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SGUL - Genomics > Mapping Mendelian Disease > Flashcards

Mapping Mendelian Disease Flashcards

1
Q

What is the Lymphatics system known as?

A

The Cinderella of the circulatory system

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2
Q

What are the functions of the Lymphatic system?

A
  • Fluid homeostasis
  • Immune function
  • Fatty acid transport
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3
Q

What is the lymphatics system in regards to the capillary bed?

A

An integral part of the interweaving network in the capillary bed

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4
Q

What is primary lymphoedema?

A
  • It is a chronic Oedema
  • Often progressive
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5
Q

What are the two causes of primary Lymphoedema?

A
  • A developmental abnormality
  • A dysfunction of the lymphatics system
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6
Q

How does the phenotypes of primary lymphoedema vary?

A
  • Age of onset
  • Site
  • Inheritance patterns
  • Associated features
  • Genetic causes
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7
Q

What are the physical implications of primary lymphoedema?

A

Lymphoedema can be
- Debilitating
- Embarrassing
- Stressful
- Causes recurrent infections

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8
Q

Why is this research important?

A

Has no medical cure

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9
Q

How do we study genetic diseases? (PART 1)

A

Clinically first Through:
- Patients
- Families

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10
Q

How do we study genetic diseases? (PART 2)

A

It then gets sent to the laboratory for:
- Genetic identification
- Functional studies

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11
Q

How do we study genetic diseases? (PART 3)

A

It then gets sent back to the clinic for:
- Diagnostic tests
- Counselling
- Treatments

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12
Q

How do we study genetic diseases?
How is gene identification carried out?

A

Gene identification by gene mapping
- Homozygosity mapping
- Linkage analysis
- GWAS

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13
Q

How do we study genetic diseases?
How do we find disease causing mutations?

A

Through Sequencing

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14
Q

How do we study genetic diseases?
How do we prove they cause disease?

A

Using in silico, in vitro and in vivo tools

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15
Q

What is genetic linkage?

A

Genetic linkage is the tendency for alleles at neighbouring loci to segregate together at meiosis. Therefore to be linked, two loci must lie very close together

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16
Q

What is a haplotype?

A
  • Defines multiple alleles at linked loci
  • Mark chromosomal segments which can be tracked through pedigrees and populations
17
Q

When is crossing over likely to happen?

A

Most likely to happen During meiosis between loci separated by some distance than those close together

18
Q

How can we use information about linked alleles to identify disease causing genes?

A

1). If an allele is linked to a disease locus, the same allele will be inherited by 2 affected relatives than expected by chance
2). If the alleles and the disease locus are linked, all the affected individuals in a family are more likely to inherit this haplotype block

19
Q

How can we use information about linked alleles to identify disease causing genes?

A

3). If the alleles and the disease locus are unlinked to the disease locus, the affected individuals in a family are less likely to inherit the same marker alleles.

20
Q

How is linkage analysis used?

A
  • Gene mapping tools
  • Using observed loci (alleles) to draw interferences about an unobserved locus (disease gene)
  • Family based design
  • The goal is to find genomic regions linked to the disease
21
Q

What two processes that identifies the cause of primary lymphoedema?

A

Traditional linkage analysis and Sanger sequencing identifies the cause of autosomal recessive form of primary lymphoedema

22
Q

What is generalised lymphatic dysplasia? Hennekam syndrome (HS)

A
  • Antenatal hydrops with ascites and pleural effusions
  • Oedematous at birth
  • Intestinal lymphangiectasia
  • Peripheral lymphoedema; arms, legs, face
  • Mild developmental delay
23
Q

Steps for something idk

A

1). First take a pedigree and get as many DNA samples as possible
2). Use some kind of tool to observe alleles (generating genotyping data for your pedigree)

24
Q

Steps for something idk (PART 2)

A

3). Generate a file with your pedigree information plus the genotyping data from the SNP array
4). Run your file in a linkage programme

25
Q

What does NPL stand for?

A
  • Nonparametric linkage
  • Gives you a plot for each chromosome
26
Q

What is the problem with NPL?

A
  • No rules are imposed
  • Inheritance pattern is not taken into consideration
27
Q

What is the advantage of using parametric analysis?

A

Imposes rules about inheritance and disease frequency
- If you have a pedigree showing autosomal recessive inheritance, you apply a rule for affected family members to be homozygous for the mutant allele
- If you have a pedigree showing autosomal dominant inheritance you apply a rule for affected family members to be heterozygous

28
Q

After carrying out an autosomal recessive model, what do you do next?

A

The parametric test results are displayed for each of the 23 chromosomes

29
Q

What happens to LOD scores above 3.0 (>3.0)?

A
  • LOD scores >3.0 are taken as significant evidence for linkage
30
Q

What does an LOD score (>3.0) mean?

A
  • These results are taken as significant evidence for linkage
  • A LOD score > 3 translates to a p-value of approximately 0.05
  • This means the genetic locus is significantly linked to disease
31
Q

What happens to LOD scores below -2.0?

A
  • LOD scores below -2.0 show significant non linkage
  • LOD scores between -2 and 3 are inconclusive
32
Q

What are some features of 4 limb lymphoedema?

A
  • Autosomal dominant
  • Pubertal/adult onset
  • Associated with venous incompetence
  • No other abnormalities
33
Q

How do we find disease causing mutations?

A
  • Traditional Sanger sequencing: Candidate gene screen
  • Next generation sequencing (NGS) (WGS (WES)
34
Q

Summary (Open answers)

A
  • Rare disease is often caused by mutations in a single gene
  • Genetic analysis can identify the causative mutations
  • Linkage analysis is an examples of such technique
  • Things are not always straight forward and a good understanding of genetics and the tools applied is necessary

SGUL - Genomics (21 decks)

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