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M2M > Genetics Review > Flashcards

Genetics Review Flashcards

1
Q

What is pharmacogenetics?

A

the study of differences in drug response due to allelic variation in genes affecting drug metabolism, efficacy, and toxicity

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2
Q

What is pharmacogenomics?

A

the genomic approach to pharmacogenetics and is concerned with the assessment of common genetic variants in the aggregate for their impact on the outcome of drug therapy

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3
Q

What are pharmacokinetics?

A

the rate at which the body absorbs, transports, metabolizes, and excretes drugs or their metabolites

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4
Q

What are pharmacodynamics?

A

the response of the drug binding to its targets and downstream targets

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5
Q

What are the two ways drugs can be modified to increase metabolism (phase I and II)?

A

Phase I - attach a polar group to make it more soluble

Phase II - attach a sugar/acetyl group to detoxify the drug and make it easier to excrete

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6
Q

What does the cytochrome P450 (CYP450) gene code for and what do they do?

A
  • CYP450 enzymes that are very active in the liver

- they metabolize a wide number of drugs

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7
Q

What enzyme activates codeine?

A

CYP2D6

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8
Q

What does a frameshift mutation of a CYP450 gene result in?

A

no activity (poor activity)

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9
Q

What does a splicing mutation of a CYP450 gene result in?

A

no activity (poor activity)

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10
Q

What does a missense mutation of a CYP450 gene result in?

A

reduced activity (poor activity)

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11
Q

What does an increase in copy number alleles of a CYP450 gene result in?

A

increased activity (ultrafast activity)

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12
Q

CYP3A (substrate, inhibitors, inducers)

A

drug - cyclosporine
inhibitors - ketconazole, grapefruit juice
inducers - rifampin

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13
Q

CYP2C9 and VKORC1

A

drug - warfarin

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14
Q

What is the indirect method for counting autosomal dominant mutations (where reproductive fitness = 0)?

A
  • all cases represent new mutations

- incidence = 2µ (µ=mutation rate)

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15
Q

What is the direct method for counting autosomal dominant mutations?

A
  • number of new cases with no family history divided by the number who do not have it
  • since each has 2 alleles for each gene then multiply denominator by two for the mutation rate
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16
Q

What is the Hardy-Weinberg equation?

A

p^2 + 2pq + q^2 = 1

p + q = 1

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17
Q

Prader-Willi Syndrome symptoms and cause.

A

cause - deletion or methylation of chr 15 paternal

  • excessive eating
  • short stature
  • hypogonadism
  • some degree of intellectual disability
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18
Q

Angelman Syndrome symptoms and cause.

A

cause - deletion or methylation of chr 15 maternal

  • short stature
  • severe intellectual disability
  • spasticity
  • seizures
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19
Q

Behwith-Wiedemann Syndrome symptoms and causes.

A

cause - chr 11 - overactive IGF-2 gene (growth factor) and/or CDKN1C (inhibitor of cell proliferation)

  • macrosomia
  • macroglossia
  • midline abdominal defects
  • can develop hemihypertrophy and increase risk of cancer
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20
Q

Russell-Silver Syndrome symptoms and causes

A

cause - hypomethylation H19 and IGF2, maternal uniparental disomy on chr 7

  • tiny size and short stature
  • mildly abnormal facial features
  • can develop hemihypertrophy and increase risk of cancer
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21
Q

IDIC 15 symptoms and causes

A

cause - inverted duplicated isodicentric 15q

  • autism
  • NOT dysmorphic
  • often hypotonic
  • seizures common
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22
Q

15q interstitial duplication

A
  • only has phenotype if inherited from the mother
  • autism
  • NOT dysmorphic
  • seizures common
  • hypotonia common during infancy
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23
Q

What causes Downs Syndrome?

A

usually error of nondysjunction

- increased risk with increasing maternal age

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24
Q

What are common medical issues for Downs Syndrome patients?

A
  • atrioventricular canal
  • GI structural anomalies (atresia)
  • GERD
  • blocked tear ducts, myopia, lazy eye, nystagmus, cataracts
  • chronic ear infections, deafness, enlarged tonsils
  • thyroid dz, diabetes, reduced fertility
  • orthopedic probs
  • increased risk of leukemia, iron deficiency anemia
  • hypotonia, speech probs
  • early Alzheimers and autism
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25
Q

What are alpha-satellite repeats?

A
  • 171 bp repeat unit
  • near centromeric region
  • may be important to chromosome segregation in mitosis and meiosis
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26
Q

Which chromosomes are hotspots for human-specific evolutionary changes?

A

chr 1, 9, 16, Y (because of tandem repeats)

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27
Q

What are Alu?

A

300 bp repetitive element

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28
Q

What are L1?

A

6 kb repetitive element

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29
Q

What are copy number variations (CNVs)?

A
  • where sections of the genome are repeated (one copy to many)
  • primary type of structural variation
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30
Q

Why is gene duplication a major mechanism behind evolutionary change?

A

when a gene duplicates it frees up one copy to vary while the other copy continues to carry out critical function

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31
Q

Describe reciprocal translocation.

A
  • results from the breakage and rejoining of non-homologous chromosomes, with a reciprocal exchange of broken segments
  • increased risk of producing unbalanced gametes
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32
Q

For a parent with reciprocal translocation, which segregation produces normal gametes?

A

Alternate segregation

  • adjacent segregation produces unbalanced gametes
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33
Q

What is robertsonian translocation?

A
  • fusion of two acrocentric chromosomes with their centromeric regions
  • results in loss of both short arms (rDNA repeats)
  • carriers often phenotypically normal
  • may lead to unbalanced karyotypes for their offspring
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34
Q

What chromosome is involved in Wolf-Hirschhorn syndrome and what are the symptoms?

A
  • del chr 4
  • facial clefting
  • prominent ears
  • microcephaly, intellectual disability
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35
Q

What chromosome is involved in Cri du chat syndrome and what are the symptoms?

A
  • del chr 5
  • microcephaly
  • characteristic cry
  • seizures, intellectual disability
36
Q

What chromosome is involved in Bechwith-Wiedemann syndrome and what are the symptoms?

A
  • dup 11 (paternal)
  • overgrowth
  • omphalocele
  • predisposition to Wilms, other tumors
37
Q

What chromosome is involved in DiGeorge syndrome and what are the symptoms?

A
  • del chr 22
  • absent or hypoplastic thymus and parathyroids
  • congenital heart disease
38
Q

What are the gene poor chromosomes?

A

13, 18, 21

39
Q

What percent of the genome is AT rich?

A

54%

40
Q

What is satellite DNA?

A
  • tandem repeats
  • alpha-satellite repeats - found near centromeric region of all human chromosomes - may be important to chromosome segregation in mitosis and meiosis
41
Q

What is the Alu family?

A
  • dispersed repetitive elements

- e.g. of SINEs (short interspersed repetitive elements)

42
Q

What is the L1 family?

A
  • dispersed repetitive elements

- e.g. of LINEs (long interspersed repetitive elements)

43
Q

Why are Alus and L1s clinically relevant?

A
  • retrotransposition may cause insertional inactivation of genes
  • repeats may facilitate aberrant recombination events between different copies of dispersed repeats leading to disease
44
Q

What are minisatellites?

A
  • insertion-deletion polymorphisms (indels)

- tenderly repeated 10-100 bp blocks of DNA

45
Q

What are macrosatellites?

A
  • insertion-deletion polymorphisms (indels)

- di-, tri-, or tetra-nucleotide repeats

46
Q

How are single nucleotide polymorphisms detectable?

A

PCR

47
Q

What are copy number variations?

A
  • variation in segments of genome from 200 bp - 2Mb

- can be one additional copy to many

48
Q

What are the limitations of nextgen DNA sequencing?

A
  • no mammalian genome has been completely sequenced
  • relies on short read sequences
  • complex, highly duplicated regions are typically not examined
49
Q

What are the limitations of genome-wide association studies?

A
  • “missing heritability” - many studies implicate loci that account for only a small fraction of the expected genetic contribution
  • many regions of the genome are unexamined by genome wide screening technologies
50
Q

What are metacentric chromosomes?

A

centromere is located in the middle of the chromosome

51
Q

What are submetacentric chromosomes?

A

centromere is slightly removed from the center

52
Q

What are acrocentric chromosomes?

A

centromere is near one end of the chromosome

53
Q

What is nondisjunction?

A

missegregation of chromosomes at metaphase in either mitosis or meiosis

54
Q

What is monosomy?

A

cell lacks one copy of a chromosome

55
Q

What is the two hit theory of maternal age effect?

A
  • diminished recombination (more susceptible to possible nondisjunction)
  • the diminishing ability of the oocyte to successfully complete chromosome segregation in the presence of unfavorable recombination events
56
Q

What is heritability of a trait?

A
  • the proportion of total variance in a trait that is due to variation in genes
  • high heritability - differences among individuals can be attributed to differences in genetic makeup
  • high heritability does not imply that non-genetic factor are not important and vice versa
57
Q

What is the disorder in Hb Kempsey?

A

mutation in beta-globin chain that binds O2 too tight

58
Q

What is the disorder in Hb Kansas?

A

mutation in beta-globin chain that binds O2 too weakly

59
Q

What are thalassemias?

A

disorders of imbalanced global levels resulting in markedly reduced or no synthesis of one globin type

60
Q

What is Hereditary Persistence of Fetal Hemoglobin?

A

group of clinically benign conditions that impair the perinatal switch from gamma to beta globe synthesis, leading to high level production of HbF in adults

61
Q

What is Hemoglobin C disease?

A
  • milder form of hemolytic anemia than sickle cell
  • HbC is less soluble than HbA and forms crystals
  • autosomal recessive
62
Q

Hemoglobin SC disease

A

compound heterozygotes of beta(s), sickle cell, and beta(c), hemoglobin C, have milder anemia than sickle cell disease

63
Q

alpha-thal-1 allele (- -)

A
  • common in Southeast Asia
  • deletion of both copies of alpha-globing genes
  • homozygous state results in hydrops fetalis
  • heterozygous - mild anemia
64
Q

alpha-thal-2 (alpha -)

A
  • common in Africa, mediterranean, Asia
  • deletion of one of the alpha-globin genes
  • no disease phenotype in heterozygotes
  • mild anemia in homozygotes
65
Q

alpha-thal-1/alpha-thal-2 (alpha -/- -)

A
  • only 25% normal alpha-globin level

- severe anemia

66
Q

Thalassemia major

A
  • severe anemia
  • enlarged liver and spleen
  • temporarily treat with blood transfusions (cause iron accumulation -> organ failure. can be treated with iron chelation therapy)
67
Q

Simple beta-thalassemia

A
  • caused by mutations or deletions that impair the production of beta-globing chain alone (other genes unaffected)
68
Q

Complex thalassemia

A
  • caused by large deletions that remove the beta-globin gene plus other genes in the beta-cluster
69
Q

beta+-thalassemia

A
  • some beta-globing is made so HbA is present
70
Q

beta0-thalassemia

A

zero beta-globing synthesis so no HbA is present

71
Q

delta-beta0-thalassemia

A
  • no delta or beta synthesis due to deletion in the coding sequence for both
  • milder clinical phenotype than beta0-thalassemia because remaining gala genes still active after birth
72
Q

What is the phenotype of phenylketonuria (PKU)?

A
  • microcephaly
  • profound mental retardation
  • seizures, tremor, gait disorders
73
Q

What is the biochemical defect in PKU?

A
  • defect of phenylalanine metabolism
  • most due to defects in PAH gene (phenylalanine hydroxyls)
  • some cases caused by BH4 defects (coenzyme)
74
Q

What is the phenotype of alpha1-antitrypsin deficiency?

A
  • 20fold increased risk of developing emphysema (more severe among smokers
  • increased risk of liver carcinoma
75
Q

Which allele results in disease symptoms for alpha1-antitrypsin deficiency?

A

Z/Z genotype

S/S genotype usually do not express symptoms

76
Q

What is the biochemical defect in alpha1-antitrypsin deficiency?

A

mutation in SERPINA1 that normally targets elastase released by neutrophils in the lung

77
Q

What is the phenotype of Tay Sachs?

A
  • progressively destroys neurons in the brain and spinal cord
  • early-onset, fatal disorder apparent in infancy
  • eye abnormality called cherry-red spot is characteristic
78
Q

What is the defect in Tay Sachs?

A

lysosomal storage disease

- defective in HexA responsible for degrading GM2 ganglioside

79
Q

What is the defect in Sandhoff disease?

A

defects in both HexA and HexB

80
Q

What is the defect in AB-variant of Tay Sachs?

A

defect in GM2 activator protein

81
Q

What do you need to know in order to do genotyping?

A
  • must know or suspect a specific genetic diagnosis

- gene must have been identified and the disorder should exhibit little or no allelic heterogeneity

82
Q

When should you use fragment analysis?

A
  • investigating small-medium deletion/insertions, repeat expansion
  • must know or suspect a specific genetic diagnosis
  • gene must have been identified
  • expected mutation must be of a type expected to result in a larger or smaller amplicon than wild type
83
Q

When should you use Sanger sequencing?

A
  • mutations in known genes
  • clinical sensitivity is below 100%
  • must know or suspect a specific genetic diagnosis
  • gene must have been identified
  • mutation must be detectable by sequencing
  • mutation must be located in a region of the gene actually sequenced
84
Q

When should you use massively parallel sequencing/nextgen sequencing?

A
  • looking at a sequence of known disease genes in highly heterogeneic diseases or clinical cases where diagnosis is uncertain
  • do not need to suspect a genetic diagnosis
  • gene must have been identified
  • mutation must be detectable by analysis algorithm
  • mutation must be located in a region of the genome that is captured
85
Q

What does allelic heterogeneity refer to?

A

multiple mutations in a particular gene can cause disease

86
Q

What is genetic heterogeneity?

A

mutations in multiple genes associated with the same phenotype

M2M (41 decks)

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