Biomarker discovery
19 important questions on Biomarker discovery
What is the definition of a biomarker?
What are false positives and what are false negatives?
false negatives: diseased individuals that are not diagnosed with the disease.
What is sensitivity? And what is specificity?
true negatives/ (true negatives + false positives). 1- specificity is the chance of a positive test in healthy people.
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What is the cut-off value?
What is the difference between the rule out limit and the rule in limit?
The rule in limit is the maximum place where you transfer the cut-off value to when you want to have as much as possible true negatives (no false positives but a lot of false negatives)
What is the receiver operating characteristics (ROC) curve?
What is the predictive value?
What is the biomarker discovery process?
What is the label-free biomarker research strategy?
What can be sources of variance in the label-free biomarker research strategy?
- influence on analytical variance (sample collection and storage)
- influence on analytical variance (sample preparation)
- influence on analytical variance (comprehensive profiling (MS settings)
- Accuracy of signal processing (data processing; classification)
- accuracy of statistical analysis (statistical analysis and validation)
- accuracy of protein identification and protein interaction network (biological validation)
- influence on analytical and biological variances (validation on large number of samples; patient cohort selection)
Summary biomarker basics:
- false positives and false negatives
- receiver operating characteristics (ROC) curve
- prevalence and predictive value
- biomarker discovery strategy & sources of variance
What is time alignment?
Summary data analysis:
- feature selection and multi-variate statistical analysis to find proteins/metabolites that contribute to group separation.
- univariate statistical analysis to assess significance of discrimination.
Summary application EAE model:
- longitudinal studies provide evidence of different protein time patterns;
- paraoxonase could be an early indicator of a relapse.
How are biomarkers validated?
- You select proteotypic peptides (peptides that only occur in the protein of interest and you compare it to a synthetic wit lc/msms)
- you get heavy labelled peptides. You choose and optimize the transitions and then you quantitatively analyse it by SRM.
What is the signature of those peptides?
- the chosen fragment peptide must ionize well and give intense fragments
- generally one transition is not enough for selective monitoring.
- for absolute quantification, stable isotope labeled internal standards must be added.
What is laser microdissection?
How do you convert the technique with tissue to blood?
- the biomarker release from tumor cells
- the biomarker release from healthy cells
- the entry of the biomarker in vasculature from tumor
- the entry of the biomarker in vasculature from healthy tissue?
- release rate from tumor cells
- release rate from healthy cells
- number of tumor cells at time
- number of healthy cells at time
so a lot of parameters.
What is the summary of the biomarker validation?
- tissue analysis after laser microdissection
- tissue analysis by immunohistochemistry (IHC)
- validation in biopsies by targeted LC-MS/MS
- translation from tissue to serum is challenging.
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