogenous ligand. Her1 = EGFR. EGF binds, Her1 forms hetero/homodimer, autophosphorylates, get effects via MAPK to cause proliferationa/angiogenesis etc. (cascade, diversifies).
116
Mechanisms of increased EGFR action?
1. Overexpressed EGFR.
2. Autocrine stimulation
3. Heterodimerisation (more stimulatory)
4. Phosphatase defect means receptor stays activated
5. Mutant EGFR.
These methods may be used by cancer cells for growth advantage and can help with chemo/radiotherapy resistance.
117
Role of EGFR in human cancer?
EGFR has key role in growth, repair, cycle, metastasis. Often over-expressed, or more heterodimers, or have point mutations which affect therapy. Makes them key targets for drugs. HER2 often massively overexpressed leading to constitutive action.
118
Targeted treatments for EGFR?
1. Trastuzumab (Herceptin) blocks signal transduction, by binding to HER2. Particularly in breast cancers. If HER-2 not overexpressed (IHC/FISH) will be harmful
2. TKIs bind to IC domain; inhibit autophosphorylation e.g. gefitinib. Used in NSCLC.
3. Immunoconjugates (toxin on ligand/Ab is internalised and kills cell; targeted to cells overexpressing EGFR).
4. Antisense approaches; bind to ligand/EGFR RNA to inhibit synthesis
119
What type of receptor is the insulin receptor?
TKL!
120
Paradoxical roles of TNFa?
In normal conditions, is ligand for death pathway along with FasL (procaspase and DNA cleavage etc.) In hypoxic conditions, causes growth and proliferation etc.
121
Basic function of Akt1?
Inhibits apoptosis
122
Four ways cancer cells acquire sustained proliferative capacity?
1. Produce growth factors to drive own proliferation (autocrine) e.g. TGF-1, PDGF. 2. Or may express more/abnormal growth receptors e.g. EGFR/Her2; may be able to signal without ligand binding.
3. Produce ligand-independent effector pathways
123
What is genetic polymorphism? And SNP?
Multiple functioning forms of a gene in a population i.e. variants of "normal"; mutations are not considered polymorphism (usuallly <1% and are disadvantage) whereas true polymorphism promotes genetic diversity and persists because no variant confers true selection advantage. Most do not alter amino acid sequence and do not refer to continuous features like height.
SNP is most common type of variation, occurring ever 300 bases so are 10 million per genome. Can be mapped by SNP arrays to associations with disease. Hence why SNP not appropriate for rare disease because would not detect truly abnormal (<1% ) variants
