24 Applied Molecular Genetics Flashcards
Define and Describe:
Personalized medicine
Personalized Medicine:
- The use of biomarkers and companion diagnostic to select the appropriate therapies for patients, based upon their “personal” disease characteristics
// typically molecular or genetic characteristics
- Decrease ineffective drug use, increase appropriate therapy use
Personalized medicine uses molecular markers to pair patients with therapies
Define and describe:
Biomarkers
Biomarkers:
- Biomarkers are measurable analytes that can be used to diagnose, prognosticate, or predict response to therapy
- “ a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention”
- Molecular pathology = typically a gene or gene product associated with a disease process, most commonly cancer
One biomarker may be used for more than one purpose, especially across cancer types
Types of Biomarkers
- ? - Presence/absense of biomarker is diagnostic/exclusive of a particular disease
- ? - Status of biomarker provides information about how the disease will behave independent of therapy
- ? - Status of biomarker provides information about how the disease will respond to a specific therapy
- Diagnostic - Presence/absense of biomarker is diagnostic/exclusive of a particular disease
- Prognostic - Status of biomarker provides information about how the disease will behave independent of therapy
- Predictive - Status of biomarker provides information about how the disease will respond to a specific therapy
Predictive biomarkers may be used as “companion diagnostics” for specific drugs
Biomarkers- caveat
- Molecular pathology biomarkers can be ?, a ?, a ?, or even a ?
- The specific biomarker can be associated with multiple ? and may have multiple types of ?, each with different disease associations
- **need to know the specifics of the ? and the ? in order to determine impact **
- Molecular pathology biomarkers can be protein, a specific mutation, a copy number alteration, or even a fusion gene product
- The specific biomarker can be associated with multiple diseases and may have multiple types of alteration, each with different disease associations
- **need to know the specifics of the biomarker and the disease in order to determine impact **
Types of Biomarkers
- Diagnostic - ?
- Prognostic - ?
- Predictive - ?
- Diagnostic- Presence/absense of biomarker is diagnostic/exclusive of a particular disease
- Prognostic - Status of biomarker provides information about how the disease will behave independent of therapy
- Predictive- Status of biomarker provides information about how the disease will respond to a specific therapy
In which cases could the biomarker BRAF V600E be Diagnostic, prognostic and predictive?
Diagnostic
-?
Prognostic
-?
Predictive
-?
In which cases could the biomarker BRAF V600E be Diagnostic, prognostic and predictive?
Diagnostic
-Hairy cell Leukemia
Prognostic
-Colorectal cancer
Predictive
-Melanoma
What is the common biomarker of the following diseases?
Diagnostic
-Hairy cell Leukemia
Prognostic
-Colorectal cancer
Predictive
-Melanoma
BRAF V600E is diagnostic, predictive and prognostic
Diagnostic
-Hairy cell Leukemia
Prognostic
-Colorectal cancer
Predictive
-Melanoma
Define and describe:
Targeted therapies
- Specific therapy that takes advantage of ?
- “Targeted”: since the ? is typically only associated with the ?, ? tissue is less affected
Targeted therapies
- Specific therapy that takes advantage of disease associated biomarkers
- “Targeted”: since the biomarker is typically only associated with the disease, normal tissue is less affected
Define and describe:
“companion diagnostics”
- FDA Definition: “A medical device, often an in vitro device which provides information that is essential for the safe and effective use of a corresponding drug or biological product.
- The test helps a health care professional determine whether a particular therapeutic product’s** benefits to patients will outweigh any potential serious side effects or risks**”
What is Chronic Myelogenous Leukemia (CML)
- Neoplastic proliferation of leukocytes (mainly neutrophils)
- Protracted course with depletion of bone marrow and associated cytopenias
- Can have sudden acceleration and conversion to a more aggressive disease
What is the molecular basis of CML?
- Mutation?
- Generation of a ? and ? (?)
- ?product? directly contributes to malignancy by acting as a constitutively active ?
- Philadelphia chromosome translocation t(9:22)
- Generation of a novel fusion transcript and protein (BCR-ABL1)
- BCR-ABL1 directly contributes to malignancy by acting as a constitutively active RTK
Chronic Myelogenous Leukemia - Neoplastic proliferation of leukocytes (mainly neutrophils)
- Protracted course with depletion of bone marrow and associated cytopenias
- Can have sudden acceleration and conversion to a more aggressive disease
RTK=Receptor Tyrosine Kinase
The detection of what biomarker is required for the diagnosis of CML?
BCR-ABL1
- Detection of BCR-ABL1 translocation is required for the diagnosis of CML
- BCR-ABL1 positivity is predictive of response to TKI Gleevec
// It is the companion diagnostic for the therapy
- The alteration of the levels of BCR-ABL1 transcript is predictive and prognostic of patients overall survival
- Philadelphia chromosome translocation t(9:22)
- Generation of a novel fusion transcript and protein (BCR-ABL1)
- BCR-ABL1 directly contributes to malignancy by acting as a constitutively active RTK
CML - Chronic Myelogenous Leukemia - Neoplastic proliferation of leukocytes (mainly neutrophils)
- Protracted course with depletion of bone marrow and associated cytopenias
- Can have sudden acceleration and conversion to a more aggressive disease
RTK=Receptor Tyrosine Kinase
BCR-ABL1
- Detection of BCR-ABL1 ? is required for the diagnosis of ?
- BCR-ABL1 positivity is predictive of response to ?
// It is the ? for the therapy
- The alteration of the levels of BCR-ABL1 ? is ? and ? of patients ?
BCR-ABL1
- Detection of BCR-ABL1 translocation is required for the diagnosis of CML
- BCR-ABL1 positivity is predictive of response to TKI Gleevec
// It is the companion diagnostic for the therapy
- The alteration of the levels of BCR-ABL1 transcript is predictive and prognostic of patients overall survival
BCR-ABL as a biomarker
- Routine ? monitoring by ? is standard of care
- ? trial established clinically relevant ? that correlated ? to ?
- Routine BCR-ABL transcript monitoring by qPCR is standard of care
- IRIS trial established clinically relevant mRNA levels that correlated patient response to survival metrics
BCR-ABL biomarker testing
- High ? detecting the exon-exon boundary of the ?
- ? probes targeting both ? and ? genes typically performed for ?
- High sensitivity qRT-PCR detecting the exon-exon boundary of the fusion mRNA
- Dual Fusion FISH probes targeting both BCR and ABL genes typically performed for initial diagnosis
What is CML targeted therapy?
- Small molecular TKI imatinib mesylate (Gleevec)
- Targets unique kinase generated by BCR-ABL
- Drastic survival improvement vs typical therapy
Lung Carcinoma Classification
-Two Major Classifications:
1. ?
2. ?
-Two Major Classifications:
1. Small cell (SCLC)
2. Non-small cell (NSCLC)
Non-small cells has two major subtypes:
1. Squamous
2. Adenocarcinoma (the most important type from a molecular pathology standpoint)
Biomarkers in Lung Adenocarcinoma
- Advanced stage NSCLC has a bad prognosis
- Stage 4: ?
- Molecular testing revealed a number of genes that were prognostic of better survival in a subset of patients
- ? mutation, ? mutation
NSCLC = non small cell lung cancer
- Advanced stage NSCLC has a bad prognosis
- Stage 4:1-2yrs
- Molecular testing revealed a number of genes that were prognostic of better survival in a subset of patients
- KRAS mutation, EGFR kinase domain mutation
EGFR in NSCLC
- Type of protein?
- Multiple activating mutations occur within the kinase domain
- Most common TKI sensitizing mutations
- Exon 21 point mutations
- Exon 19 deletions
- These are predictive and now almost diagnostic
NSCLC = non small cell lung cancer
- Receptor tyrosine kinase
- Multiple activating mutations occur within the kinase domain
- Most common TKI sensitizing mutations:
1.Exon 21 point mutations
2.Exon 19 deletions
//These are predictive and now almost diagnostic
EGFR targeted therapy:
- ? and ? target the abnormally active ? and ?
- Significant ? advantage
EGFR targeted therapy:
- TKIs Erlotinib and Gefitinib target the abnormally active EGFR kinase and block activity
- Significant Initial survival advantage
- inhibition of cancer-cell proliferation and invasion, metastasis, and tumor induced neoangiogenesis
- Induction of cancer-cell cycle arrest and potentiation of antitumor activity of cytotoxic drugs and radiotherapy
Most patients develop resistance to standard EGFR TKIs
// ~50% develop a new ?
- Newer ? target this mutation specifically
- Switching to a ? after ? identification ? survival
Most patients develop resistance to standard EGFR TKIs
// ~50% develop a new EGFR mutation T790M
- Newer TKIs target this mutation specifically
- Switching to a new TKI after T790M identification increases survival
Other lung biomarkers
- ? chromosomal inversion creates a novel kinase in 2-3% of lung adenocarcinoma
- ? contributes to tumorigenesis
- Mutually exclusive of EGFR mutations
- Kinase sensitive to a specific ?
- EMLK4-ALK chromosomal inversion creates a novel kinase in 2-3% of lung adenocarcinoma
- ALK fusion contributes to tumorigenesis
- Mutually exclusive of EGFR mutations
- Kinase sensitive to a specific TKI crizotinib
Other lung biomarkers
- EMLK4-ALK chromosomal inversion creates a ?
- ALK fusion contributes to ? in 2-3% of lung adenocarcinoma
- Mutually exclusive of ?
- ? sensitive to a specific TKI crizotinib
- EMLK4-ALK chromosomal inversion creates a novel kinase in 2-3% of lung adenocarcinoma
- ALK fusion contributes to tumorigenesis
- Mutually exclusive of EGFR mutations
- Kinase sensitive to a specific TKI crizotinib
Cell Free DNA NGS
-Benefit of Cell Free DNA NGS?
- Patient known to have EGFR lung mutation and is on TKI
-Develops resistance - T790M mutation present?
-Typically, stage 4 patients aren’t ideal candidates for biopsy - Easier sample to test: Blood or urine (cfDNA analysis)
cfDNA analysis:
- Tumor (and normal tissue) releases circulating DNA into bloodstream
- Small percentage contains resistance mutation
- Need high sensitivity assay (specifically designed) to detect biomarker in the normal background
cfDNA analysis:
- Tumor (and normal tissue) releases ? into bloodstream
- Small percentage contains ?
- Need ? assay (specifically designed) to detect ? in the normal background
cfDNA analysis:
- Tumor (and normal tissue) releases circulating DNA into bloodstream
- Small percentage contains resistance mutation
- Need high sensitivity assay (specifically designed) to detect biomarker in the normal background
Describe the concept of cell-free DNA and list three ways that it might be used for cancer diagnostics/monitoring
- Cell free DNA may be used as a minimally invasive way to look for driver and/or resistance mutations in patients with cancer
- Detection of mutations in cfDNA requires remarkable sensitivity (and therefore deep coverage)
Detection of resistance mutations in cfDNA may precede the radiographic evidence of progression
The analysis of a patient’s cfDNA can therefore provide information that is useful for the diagnosis and monitoring of cancer, the assessment of transplant-graft rejection, and the diagnosis of infectious diseases — in addition to prenatal screening for trisomies.
Urinary detection of EGFR T790M Resistance Mutation
Analysis of cfDNA can be applied to evaluate the mutational makeup of cancer lesions and monitor cancer progression at the molecular level with no need of invasively acquired tissues from primary or metastatic lesions.
