Exam 2 Flashcards
(218 cards)
1
Q
Loss of function mutation
A
A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene.
Can be caused by a nonsense or missense mutation
2
Q
Gain of function mutation
A
the altered gene product possesses a new molecular function or a new pattern of gene expression
Achondroplasia (ACH), the most common genetic dwarfism in human, is caused by a gain-of function mutation in fibroblast growth factor receptor 3 (FGFR3)
3
Q
Genotype-phenotype correlation
A
the association between specific germline mutations (genotype) and the resulting spectrum of disease expression (phenotype)
4
Q
Allelic Heterogeneity
A
Different mutations in the same gene affect phenotype
PKU - allelic heterogeneity - different mutations cause different
tolerance of phenylalanine
5
Q
Mutations Associated with Heterochronic or Ectopic Gene Expression
A
Mutations in heterochronic genes cause certain cells to adopt cell fates normally associated with earlier or later times in development
“ectopic” expression refers to the expression of genes at locations where the target gene is not known to have a function
6
Q
Modifier Genes
A
Mutations/variants in other genes affect phenotype
7
Q
When does alpha thalassemia start to be observed?
A
alpha thalassemia seen in utero
8
Q
Hemoglobin Electrophoresis for Sickle Cell
A
Thick band for HbS because Autosomal recessive so both copies of beta-hemoglobin express HbS
9
Q
What happens if you are heterozygous with HbC and HbS?
A
HbC can be phenotype if paired HbS - so pt 7 probably has some sort of hemoglobinopathies
10
Q
What determines if condition included in Newborn Screen?
A
Condition has to be
1) treatable
2) has to be easily identified through test
3) there has to be a benefit to treating before disease is identified ->therefore worth doing right after birth vs waiting for symptoms to arise
Reproductive information about a future pregnancy is not a good reason
11
Q
sticky clear mucus is a sign of what?
A
mutations in CFTR
12
Q
Why does pancreatic insufficiency lead to digestive problems
A
because digestive enzymes not made
13
Q
Categories of Metabolic conditions
A
Amino Acid disorders
PKU
Organic Acidemias
Urea cycle disorders
OTC deficiency
Fatty Acid Oxidation disorders
MCAD deficiency
Mitochondrial disorders
MELAS
mtDNA vs nuclear DNA
Lysosomal storage disorders
MPSs -> know them all
Tay Sachs
Fabry
“Other”
Biotinidase deficiency
Galactosemia
14
Q
MN CF Newborn Screening Method
A
If IRT is normal -> STOP
If IRT is elevated -> Genetic Panel Test
If at least one mutation found -> Follow up
sweat test
15
Q
If Sweat test is >60 mmol/L
A
Automatic Diagnosis of CF
16
Q
If sweat test 30-60 mmol/L
A
Borderline Sweat test
17
Q
MN CF Newborn Screening Method
A
If IRT is normal -> STOP
If IRT is elevated top 4% of the day -> Genetic Panel Test
If at least one mutation found -> Considered positive newborn Screen ->Follow up with sweat test
18
Q
If sweat test 30-60 mmol/L
A
Borderline Sweat test
19
Q
Positive Newborn screen
Normal or borderline Sweat test 30-60 mmol/L (Borderline)
1 CF causing mutation or 2 mild CF mutations (e.g. 2 copies of 5T in trans by themselves)
2 5T in trans and borderline
A
CRMS
20
Q
Sweat test 30-60 mmol/L (Borderline)
1 CF mutation or 2 possible CF mutations (e.g. 2 copies of 5T in trans by themselves)
But no Positive Newborn screen
A
CFTR related disorder
21
Q
POSITIVE sweat test OR 2 cf causing mutations
A
CF diagnosis
22
Q
ABSENT OR NEGATIVE NEWBORN SCREEN, fewer than 2 classic cf mutations, and borderline sweat test
A
CFTR-related disorder
23
Q
positive newborn screen, fewer than 2 cf mutations, and borderline sweat test
A
CFTR-related metabolic syndrome
24
Q
5T on its own in trans
A
concidered mild mutation of CFTR
25
CBAVD stands for
Congenital bilateral absence of the vas deferens
26
How does CF affect the reproductive system?
As the movement of salt and water in and out of cells is altered, mucus becomes thickened. In the reproductive system, the thickened secretions can cause blockages. These can affect how the sex organs develop and work. For most men with CF, the tube (vas deferens) that carries sperm to the penis does not develop.
27
presentation with F508del and R117H and 5T in CIS
Classic CF
28
5T on its own in trans
considered mild mutation of CFTR
29
Poly-T/TG Tract Consequences
worsens phenotype if in CIS with both 5T and R117H mutation
30
which is worse TG11 or TG13
TG13
31
Central Nervous System consists of
Brain and spinal cord
32
Central Nervous System consists of
Brain and spinal cord
33
R117H and 5T in CIS + TG13
even worse presentation
34
Two sections of Peripheral Nervous System
1) Autonomic nervous system
Unconscious body functions
2) Somatic nervous system
Conscious control of the muscles
35
Neuromuscular disorders affect what?
parts of the CNS and PNS
36
Three types of neuron
1) Sensory Neuron
2)
3)
37
What does Sensory Neuron do?
Sensory organs
| Touch, taste, smell, pain, temperature
38
What does Interneuron do?
Communication between CNS and the sensory and motor neurons of the PNS
39
What does Motor Neuron do?
1) Signals from the brain through the neuromuscular junction to the muscles
2) Movement
40
Three types of neuron
1) Sensory Neuron
2) Interneuron
3) Motor Neuron
41
most common type of mutation in SMN1 gene
Homozygous deletion of exon 7 in ~ 95% of people (tested on NBS)
42
How common are de novo deletions in SMA?
2% have de novo deletions in one allele
43
How common are non deletion mutations in SMA?
3-5% non deletion mutations in one allele, typically with a deletion in the other allele
44
Will non deletion mutations in SMA be picked up on NBS?
will NOT be picked up on NBS, only deletions
45
which gene modifies phenotype of SMA but not causative
SMN2 copy number
46
Reasons father of child with SMA not picked up on with carrier screen?
1) DAD WHO IS SILENT CARRIER, because he has 2 copies of SMN1 in CIS on a single chromosome (most common)
2) den novo mutation (2% of cases - more common than usual because SMN2 is so similar that can get deleted by accident)
3) this dad has non-deletion mutation that is not on carrier screen (3-5% of cases)
47
Reasons father or mother of a child with SMA not picked up on with carrier screen?
1) parent WHO IS SILENT CARRIER, because he has 2 copies of SMN1 in CIS on a single chromosome (most common) and zero copies on the other -> microarray does not pick this up
2) den novo mutation (2% of cases - more common than usual because SMN2 is so similar that can get deleted by accident)
3) this dad has non-deletion mutation that is not on carrier screen (3-5% of cases)
48
What other disease besides SMA can occur with a parent who tested negative on carrier screen but kid has disease anyway?
CAH (Congenital adrenal hyperplasia) also autosomal recessive and has the same problem where parent can be SILENT CARRIER, because he has 2 copies of gene in CIS on a single chromosome (most common) and none on the other chromosome
49
What is the relationship between severity of SMA and SMN2 copy number?
Inverse relationship between severity of SMA and SMN2 copy number
50
Why do genetic testing in patient with Amyotrophic Lateral Sclerosis (ALS) if it is a clinical diagnosis?
1) Determine familial cause because will effect relatives,
| 2) Certain variants are appropriate for certain treatment but not others
51
Symptoms of ALS
Progressive loss of muscle movement
| Speech, swallowing, skeletal muscle
52
ALS weakness is symmetric or asymmetric?
Asymmetric weakness in most cases
53
limb onset ALS vs bulbar onset ALS
If symptoms begin in the arms or legs, doctors refer to this as “limb onset ALS”
If disease starts affecting speech or swallowing, they call it “bulbar onset ALS”
54
Familial vs sporadic ALS
"familial" ALS means that there is more than one occurrence of the disease in a family.
"sporadic" when there is no known history of other family members with the disease
"genetic" can apply to both familial and sporadic ALS.
55
Does ALS always occur with FTD?
Can be isolated or occur in association with frontotemporal dementia (FTD)
56
What is frontotemporal dementia (FTD)?
Damage to frontal and temporal lobes of the brain
57
What is the clinical presentation of frontotemporal dementia (FTD)?
Associated with personality, behavior and language
58
How many susceptibility genes associated with ALS?
>30 susceptibility genes (and counting)
59
Most common genetic cause of ALS and FTD?
C9orf72
| The expansion of a hexanucleotide (GGGGCC) in C9orf72 is the most common known cause of ALS
60
Hexanucleotide expansion of C9orf72 seen in familial or sporadic ALS?
Seen in both ~ 40% familial cases and ~ 7% sporadic ca
61
Age of onset for ALS?
Variable age of onset (20s-90s)
62
What is the age related penetrance of ALS?
Age related penetrance, almost complete by age 83
63
Hexanucleotide expansion of C9orf72 seen in familial or sporadic ALS?
Seen in both ~ 40% familial cases and ~ 7% sporadic ca
64
Does Hexanucleotide repeat expansion repeat number correlate with age of onset, severity or progression of ALS?
No it does not
| More does not mean worse, but >30 means ALS
65
how many Hexanucleotide repeats is considered pathogenic in ALS?
>30 repeats-pathogenic
66
What rare event can explain variability in ALS phenotype?
SOMATIC MOSAICISM
Somatic mutations, arising in early embryonic development and leading to mosaicism, have emerged as pathogenic drivers for neurodevelopmental and neurodegenerative disorders. Although these mutations may be absent or undetectable in DNA isolated from peripheral blood, they might be present in subsets of neurons and glia in the CNS, driving diverse clinical outcomes. The much milder clinical phenotype in case 1 might be explained by mosaicism of this mutation in her CNS.
67
What other gene besides C9orf72 is associated with ALS?
VCP
Mutations in the valosin-containing protein (VCP) gene were recently reported to be the cause of 1%-2% of familial amyotrophic lateral sclerosis (ALS) cases. VCP mutations are known to cause inclusion body myopathy (IBM) with Paget's disease (PDB) and frontotemporal dementia (FTD).
68
Duchenne Muscular Dystrophy symotoms
Delayed motor milestones
waddling gait
Gower maneuver
Large calf muscles
69
Serum CK levels in DMD
>10x normal
70
Big Physical sign in DMD
Hypertrophic calf muscles
71
Serum CK levels in DMD
>10x normal
72
When does Cardiomyopathy happen in a child with DMD
teenage years
73
What are intellectual consequences in some children with DMD?
Some can have mild ID, learning disability, ADHD
74
When does Cardiomyopathy happen in a child with DMD
teenage years
75
Median survival with DMD
24 years
76
CK levels of female carriers of Dystrophinopathies like DMD and Becker?
Elevated
77
Difference between DMD and Becker?
Later-onset muscle weakness
78
Serum CK levels in Becker?
>5x normal
79
When does Cardiomyopathy happen in a child with Becker?
teenage years
80
Median survival with Becker?
mid-40’s
81
Median survival with Becker?
mid-40’s
82
What is DMD-associated DCM?
Dilated cardiomyopathy (DCM) is a common complication of Duchenne muscular dystrophy (DMD), but it usually does not present with clinically significant symptoms until the later stages of the disease
83
How does DMD-associated Dilated Cardiomyopathy present?
Left ventricular dilation and congestive heart failure
84
When do DMD patients present with Dilated Cardiomyopathy?
Males present between ages 20-40
Females present later
Progression is faster in males
85
if DMD is X-linked why do some females have problems?
Duchenne muscular dystrophy usually affects males. However, females are also affected in rare instances
~15-20% are manifesting carriers and have muscle weakness to some extent.
86
Female carriers of DMD/BMD
Some can have symptoms:
~15-20% have mild-moderate muscle weakness in adulthood
Can have elevated CK (2-10x normal)
Increased risk for DCM
87
Is cardiac screening recommended for Female Dystrophinopathy Carriers?
For symptomatic and asymptomatic individuals
Initially in adolescence/ early adulthood or when symptoms begin
At least every 5 years
88
Myotonic dystrophy type 1 (DM1) genetics
CTG trinucleotide repeat expansion in DMPK gene
89
Does size of trinucleotide repeat expansion in DMPK gene matter?
YES! Increased severity of DM1 with increased repeat size
90
Intellectual ability with Myotonic Dystrophy Type 1 (DM1)
Only minor intellectual deficits in some individuals (can sometimes be wrongly assumed to have ID due to myopathic facies)
91
Personality traits with Myotonic Dystrophy Type 1 (DM1)
1) avoidant
2) obsessive-compulsive
3) passive-aggressive
4) dependent
5) paranoid personality
92
GI concerns with Myotonic Dystrophy Type 1 (DM1)
dysphagia, constipation, or diarrhea
93
Endocrine dysfunction with Myotonic Dystrophy Type 1 (DM1)
thyroid dysfunction, diabetes, calcium dysregulation, testicular atrophy
94
Lungs with Myotonic Dystrophy Type 1 (DM1)
Progressive impairment of lung function
95
Genetics cause of Myotonic Dystrophy Type 2 (DM2)
Caused by CCTG repeat within a complex repeat motif, (TG)n(TCTG)n(CCTG)n in CNBP gene
96
Normal level of CCTG repeats in CNBP gene
≤30 CCTG repeats
97
Pre-mutation level of CCTG repeats in CNBP gene
~30-74 CCTG repeats
98
Pathogenic DM2 level of CCTG repeats in CNBP gene
~75-11,000 CCTG repeats
99
Number of DMPK trinucleotide repeats in DM1?
50 to ~150 mildly affected
150-1000 classic
Congenital >1000
100
Clinical features of DM2
1) Myotonia and muscle weakness
2) Cataracts
3) Type 2 diabetes
Other features: cardiac conduction defects and/or cardiomyopathy, hearing loss, endocrine dysfunction, GI complications
101
What is Charcot Marie Tooth?
Peripheral neuropathy with Demyelination, Axonal or both
102
Symptoms of Sensory nerve damage in Charcot Marie Tooth?
1) Numbness and Tingling
| 2) Balance problems
103
Symptoms of Motor nerve damage in Charcot Marie Tooth?
1) Muscle weakness
2) Muscle atrophy
3) Foot Drop
4) Pes Cavus/Hammertoes
104
Why are there Length dependent symptoms in Charcot Marie Tooth?
The longer the nerve the more it is affected by slow (demyelination) or weak conductance (axon damage)?
105
What class of disorder is PKU?
Amino acid disorder
106
Gene for PKU
PAH - phenylalanine hydroxylase
107
Inheritance of PKU
Autosomal recessive
108
Common treatment for PKU
Kuvan
109
Limitation of Kuvan
Requires residual activity of Phenylalanine hydroxylase
110
What are Organic acidemias?
Disrupted amino acid metabolism, particularly branched-chain amino acids, causing a accumulation of acids
Organic acids are produced from the catabolism of amino acids
111
Inhertiance of organic acidemias
Autosomal recessive
112
Example of an organic acidemia disorder
Isovaleric acidemia (IVA)
113
What is not broken down in individuals with IVA?
Leucine
114
What builds up in urine for IVA individuals?
Isovaleric acid
115
Treatment for PKU?
Low-protein diet, eliminate phenylalanine, kuvan, formula
116
Treatment for IVA?
Low protein diet, treatment with glycine, formula
117
How does glycine treat IVA?
glycine augments conversion of isovaleric acid (IVA) to isovalerylglycine (IVG) through glycine-N-acylase
118
What are the inheritance patterns of Urea cycle disorders?
Autosomal recessive and X linked
119
What builds up in individuals with urea cycle disorders?
Ammonia
120
What is OTC?
Ornithine transcarbamylase (OTC) deficiency. OTC is 1 of 6 enzymes in urea cycle, which breaks down and removes nitrogen from the body
121
What is the inheritance pattern of OTC deficiency?
X-linked
122
What is the treatment for OTC deficiency?
Low protein diet, ammonia scavengers, liver transplant, Ravicti
123
How does Ravicti treat OTC?
Ravicti is converted to phenylacetate. Phenylacetate attaches to glutamine so that it can remove from the body. This removal of amino acids (glutamine in this case) decreases nitrogen in the body, reducing the amount of ammonia produced.
124
What are the symptoms of OTC?
Buildup of ammonia causes neurotoxicity leading to episodes of delirium, erratic behavior, a reduced level of consciousness, headaches, vomiting, and seizures
125
Can females exhibit symptoms of OTC?
Yes; often mild, like protein avoidance
126
What is fatty acid oxidation?
breakdown of fatty acids to acetyl CoA; (fatty acids to energy in the mitochondria)
127
Why are there different enzymes used for fatty acid oxidation?
Different size (or chain length) of fatty acids use different enzymes
128
What is the inheritance pattern of fatty acid oxidation disorders?
Autosomal recessive
129
What does MCAD stand for?
medium chain acyl-CoA dehydrogenase
130
What is the gene that codes for MCAD?
ACADM
131
Treatment for MCAD deficiency
Avoidance of fasting, low fat/high carb, overnight cornstarch
132
Common mutations for MCAD deficiency
c.985A>G, c.199T>C
133
What are the two "ways" to get a mitochondrial disease?
Mutations in mtDNA and mutations in nuclear DNA
134
What are the inheritance patterns of mitochondrial diseases?
Pretty much everything; AR, AD, X linked, maternal (mitochondrial)
135
What is an example of mitochondrial disease?
MELAS
136
What are the symptoms of MELAS?
In the name; Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes
137
What is the most common MELAS gene?
Mt-TL1 a t-RNA gene
138
What happens in MELAS?
Mutation in t-RNA gene, MT-TL1 impair ability of mitochondria to make proteins, use oxygen, and produce energy
139
Can red ragged fibers be used to diagnose mitochondrial disease later in life?
No; red ragged fibers can occur naturally with aging in healthy individuals
140
Which category of metabolic conditions (so far) has progressive symptoms?
Lysosomal storage diseases
141
What are Lysosomal storage diseases?
Defective lysosomal enzymes, cofactors or transport causes buildup of metabolites in lysosomes
142
What is the inheritance of lysosomal storage diseases?
Autosomal recessive and X linked
143
What is the treatment for lysosomal storage diseases?
enzyme replacement therapy
| and Bone marrow transplant for MPS1
144
What are mucopolysachharidoses?
mucopolysaccharidoses caused by deficiency in enzymes that break down glycosaminoglycans (mucopolysaccharides) —long chains of sugars
145
MPSI is also known as?
Mucopolysarcharidosis type I is also known as Hurler syndrome
146
MPSII is also known as
Mucopolysarcharidosis type II is also known as Hunter syndrome
147
MPSIII is also known as
Sanfilippo Syndrome
Milder dysmorphic features
Coarse facial features
148
MPSIV
Morquio Syndrome
| Mostly skeletal problem
149
MPSVI
Maroteaux-Lamy Syndrome
| intellectually intact
150
What do MPS I, II, and III have in common
1) Regression
| 2) Intellectual disability
151
What are the two "ways" to get a mitochondrial disease?
Mutations in mtDNA and mutations in nuclear DNA
152
What are the inheritance patterns of mitochondrial diseases?
Pretty much everything; AR, AD, X linked, maternal (mitochondrial)
153
Examples of lysosomal storage diseases
Tay Sachs
Mucopolysaccharidoses
Fabry disease
154
What is Tay Sachs?
AR caused by mutations HEXA gene. HEXA codes for the alpha subunit of β-hexosaminidase A. Leads to accumulation of fats (lipids) known as gangliosides in lysosomes of brain and nerve cells.
155
What is Fabry disease?
X-lnked disorder of glycosphingolipid (fat) metabolism resulting from the absent or markedly deficient activity of the lysosomal enzyme, α-galactosidase A (α-Gal A) leads to buildup of fat in lysosomes
156
What is a common mutation for Tay Sachs?
1278insTATC (infantile)
| in HEXA gene
157
What is the inheritance pattern of Fabry disease?
X linked
158
What are the barriers to treating Fabry disease?
Cost, time, reactions
159
What is the basic mechanism of biotinidase deficiency?
Mutated BTD gene, reduction in enzyme functionality that can't free up biotin
160
How is biotinidase treated?
Biotin
161
What is the common partial, or mild, mutation for BTD?
D444H
162
What is the inheritance pattern of biotinidase deficiency?
Autosomal recessive
163
What genes are associated with galactosemia?
GALT
GALE
GALK1
164
What is the inheritance pattern of Galactosemia?
Autosomal recessive
165
What is the Duarte variant?
N314D; asymptomatic/mild phenotype (GALT)
166
What is the most common mutation for classic galactosemia?
Q188R (GALT)
167
CMT1A
| Charcot Marie Tooth Type 1
Most common type
168
Inherirance of CMT1A
AD
169
CMT1A gene
PMP22 duplication
PMP22 deletions and point mutation cause a different phenotype
170
CMT1A onset
Childhood
171
CMT1X
Second most common
| X-linked inheritance
172
CMT1X presentation
Men: Intrinsic hand muscle (close to writst) weakness starts in childhood
Stroke-like episodes <20 years
Women: Spectrum of symptoms, may be asymptomatic
173
CMT4C
AR
| Most common Recessive type
174
CMT4C symptoms
Spine deformities
foot deformities
hearing loss
sensory ataxia
proximal muscle weakness
175
Ataxia Telangiectasia (AT) symptoms and onset
progressive cerebellar ataxia, jerking, and tremors, swallowing difficulties; immunodeficiency, increased risk for malignancy; onset 1-4 years
176
AT genetics
Autosomal Recessive, ATM gene (ATM serine/threonine kinase), carriers at risk for breast, pancreatic, and prostate cancer
ATM can’t correct mistakes
ATM serine/threonine kinase, symbol ATM, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks. It phosphorylates several key proteins that initiate activation of the DNA damage checkpoint, leading to cell cycle arrest, DNA repair or apoptosis
177
Spinocerebellar ataxias (SCAs)
degeneration of the cerebellum and spinal cord; progressive incoordination of walking
178
SCA symptoms
ataxia, poor coordination of hand and eye movements
179
SCA (Spinocerebellar ataxia) genetics
Autosomal Dominant, some types due to repeat expansions
180
Friedreich ataxia
slowly progressive ataxia with onset before age 25
181
Typical Friedreich ataxia symptoms
progressive ataxia, peripheral neuropathy, muscle weakness, dysphagia, cardiomyopathy
182
Atypical Friedreich ataxia
late onset (after 25 years)
183
Friedreich ataxia genetics
Autosomal Recessive, mutations in FXN gene, GAA expansion in intron 1
FXN Frataxin gene codes for a protein that affects mitochondria. Frataxin mRNA is mostly expressed in tissues with a high metabolic rate.
184
Neuronal ceroid lipofuscinosis (NCL, Batten disease)
many types, mostly autosomal recessive, vision loss, epilepsy, dementia
Neuronal ceroid lipofuscinosis is the general name for a family of at least eight genetically separate neurodegenerative lysosomal storage diseases that result from excessive accumulation of lipopigments (lipofuscin) in the body's tissues. These lipopigments are made up of fats and proteins.
185
CLN1 (NCL)
Infantile onset, floppy, epilepsy, death by mid-childhood (7 y.o.)
186
CLN3 (NCL)
juvenile onset, vision loss, epilepsy, unsteady gait, death 15-35 years
187
Huntington's disease
progressive breakdown (degeneration) of nerve cells in the brain
mood, memory, movement
188
Huntington's disease genetics
HTT gene, CAG repeat expansion, inverse relationship between disease severity and repeat number, anticipation (most commonly maternal)
189
Epilepsy types of seizures
generalized versus focal/partial
190
Tonic clonic seizure
generalized seizure, unconsciousness, convlusions, muscle rigidity
191
Absence seizure
staring into space
192
Epilepsy genetic testing yield
higher for rare forms, neonatal onset, and uncontrolled types
193
Epilepsy genetic testing options
CMA (Chromosomal Microarray Analysis)
epilepsy panel (del/dup analysis but many VUS (variants of uncertain significance))
WES (Whole Exome Sequencing)
194
Age of Onset for epilepsy and testing
neonatal seizures-highest yield
| prior to age 2-generally high
195
Severity genetic testing yield for epilepsy
higher yield with uncontrolled seizures and multiple types
196
Seizure type testing yield for epilepsy
lower yield for common epilepsies such as childhood absence epilepsy and juvenile myoclonic epilepsy
197
Genetic testing yield for epilepsy Complicated by:
Trauma
birth history
accidents
abuse
Non mendelian genetic contribution
198
Epilepsy Genetic Testing Chromosome Microarray (CMA)
3-10% yield reported
higher in patients with dysmorphic features, congenital anomalies, intellectual disability, autism spectrum disorder, history of recurrent miscarriage (in parent) and other health concerns
199
Epilepsy Genetic Testing Epilepsy Panel
sponsored and non sponsored
deletion/duplication analysis
higher read depth
typically 300-500 genes
200
Epilepsy Genetic Testing Whole Exome Sequencing
17%-33% with severe epilepsy
58% when seizure onset is in neonatal period
Trio
less VUSs
do not use if del/dup condition is suspected
201
Epilepsy Genetic Testing Whole Genome Sequencing
to be determined
| Consensus has not been reached regarding whether to start with panel vs WES
202
Are seizure disorders easy to clinically distinguish?
Many seizure disorders are clinically indistinguishable
203
11.1) A child dies of hydrops fetalis. Draw a pedigree with genotypes that illustrates to the carrier parents the genetic basis of the infant’s thalassemia. Explain why a Melane- sian couple whom they met in the hematology clinic, who both also have the α-thalassemia trait, are unlikely to have a similarly affected infant.
The pedigree should contain the following informa- tion: Hydrops fetalis is due to a total absence of α chains. The parents each must have the genotype αα/−−. The α− genotype is common in some pop- ulations, including Melanesians. Parents with this genotype cannot transmit a − −/− − genotype to their offspring.
If in cud they could have Hb Barts in both hba1 and hba2
204
11.2) Why are most β-thalassemia patients likely to be genetic compounds? In what situations might you anticipate that a patient with β-thalassemia would be likely to have two identical β-globin alleles?
Except in isolated populations, patients with β-thalassemia will often be genetic compounds because there are usually many alleles present in a population in which β-thalassemia is common. In isolated populations, the chance that a patient is a true homozygote of a single allele is greater than it would be in a population in which thalassemia is rare. In the latter group, more “private mutations” might be expected (ones found solely or almost solely in a single pedigree). A patient is more likely to have identical alleles if he or she belongs to a geographical isolate with a high frequency of a single allele or a few alleles, or if his or her parents are consanguineous. - See text...
A homozygous mutation is the presence of the identical mutation on both alleles of a specific gene. However, when both alleles of a gene harbor mutations, but the mutations are different, these mutations are called compound heterozygous. Also called a genetic compound
205
11.3) Tony, a young Italian boy, is found to have moderate β-thalassemia, with a hemoglobin concentration of 7 g/dl (normal amounts are 10 to 13 g/dl). When you perform a Northern blot of his reticulocyte RNA, you unexpectedly find three β-globin mRNA bands, one of normal size, one larger than normal, and one smaller than normal.
What mutational mechanisms could account for the presence of three bands like this in a patient with β-thalassemia? In this patient, the fact that the anemia is mild suggests that a significant fraction of normal β-globin mRNA is being made. What types of mutation would allow this to occur?
Three bands on the RNA blot could indicate, among other possibilities, that (a) one allele is producing two mRNAs, one normal in size and the other abnormal, and the other allele is producing one mRNA of abnormal size; (b) both alleles are making a normal- sized transcript and an abnormal transcript, but the aberrant ones are of different sizes; or (c) one allele is producing three mRNAs of different sizes, and the other allele is making no transcripts.
Scenario (c) is highly improbable, if possible at all. Two mRNAs from a single allele could result from a splicing defect that allows the normal mRNA to be made, but at reduced efficiency, while leading to the synthesis of another transcript of abnormal size, which results from either the incorporation of intron sequences in the mRNA or the loss of exon sequences from the mRNA. In this case, the other abnormal band comes from the other allele. A larger band from the other allele could result from a splicing defect or an insertion, whereas a smaller band could be due to a splicing defect or a deletion. Hb E is caused by an allele from which both a normal and a shortened transcript are made (see Fig. 11-10); the normal mRNA makes up 40% of the total β-globin mRNA, producing only a mild anemia.
Pg 209
Table 11-5
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11.5) A child has a paternal uncle and a maternal aunt with sickle cell disease; both of her parents do not. What is the probability that the child has sickle cell disease?
2/3 ×2/3 ×1/4 =1/9
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11.6) A woman has sickle cell trait, and her mate is heterozy- gous for Hb C. What is the probability that their child has no abnormal hemoglobin?
1/4
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11.7) Match the following:
complex β-thalassemia
β+-thalassemia
number of α-globin genes missing in Hb H disease
two different mutant alleles at a locus
ATR-X syndrome
insoluble β chains
number of α-globin genes missing in hydrops fetalis with Hb Bart’s
locus control region
α−/α− genotype
increased Hb A2
1. detectable Hb A 2. three
3. β-thalassemia
4. α-thalassemia
5. high-level β-chain expression
6. α-thalassemia trait
7. compound
heterozygote
8. δβ genes deleted
9. four
10. mental retardation
```
8
1
2
7
10
4
9
5
6
3
```
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12.3) In discussing the nucleotide changes found to date in the coding region of the CF gene, we stated that some of the changes (the missense changes) found so far are only “putative” disease-causing mutations. What criteria would one need to fulfill before knowing that a nucleotide change is pathogenic and not a benign polymorphism?
A nucleotide substitution that changes one amino acid residue to another should be termed a putative pathogenic mutation, and possibly a polymorphism, unless (1) it has been demonstrated, through a functional assay of the protein, that the change impairs the function to a degree consistent with the phenotype of the patient, or (2) instead of or in addition to a functional assay, it can be demonstrated that the nucleotide change is found only on mutant chromosomes, which can be identified by haplotype analysis in the population of patients and their parents and not on normal chromosomes in this population.
The fact that the nucleotide change is only rarely observed in the normal population and found with significantly higher frequency in a mutant population is strong supportive evidence but not proof that the substitution is a pathogenic mutation.
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12.4) Johnny, 2 years of age, is failing to thrive. Investigations show that although he has clinical findings of CF, his sweat chloride concentration is normal. The sweat chloride concentration is normal in less than 2% of patients with CF. His pediatrician and parents want to know if DNA analysis can determine whether he indeed has CF. a. Would DNA analysis be useful in this case? Briefly
outline the steps involved in obtaining a DNA diagnosis for CF.
b. If he has CF, what is the probability that he is homozygous for the ΔF508 mutation? (Assume that 85% of CF mutations could be detected at the time you are consulted and that his parents are from northern Europe, where the ΔF508 allele has a frequency of 0.70.)
c. If he does not have the ΔF508 mutation, does this disprove the diagnosis? Explain.
If Johnny has CF, the chances are approximately 0.85 × 0.85, or 70%, that he has a previously described mutation that could be readily identified by DNA analysis. His parents are from northern Europe; therefore the probability that he is homozygous for the ΔF508 mutation is 0.7 × 0.7, or 50%, because approximately 70% of CF carriers in northern Europe have this mutation. If he does not have the ΔF508 mutation, he could certainly still have CF, because approximately 30% of the alleles (in the northern European population, at least) are not ΔF508. Steps to DNA diagnosis for CF include the following: (1) look directly for the ΔF508 mutation; if it is not present, (2) look for other mutations common in the specific population; (3) then look directly for other mutations based on probabilities suggested by the haplotype data; (4) if all efforts to identify a mutation fail (or if time does not allow), perform linkage analysis with polymorphic DNA markers closely linked to CF.
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12.5) James is the only person in his kindred affected by DMD. He has one unaffected brother, Joe. DNA analysis shows that James has a deletion in the DMD gene and that Joe has received the same maternal X chromo- some, but one without a deletion. What genetic counsel- ing would you give the parents regarding the recurrence risk for DMD in a future pregnancy?
James may have a new mutation on the X chromo- some because Joe inherited the same X chromosome from his mother, and the deletion was present in neither Joe nor his mother. If this is the case, there is no risk for recurrence. Alternatively, the mother may be a mosaic, and the mosaicism includes her germline. In this case, there is a definite risk that the mutant X could be inherited by another son or passed to a carrier daughter. Approximately 5% to 15% of cases of this type appear to be due to mater- nal germline mosaicism. Thus the risk is half of this figure for her male offspring because the chance that a son will inherit the mutant X is 1/2 × 5% to 15% = 2.5% to 7.5%.
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12.6) DMD has a high mutation rate but shows no ethnic variation in frequency. Use your knowledge of the gene and the genetics of DMD to suggest why this disorder is equally common in all populations.
For DMD, as a classic X-linked recessive disease that is lethal in males, one third of cases are pre- dicted to be new mutations. The large size of the gene is likely to account for the high mutation rate at this locus (i.e., it is a large target for mutation). The ethnic origin of the patient will have no effect on either of these phenomena.
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12.7) A 31 2 -year-old girl, T.N., has been noted to have increasing difficulty standing up after sitting on the floor. Her serum level of creatine kinase is grossly elevated. Although a female, the presumptive clinical diagnosis is Duchenne muscular dystrophy. Females with DMD are rare. Identify three mechanisms of mutation that could account for the occurrence of DMD in a female.
A DMD female like T.N. might have the disease because she carries a DMD gene mutation on the X chromosome inherited from her mother. (Skewed inactivation) T.N. could show clinical symptoms if her paternal X (carrying a normal allele at this locus) was subject to nonran- dom inactivation in most or all cells. An alternative explanation would be that she has Turner syndrome and that her only X chromosome (inherited from her mother) carries a DMD gene mutation. A third explanation would be that she has a balanced X;autosome translocation that disrupts the DMD gene on the translocated X chromosome. Although her normal X chromosome carries a normal allele at the DMD locus, balanced X;autosome transloca- tions show nonrandom inactivation of the structur- ally normal X due to secondary cell selection (see Chapter 6).
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12.11) The effect of a dominant negative allele illustrates one general mechanism by which mutations in a protein cause dominantly inherited disease. What other mechanism is commonly associated with dominance in genes encoding the subunits of multimeric proteins?
Haploinsufficiency. Thus, in some situations, the contributions of both alleles are required to provide a sufficient amount of protein to prevent disease. An example of haploinsufficiency is provided by hetero- zygous carriers of LDL receptor deficiency.
Haploinsufficiency - The situation that occurs when one copy of a gene is inactivated or deleted and the remaining functional copy of the gene is not adequate to produce the needed gene product to preserve normal function.
Dominant negative- A mutation whose gene product adversely affects the normal, wild-type gene product within the same cell. This usually occurs if the product can still interact with the same elements as the wild-type product, but block some of its function
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12.16) What are the possible explanations for the presence of three predominant alleles for Tay-Sachs disease in Ashkenazi Jews? Does the presence of three alleles, and the relatively high frequency of Tay-Sachs disease in this population, necessarily accord with a heterozygote advantage hypothesis or a founder effect hypothesis?
The presence of three common alleles for Tay-Sachs disease in the Ashkenazi population seems likely to be due either to a heterozygote advantage or to genetic drift (one form of which is the founder effect, as explained in Chapter 9). The high fre- quency of these alleles might also be due to gene flow, although the population of origin of the three common mutations is not apparent, making this explanation seem less likely (in contrast, say, to the evidence indicating that the most common PKU alleles in many populations around the world are of Celtic origin).
Founder effect - the reduced genetic diversity which results when a population is descended from a small number of colonizing ancestors.
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13.3) A 3-year-old girl, Rhonda, has familial hypercholesterolemia due to a deletion of the 5′ end of each of her low-density lipoprotein (LDL) receptor genes that removed the promoter and the first two exons. (Rhonda’s parents are second cousins.) You explain to the parents that she will require plasmapheresis every 1 to 2 weeks for years. At the clinic, however, they meet another family with a 5-year-old boy with the same disease. The boy has been treated with drugs with some success. Rhonda’s parents want to know why she has not been offered similar pharmacological therapy. Explain.
Rhonda’s mutations prevent the production of any LDL receptor. Thus the combination of a bile acid– binding resin and a drug (e.g., lovastatin) to inhibit cholesterol synthesis would have no effect on increasing the synthesis of LDL receptors. The boy must have one or two mutant alleles that produce a receptor with some residual function, and the increased expression of these mutant receptors on the surface of the hepatocyte reduces the plasma LDL-bound cholesterol.
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13.4) What classes of mutations are likely to be found in homocystinuric patients who are not responsive to the administration of large doses of pyridoxine (vitamin B6)? How might you explain the fact that Tom is completely responsive, whereas his first cousin Allan has only a partial reduction in plasma homocystine levels when he is given the same amount of vitamin B6?
Unresponsive patients probably have alleles that do not make any protein, that decrease its cellular abun- dance in some other way (e.g., make an unstable protein), or that disrupt the conformation of the protein so extensively that its pyridoxal-phosphate binding site has no affinity for the cofactor, even at high concentrations. The answer to the second part of this question is less straightforward. The answer given here is based on the generalization that most patients with a rare autosomal recessive disease are likely to have two different alleles, which assumes that there is no mutational hot spot in the gene and that the patients are not descended from a “founder” and are not members of an ethnic group in which the disease has a high frequency. In this context, Tom is likely to have two alleles that are responsive; first cousins with the same recessive disease are likely to share only one allele, so that Allan is likely to have one responsive allele that he shares with Tom and another allele that is either unresponsive or that responds more poorly to the cofactor than Tom’s other allele.
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13.6) Both alleles of an autosomal gene that is mutant in your patient produce a protein that is decreased in abundance but has residual function. What therapeutic strategies might you consider in such a situation?
One must consider the kinds of mutations that decrease the abundance of a protein but that are associated with residual function. One class of such mutations are those that decrease the abundance of the mRNA but do not alter the protein sequence (i.e., each protein molecule produced has normal activity, but there are fewer molecules). Mutations of this type might include enhancer or promoter mutations, splice mutations, or others that destabilize the mRNA. In this case, one could consider strategies to increase expression from the normal allele and perhaps also the mutant allele, as is done with hereditary angio- edema, in which danazol administration increases the expression of the product from both the wild-type and mutant alleles. A second class of such mutations are those within the coding sequence that destabilize the protein but still allow some residual function. Here, a strategy to increase the stability or the function of the mutant protein should be considered. For example, if the affected protein has a cofactor, one could administer increased amounts of the cofactor, provided such an approach would not have unacceptable side effects.
