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4.1 Molecular Biology > Molecular Diagnostics - Cancer Genomics > Flashcards

Molecular Diagnostics - Cancer Genomics Flashcards

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1
Q

What type of disease is cancer classified as?

A

Cancer is a genetic disease: both inherited and somatic (acquired).

This classification highlights that cancer can arise from genetic mutations passed down through generations or acquired during an individual’s life.

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2
Q

How many ‘driver’ mutations can be present in cancer?

A

Up to 10-20 ‘driver’ mutations.

Driver mutations are genetic alterations that contribute to the development and progression of cancer.

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3
Q

What is the significance of sequencing genomes in cancer research?

A

Sequence genomes (cancer tissue and normal) to find genetic changes and suggest possible therapies.

This process helps identify specific mutations that may be targeted for treatment.

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4
Q

What are somatic mutations?

A

Somatic mutations are inherited throughout a lifetime.

These mutations occur in non-germline cells and are not inherited by offspring.

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5
Q

What are germline mutations?

A

Germline mutations are inherited cancer mutations.

These mutations are present in the reproductive cells and can be passed to the next generation.

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6
Q

What is a key factor that leads to cancer development?

A

Polymerase makes mistakes in key genes involved in cell proliferation.

Errors in DNA replication can lead to the accumulation of mutations that promote cancer.

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7
Q

What advantage do tumor cells gain from mutations?

A

Tumor cells gain a selective growth advantage.

This advantage allows cancer cells to proliferate more rapidly than normal cells.

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8
Q

True or False: The same type of cancer can have different mutations in different patients.

A

True.

Each cancer patient may have their own unique mutations, even if they have the same type of cancer.

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9
Q

What is the trend in targeted therapies for cancer?

A

There has been a huge increase in small molecule inhibitors that inhibit specific cancers.

These targeted therapies are designed to attack specific genetic mutations found in cancer cells.

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10
Q

What is The Cancer Genome Atlas (TCGA)?

A

A cancer sequencing project collecting tissues from 11,000 patients

TCGA provides genomic data for various cancers, facilitating research and treatment.

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11
Q

When did The Cancer Genome Atlas project start and complete?

A

Started in 2009 and completed in 2016

This timeline reflects the extensive research and data collection involved in the project.

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12
Q

How many patients’ tissues were collected for The Cancer Genome Atlas?

A

11,000 patients

This large sample size allows for a comprehensive analysis of cancer genomics.

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13
Q

What type of cancers were studied in The Cancer Genome Atlas?

A

Cancers included:
* Brain (Glioma, Glioblastoma)
* Breast
* Gastrointestinal (Colon, Rectal, Stomach)
* Gynaecologic (Ovarian, Cervical, Uterine)
* Head and Neck
* Hematologic (AML)
* Melanoma
* Lung
* Urologic (Kidney, Prostate)

These categories encompass a wide range of cancer types for comprehensive research.

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14
Q

Where is all TCGA data currently stored?

A

Genomic Data Commons

The GDC portal provides public access to genomic data for further research.

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15
Q

What is the European equivalent of The Cancer Genome Atlas?

A

COSMIC

COSMIC (Catalog of Somatic Mutations in Cancer) is a database of somatic mutations in cancer.

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16
Q

What type of data was primarily compared in The Cancer Genome Atlas?

A

Cancer biopsies and normal biopsies

This comparison helps identify genetic differences that may drive cancer.

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17
Q

What percentage of patients in TCGA were subjected to whole genome sequencing?

A

22%

This indicates a focused approach on a subset of patients for detailed genomic analysis.

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18
Q

True or False: The data from The Cancer Genome Atlas is freely available.

A

True

This accessibility supports global research initiatives in cancer biology.

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19
Q

What is the purpose of cancer genome sequencing?

A

To identify key mutations by comparing tumor DNA/RNA to normal DNA/RNA

This process helps in understanding the genetic variations specific to cancer.

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20
Q

What samples are typically collected for cancer genome sequencing?

A

Tumor biopsy and normal biopsy taken at the same time

This dual sampling allows for a direct comparison between cancerous and healthy cells.

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21
Q

Why is it important to differentiate between normal genetic variation and cancer mutations?

A

To accurately identify mutations that contribute to cancer development

Genetic variation can exist in everyone, making it crucial to distinguish between benign variations and those that indicate cancer.

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22
Q

What is one of the main analyses performed during cancer genome sequencing?

A

Sequencing and alignment to a reference genome

This step helps in identifying mutations by comparing sequenced data against a standard genome.

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23
Q

What is the role of treatments available for common cell signaling inhibitors?

A

To target specific pathways involved in cancer cell proliferation

These treatments aim to disrupt the signals that promote tumor growth.

24
Q

Fill in the blank: Cancer genome sequencing involves the analysis of _______ and RNA.

A

DNA

DNA analysis is a critical component in understanding the genetic basis of cancer.

25
Q

True or False: Tumor and normal biopsies are collected at different times during cancer genome sequencing.

A

False

Both biopsies are collected simultaneously for accurate comparison.

26
Q

What is a key step in the integration and interpretation phase of cancer genome sequencing?

A

Identifying genetic variations that are specific to cancer

This step assists in determining the relevance of identified mutations.

27
Q

What does the term ‘cell proliferation’ refer to in the context of cancer?

A

The process of cancer cells multiplying and growing

Understanding cell proliferation is essential for developing effective treatments.

28
Q

How many single nucleotide variations (SNVs) are typically found in many cancer types?

A

10-100,000 SNVs

This range indicates the high variability of mutations present in different cancers.

29
Q

How many cancer genes have been identified?

A

> 400 cancer genes

This includes well-known genes associated with various cancers.

30
Q

Name three of the most common cancer genes.

A
  • p53
  • RB1
  • KRAS
  • BRCA1/2

These genes are frequently studied due to their roles in cancer development.

31
Q

True or False: Every patient with cancer has the same spectrum of mutations.

A

False

Each patient exhibits a unique selection of mutations.

32
Q

What is the significance of the 100,000 genome project in cancer genomics?

A

It helps determine normal variation vs cancer variations

This project aids in distinguishing between benign genetic variations and those associated with cancer.

33
Q

What are common structural variants found in cancer?

A
  • Deletions
  • Rearrangements of genes

These structural changes can significantly impact gene function and contribute to cancer progression.

34
Q

Fill in the blank: Every patient often has one common mutation associated with the disease along with ______ mutations specific to that individual.

A

10-20 other mutations

This highlights the complexity of cancer genetics and individual patient profiles.

35
Q

What is the challenge in distinguishing between normal genetic variation and cancer-related mutations?

A

Hard to figure out what is normal variation and what is cancer

The overlap between benign and malignant genetic changes complicates diagnosis and treatment.

36
Q

Cite one key publication related to cancer genomics from the Cancer Genome Atlas Research Network.

A

Nature 474, 603-15 (2011)

This publication integrates genomic analyses of ovarian carcinoma.

37
Q

What types of mutations are often present in cancer?

A

Single nucleotide variations and structural variants

Both types of mutations play significant roles in cancer development and progression.

38
Q

What are common pathways where mutations often fall?

A
  • Wnt
  • PI3K/AKT
  • Ras/Raf
  • TP53
  • RB

These pathways are critical in various cellular processes and are frequently implicated in cancer development.

39
Q

How many key pathways are mentioned in the context of mutations?

A

12

The specific pathways are important for understanding the molecular basis of different cancers.

40
Q

True or False: Different types of cancer can have the same mutated gene.

A

True

An example is the EGFR gene, which can be mutated in both non-small cell lung cancer (NSCLC) and colon cancer.

41
Q

What is a common outcome from sequencing in cancer research?

A

Finding a potentially ‘druggable’ mutation

This refers to mutations that can be targeted by specific therapies.

42
Q

Fill in the blank: Different kinds of cancers can have the same gene mutated, e.g., _______ in NSCLC and colon cancer.

A

EGFR

EGFR stands for Epidermal Growth Factor Receptor, a significant target in cancer treatment.

43
Q

What are some examples of genetic variations associated with cancer?

A
  • EGFR mutations
  • HER2 mutations
  • BRAF mutations
  • MET amplification
  • RET rearrangements

These genetic variations can influence treatment options and patient responses.

44
Q

Name some targeted therapy agents used in cancer treatment.

A
  • Gefitinib
  • Erlotinib
  • Afatinib
  • Trastuzumab
  • Vemurafenib
  • Dabrafenib
  • Crizotinib
  • Cabozantinib

These agents are designed to target specific genetic mutations in cancer cells.

45
Q

True or False: Only some lung cancer patients have EGFR gene mutations.

A

True

Only patients with these mutations will respond to drugs targeting them.

46
Q

What is the importance of identifying mutations in cancer patients?

A

It allows for the possibility of treating with specific inhibitors.

Knowing the sequence of mutations can guide targeted therapy.

47
Q

Fill in the blank: Protein kinases transfer _____ from one protein to another.

A

Ks

This function is crucial in various cellular processes, including cell division.

48
Q

What is the potential outcome of blocking protein kinases in cancer treatment?

A

It can stop cells from dividing.

Inhibiting these kinases can disrupt cancer cell proliferation.

49
Q

What is the focus of the development of small-molecule inhibitor drugs?

A

Targeting mutated protein kinases.

These drugs are designed to interfere with specific pathways involved in cancer.

50
Q

What is the mechanism of action of Gleevec in treating CML?

A

Gleevec binds to the active site of Abl protein kinase and inhibits its activity

This inhibition leads to remission in Chronic Myeloid Leukemia.

51
Q

What chromosome translocation is involved in Chronic Myeloid Leukemia?

A

BCR-ABL translocation

This translocation results in the hyperexpression of a protein kinase.

52
Q

What other kinases can Gleevec bind to besides Abl?

A

Kit

Gleevec can also be used to treat cancers with Kit mutations.

53
Q

True or False: Gleevec has been on the market for a long time and is well studied.

A

True

Gleevec has a long history of use and research.

54
Q

What percentage of patients can build up resistance to Gleevec?

A

20%

This resistance can limit the effectiveness of the treatment.

55
Q

Fill in the blank: Gleevec is primarily used to treat ______ in patients.

A

[Chronic Myeloid Leukemia]

CML is a type of cancer that affects the blood and bone marrow.

56
Q

What has the success of Gleevec led to in the pharmaceutical industry?

A

The funding of many other small molecule inhibitors

Gleevec’s success created a significant market for targeted cancer therapies.

57
Q

What type of drug is Gleevec considered?

A

A small molecule inhibitor

It specifically targets certain proteins involved in cancer cell proliferation.

4.1 Molecular Biology (14 decks)

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