Week 1 Flashcards

(151 cards)

1
Q

Penetrance

A

on/off switch

  • If person has mutation they either effected or not effected
  • NOT influenced by level of phenotype expression
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2
Q

Expressivity

A

dimmer function

  • Light is on, but trying to determine SEVERITY / range of expressivity
  • Patient has mutation, but there is a range of severity levels
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3
Q

Pleitropy

A

gene that has multiple effects within the body

  • How broad/how many different areas are effected
  • Polysystemic or Monosystemic
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4
Q

Mendel’s 2 laws are…

A
  • Mendel’s Law of Segregation: Alleles segregate (at meiosis) into the gametes
  • Mendel’s Second Law of Independent Assortment: the segregation of each pair of alleles is independent
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5
Q

3 threats to mendelian inheritance

A

penetrance
pleitropy
expressivity

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6
Q

The human genome is _________ and organized in a ______________

A

dynamic

non-random manner

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7
Q

There is an average of _______ SNPs every _________ bp between any two randomly chosen human genomes.

We are 99.9% identical but this still means we have _________ differences

A

1
1000 bp

3 million

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8
Q

The 4 types of variations that can occur between genomes are…

A

1) Insertion/Deletion Polymorphisms
2) Single Nucleotide Polymorphisms
3) Copy Number Variations
4) Other structural variations (inversion, duplications, translocations, large scale insertions/deletions)

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9
Q

Minisatellites are ____________ polymorphisms and consist of ___________. They are also known as _____________

A

insertion-deletion polymorphisms

consist of tandemly repeated 10-100 bp blocks of DNA

(aka Variable Number Tandem Repeats VNTR)

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10
Q

Microsatellites are _____________ polymorphisms and consist of __________. They are also known as ___________ and a common example is ____________

A

insertion-deletion polymorphism

di-, tri-, tetra- nucleotide repeats

AKA Short Tandem Repeat Polymorphisms (STRP)

EX) CAG repeats - abnormal CAG repeats in Huntington’s disease dictate if individual gets disease or not

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11
Q

SNPs can be detected by _________, and are used in _________ because they are so widely distributed

A

PCR

can be used in genetic fingerprinting

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12
Q

Copy Number Variations can vary in size from _______-______ and are the primary type of ________ variation.

A

200bp - 2 Mb

structural

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13
Q

CNV can be identified using ________

A

array comparative genomic hybridization

microarray, but with DNA

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14
Q

1q21 is a region on the genome that is _______ and is associated with _______ different diseases

A

unstable

12 different diseases

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15
Q

1q21

A
  • contains duff 12-20, highly variable protein coding region
  • humans have most copies
  • farther you get from humans the less copies
  • thought to be involved in human brain evolution
  • more instability in 1q21 = increase duff 1220 copy number –> increase in brain size
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16
Q

1q21 deletion –>

1q21 duplication –>

A

deletion –> schizophrenia, microcephaly

duplication –> autism, macrocephaly

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17
Q

G-C rich regions make up ____% of the genome, and A-T rich regions make up ____%

A
GT = 38%
AT = 54%
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18
Q

GC and AT rich regions are used in finding _________

A

chromosomal banding patterns

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19
Q

Genome sequencing is focused on _____ regions with > ______ sequence gaps still remaining, and there is no completely sequenced and assembled human genome.

A

euchromatic, >200

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20
Q

Genome Composition:

1) _____ = translated (protein coding)
2) 20-25% = __________
3) ______% = “single copy” sequences
4) 40-50% = _________

A

1) 1.5% is translated (protein coding)
2) 20-25% is represented by genes (exons, introns, flanking sequences involved in regulating gene expression)
3) 50% “single copy” sequences
4) 40-50% classes of “repetitive DNA”

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21
Q

NextGen sequencing relies on ______ sequences, therefore _________ regions are typically unexamined such as _______

A

short read

complex, highly duplicated regions

such as 1q21

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22
Q

Missing Heritability

A

defined as the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes.

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23
Q

Explain the relationship between gene duplication and evolution and problems with this

A
  • CNV involved in rapid, recent evolutionary change
  • link between evolutionarily adaptive copy number increases and increase in human disease
  • one gene copy carries out critical function, the other is free to vary
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24
Q

CNV regions are often enriched for _________, __________, and __________

A

human specific gene duplication
genome sequence gaps
recurrent human diseases

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25
Gene families
- composed of genes with high sequence similarity that may carry out similar but distinct functions - Arise through gene duplication - play major role in evolutionary change
26
____% of the genome is comprised of segmental duplications
5
27
Tandem Repeats (aka satellite DNAs) are used for _________ and some are found as part of ___________ on long arms of Chromosome 1, 9, 16, and Y
cytogenetic banding human-specific heterchromatin
28
a-satellite repeats are _______ bp repeat units found _______. They are important for ________ and ________.
171 found near centromeric regions of all human chromosomes important for chromosome segregation in mitosis and meiosis
29
Dispersed Repetitive Elements include _____ and _______ families. These can be responsible for _________
Alu L1 responsible for aberrant recombination events between different copies of dispersed repeats (--> disease)
30
Alu Family, aka _________. Comprised of _____ bp, with ________ copies in the genome
SINE (short interspearsed repeat elements) 300 bp, 500,000 copies
31
L1 Family, aka _________. Comprised of _____ kb, with ________ copies in the genome
LINE (long interspersed repeat elements) 6kb, 100,000 copies
32
Retrotransposition may cause _________ of genes, and is due to what process?
insertional activation mRNA --> cDNA (introns all gone) --> cDNA reinserted into genome -can be innocuous or detrimental
33
There are ____ (#) of cross-over events of homologous chromosomes, and each cross-over contains a physical link between homologs called a ________
2-3 chiasma
34
Genetic variability among offspring is due to ________ and _________
Recombination/Crossing-over and Independent assortment
35
Independent assortment
Chromosomes can align in many different ways before being pulled apart (2^23 possible combinations)
36
In Prophase I of meiosis, ______ and _______ occur, such that homologous chromosomes are brought into alignment along the entire length of the chromosome and swap parts. These ______ are held together in _________.
synapsis and recombination bivalents, held together in syntaptonemal complex
37
In metaphase I chromosomes undergo _________ when they line up at the metaphase plate
independent assortment
38
Homologous chromosomes separate in _________, and this process can result in ________
anaphase I | disjunction
39
At the end of meiosis I you go from _______ to __________
1 4n cell --> 2 2n cells
40
Sister chromatids separate in ________
anaphase II
41
At the end of meiosis II you create ________
4 haploid cells that are all genetically different
42
Nondisjunction in meiosis I =
100% abnormal gametes 2 cells = N+1 2 cells = N-1
43
Nondisjunction in meiosis II =
50% abnormal gametes 2 cells = N 1 cell = N+1 1 cell = N-1
44
Two possible mechanisms of nondisjunction
chiasmata positioning | freqeuncy of cross-over events
45
Chiasmata positioning results in nondisjunction because
cross over event occurs too near or too far from the centromere
46
Metacentric
centromere is located in the middle of the chromosome, such that the two chromosome arms are approximately equal in length.
47
Submetacentric
centromere is slightly removed from the center.
48
Acrocentric
- centromere is near one end of the chromosome. | - everything on short arm is repetitive satellite and ribosomal DNA
49
_____ and ______ are dyes used in banding pattern staining to allow unequivocal identification of each chromosome
Giemsa and DAPI
50
Polyploidy
“many-ploidy” having a chromosome number that is more than double the basic or haploid number – 69, etc. - Triploid (3 sets) – 69 - Tetraploid (4 sets) – 92
51
Aneuploidy
abnormal number of chromosomes | EX) Monosomy, trisomy
52
Mosaicism
presence of at least two genetically different cells in a tissue that is derived from a single zygote
53
Maternal age effect: Two-Hit Theory
1) More risk of non-disjunction because of diminished recombination due to lack of chiasma or mislocalization 2) Diminished ability of oocytes to successfully complete chromosome segregation in the presence of unfavorable recombination events
54
Maternal Age effect: Cohesion Complex Theory
- Degradation of cohesion complexes established during fetal development between sister chromatids and homologs with age because of extended meiosis I - -> Terminalization (premature separation of homologs/sister chromatids --> aneuplodiy)
55
Balanced Structural Rearrangments
- all genomic material is present, even though it is arranged differently - No loss or gain of genetic material - No phenotypic effect for heterozygote carrier - EXCEPTION: breakpoint in a gene, disrupting function - Can increase risk of producing abnormal gametes, risk to subsequent generations
56
3 examples of balanced structural rearrangments
1) Robertsonian Translocations 2) Inversions 3) Reciprocal translocations
57
Reciprocal translocations results in ________ formation when chromosomes of a carrier pair in meiosis, leading to either _______ or _______ segregation
quadrivalent formation adjacent alternate
58
Reciprocal translocation
- reciprocal exchange of broken segments between non-homologous chromosomes - balanced structural rearrangement
59
When adjacent segregation of quadrivalents occurs this leads to the formation of __________
100% unbalanced gametes
60
When alternate segregation of quadrivalents occurs this leads to the formation of __________
1/2 normal gametes, 1/2 balanced reciprocal translocation gametes
61
Robertsonian translocation
- Most common structural chromosomal rearrangement - Fusion of two acrocentric chromosomes → loss of both short arms (NOT deleterious, only satellite DNA) → reduction of chromosome number, but still considered balanced -Normal phenotype in carrier, but can lead to unbalanced karyotypes in offspring (monosomies and trisomies)
62
Two types of inversions
pericentric | paracentric
63
Inversions
- chromosome undergoes two double strand breaks of the DNA backbone, and the intervening sequence is inverted prior to the rejoining of the broken ends - formation of loop when homologous chromosomes are paired in recombination - can increase risk of abnormal gametes
64
Pericentric Inversions
- Include the centromere - Can result in gametes with duplication and deficiency of chromosome segments -½ balanced, ½ unbalanced
65
Peracentric Inversions
- excludes centromere - can result in acentric or dicentric chromosomes after crossing over (unstable) -1/2 balanced, 1/2 inviable
66
Unbalanced Structural Rearrangements
abnormal chromosomal content, deletion or duplication in multiple genes
67
Duplication results in gametes with _________ and deletion results in gametes with _________ (after fertilization with a normal gamete)
duplication --> partial trisomy | deletion --> partial monosomy
68
Del (22)(q11.2) results in ________ and _______ syndromes due to a deletion of 3 Mb within 22q11.2 in one cope of chromosome 22. Symptoms include _______, ________, _________, _________
- DiGeorge Syndrome, Vel-Cardio-Facial Syndrome | - Results in: heart defects, craniofacial anomalies, intellectual disability, and immunodeficiency
69
DiGeorge Syndrome and Vel-Cardio-Facial Syndrome are a result of ___________
Del(22)(q11.2) -deletion of approximately 3 Mb within 22q11.2 in one copy of chromosome 22
70
Epigenetics
mitotically and meiotically heritable variations in gene expression not caused by changes in DNA sequence EX) reversible, post-translational modifications of histones and DNA methylation
71
DNA methylation of CpG islands results in ______, but some DNA methylation can result in __________
recruitment of silencing complexes, and silencing of gene expression gene expression activation
72
Genetic imprinting is _________ and is present in ___% of genes in the human genome
sex dependent epigenetic modulation of regulatory regions such as promoter sequences 10%
73
DNA methylation of genetically imprinted genes have 3 main qualities...
1) established in the gamete 2) stably maintained in somatic cells after fertilization 3) reversible
74
Imprinted DNA methylation is maintained in somatic cells by ________ when DNA is replicated
maintenance methyltransferases
75
Imprinted DNA methylation is reversible because _________
it can be reset during gametogenesis to transfer the appropriate sex-specific imprint to progeny (based on their sex)
76
Uniparental Disomy is _____________ and often results due to __________
the presence of two chromosomes only inherited from one parent trisomy rescue
77
Types of FISH probes include ________, _________ and __________
Centromere, Locus Specific, and Dual Fusion
78
FISH probes use _________ which hybridize to cells and can identify _______ by looking for ________
fluorescently labeled specific DNA probes (no more than 200kb) -can identify translocations by looking for fusion signals
79
Centromere FISH probe is used for ________ | EX) ______
enumeration | EX) ALL panel
80
Locus Specific FISH probe is used for _________ | EX) ______
identifying deletions/duplications | EX) p53
81
Dual Fusion FISH probe is used for __________ EX) ______ and _______
identifying translocations | EX) BCR-ABL and PML-RARa
82
Chromosomal microarray (CMA) can detect _______ but not ________, and has limited ability to detect _________
genomic deletions and duplications NOT translocations mosaicism
83
Lab test diagnosis protocal includes these 3 steps:
1) Chromosomal Microarray (CMA) - If duplication/deletion detected → consult Database of Genomic Variants (DGV) to see if it is a known disease region 2) Parental FISH studies – determine if finding is normal, rare, or familial - Deletion/Duplication found on parent → further FISH testing of other family members 3) No deletion/duplication found, and no DGV hits, then do further data-base mining
84
Pharmacogenetics
- Variable response to individual genes - The study of differences in drug response due to allelic variation in genes affecting drug metabolism, efficacy, and toxicity
85
Pharmacogenomics
- variable response due to MULTIPLE LOCI across the genome | - Concerned with assessment of common genetic variants in the aggregate for their impact on the outcome of drug therapy
86
Pharmacokinetics
- absorption, distribution, metabolism, and excretion of drugs - whether, or how much drug reaches its target
87
Drug Metabolism Steps (2)
Phase 1: polar group added to compound --> makes more soluble (usually hydroxylation) Phase 2: add sugar/acetyl group to detoxify drug --> easier to excrete
88
Pharmacodymanics
- relationship between drug concentration at site of action and the observed biological effects - what happens when drug successfully reaches target
89
CYP450 gene family (50+ types): most function to _________, and 90% are active in ___________.
inactivate drugs | phase I metabolism of common drugs
90
______% of Codeine is inactivated by ______ and _____% of codeine is activated by _________
80% inactivated by CYP3A4 | 10% activated by CYP2D6
91
grapefruit juice acts to _______ CYP3A activity. Therefore, when grapefruit juice is combined with Felodipine (treats HTN) the result is _______________
inhibit significant hypotension - low metabolism of drug because CYP3A is inactivated, thus over-activation of drug effects
92
_______ is used to treat fungal infections and acts to temporarily inhibit _______ metabolism of cyclosporine
Ketoconazole | CYP3A
93
When Ketocanazole is combined with ________, you must _________ or risk neprotoxicity because ________ is inhibited
cyclosporine must decrease cyclosporine dose CYP3A metabolism of cyclosprine
94
________ is a TB prophylaxis drug that acts to _______ thus ___________. Therefore, you must ________
Rifampin CYP3A inducer thus increasing metabolism of cyclosporine. Must increase dose of cyclosporin
95
CYP2D6
needed to activate codeine into morphine
96
VKORC1 = ? and is metabolized by _______
Warfarin (narrow therapeutic window) | CYP2C9
97
NAT = is a __________ enzyme whose rate is determined by ________. _______ (drug) is a TB prophylactic drug metabolized by NAT. If drug is metabolized to fast --> ? If drug is not metabolized enough --> ?
N-Acetyltransferase enzyme (important in phase II metabolism), reate determined by genetic polymorphisms Isoniazid If drug is metabolized to fast --> not effective in preventing TB If drug is not metabolized enough --> liver damage/failure
98
TPMT (Thiopurine-S-methyltransferase) is used to treat ______ If drug is metabolized to fast --> ? If drug is not metabolized enough --> ?
treats childhood leukemia If drug is metabolized to fast --> not effective in treating leukemia If drug is not metabolized enough --> immunosuppressant can cause death from bone marrow failure
99
G6PD deficiency
- X-linked Recessive - most common human enzyme deficiency - Increases malarial resistance (common among blacks) - subject to hemolytic anemia after certain drug exposures
100
Population genetics
the study of allele frequencies and changes in allele frequencies in populations
101
Polymorphism
genetic variant (mutation) which is common (>1%) in the populations
102
Mutation rate (u)
Frequency of new mutations at a given genetic locus
103
Calculating mutation rate: Direct method Indirect Method
Direct method: u = number of cases without family history/ (total population x 2 allels) Indirect Method: used when f=0 I=2u
104
Fitness (f) If F=1 ? If F=0 ?
o Probability of transmitting one’s genes to the next generation F=1 (same as normal population) F=0 (gene(s) not passed on)
105
Coefficient of Selection (S)
S = 1 - f
106
Hardy-Weinberg Assumptions
1) Population is large and matings are random 2) Allele frequencies remain constant over time because: - No appreciable rate of mutation - All genotypes are equally fit (equal chance to pass alleles to next generation) - No significant immigration/emigration of individuals with different allele frequencies
107
Carrier frequency =
2pq when q is more rare than 1/10,000 can use 2q as an estimate for carrier frequency
108
p=? | q= ?
``` p = frequency of common allele q = rare allele ```
109
3 Types of Down Syndrome
- Trisomy 21 (95% of the time) (maternal nondisjunction in meiosis I usually) - Unbalanced Translocation (3-4%) between chr21 and another acrocentric chromosome - Mosaic Trisomy 21 (1-2%) – more mild phenotype
110
Down Syndrome Physical Features
- Flat faces - prominent epicanthal folds - Upslanting palpebral fissures - Single palmar crease - small ears - gap between 1st 2 toes - Large-appearing tongue - Low muscle tone - Increased joint mobility
111
Down Syndrome Medical Problems
``` Duodenal atresia Hirschsprung disease (constipation) Congenital heart disease (atrial septal defect) Early onset Alzheimer's Increased ALL risk ``` Other: - Eye: myopia (near-sightedness), lazy eye, blocked tear ducts, nystagmus, cataracts - ENT: ear infections, deafness, enlarged tonsils/adenoids - Endocrine: diabetes, thyroid, reduced fertility - Ortho: hips, joint subluxation, atlantoaxial subluxation
112
Down Syndrome Developmental and Behavior Phenotypes (6)
- Hypotonia – gross motor development effects - Spectrum of intellectual disability (Mild-moderate usually) - Speech problems - Seizures - Alzheimer’s - Autism
113
Trisomy 18 (Edwards Syndrome) Clinical Features (4)
- Small for gestational age - Small jaw - low-set ears - Clenched fingers - Rocker-bottom feet -Very high lethality within 1 year
114
Trisomy 13 (Patau Syndrome) Clinical Features
- Characteristic faces - Severe intellectual disabilities - facial clefts - polydactyly - renal anomolies
115
45XO is ___________
Turner Syndrome
116
47XXY is ___________
Kleinefelter Syndrome
117
Turner Syndrome clinical features
- short stature - webbed neck - broad chest - low set ears - cubitus valgus - inner canthal folds - blue sclera - NORMAL INTELLIGENCE - hormone dysfunction - gonadal dysgenesis - coarctation of the aorta - Prolonged QTc - scoliosis
118
Turner Syndrome prevalence
1/2500 newborn girls 99% do not survive to term mosaic karyotypes thought to contribute to survival
119
Klinefelter Syndrome prevelance
47XXY 1/500-1/1000 newborn boys can occur due to maternal or paternal meiosis I
120
Klinefelter Syndrome Clinical Features
- Tall stature - Hypogonadism (small testes) - gynecomastia - usually sterile - learning disabilities - delayed speech/language
121
Prader-Willi Syndrome (PWS) can be caused 3 ways
1) 15q11-q13 deletion on paternal chromosome (70%) 2) Maternal uniparental disomy (20-30%) 3) Abonormalities in imprinting center (2.5%)
122
PWS 15q11-q13 deletion can be caused by _______ and can be detected with ______ and ________
Caused by misalignment during homologous recombination of repeats flanking 15q11-q13 Detect with FISH and Microarray
123
Maternal uniparental disomy is 2 copies of the ______ allele and can be detected with __________
maternal detect with methylation testing
124
PWS abnormalities in imprinting center results when fertilization occurs by _________ causing the cell to think there is maternal UPD
sperm with abnormally persistent female imprinting
125
Detect abnormalities in imprinting center with ___________
methylation testing
126
PWS physical features (4)
-Changes in facial features (almond shaped eyes) -Undescended testicles (males) -Severe feeding problems (require G-tube) until 2-4 years when they completely reverse (insatiable appetite) → Obesity (can treat with Growth Hormone)
127
PWS medical problems
- Ortho: Scoliosis common - Eyes: Nystagmus, strabismus - Resp: obstructive sleep apnea
128
PWS developmental and behavioral problems
- mild-moderate cognitive disabilities | - behavioral issues are common
129
Angelman Syndrome can be caused 4 ways
1) 15q11-q13 deltion on maternal chromosome (70%) 2) Paternal uniparental disomy (7%) 3) Abnormalities in imprinting center (abnormally persistent male imprint) (3%) 4) Genetic mutation in UBE3A (10%)
130
UBE3A is usually only expressed from the ______ allele, so mutation can cause _______ 10% of the time
maternal | Angelman Syndrome
131
AS phenotype (6)
- mildly dysmorphic facial features - hypotonia - spasticity in older patients - Intellectual Disability - seizures - autism
132
IDIC 15 (15q11-q13) is a _________ derived abnormality that causes ________. These patients are NOT ______ but often suffer from _______ and ________
maternally causes autism NOT dysmorphic suffer seizures, and are hypotonic
133
Maternal 15q Interstitial Duplication only results in phenotypic effects if it is __________
maternally inherited
134
Maternal 15q Interstitial Duplication results in ______, with _____ and ______ common,. These patients are NOT _________
autism seizures, hypotonia common NOT dysmorphic
135
Chronic Myeloid Leukemia (CML) results from a ________ translocation involving chromosomes _____ and _____
BCR-ABL, chr 9 and 22
136
CML can be treated by ________
Gleevec
137
Gleevec is a _______ and acts to _________
- tyrosine kinase inhibitor - targets novel protein (tyrosine kinase signaling molecule) generated by translocation - -> Gleevec binds ATP binding site, inhibiting action
138
Acute Pro-Myeloid Leukemia (APML) results from a _______ balanced translocation involving chromosome _____ and _____
RERalpha and PML translocation chr 15 and 17
139
RERa and PML translocation results in a _________ that acts to _________
- novel transcription factor | - bind to promoter elements in DNA, inhibiting transcription downstream
140
Acute Pro-Myeloid Leukemia is treated with ________ which acts to _________
Vitamin A | -bind novel protein TF--> changes protein conformation --> allows transcription to continue when coactivators bind
141
Childhood B-cell Leukemia: ``` Hypodiploid = ? Hyperdiploid = ? ```
Hypodiploid = 38 chromosomes in cancer cells (poor prognosis, needs aggressive treatment) Hyperdiploid = 55 chromosomes in cancer cells (more favorable diagnosis)
142
47XYY = ?
Jacobs Syndrome
143
Jacobs syndrome clinical features and prevalence
-Learning disabilities -Speech delays -developmental delays -emotional/behavioral difficulties autism -tall stature 1/1000 newborn boys
144
47XXX = ?
Triple X syndrome
145
Triple X syndrome clinical features/risks and prevalence
- Tall stature - risk of learning disabilities, delayed speech/motor, seizures, kidney abnormalities 1/1000 newborn girls
146
Androgen Insensitivity Syndrome
46XY - x-linked gene - Androgen Receptor mutation - Androgens (testosterone) is present, but body does not recognize/respond to it
147
5-alpha reductase deficiency
46XY -Body can’t convert testosterone to dihydrotestosterone -Phenotype: undervirilized male with increased virilization at the time of puberty
148
SRY disorders: SRY deletion = ? Presence of SRY in 46XX = ? Mutations in SRY = ?
Deletion/Absence of SRY → phenotypically normal female Presence of SRY in 46XX → phenotypically normal male Mutations in SRY → decreased/absent AMH, under-virilization of a male
149
Denys-Drash and Frasier Syndrome (genotype = ?) results from a mutation in ________ which is a _________. Can result in ________, _________, and ______
46XY WT1 gene, an SRY transcription factor Can result in: kidney disease, increased tumor risk, and sex reversal
150
Congenital Adrenal Hyperplasia (genotype = ?) and results in ________, ________, and _________
46XY ambiguous genitalia 21-hydroxylase deficiency risk of salt wasting
151
Who am I? - short stature - webbed neck - broad chest - low set ears - cubitus valgus - inner canthal folds - blue sclera - NORMAL INTELLIGENCE - hormone dysfunction - gonadal dysgenesis - coarctation of the aorta - Prolonged QTc - scoliosis
Turner Syndrom XO