7: Investigating Cancer Genomes Flashcards

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1
Q

What is a main motivation for large-scale cancer genome sequencing studies?

A

Identify cancer driver genes
They provide cells with a growth advantage when mutated

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2
Q

Why are cancer bio banks paired with blood samples from the same patient so valuable to clinicians?

A

Shows the progress/regression of a patient, and can identify what is going on from diagnosis > flow up/relapse

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3
Q

At what points through the cancer patient’s journey are blood samples taken?

A

Diagnosis
Surgery
Chemo start
Chemo end
Follow - Up
Relapse, if applicable

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4
Q

Outline the steps of workflow of NGS data anaylsis

A
  • Assessment of Quality
  • Aligning sequences
  • Identifying variants
  • Annotating variants
  • Visualizing NGS data
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5
Q

What is NGS data analysis?

A

Next-generation sequencing

emerging technology which determines DNA/RNA sequences for whole genome or specific regions of interest

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6
Q

What happens during assessment of quality in NGS data analysis?

A
  • NGS reads are evaluated to remove, correct, or trim reads that don’t meet standards
  • Errors include base calling errors, poor quality reads.
  • This is mostly automated.
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7
Q

What are NGS reads?

A

Short reads from chopping genome randomly and re-assembling them

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8
Q

What happens during the aligning sequences phase of NGS data analysis?

A

Reads as aligned to reference genome, eg to GRC (genome reference consortium).

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9
Q

What happens during the identifying variants phase of NGS data analysis?

A

Compares the difference between patient tumour and reference.
Sequence coverage is important in this stage as identified mutations hound be supported by multiple reads.

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10
Q

What is Coverage in NGS?

A

The average number of reads that align to/cover known reference bases

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11
Q

What is depth of coverage?

A

The number of reads of a given nucleotide in an experiment

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12
Q

Why is coverage an important factor for variant detection?

A
  • Determines wether discovery can be made with a certain degree of confidence at particular base positions
  • The higher the depth of coverage, the more likely you are to find all mutants
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13
Q

What are the preferred depths of coverage for normal versus cancer DNA?

A

Normal: 30x
Cancer: 60x

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14
Q

Why is the preferred depth of coverage for Cancer DNA higher than for normal DNA?

A

Due to tumour heterogeneity.

Some parts of the tumour may have a mutation present, whilst other areas may not. You therefore need more coverage as normal tissues tend to be more homogenous.

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15
Q

What are the 3 different groups of genomic changes in cancer?

A
  • small variants (SMPs, indels. <50bp change)
  • copy number alterations (amplifications, deletions)
  • structural variations (inversions, translocations)
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16
Q

What happens during the annotating variants of NGS data analysis?

A

Identifies disease causing variants. Annotation of SNPs and INDELs provided via computational annotation tools.

17
Q

What happens during the visualization NGS data phase of NGS data analysis?

A

Use visualization tools and genome browsers to visualize variants.
Obtain information about variants.

18
Q

What variants can we obtain by visualizing variants?

A
  • Mapping quality
  • Aligned reads
  • Annotation information ( consequence, impact of variance, scores of annotation tools)
19
Q

How may a genome be visualization using a UCSC genome browser?

A
  • Gene as a long horizontal line, and exons as small vertical lines along it.
  • Arrows to denote direction of gene from promoter to 3’ end.
20
Q

What is the overall idealized pipeline Fiordland cancer genome analysis?

A
  • Sequence data prep and processing (sequencing of matched tumour/normal DNA, alignment to reference genome)
  • Dissect and catalogue genomic changes (Nucleotide changes, copy number alterations, structural variation)
  • Consequence analysis (recurrent changes, significantly altered genes, biological pathways)
21
Q

What is the challenge of genome sequencing glioblastomas?

A

There is strong intra- and inter- tumoural heterogeneity

22
Q

What % of the mutations in cancer occur in non-coding parts of the genome?

A

98.5%

23
Q

Outline the idea of evolutionary conservation

A
  • Conserved genome positions for 100 million years implies these areas are important, and have a specific function
  • We can observe conserved invariant sequences across species and evolution
  • We can use this to identify novel candidate driver genes