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Cancer > Introduction to Bioinformatics - Part 2 > Flashcards

Introduction to Bioinformatics - Part 2 Flashcards

1
Q

What causes cancer?

A

Damage to our DNA / genes

  • Natural accumulation of DNA damage (cancer occurs more often in older people)
  • Exposure to factors that damage DNA (eg: UV, smoking)
  • Inheriting faults in genes that increases risk of developing cancer
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2
Q

Does all DNA damage cause cancer?

A

No

Damage to certain genes, so called cancer driver genes, contribute to cancer

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3
Q

How do we identify what went wrong in cancer genome?

A

Compare DNA of cancer cells to DNA from healthy cells

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4
Q

To understand cancer, can look for association of genetic and genomic factors with what?

A

human health and disease,

their prevalence within families and populations,

their interactions with environmental factors,

and their contribution to disease risk.

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5
Q

Studying genetic and genomics may help to…

A

.) diagnose the disease
.) predict how severe the disease might be
.) choose the best medicine and correct dose
.) could find genetic factors that could be passed on to the next generation

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6
Q

What change is often found in the cancer genome?

A

Aneuploidy- quantity of genome changes

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7
Q

DNA& RNA sequencing is the process of what?

A

Determining the precise order of nucleotides within a DNA & RNA molecule

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8
Q

What four bases is DNA composed of?

A

Adenine, guanine, cytosine, and thymine (A,G,C,T )

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9
Q

What four bases if RNA composed of?

A

Adenine, guanine, cytosine, and uracil

A,G,C, U

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10
Q

What do NGS technologies facilitate?

A

Massively Parallel Sequencing

- multiple sequencing reactions are running simultaneously

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11
Q

What are the predominant applications of whole genome sequencing?

A

Structural variants

Point mutations

Copy number variation

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12
Q

What are the predominant applications of whole exome sequencing?

A

Point mutations

Copy number variation

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13
Q

What are the predominant applications of PCR amplicon?

A

Point mutations

Deletions

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14
Q

What are the predominant applications of transcriptome RNA?

A

Gene expression

Gene fusions

Splice variants

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15
Q

What are the predominant applications of exon capture transcriptome?

A

Gene expression

Gene fusions

Splice variants

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16
Q
  1. What is single cell sequencing?

2. What is advantage of this?

A
  1. Tissue first separated into individual cell

Cells then sequenced separately. DNA methylation, Intracellular protein etc can be measured

  1. Allows specific investigation of molecular landscape of cells
17
Q

What are the four steps of NGS workflow in clinical oncology?

A
  1. Sample processing
  2. Data processing
  3. Variant calling and annotation
  4. Data utilisation
18
Q

What is MSK?

A

Gene panel used

Overall analyses up to 500 genes – genes are nominated by researchers and experts across MSK (Memorial Sloan Kettering). Are all actionable targets, aim is that gene list is updated to include new genes in this panel.

Capable of detecting several classes of genomic changes

Provides comprehensive picture of full spectrum of genetic changes in tumour

19
Q

What are the 8 steps involved in MSK?

A
  1. Patient consent
  2. Sample accessing
  3. Sample preparation
  4. Sequencing
  5. Bioinformatic analysis
  6. Case review and sign out
  7. Genomic variant database e.g OncoKB used to compared variants found
  8. Findings used for clinical report, clinical trial matching and data mining and interpretation
20
Q

One example of bioinformatics is Foundation medicine gene panel

What are the tests available?

A

FoundationOne CDx-

  • For all solid tumours
  • Uses a tissue sample (tissue biopsy)
  • Tests the DNA of over 300 genes

Foundation Liquid CDx-

  • For all solid tumours
  • Uses a blood sample (liquid biopsy)
  • Tests the DNA of over 300 genes

FoundationOne Heme-

  • For blood cancers and sarcomas
  • Uses a tissue or blood sample
  • Tests DNA of over 400 and RNA of over 260 genes
21
Q

What does the FDA approve for adults and children with TMB-H solid tumours?

A

Pembrolizumab

22
Q

What does Tumor mutational burden (TMB) refer to?

A

Number of somatic gene mutations present in a tumour.

23
Q

What is TMB-H (high) defined as?

A

TMB ≥10 mut/Mb.

24
Q

What is an alteration in the nucleotide sequence of the genome of an organism or a virus called?

25
Q

What is the difference between germline and somatic mutations?

A

Germline are inherited and found in all ells

Somatic are not inherited and found within the tumour

26
Q

What is one of the major mechanisms of defective DNA repair?

A

Homologous recombination

27
Q

What does Homologous recombination deficiency (HRD) status reflect?

A

Whether there are mutations in BRAC1 and BRCA2 genes or if the cancer genome shows high Genomic Instability.

28
Q

With a positive HRD status, a patient’s DNA is what?

A

Unable to repair, and DNA damage- targeting drugs may be beneficial.

29
Q

What are two current tests that are able to detect homologous recombination deficiency (HRD)

A

Myriad Genetics’ myChoice CDx for olaparib and niraparib in ovarian cancer
Foundation Medicine’s FoundationOne CDx for olaparib in mCRP

30
Q

What is olaparib and niraparib?

A

PARP inhibitors:a type of targeted cancer drug.

They are a treatment for some women with ovarian cancer.

31
Q

What are two different novel precision medicine trial designs?

A

Umbrella trial:
1 type of cancer
Different genetic mutations
Test different drugs

Basket trial:
Multiple types of cancer with one genetic mutation
Test drug

32
Q

What can cancer screening detect and prevent?

A

Cancers at an early stage and in some

cases, even prevent cancers from developing in the first place.

33
Q

What is the most common cancer among men?

34
Q

What is the 2nd leading cause of cancer death?

A

Prostate cancer

35
Q

Prostate cancer risk goes up with age, as around 6 out of every 10 cases “are found in men older than 65.”

True or false

36
Q

Prostate cancer is more common in people without a family history of the disease?

True or false

A

False

More common in people with a family history of the disease

37
Q

What might make it easier to determine the necessity, as well as the rate, of regular prostate cancer screenings?

A

A 6-year research project identifies 63 gene changes that could help to indicate an increased risk of prostate cancer in certain men.

38
Q

How can computational science help speed up cancer research?

A

To store and retrieve data
To analyse data
To interpret data

39
Q

What are new technologies involved in cancer research?

A

Drug screening- CRISPR/Cas9 for Drug Discovery

Immune cell profiling

Digital Pathology

Genomics Data

Microbiome

Imaging

Cancer (20 decks)

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