Midterm 2 - Notes 5 (Part 1) Flashcards
Cancer critical genes
Gene that contribute to cancer formation when mutated
What do individual cancers have?
Individual mutations
What does an alteration in a given gene that contribute to cancer depend on? (4)
- Type of mutation
- Cell type
- Interaction with other mutated gene products
- Differentiation status
Identification of mutations in a given cancer is starting point for what 3 things?
- Identification of the mutation in cancer
- Understanding cancers on a molecular level
- Targets for diagnosis and drug development or other treatments
What is the benefit of identifying the mutation in cancer?
It can be cataloged to see what went wrong, how it started and identify how to prevent them
- its the holy grail
Why is it better to used short sequences when comparing genomes?
It makes it easier
What can you conclude if the reference genome is different than the normal genome and not from higher up?
That is it a somatic mutation and not inherited
What was detected in the cancer genome sequencing experiment?
Types of alterations in both coding and non-coding regions
What can you discover information about when you compare cancer with normal genomes of the same individual?
You can identify the somatic mutation information
What does it mean if a sequence map contains no reads?
We can conclude there was a homo deletion in the tumour DNA
What does it mean if a sequence map contains a few reads?
We can conclude there was a hetero deletion in the tumour DNA
- will get 1/2 the amount of reads
- more than one copy leads to genome duplication
What can you conclude from jumping from chromosome 1 to chromosome 5?
That there was some sort of gene translocation that took place
What was being dealt with in the first attempt of cancer genome sequencing?
Highly malignant leukemia
What are 3 things they found in the case study involving cancer genome sequencing?
- No large alterations
- chromosomes look fairly normal - Typical symptoms
- Used both tumour (test) and skin (control) samples for sequencing
- used this to identify the inherited gene
What kind of sequencing did they use in the caner genome sequencing experiment?
Illumina sequencing
What happened in the tumour sequencing for the experiment? (2)
- Used short reads
2. Did quality filtering
What did quality filtering allow?
Detection of heterozygous mutations
What happened in the skin (control) sequencing for the experiment? (2)
- Expected them to be similar to the reference
2. Didn’t need as much and wanted to save money
What was the 2nd experiment sequencing mapping and variant calling about?
It was a proof of concept experiment
- needed to prove that it did work
What did they do in the sequencing mapping and variant calling experiment? (3)
- Aligned sequences to human reference genome
- 3.8 million single nucleotide differences
- could be SNP or SNV - Compared it to 2 other individual human genomes
- number of SNP variants to hg18
- used sanger and illumina sequencing - Used SNP array to determine variants
What human genome did they use as a reference in the sequencing mapping and variant calling experiment?
hg 18
- human genome 18
SNP
Single nucleotide polymorphism
- inherited differences
SNV
Single nucleotide tumour variants
- somatic differences (but sometimes can also be inherited)
What was the final conclusion about the sequencing mapping and variant calling experiment?
Was that yes we can use it to determine whole genome sequencing
What did a high quality data filter do?
Reduced the number of SNPs
- different though from human genome sequencing
Passenger mutations
Are mutations that do not provide a growth advantage to cancer
- do not contribute to cancer formation
What is the type of mutation that is dealt with the most in this experiment?
Passenger mutations
What are the candidate mutations?
Candidates for being somatic mutations
- higher than expected
What does it mean that the candidates for somatic mutations were higher then expected?
That the tumour accumulated 10s of thousands of somatic mutations on its way to becoming cancerous
What did they expect in this experiment?
Most were passenger mutations
What did they focus on?
Protein coding gene regions
SNVs filtered out due to what 3 things?
- Present in the germ line of other individuals
- unlikely this caused it to be cancerous - In non-coding regions
- introns - Synonymous
Synonymous
Silent mutations where codon changes but still produced the same amino acid protein
- unlikely to change the protein function
What 2 things did they use to validate SNVs?
- Targeted PCR
2. Sanger sequencing
What did they find a large majority of?
False positives
- which created a high error rate
Was the proof of concept successful?
Yes
