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Exam 2 > Genetics 2 > Flashcards

Genetics 2 Flashcards

1
Q

p

A

Short arm.

Up.

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2
Q

q

A

Long arm.

Down.

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3
Q

aneuploidies compatible with life

A

Trisomy 13, 18, 21.
+X
+Y
Loss of a sex chromosome

All other trisomies associated with infertility or pregnancy loss.

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4
Q

prenatal testing

A

Serum screen.
Ultrasound (look at nuchal translucency).
Amniocentesis (cells take 7 days to grow for analysis).
FISH probe-mix: looks for frequent trisomies in cells that aren’t growing; helps with mother’s anxiety for waiting for 7 days for cells to grow.

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5
Q

trisomy 18

A

Edwards Syndrome.
1 in 6,000.
Small size, small head circumference, low weight.
Overlapping fingers.
Rockerbottom feet.
Congenital heart defects.
Very poor prognosis (only 5% live past 1 year).

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6
Q

trisomy 21

A 
Down Syndrome.
1 in 700.
Flat facial profile, upslanted palpebral fissures.
Anomalous auricles.
Nuchal skin fold.
Single palmar crease, clinodactyly.
Hypotonia.
Hyperflexibility of joints.
Life expectancy: 60 years.

Associated findings: intellectual disability, congenital heart disease, gastrointestinal abnormalities, atlantoaxial instability, strabismus, thyroid abnormalities, leukemia.

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7
Q

trisomy 13

A

Patau Syndrome.
1 in 10,000.
Scalp defects, microcephaly, micropthalmia, holoprosencephaly, cleft lip/palate.
CHD.
Polydactyly.
Renal anomalies.
Very poor prognosis (only 5% survive 6 months).

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8
Q

Turner Syndrome

A

1 in 2,000 females.
Too few X genes.
Lymphedema.
Bicuspid aortic valve, coarctation of aorta.
Short stature.
Gonadal regression.
Low posterior hairline, webbed neck, widely spaced hypoplastic nipples.
Horseshoe kidney.
Cubitus valgus of elbow.
Karyotypes: 45, X (most common, 50%)/ 46,X, abnormal X/ mosaicism

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9
Q

Klinefelter Syndrome

A 
1 in 500 males.
Extra X in males.
Tall stature, long limbs.
Learning differences.
Gynecomastia (breast development).
Small testicles.
Infertility due to hypogonadism with oligospermia or azoospermia.
Karyotype: 47,XXY
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10
Q

47, XXX

A

1 in 1,000 females.
Speech delay, lower IQ than siblings.
Increased risk for infertility.
Most offspring are chromosomally normal.

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11
Q

X-inactivation

A

Compensates for dosage difference between males and females.
Steps: counting, choice, cis inactivation.

Counting - assesses how many X chromosomes are present; must be at least 1 active X chromosome.

Choice - random if both are normal; abnormal X inactivated if has XIST; Normal X is inactivated if there’s a translocation between X and an autosome; abnormal X inactivated if an unbalanced translocation.

Cis activation - XIST locus in Xq13 is responsible.

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12
Q

meiosis I nondisjunction

A

gametes: heterodisomy (ABC)
Zygote: trisomy

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13
Q

meiosis II nondisjunction

A

gametes: isodisomy (AAC, BBC).
Zygotes: trisomy

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14
Q

uniparental disomy

A

2 chromosomes from 1 parent, 0 from other.

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15
Q

47, XYY

A

1 in 1,000 males.
Lower IQ than siblings.
Increased risk of behavior problems.
Most offspring are chromosomally normal.

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16
Q

microdeletion syndromes

A

Submicroscopic deletions of more than 1 gene.
Bigger deletion = more features.
Need FISH to diagnose.
Genes are physically contiguous on chromosomes.
Usually sporadic, sometimes dominant.

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17
Q

DiGeorge Syndrome

A

del(22)(q11.2)

Narrow face, narrow eye openings, flat cheeks, prominent nasal root.

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18
Q

Williams Syndrome

A

Deletion of elastin gene on chromosome 7.

Broad forehead, short palpebral fissures, supravulvar aortic stenosis.

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19
Q

Duplication 7q

A

Frontal bossing, abnormal ears, hydronephrosis.

Duplication with multiple deletions.

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20
Q

translocations

A

Exchange of material between 2 or more chromosomes.
Can be balanced/reciprocal or unbalanced.
Balanced translocations can survive but are often infertile (high chance offspring will not be balanced).

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21
Q

robertsonian translocation

A

Occur between acrocentric chromosomes (13, 14, 15, 21, 22).
Results in loss of non-critical genes in short arms of chromosomes.
Count is reduced to 45.
ex: 45, XY, der(15;22)(q10;q10)

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22
Q

pericentric inversion

A

Around the centromere.

p and q breakpoints.

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23
Q

paracentric inversion

A

Outside the centromere.

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24
Q

acquired changes

A

Not present at birth.
Only occur in the organ affected.
Trisomy origin: mitosis.

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25
Q

constitutional changes

A

Trisomy: 13, 18, 21.
Trisomy origin: meiosis.
Monosomy: X
Balanced translocation: no impact on phenotype.
Unbalanced translocation: abnormal phenotype.

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26
Q

Philadelphia translocation

A

90-95% of CML cases.
Balanced translocation: t(9;22) (q34,q11.2).
First cancer abnormality described.

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27
Q

cancer and translocations

A

Breakpoints occur at oncogenes.
Abnormal protein is produced and cannot be regulated.
Overproduction of a normal protein.

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28
Q

cancer and deletions

A

Result in loss of genes, typically tumor suppressors.

Loss of 1 gene and possible inactivation of the other removes cell cycle control.

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29
Q

types of deletions

A

Single base substitutions.
Deletions (single base & microdeletions).
Duplications (single base & microduplications).
Frameshift (insertion, deletion, duplication).
Regulatory (promoters, enhancers, UTR).
Tandem repeat expansions.

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30
Q

conservative missense mutations

A

new amino acid has the same properties.

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31
Q

nonconservative missense mutation

A

new amino acid has new properties

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32
Q

Charcot-Marie-Tooth

A

Duplication on chromosome 17.

Clawed hand, arched feet.

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33
Q

promoter mutations

A

Affect binding of RNAP to promoter.

Results in reduced production of mRNA and decreased protein production.

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34
Q

dyskeratosis

A

Promoter mutation.

Causes premature ageing and bone marrow disease.

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35
Q

null mutation

A

Loss of function mutation.
Classic autosomal recessive inheritance.
50% function is sufficient.
Carriers are healthy.

Ex: PKU

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36
Q

haploinsufficiency

A 
Loss of function mutation.
Autosomal dominant.
Half of normal product is insufficient.
Heterozygous = mild disease.
Homozygous = severe disease.
AKA incomplete dominance.

Ex: familial hypercholesterolemia

37
Q

dominant negative

A

Loss of function mutation.
Autosomal dominant.
Mutant protein interferes with function of normal protein.

Ex: Marfan’s syndrome

38
Q

gain of function

A

Usually due to a very particular change in gene.
Only 1 mutant gene necessary.
Autosomal dominant.

Ex: Achondroplasia

39
Q

benefits of DNA based testing

A

Confirm clinical diagnosis.
Presymptomatic diagnosis.
Pre-implantation and prenatal diagnosis.
Genotype-phenotype correlation.

40
Q

challenges of DNA based testing

A 
Genetic heterogeneity.
Allelic disorders.
Variable expression.
Non-paternity.
Concerns regarding genetic discrimination.
Mitochondria.
41
Q

DNA sources

A 
Blood (WBC).
Saliva, buccal cells.
Skin, hair, sperm.
Amniocytes.
Chorionic villus.
42
Q

karyotype analysis

A

Visible chromosome abnormalities (>3 MB).

Deletions, duplications, translocations, inversions, insertions.

43
Q

FISH

A

Fluorescent In-Situ Hybridization.
Known submicroscopic deletion/duplication syndromes.
Subtelomeric deletions/duplications.

44
Q

Methylation Testing

A

Bisulfite treatment + MSP.
Shows methylation.
Determine if maternal or paternal.

45
Q

Allele Specific Oligonucleotide Testing

A

Look for a panel of common mutations.

46
Q

Short Tandem Repeat Polymorphisms (STRPs)

A

Polymorphic markers for indirect DNA testing.

Crime scenes, paternity testing, twin testing.

47
Q

Multiple Ligation-Dependent Probe Amplification (MLPA)

A

Multiple exons at once.

Detect large deletions (many exons), small deletions (1 exon), single base change.

48
Q

haplotype

A

SNPs observed in groups.
Inherited together from 1 parent.
Can be used for gene mapping.

49
Q

comparative genomic hybridization (CGH) array

A

Compares patient DNA with control DNA.
Duplication: more patient DNA than control (red).
Deletion: more control DNA than patient DNA (green).

50
Q

SNP array

A

Asks which SNPs are present.
If a duplication/deletion, it shows how many copies.
Provides more info than a CGH array.
Reports amount of DNA (deletions more easily recognized).
Can identify loss of heterozygosity.

51
Q

importance of identifying loss of heterozygosity

A 
(SNP array identifies loss of heterozygosity).
For UDP (heterodisomy, not isodisomy).
Imprinting.
Consanguinity.
AR conditions.
52
Q

Expression array

A

Measures changes in gene regulation via gene expression level.
Used for tumor characterization.
Can use it to guide treatment based on response of cells.

53
Q

use of arrays

A

When no clear, clinical picture.
Developmental delay, dysmorphic features.
Characterization of tumors.
Identification of genes (GWAS).

54
Q

limitations of arrays

A

Might not detect low-level mosaicism.
Only look at quantity, not location.
Cannot detect translocations or inversions (but can be used to follow up an inversion: is there a small deletion as a result?)

55
Q

Sanger sequencing

A 
Slow.
Expensive.
Highly accurate.
Gold standard for validation of NGS.
Used in human genome project.
56
Q

NGS (next generation sequencing)

A

Faster.
Cheaper.
Less accurate.

57
Q

clinical uses of NGS

A

WGS (whole genome): research, now moving to clinical use.
WES (whole exome): loos for disease-causing mutations.
Panels: sequencing for a list of genes associated with a phenotype.

58
Q

possible NGS results

A

Benign: does not affect gene function; not included in report.

VUS (variant of uncertain significance): not enough evidence for benign or pathogenic decision.

Pathogenic: disrupts gene function; potential to cause health effects.

59
Q

secondary findings

A

Not what you were looking for, but has health implications.
Pathogenic mutations in medically actionable genes.
Have established interventions to reduce morbidity.

60
Q

Limitations of NGS

A

Cannot detect trinucleotide repeat expansions, methylation/imprinting, structural rearrangements, or copy number variations.

Not a “one size fits all” test.

61
Q

epigenetics

A

Modification of gene expression without alteration of DNA sequence.
Change over time.
Reversible.

62
Q

3 types of epigenetic changes

A

1) Methylation: on DNA; reduces expression.
2) nucleosome positioning: move nucleosomes to expose an area for translation.
3) histone modifications: alteration of chromatin structure.

63
Q

karyotypes can detect:

A

Large deletions.

2-3 mbs

64
Q

FISH can detect:

A

120-400 kb

65
Q

Arrays can detect:

A

500 bp

66
Q

NGS can detect:

A

1 bp

67
Q

% of cancers that are hereditary

A

5-10%

MOST are NOT hereditary.

68
Q

Knudsen’s two-hit hypothesis

A

Sporadic cancer: requires 2 acquired mutations before tumor forms.
Have 2 genes, and loss of function is AR.

Hereditary cancer: only need 1 acquired mutation before tumor forms.
Already have 1 bad gene.

69
Q

oncogenes

A

Promote excessive cell growth.

Mutated form of a gene involved in normal cell growth.

70
Q

red flags for hereditary cancers

A 
Early onset tumors (<50 years).
Multiple/bilateral tumors.
Rare/unusual tumors.
Combinations of certain cancers.
Multiple generations affected (AD inheritance).
Lack of known contributing factor.
71
Q

HBOC (hereditary breast and ovarian cancer)

A

Due to mutated BRCA1/2 gene.
Females: increased risk of breast/ovarian cancers, increased risk of having a 2nd breast tumor.
Males: increased risk of breast/prostate cancers.

72
Q

colorectal tumors - genes affected

A

(in order)
APC
KRAS (increases size/dysplasia)
p53 (carcinomas)

73
Q

Lynch Syndrome

A

Caused by mismatch repair genes.
Increased risk for colon cancer (also stomach, endometrial, uterine, ovary).

Prevention: increase screening, do surgical procedures.

74
Q

risks/concerns of testing for cancers

A

Psychological stress.
Ethical concerns.
Life insurance discrimination.
Expensive.

75
Q

objectives of prenatal diagnosis

A

Provide info to prospective parents regarding fetal diagnosis.
Counsel and support parents in personal reproductive decisions.
Offer fetal therapy / prevent postnatal medical implants.

76
Q

screening tests (general, names)

A

PROBABILITY, not definitive.
Provides an individual risk assessment.

Ex: ultrasound, maternal serum marker screening, NIPT.

77
Q

diagnostic tests (general, names)

A

Definitive.
Procedure-related risk of pregnancy loss.

Ex: CVS, amniocentesis, cordocentesis, PUBS

78
Q

nuchal translucency ultrasound

A

11-13 weeks.
Measures fluid under skin behind fetal neck.
Increased nuchal translucency associated with increased risk for aneuploidies, heart defects.
Many false positives.

79
Q

Fetal Anatomic Survey

A

18+ weeks.

Detects structural fetal anomalies, “soft marker” for aneuploidies.

80
Q

Level II Ultrasound

A

After 18 weeks.

Detects open neural tube defects, congenital heart defects, trisomy 21, trisomy 18.

81
Q

Maternal Serum Marker Screening

A

11-13 weeks (but can’t look at neural tube defects yet).
15-21 weeks (CAN look at neural tube defects).
Offered to all pregnant women.
Evaluates chances for trisomy 21/18, open neural tube defects.

82
Q

Non-Invasive Prenatal Testing (NIPT)

A

10 weeks to delivery.
Offered to women at increased risk of aneuploidy.
Evaluates chances for trisomies 13/18/21, monosomy X.
Higher detection rate, lower false positive rate.

83
Q

Chorionic Villus Sampling (CVS)

A

10-13 weeks.
Can NOT test for neural tube defects.
Testing includes FISH, karyotype analysis, microarray, targeted testing for single gene disorders.

1/300 to 1/500 chance of miscarriage.

84
Q

Amniocentesis

A

15+ weeks.
Can detect neural tube defects.
Testing includes FISH, karyotype analysis, microarray, targeted testing for single gene disorders, neural tube defects.

1/300 to 1/500 chance of miscarriage.

85
Q

Pre-implantation Genetic Testing

A

Embryos in IVF can be screened for aneuploidy or single gene disorders.
PGS or PGD.

86
Q

PGS (pre-implantation genetic screening)

A

Microarray based.

Screens for aneuploidies.

87
Q

PGD (pre-implantation genetic diagnosis)

A

NOT DIAGNOSTIC, still just a screening.
Uses a family-specific test.
Screens for single gene disorders.
Confirmed via CVS or amniocentesis.

88
Q

indications for additional testing

A 
Advanced maternal age (>35).
Fetal ultrasound finding.
Prior pregnancy with aneuploidy.
Prenatal chromosome translocation.
Positive maternal serum screen results.
Positive non-invasive prenatal testing results.

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