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M2M Unit 2 > Learning Objectives (not comprehensive) > Flashcards

Learning Objectives (not comprehensive) Flashcards

1
Q

autosomal dominant pedigree

A

i. One copy of disease allele needed to express phenotype
ii. 50% chance offspring will inherit disease allele
iii. all affected individuals have at least one parent who carries disease allele
iv. males and females equally affected
v. male-to-male transmission observed
vi. ie: muscular dystrophy, Huntington’s

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2
Q

autosomal recessive

A

i. Two copies of disease allele needed to express phenotype
ii. 25% change offspring inherits disease allele (has phenotype); 50% chance offspring inherits one copy of disease allele (carrier); 25% chance offspring inherits no copies of disease allele (not carrier)
iii. Parents of affected individual are not typically affected but are gene carriers
iv. Males and females equally affected
v. Often seen in consanguineous couples (related by blood)
Ie: sickle cell anemia, CF

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3
Q

x-linked dominant

A

i. One copy of disease allele on x-chromosome required for individual to be susceptible
ii. 50% chance for offspring to inherit disease allele from affected female
iii. affected male: all daughters will be affected but none of his sons
iv. Males and females affected (may be more severe or lethal in males)
Ie: Fragile X syndrome

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4
Q

x-linked recessive

A

i. Two copies of diseased allele on X chromosome are required for female to be affected; one copy for male
ii. Females are usually carriers because they have one copy of diseased allele
iii. Carrier female: 50% chance that sons will inherit disease from mom and 50% chance that daughters will be carriers
iv. Affected female: all sons will be affected, all daughters will be unaffected carriers
v. Affected men transmit disease to all daughters (who are then carriers) but none to sons
Ie: Duchenne muscular dystrophy, hemophilia A

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5
Q

What is mendel’s first law?

A

segregation; alleles segregate at meiosis into gametes

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6
Q

What is mendel’s second law?

A

law of independent assortment; segregation of each pair of alleles is independent (except linked genes)

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7
Q

How is penetrance like a light switch?

A

on/off (affected/unaffected)
i. Could have mutation but not be affected (no visible phenotype)
ii. 80% penetrance: 80% of individuals with mutation are affected
Fraction of individuals with trait (disease) genotype who show manifestations of disease

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8
Q

What is age-dependent penetrance?

A

likelihood of manifesting disease in mutation carriers depends on age

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9
Q

How is expressivity like a light switch?

A

light is on but you’re trying to figure out how severe (dimmer function)
i. Affected individual (gene mutation led to disease) looking at severity
Degree to which trait is expressed in an individual (severity)

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10
Q

What is the influence of sex on Mendelian inheritance patterns?

A

manifestation of a trait depends on individual’s sex

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11
Q

What is the influence of stochastic effects on Mendelian inheritance patterns?

A

random effects can influence expression of phenotypes

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12
Q

What are modifier genes?

A

genetic factors that influence phenotype

Ie: one gene affects eye color but another also influences it by changing amount or distribution of pigment in iris

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13
Q

What are phenocopies?

A 
same phenotype (as a genetic condition) due to non-genetic factors
Ie: some animals change fur color (phenotype) depending on temperature where they live
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14
Q

What is pleiotropy?

A

Some mutation leads to multiple and different phenotypes (different organ systems); genes that have multiple effects within the body

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15
Q

How frequent are SNPs?

A

1 per 1,000 base pairs between any human genomes

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16
Q

What are insertion-deletion polymorphisms?

A

lots of variation in genome comes from variation in these large blocks of small repeating segments instead of variation between important genes

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17
Q

Mini-satellites are tandem repeats of ________ base pairs of DNA

A

10-100

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18
Q

How many base pairs does the haploid human genome have?

A

3x10^9

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19
Q

Evolution and adaptation are fueled by __________

A

random genomic variation

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20
Q

How do individuals get new mutations?

A

shuffling of regions during meiosis (recombination)

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21
Q

VNTR (variable number of tandem repeats) are found in _________

A

minisatellites

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22
Q

Microsatellites contain ________ repeats

A

2-,3-,4-bp

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23
Q

STRP (short tandem repeat polymorphisms) are found in ____________

A

microsatellites

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24
Q

What is the primary type of structural variation in the human genome?

A

copy number variation

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25
Q

Genomic DNA copy numbers are measured using _____________

A

array comparative genomic hybridization (array CGH)

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26
Q

What protein coding sequence exhibits the greatest human specific copy number expansion?

A

DUF1220

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27
Q

Gene-rich genome

A

Chr19

how many genes (expressed segments) each contains

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28
Q

Gene-poor genome

A

Chr13,18,21

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29
Q

____% of the genome is G-C rich

A

38%

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30
Q

____% of the genome is A-T rich

A

54%

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31
Q

Euchromatic has (more/less) repeats and makes up (more/less) of genome

A

less, more

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32
Q

Categories and frequencies of genomic DNA sequences

A

a. 1.5% translated (protein coding)
b. 20-25% represented by genes (exons, introns, flanking sequences involved in regulating gene expression)
c. 50% “single copy” sequences
d. 40-50% classes of “repetitive DNA”

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33
Q

Tandem repeats are the basics for ________ techniques

A

cytogenetic banding

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34
Q

Tandem repeats are often found on _________ (hotspots for evolutionary change)

A

Chr1,9,16,Y

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35
Q

“Alpha satellite” repeats are found near the _________ region of all human chromosomes

A

centromeric

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36
Q

“Alpha satellite” repeats may play a role in _________ during mitosis and meiosis

A

chromosome segregation

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37
Q

What do retrotransposon elements in DNA do?

A

copy their own sequences into other locations in DNA (can cause inactivation of genes)

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38
Q

Two examples of dispersed repetitive elements are …

A
  • Short interspersed repetitive elements (SINES)

- Long interspersed repetitive elements (LINES)

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39
Q

Short interspersed repetitive elements (SINES) are part of the ______ family

A

alu

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40
Q

Long interspersed repetitive elements (LINES) are part of the _________ family

A

L1

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41
Q

Alu’s and L1’s can lead to non-allelic homologous recombination (NAHR), which is ___________

A

aberrant recombination events between different copies of dispersed repeats leading to diseases

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42
Q

How many human genes are there?

A

25,000-30,000

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43
Q

The three types of human genes are…

A
  • protein-encoding
  • RNA-encoding
  • pseudogenes
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44
Q

Gene families arise through __________

A

gene duplication

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45
Q

Meiotic recombination involves ________ crossing-over between _________

A

homologous; non-sister chromatids

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46
Q

What is the most common contiguous gene syndrome in humans?

A

del 22q11 (overexpression of multiple loci next to each other)

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47
Q

Methylation binding proteins attract ________ to _______ transcription and compact ________

A

HDACs, silence, chromatin

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48
Q

DNA methylation marks are established in the _______

A

gamete

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49
Q

DNA methylation is stably maintained in ______ cells after fertilization

A

somatic

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50
Q

Methylation in somatic cells is maintained by ____________

A

methyltransferase

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51
Q

Prader-Willi and Angelman Syndromes involve deletions in long arm regions of chromosome _____

A

15

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52
Q

Prader-Willi causes (%s)

A
  • 70% deletion of paternal chromosome
  • 28% maternal uniparental disomy
  • 2% mutation on imprinting center
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53
Q

Angelman Syndrome causes (%s)

A
  • 70% deletion of maternal chromosome
  • 4% paternal uniparental disomy
  • 18% (ish) imprinting center mutation on maternal allele
  • 8% mutated gene
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54
Q

FISH Probe: Centromere (name, use, example)

A

Name: cen
Use: enumeration of chromosomes
Example: ALL panel, prenatal dx

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55
Q

FISH Probe: Locus specific identifier (name, use, example)

A

Name: LSI
Use: deletion/duplication of gene (loci)
Example: p53, cancer

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56
Q

FISH Probe: Fusion (name, use, example)

A

Name: F, DF
Use: detecting translocation
Example: BCR;ABL, PMR;RARa

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57
Q

FISH Probe: Break apart (name, use, example)

A

Name: BAP
Use: detecting translocation and rearrangement
Example: MLL (cancer)

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58
Q

FISH Probe: Whole chromosome point (name, use, example)

A

Name: WCP
Use: identifying translocations or markers
Example: WCP 1-22, X, Y

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59
Q

The target DNA in chromosomal microarray is …

A

a single-stranded oligomer

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60
Q

CMA can only detect ________ and _________

A

gains, losses

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61
Q

CMA cannot detect _________________

A

balanced rearrangements (limited mosaicism)

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62
Q

The CYP450 enzyme is active in the _______ and ___________

A

liver, intestinal epithelium

63
Q

Cyclosporine is a(n) ________ of _______ gene.

A

immunosuppressant, CYP3A

64
Q

Grapefruit juice and ketoconazole are _________ of CYP3A gene

A

inhibitors

65
Q

Rifampicin is a(n) ________ of CYP3A gene

A

inducer

66
Q

tricyclic antidepressants and opioids such as codeine act on _______ gene

A

CYP2D6

67
Q

Warfarin acts on _______ gene

A

CYP2C9

68
Q

Proton pump inhibitors and fluoxetine act on ________

A

CYP2C19

69
Q

__________ drugs act on NAT gene

A

isoniazids for TB

70
Q

TMPT gene experiences _______ mutations that destabilize the genome

A

missense

71
Q

If you give kids with ALL a standard dose of ________, it will kill them.

A

6-mercaptopurine (for TMPT gene)

72
Q

Butyrylcholinesterase hydrolyzes _________, which acts on BCHE gene

A

succinylcholine

73
Q

G6PD is a ________ enzyme

A

x-linked

74
Q

people are susceptible to hemolytic anemia after exposure to _________ drug

A

sulfonamide, dapsone

75
Q

Rare mutations in RYR1 lead to _________

A

malignant hyperthermia

76
Q

Warfarin acts on the _______ gene by reducing vitamin K so it can be recycled and used to make more coagulation factors

A

VKORC1

77
Q

Hardy Weinberg assumptions

A
  • large population, random mating
  • constant allele frequencies
  • no mutation rate
  • all genotypes equally fit
  • no significant immigration/emigration
78
Q

Turner and Klinefelter’s syndromes are normally driven by ____________

A

meiotic nondisjunction

79
Q

Centromeres (are/are not) repeat rich

A

are

80
Q

The classes of DNA include __________ and _________________

A

tandem repeats, dispersed repetitive elements

81
Q

Types of DNA variation (3)

A
  • insertion/deletion polymorphisms
  • SNPs
  • copy number variation
82
Q

Increases in DUF1220 copy number led to an increase in _________ instability

A

1q21.1

83
Q

1q21.1 duplications lead to ________ and _________

A

macrocephaly, autism

84
Q

1q21.1 duplications lead to _______ and __________

A

microcephaly, schizophrenia

85
Q

Aneuploidy can occur…(3)

A
  • meiosis I
  • meiosis II
  • post-zygotically
86
Q

What percent of Turner’s Syndrome karyotypes are pure 45X?

A

50%

87
Q

75% of Klinefelter Syndrome comes from errors in _____________

A

maternal meiosis I

88
Q

Mosaicism is most commonly caused by ___________

A

nondisjunction

89
Q

In chromosomes, which are more common: structural rearrangements or numerical aberrations?

A

numerical aberrations

90
Q

75% of Robertsonian translocations involve chromosomes ____ and ____

A

13, 14

91
Q

Inversions with chromosomes 1,9,16, and Y are almost always ______ in nature

A

familial

92
Q

Pericentric inversions give rise to ___________

A

two complementary recombinants

93
Q

Imprinted genes make up less than ___% of the human genome

A

10%

94
Q

During crossing over, deletions are caused by __________________

A

low copy repeat misalignment

95
Q

Cytogenetics are important in diagnosing ________ while CMA are important in diagnosing __________

A

leukemia, lymphoma; children with delays

96
Q

APML is caused by gene fusion of ___________ and CML is caused by gene fusion of ____________

A

PML-RARalpha (t(15;17))

BCR-ABL (t(9;22))

97
Q

CML is treated with ___________

A

Gleevec

98
Q

Gleevec (CML treatment) binds at the ____ binding site in the BCR/ABL ___________ and the effect is __________

A

ATP, tyrosine kinase, inhibited cell proliferation

99
Q

DS infant and children have a _______ increased risk for developing AML or ALL and a _______ increased risk for developing AMKL

A

20-100 fold

500x

100
Q

Cytogenetics detects ____________ while CMA detects _____________

A

balanced rearrangements, runs of homozygosity

101
Q

CMA determines the _________ and _________ of deletions/duplications

A

size, location

102
Q

T/F You can see mutations in FISH

A

false (identifies number of a specific chromosome or translocation)

103
Q

What is inverted duplicated isodicentric 15Q (IDIC15)?

A

autism, not dysmorphic, often hypotonic seizures

104
Q

What are 15Q interstitial duplications?

A
  • maternally inherited
  • within one arm of chromosome
  • autism, not dysmorphic, hypotonic seizures
105
Q

Pharmacogenetics looks at variable responses due to ____________

A

individual genes

106
Q

Pharmacogenomics looks at variable responses due to ____________

A

multiple loci across the genome

107
Q

Pharmacokinetics describes the ___________ of drugs

A

absorption, distribution, metabolism, and excretion

108
Q

Pharmacodynamics describes the relationship between ___________

A

concentration of a drug (at active site) and biological effects

109
Q

Expected DNA mutations for poor metabolizers (4)

A
  • frameshift
  • missense
  • nonsense
  • splicing
110
Q

Expected DNA mutations for ultrafast metabolizers (2)

A
  • increased copy number

- missense

111
Q

Mendelian disease looks at the _____ of genetic effect and population genetics looks at the _________ of disease

A

size, frequency

112
Q

What can NextGen DNA sequencing determine?

A

if estimates of mutation rates from Hardy-Weinberg are correct

113
Q

Genes present for development of testes

A

SRY, SOX9, SF1, DAX1

114
Q

SF1/NR5A1 cause the genital ridge to differentiate into ___________ and __________

A
  • sertoli cells (AMH, spertm)

- Leydig cells

115
Q

Production of anti-mullerian hormone (AMH) is stimulated by…(2)

A

SRY, SOX9

116
Q

________ is important for differentiation of the testes

A

FGF9

117
Q

WNT4 protein is important in females for __________

A

differentiation of ovary

118
Q

WNT4 is inhibited by _______

A

SOX9

119
Q

CYP2D6 inhibitors (3)

A
  • quinidine
  • fluoxetine
  • paroxetine
120
Q

How are imprinting patterns maintained in offspring?

A

maintain methylation

121
Q

_______% of babies with DS have congenital heart defects

A

30-50

122
Q

Copy number variations are often enriched with __________ and __________

A
  • specific duplications

- sequence gaps

123
Q

First degree relatives include __________

A

parents, siblings, children

124
Q

Patau syndrome is trisomy ____

A

13

125
Q

Edwards syndrome is trisomy ____

A

18

126
Q

In adjacent 1 segregation, homologous centromeres go to _________ daughter cells

A

different

127
Q

In adjacent 2 segregation, homologous centromeres go to _________ daughter cells

A

the same

128
Q

Individuals with androgen insensitivity have _____________

A

extra female genitalia with male gonads

129
Q

The incidence of inversion is as high as ___%

A

1%

130
Q

Leydig cells produce _________ and Sertoli cells produce ________

A

testosterone, anti-Mullerian hormone

131
Q

Androgen insensitivity syndrome is caused by a _______________ gene

A

x-linked

132
Q

What is 5-alpha reductase deficiency?

A

inability to convert testosterone to dihydrotestosterone

133
Q

5-alpha reductase deficiency is caused by a ________________ gene

A

autosomal recessive

134
Q

allelic heterogeneity

A

existence of multiple alleles of a single gene causing a similar phenotype

135
Q

compound heterozygote

A

person who carries different mutant alleles at the same gene locus

136
Q

Alpha1-antitrypsin deficiency (ATD) is (early/late) onset

A

late

137
Q

Tay-Sachs has a defect in the ability to get rid of ___________, which makes up 5% of brain mass

A

ganglioside

138
Q

Qualitative hemoglobinopathies (3)

A

HbS, HbC, HbE

139
Q

Quantitative hemoglobinopathies (4)

A

alpha, beta, gamma, delta thalassemias

140
Q

Patients with Denys-Drash and Frasier Syndromes are genetically ______ but exhibit sex reversal because of a mutation in the _____ gene

A

male, WT1

141
Q

WT1 is a ____________ for the SRY gene

A

transcription factor

142
Q

Salt wasting in the first few weeks of life and metabolic stress are symptoms of ____________

A

congenital adrenal hyperplasia

143
Q

What is a genetic linkage study?

A

search genome for segments disproportionately co-inherited along with diseases in multiplex families

144
Q

What is log of odds?

A

a statistical measure of the likelihood that loci are linked together given the inheritance/disease pattern

145
Q

Gene linkage studies are most powerful for…

A

uncommon risk alleles with strong effects

146
Q

most commonly used DNA polymorphisms for finding genes (3)

A
  • microsatellites
  • SNPs
  • CNVs
147
Q

Candidate gene association studies are best for…

A

common risk alleles with small to moderate effects

148
Q

In sickle cell (HbS), the amino acid change is _______ to _________

A

glu(-) to val(neutral)

149
Q

In HbC, the amino acid change is ________ to ____________

A

glu(-) to lys(+)

150
Q

Alpha-thalassemias are usually caused by ________ and beta-thalassemias are usually caused by __________

A

deletions, point mutations

151
Q

4 main characteristics of epigenetic phenomena

A
  • different gene expression pattern/phenotype, identical genome
  • inheritable through cell division
  • on/off switch
  • erase-able (therapeutic potential)
152
Q

In a person with PWS, treatment with GH should be started….

A

at onset of excessive eating symptoms

153
Q

Paternal errors in meiosis I result in …

A

XXY (Klinefelter’s)

154
Q

What is the recurrence risk for Trisomy 21?

A

1/100 + maternal age risk

M2M Unit 2 (2 decks)

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