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Medical genetics > Identifying disease genes > Flashcards

Identifying disease genes Flashcards

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USMLE® Step 1 flashcards Biology 101 flashcards
1
Q

How can we identify candidate gene for single gene defect if protein sequence known, what is one gene found this way?

A

cDNA sequence can be worked out

Probe used to screen cDNA library to isolate clone for gene, e.g alpha/beta globin genes

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2
Q

How can candidate genes be identified from a gene family?

A

If one member of gene family shown to cause disease, other members of family are candidate genes for related diseases

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3
Q

How can animal phenotypes be used to identify disease genes?

A

If a gene causes a phenotype in an animal, its human homologue is a candidate gene for similar human conditions

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4
Q

How can candidate genes be identified based on metabolic pathways?

A

If a gene product is part of a metabolic pathway, and that gene is mutated in some but not all people with a certain disease, other genes in the pathway are candidate genes for the remaining cases

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5
Q

If a disease shows anticipation, what is likely to cause it

A

Unstable expanding DNA repeat

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6
Q

How can cytogenic clues indicate a candidate gene?

A

Individuals with deletions/mutations in specific chromosome region may share particular phenotype

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7
Q

What method is used to identify single genes for conditions such as CF and HD?

A

Whole genome sequencing

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8
Q

What method is used to locate candidate genes ?

A

Genetic linkage

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9
Q

What is anticipation?

A

Not expressed till certain age, each generation age of onset younger

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10
Q

When is genetic linkage for discovery of single genes easier?

A

When populations have relatively restricted gene pool and long known pedigrees

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11
Q

How can we use genetic linkage for a large family affected by specific disease?

A

Polymorphisms in genotype of each family member determined.

Statistical analysis establish strength of linkage between marker and disease (i.e is polymorphism only in diseased individuals).

Strong association suggests marker is either within, or close to (in linkage disequilibrium with) a gene involved in pathogenesis of disease

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12
Q

How do we quantify how likely 2 loci are to be linked based on co-inheritance patterns of a family?

A

LOD score (statistical estimate of whether two genes, or a gene and a disease gene, are likely to be located near each other on a chromosome and are therefore likely to be inherited.)

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13
Q

What is the LOD score?

A

Statistical estimate of how likely 2 loci are to be linked based on coinheritance patterns of a family.

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14
Q

What is linkage analysis?

A

Mapping of trait based on its tendency to be coinherited with polymorphisms.

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15
Q

What do we have to determine before using linkage analysis?

A

Determine the genotype of each family member for polymorphic markers across the genome

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16
Q

Will loci on different chromosomes will be co-inherited?

A

No

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17
Q

What effects how likely two genes on the same chromosome will be co-inherited, why?

A

The closer 2 loci are on the same chromosome (smaller chance of recombination)

18
Q

What are polymorphism markers?

A

Genetic variants, occurring at fairly high frequency in population

They are not pathological

19
Q

What is the benefit of polymorphic markers being heterozygous in population?

A

So two copies of genes someone inherits can be distinguished

20
Q

What do we use polymorphic markers for?

A

Points of reference to determine which stretches of DNA are coinherited with certain diseases

21
Q

3 types of markers (biggest to smallest)

A

VNTRs
Microsatellites (short satellite repeats)
SNPs

22
Q

What are VNTR?

A

Changes in the numbers of repeated DNA sequences arranged in tandem arrays

23
Q

What sort of polymorphism is used for genetic fingerprinting?

A

VNTR

24
Q

What are microsatellites?

A

Class of VNTRs that have repeat units 1-6bps in length

25
Q

What are SNPs?

A

Polymorphism due to base substitution/insertion/deletion of a single base (not in coding region)

26
Q

What sort of mapping is used for consanguineous mapping?

A

Homozygosity/autozygosity mapping

27
Q

What does homozygosity/autozygosity mapping do?

A

Detects region of genome that affected people have in consantuineous families

Markers identified in these region and candidate genes then identified and sequenced

28
Q

Describe consanguineous family pedigrees compared to normal ones?

A

More complex

29
Q

When is whole exome/genome sequencing used?

A

Used for gene identification when no clues for suggesting candidate genes

(i.e. rare diseases used to find new genes for condition or find drug target in cancer)

30
Q

How can susceptibility (polygenic) genes be identified ?

A

Sibling pair association studies

Siblings must both be affected

Find region of maximum linkage, list genes here

31
Q

What do you do after identifying candidate genes for polygenic gene (clue: polymorphism)?

A

Polymorphisms within gene are genotyped in affected individuals and controls to test for association

32
Q

Why when using sibling pair method to find polygenic genes do you find region of maximum linkage?

A

Markers shared more often in affected sibling pairs could be associated with the disease.

33
Q

Why do sibling pair studies looking for susceptibility genes often give false positive associations?

A

Polygenic diseases are more influenced by environmental factors and have more variable phenotypes

34
Q

What is GWAS?

A

Genetic variants compared across entire genome so common alleles contributing to polygenic disorders can be identified in population studies.

35
Q

What does GWAS allow?

A

Can isolate candidate genes which may confer susceptibility to the condition.

36
Q

What is a criteria for GWAS?

A

Large sample size needed as p value is very small to avoid false positives.

37
Q

What is the general idea in how GWAS identifies susceptibility genes in populations?

A

Particular polymorphisms occur more commonly in affected individuals than in population

38
Q

GWAS has superseded linkage analysis as…

A

A more powerful way of identifying loci for polygenic traits

39
Q

What does GWAS rely on?

A

High density of SNPs (up to 700,000) used for a genome wide association scan

40
Q

Advantages of GWAS?

A

No prior hypothesis about which variants could be associated needed

Population stratification can be identified

Imputation: by genotyping 500,000 SNPs, genotypes for most other common SNPs can be inferred

41
Q

What is meant by population stratification?

A

Population contains subgroups of different ancestries in which both disease and variant may be common, but not genuinely associated.

42
Q

What is more difficult to identify with GWAS, what is the solution?

A

Rarer variants

Use exome chimps and imputation to identify rare variants in coding and non coding regions respectively.

Medical genetics (6 decks)

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