Study Guide for BTEC 444 (Mid_Term_Exam_2)

Cancer Biomarkers

Measurable biological molecules used to detect, classify, or predict aspects of cancer. They can be found in tissues, blood, or other body fluids. Different categories based on their purpose.

Diagnostic biomarkers

Prognostic biomarkers

Diagnostic Biomarkers

Help detect or confirm the presence of cancer, distinguish

Role:

Distinguishes malignant from benign lesions. (identify whether a lesion is likely cancerous or not)

Identifying cancer subtype or tissue origin (CDX2 expression - confirms colorectal origin in metastatic adenocarcinoma)

Guide diagnosis and staging

Prognostic Biomarkers

Provides information about the likely course or natural progression of the disease, regardless of treatment.

Role:

Predicts survival, recurrence, or progression

Stratifies patients into risk categories (sorts patients into groups based on how high or low their risk is for: treatment failure, death, etc.)

Informs intensity of follow-up or adjuvant therapy (helps doctors decide how aggressive the after-treatment plan should be. What actions to take next)

Analytical Validation

The process of confirming that a diagnostic test or biomarker assay accurately and reliably measures the intended target (such as a DNA mutation, RNA expression, or protein level) under defined laboratory conditions. It ensures the test performs consistently and reproducibly before it is used in clinical decision-making

Key components of Analytic Validation

Accuracy: How close the test result is to the true value

Precision: Reproducibility across different runs, operators, and instruments

Sensitivity: Ability to detect low levels of the target

Specificity: Ability to distinguish the target from similar non-targets (e.g., wild-type vs. mutant)

Limit of Detection (LoD): The smallest amount of analyte that can be reliably detected (good sensitivity)

Linearity: Whether the test produces results proportional to analyte concentration (Should be consistent)

Robustness: Performance under variable conditions (e.g., different sample types or reagent lots) (Reliable/Consistent)

Clinical Validation

Process of demonstrating that a biomarker test provides meaningful medical information that correlates with clinical outcomes (Shows test results that are linked to real clinical significance, not just laboratory measurements)

Diagnosis

prognosis

Treatment Response

Disease Monitoring

Example of Clinical Validation

Oncotype DX breast cancer assay - validated to predict 10 year recurrence risk and chemotherapy benefit in early stage ER-positive, HER2 negative breast cancer patients

1. Tested in real patients

2. Proven to predict a real clinical outcome

(recurrence and treatment benefit)

3. Shown to be useful for guiding treatment

(who does or does not need chemotherapy)

Oncotype DX

A test that looks at the activity of certain cancer-related genes in a breast tumor. It helps decide whether a patient needs chemotherapy in early-stage ER-positive, HER2-negative breast cancer

What does the Oncotype DX Recurrence Score indicate?

It predicts a patient's 10-year risk of distant breast cancer recurrence and how much they are likely to benefit from adding chemotherapy to hormonal therapy. Low scores suggest chemo isn't needed; high scores suggest chemo is beneficial.

What does Oncotype DX measure?

It measures the activity of 21 genes in the tumor (16 cancer-related + 5 reference genes) to generate a Recurrence Score

What do the Oncotype DX Recurrence Score ranges mean?

0-17: Low risk → hormonal therapy usually enough

18-30: Intermediate risk → treatment depends on patient factors

31-100: High risk → chemotherapy likely beneficial

What does "node-negative" mean?

No cancer cells are found in the lymph nodes near the primary tumor

What does "node-positive" mean?

Cancer has spread to one or more nearby lymph nodes

What are lymph nodes?

Small, bean shaped immune structures that filter harmful substances and are common sites where cancer spreads

Why do node-negative patients generally have a better prognosis?

Because cancer hasn't spread beyond the original tumor area

cancer hasn't "escaped" the site → better outcomes

How does lymph node status affect treatment decisions?

Node status can influence whether chemotherapy is recommended.

Example: early stage ER+ breast cancer uses Oncotype DX to decide if chemo is needed for node negative women

What does T1N0M0 mean?

Small tumor (T1), no lymph nodes involved (N0), no metastasis (M0)

(Example for stage 0 - I of tumors)

What characterizes Stage 0 - I tumors?

Node-negative; tumor is localized to the primary site with no lymph node involvement

What characterizes Stage II - III tumors?

Node-positive; cancer has spread to nearby lymph nodes (axillary; armpits, sentinel; first checkpoint)

How many lymph nodes correspond to N1, N2, and N3?

N1: 1-3 nodes

N2: 4-9 nodes

N3: 10+ nodes

Why do node (+) patients have a higher recurrence risk?

Cancer has already spread beyond the primary tumor, increasing the chance of return

What is Stage IV cancer defined by?

Distant metastasis (spread to organs like live, bone, or lungs)

In Stage IV, what is the main factor determining treatment?

The presence of distant metastasis, not lymph node status

What is the treatment goal for stage IV cancer?

Disease control and improved quality of life

Clinical Utility

How useful a test is for improving patient care

What is Clinical Utility essential for?

Treatment decisions (e.g., selecting targeted therapies)

Prognostic stratification

Early detection or monitoring

Avoiding ineffective or harmful interventions

what are Microsatellite?

Short, repetitive DNA sequences (1-6 bp) normally kept stable during cell division

What causes Microsatellite Instability (MSI)?

Defects in mismatch repair genes (MLH1, MSH2, MSH6, PMS2), Lynch Syndrome, or MLH1 promoter hypermethylation

Which cancers are commonly linked to MSI?

Colorectal cancer (15-20%)

Endometrial cancer (up to 30%)

Gastric cancer (~15%)

What was the purpose of the TAILORx trial?

To determine whether women with early stage ER+, HER2 - negative breast cancer can safely avoid chemotherapy based on their Oncotype DX Recurrence Score

What does TAILORx stand for?

Trial Assigning Individual Options for Treatment

What patients group was studied in TAILORx?

Women with early stage, estrogen receptor positive (ER+), HER2-negative, node-negative breast cancer

How many patients participated in the TAILORx trials?

Over 10,00 women across 1,182 sites globally

What treatment was recommended for patients with a Recurrence Score of 0-10 in TAILORx?

Hormone therapy only (no chemotherapy)

What happened to patients with a Recurrence Score of 11-25 in TAILORx?

They were randomized to hormone therapy alone vs. hormone therapy + chemotherapy

What treatment was recommended for patients with a Recurrence Score of 26-100 in TAILORx?

Chemotherapy plus hormone therapy

What was the major outcome of the TAILORx study?

Many women with intermediate recurrence scores do not benefit from chemotherapy, allowing more personalized and less toxic treatment decisions

What is Cancer Precision Medicine?

An approach to treatment where therapies are tailored to subset of patients based on specific molecular features of their cancer, such as genetic mutations or changes in gene or protein expression

What is companion diagnostic?

A test used to determine whether a specific drug is likely to be safe and effective for a patient. These tests must be clinically validated before being approved for use

What are the two main regulatory path for molecular diagnostic tests?

Laboratory Developed Tests (LDTs) and FDA approved tests

Who regulates laboratory developed tests (LDTs)?

The Centers for Medicare & Medicaid services (CMS) through CLIA-certified laboratories

Who regulates FDA approved molecular diagnostic tests?

FDA

Trick to remember sensitivity

SnOUT: High Sensitivity -> a Negative result rules OUT disease

Trick to remember specificity

Spln: High Specificity -> Positive result rules IN disease

Sensitivity Formula?

true positive/(true positive + false negatives)

Specificity Formula?

true negatives / (true negatives + false positives)

Accuracy Formula?

(true positives + true negatives) / (all positives and negatives)

What does Positive Predicative Value (PPV) measure?

The probability that a patient actually has the disease when the test result is positive

Positive Predicative Value (PPV) Formula?

true positive / (true positive + false positive)

What does Negative Predicative Value (NPV) measure?

The probability that a patient does not have the disease when the test result is negative

Negative Predicative Value (NPV) Formula?

true negative / (true negative + false negative)

What is the main goal in defining the intended use of a molecular diagnostic test early in development?

To ensure the test is actionable and appropriate for the population being tested

What does "Fit for Purpose" mean in molecular diagnostics?

It refers to matching the test to its clinical context, such as addressing an unmet need or improving over existing tests

Why is building a development plan important for molecular diagnostics?

It ensures the test is designed around real - world use, such as user training and clinical workflow

Why is reimbursement is consideration in molecular diagnostics?

Because even clinically useful tests may not be adopted if insurance or healthcare systems won't cover them

What is Clinical histopathology?

The study of diseased cells and tissues using a microscope to identify abnormalities and diagnose diseases

What is Clinical molecular pathology?

The study of diseased cells and tissues at the molecular level, including DNA, RNA, and protein changes, to help diagnose and guide treatment

What are examples of FDA-approved molecular tests and what do they detect?

IHC (Immunohistochemistry) - detects protein expression and FISH (Fluorescence In Situ Hybridization) - detects specific DNA changes

What kinds of genomic alterations can next-generation sequencing (NGS) detect?

Mutations, copy number alterations, translocations, and gene fusions.

What are the advantages of NGS in molecular testing?

Efficient, cost-effective, saves tumor tissue, and allows simultaneous analysis of many genomic changes.

What are some types of sequencing used in molecular testing?

WES (whole exome sequencing), WGS (whole genome sequencing), targeted sequencing, RNAseq, and epigenomics.

Driver Mutations

Mutations that directly contribute to cancer development by giving cells a growth or survival advantage.

Passenger Mutations

Mutations that occur in cancer cells but do not contribute to tumor growth

Why is patient education important in molecular testing?

Because genetic information is complex, and patients may have difficulty understanding results and their implications.

What challenge can arise with patient expectations in molecular testing?

Patients may expect actionable results, but disappointment can occur if no actionable mutations are found.

Why is access to genetic counselors important?

Counselors help interpret results, but access may be limited, leaving patients without expert guidance.

What is the significance of germline findings in molecular testing?

Sequencing may reveal inherited mutations that affect health beyond cancer, including risks for family members.

What is a master protocol in clinical trials?

A trial framework designed to evaluate multiple therapies, biomarkers, or disease subtypes under one overarching protocol.

What is a basket trial?

A trial that uses one investigational drug (or drug combination) tested across multiple cancer types that share the same genomic mutation or biomarker.

What type of patients are included in a basket trial?

Patients with different tumor types but who all share the same genomic alteration (e.g., a mutation).

What is the main goal of a basket trial?

To test whether one targeted treatment works across multiple cancers driven by the same biomarker.

What is an umbrella trial?

A trial that analyzes multiple investigational drugs in a single type of cancer, with patients assigned based on specific genomic alterations

What type of patients are enrolled in umbrella trials?

Patients with the same tumor type but different genomic alterations, each linked to a specific therapy.

What is the main goal of an umbrella trial?

To match patients within the same cancer type to the most effective personalized treatment based on their genetics.

Basket vs. Umbrella Trial — what's the key difference?

Basket: Same mutation, different cancer types.

Umbrella: Same cancer type, different mutations.

What is the purpose of molecular profiling in cancer treatment?

To identify genetic mutations in a patient's tumor so therapy can be matched to the specific genotype

What major challenge exists at the start of molecular profiling?

Tumor heterogeneity - different cells in the tumor may have different mutations

What step follows molecular profiling in the matching process?

Variant interpretation - determining whether mutations are clinically meaningful (driver vs passenger mutations)

What does Pharmacokinetics describe?

What the body does to the drug

What does Pharmacodynamics describe?

What the drug does to the body

What are the four steps of ADME?

1. Absorption

2. Distribution

3. Metabolism

4. Excretion

Which PK step describes how a drug spreads through tissues?

Distribution

What is a mechanism of action in PD?

How the drug works at the molecular/cellular level

What is dose-response relationship?

How drug dose relates to its biological effect

Why do PK and PD matter together?

They help optimize dosing to maximize tumor killing while minimizing toxicity

What is bioavailability?

The fraction of the active drug that enters circulation and is available to have an effect.

What is absorption in pharmacology?

The movement of the drug from the administration site into systemic circulation.

What factor mainly affects bioavailability?

Absorption.

What is distribution?

The process where the unmetabolized drug moves from the bloodstream to tissues/organs.

What is metabolism?

The chemical alteration of a drug, making it easier to excrete.

Why is water solubility important for drugs?

It improves absorption, distribution, and excretion

What is drug formulation?

The process of combining chemicals and inactive ingredients with the API to create a final drug product.

Why is drug formulation important?

It improves solubility, drug stability, release timing, and pharmacokinetic properties.

What does API stand for?

Active Pharmaceutical Ingredient

Do pharma companies spend a lot of time on formulation?

Yes — often as much time and effort as discovering the API

What makes nanoparticles useful for drug delivery?

Their large surface-to-volume ratio, which affects drug solubility, stability, and biodistribution.

What is the main purpose of nanoparticle-based drug delivery systems?

To improve drug formulation and allow better targeting, delivery, and release of therapeutics.

What are liposomes made of?

Spherical vesicles composed primarily of phospholipids.

What type of nanoparticle involves attaching drugs to polymers?

Polymer-based nanoparticles (e.g., polymer-drug conjugates).

What are micelles used for in drug delivery?

They are polymeric carriers that help encapsulate hydrophobic drugs.