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Bench to bedside and beyond > 16. Genetics in Haematology > Flashcards

16. Genetics in Haematology Flashcards

1
Q

What are rare genetic diseases caused by?

A
  1. usually germline varients
  2. Will affect every cell in the body including the gametes
  3. Heritable
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2
Q

What is cancer caused by?

A
  1. Somatic variants
  2. Affects the cell with the mutation and all its progeny
  3. The mutation will confer a growth advantage
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3
Q

What is Clonal evolution?

A
  1. 1 cell will have a genetic change that gives it a growth advantage. This grows and increases the cell count.
  2. Due to very fast replication they pick up more genetic changes that gives more growth advantages.
  3. Most modern cancer treatments target specific genetic changes.
  4. This creates escape clones that have developed resistance to treatment and reform the cancer and cause relapse.
  5. All cancers have the founder clone and then additional mutations.
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4
Q

What is genomics?

A

The study of an organism’s complete set of genetic information including non-coding regions.

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5
Q

what is genetics?

A

The study of heredity

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6
Q

What are some of the clinical applications of genomic technology?

A
  1. Identifying rare diseases
  2. characterising malignant disease
  3. looking at infectious agents
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7
Q

What is sanger sequencing good for?

A
  1. when there is one gene that is/could be the cause of the symptoms
  2. genetics and inheritance
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8
Q

What is sanger sequencing bad for?

A
  1. symptoms that could be caused by multiple different mutations. 1 or them or a combination
  2. genomics studies
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9
Q

What is Glanzmann thrombasthenia?

A
  1. Caused by a mutation in the ITGB3 gene
  2. A disorder of the platelets that causes excess bleeding
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10
Q

How is Sanger sequencing used to sequence candidate genes?

A
  1. The disorder will likely be caused by this candidate gene so
  2. You PCR amplify the candidate gene
  3. Use Sanger to detect the mutation
  4. Use bioinformatics to find out whether that mutation causes the disorder you are testing for.
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11
Q

How is next generation sequencing used in genomics?

A
  1. The most common method of testing
  2. Use manufactured nucleotides called baits to amplify bits of the genome you are interested in
  3. Use parallel sequencing and bioinformatics to identify mutations and what disorders they could cause.
  4. can do 1000s of genes in 1 go.
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12
Q

What is important in bait design?

A

Have a number of overlapping baits to be suitable for around 6 different types of reactions

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13
Q

What are gene panels?

A
  1. These are done for most solid tumours.
  2. Simultaneously analyse 50-1000 genes by sequencing the exons.
  3. Useful for when selection of a candidate gene is difficult.
  4. Different mutations cause different cancers but we can test for all of them in every cancer to cover bases
  5. This is due to next generation sequencing speed and cost.
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14
Q

How is whole genome sequencing used in cancer genetic analysis?

A
  1. Covers the exons plus introns, untranslated regions and regulatory regions like enhancers and promoters.
  2. can be applied to somatic and germline samples.
  3. rapid and inexpensive.
  4. detect single nucleotide variants, insertions, deletions, copy number variants.
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15
Q

What are the benefits of whole genome sequencing in haematological malignancy?

A
  1. Somatic genotyping to identify genetic changes in cancer susceptibly genes and find specific chemotherapies.
  2. Gives an overview of total variant burden of the disease. Circos plot to represent all the genetic changes in 1 cancer including translations.
  3. Additional information that takes longer to get in serological tests like HLA screening, ABO, pharmacogenetic safety, finding other diseases or risk factors.
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16
Q

What other omics technology can be used?

A
  1. Transcriptomics to detect genetic changes and gene fusions through abnormal RNA. Use techniques like RT-PCR or mRNA-seq.
  2. Detect biochemical modifications that can alter gene expression. Epigenetic changes are implicated in the pathogenesis of multiple tumours.
17
Q

What can cancer susceptibility disorders be?

A
  1. Silent like BRCA1/2
  2. Cause detectable abnormalities first before causing cancer
18
Q

What will initiating mutations do?

A

Give the cells a growth advantage causing them to have abnormal progeny.

19
Q

Chronic myeloid leukaemia information

A
  1. Peak incidence at 40-60 years
  2. 15% of all leukaemias
  3. clonal proliferation of late myeloid cells, takes over the bone marrows and causes failure.
  4. increases the circulating white cell count
  5. causes painful and serious spleen enlargement.
20
Q

What makes a leukaemia chronic?

A
  1. It develops slowly at first
  2. then it will acquire a genetic change that makes it develop faster.
  3. It will then become an acute leukaemia
21
Q

What is the Philadelphia chromosome?

A
  1. The initiating event in CML.
  2. a translocation between chr9 and chr22.
  3. Causes a fusion protein of BCR/ABL on the derived chr22.
  4. moves ABL next to BCR causing ABL to always be expressed
  5. this means abnormal proliferation
22
Q

What is ABL?

A
  1. a mediator of cell growth and division.
  2. normally tightly controlled on chr9
  3. only on when you really need cell division.
23
Q

What is Imatinib?

A
  1. A synthetic inhibitor of BCR-ABL.
  2. discovered using genomics.
  3. Have saved 1000s of lives.
24
Q

How can we use genetic testing to diagnose CML?

A
  1. Look at the abundance of abnormal mRNA in the cells.
  2. BCR-ABL should be 0
  3. Results are given as a percentage of the transcripts in the cell.
  4. presence of more then about 5-10% would indicate active CML.
25
Q

How can genetic testing be used to monitor CML?

A

Constantly monitor the levels of BCR-ABL being expressed. This can be used to indicate successful treatment or show when a patient is entering relapse. Relapse due to resistance to treatment.

26
Q

How does imatinib work?

A

It sits in the active site of BCR-ABL to prevent its function.

27
Q

How does BCR-ABL acquire resistance?

A

Missense mutations that change the structure to prevent Imatinib binding.

28
Q

How can we overcome imatinib resistance?

A

develop lots of new drugs that can inhibit the new BCR-ABL

29
Q

Why are drugs like imatinib used?

A

To reduce the levels of cancerous cells in the blood to be low enough that we can give curative treatment like stem cell transplants.
They are well tolerated and cause not bad side effects.

30
Q

How has genetic testing help the treatment of CML?

A
  1. Confirmed the diagnosis
  2. Inform the choice of treatment
  3. Monitored the disease activity
  4. Selection of personalised therapy for relapsed disease.
31
Q

What is familial thrombocytopenia with predisposition to myeloid malignancy?

A
  1. An inherited mutation
  2. Germline variants of transcription factor RUNX1
  3. 1 in 100,000
  4. autosomal dominant
  5. mild or moderate bleeding
  6. Predisposes to myeloid malignancy (AML or MDS)
32
Q

What does familial thrombocytopenia cause?

A
  1. increased bleeding
  2. reduced platelet number
  3. abnormal platelet function for those that are made
33
Q

What is the usual clinical testing for these platelet disorders?

A
  1. Complete blood count and observe reduced platelets.
  2. Blood film to see enlarged platelets.
  3. Function testing to see how they are working.
  4. Then genetic testing
34
Q

What genetic testing is done for platelet disorders?

A
  1. There are lots of platelet disorders caused by lots of different genes.
  2. Cannot do Sanger due to the number of genes.
  3. Run a genetic panel of germline DNA to identify the disorder and whether it also has a cancer risk
35
Q

How many different genes could cause a platelet disorder?

A

around 100

36
Q

How has genetic testing helped treat the platelet disorder?

A
  1. Enables correct diagnosis and gives prognostic information.
  2. Can only diagnose these kinds of disorders with genetic testing.
  3. Family counselling and testing for other family members.
  4. Enhanced surveillance
  5. inform reproductive choice to future family
37
Q

Clinical applications of genomic technology: rare diseases

A

detect germline mutations to help diagnosis and treatment

38
Q

Clinical applications of genomic technology: malignant disease

A
  1. Testing to see if chemotherapy effects metabolism.
  2. Detect where you haven’t got cancer but can increase the susceptibility
  3. characterise genomic changes
  4. detect abnormalities very sensitively
38
Q

Clinical applications of genomic technology: Infection

A
  1. Genetic PCR like in covid detection
  2. can see if the person has changes elsewhere in the body

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