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MCT > Genetics > Flashcards

Genetics Flashcards

1
Q

What is apparently the main factor influencing de novo mutations?

A

Father’s age

Positive correlation

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2
Q

What is the difference between SNV and SNP?

A

Single nucleotide:
Variant - any frequency
Polymorphism - commonly different (>1-5%)

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3
Q

What is the difference between functional and non-functional SNVs?

A

Functional: aa change

  • non-synonymous (missense)
  • stop gain (nonsense)
  • stop loss
  • splice site

Nonfunctional: no aa change

  • synonymous (silent)
  • intronic
  • intergenic
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4
Q

What are short tandem repeats/ microsatellites?

A

Repeat of 2,3, 4 or more NTs 10-100x
Highly polymorphic (used in forensics, linkage studies)
Generated though error during replication (slippage of DNA pol - DNA melts and reanneals incorrectly)

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5
Q

What are retrotransposons?

A

RNA intermediate required to copy, then jump around
Repetitive sequences in genome
LINE-long interspersed repetitive elements (makes copies)
SINE-short interspersed repetitive elements (Alu sequence around 300 bp)
LTR-long terminal repeats
Total ~40% of genome

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6
Q

What are copy number variants (CNVs)

A

Deletions/duplications

  • longer (can be millions of bases long)
  • usually fine until 2 million bp range, then start to see phenotypic problems
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7
Q

What effects do inversions and translocations have?

A

Impact depends on break point

Inversions can sometimes be harmless, but can cause problems other times

Reciprocal translocations (switching) less likely to cause problems, but reproduction can be a problem

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8
Q

Describe the map-based (indirect) strategy to finding genetic variants that influence disease?

A

Used to narrow down portion of genome responsible for trait
Use a set of markers (variants) spread throughout genome
Markers themselves not expected to influence trait

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9
Q

Describe the direct strategy to finding genetic variants that influence disease?

A

Test potential causal variants

  • previously in canditate genes with biological plausibility (often flawed)
  • now by complete genome or exome sequencing (difficulties in correct interpretation)
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10
Q

What are examples of indirect causal variant identification strategies?

A 
Linkage studies (rare variant) 
Canditate genes (frequent variant)

Both used with there is a large effect on phenotype

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11
Q

For what kind of diseases would you map using linkage?

A

Mendelian

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12
Q

How would you map using linkage?

A

Genotype 300-400 microsatellite markers for affects and unaffected family members
Identify makers that cosegregate with the disease
Get down to ~10mB region
(now cheaper to use SNPs instead of microsatellites)

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13
Q

What can you NOT find with linkage?

A

Dominant variants compromising reproduction
Atypical presentations

(use exome or genome sequencing)

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14
Q

Describe mapping using common variants through Genome-Wide Association Studies (GWAS).

A

Designed to interrogate all common genetic variation (tagging SNPs)
Large sample sizes (1000-100K or more)
Unrelated individuals
Genotype cases and controls (or continuous trait)
Strict statistical procedures

Have largely not found variants of medical importance

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15
Q

What is a main difference between map-based and direct methods?

A

Map-based focus on variants that can identify the genomic region of interest and do not usually affect the trait themselves.

  • linkage
  • GWAS

Direct focus on causal variants themselves

  • candidate gene studies
  • whole-gemone or exome sequencing
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16
Q

What is G banding?

A

Pattern obtained using protease pretreatment of chromosomes followed by staining with Giemsa
Dark bands AT rich, heterochromatin, late replication
Light bands GC rich, euchromatin, early replication
Resolve 3-10 Mb

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17
Q

Short arm

A

p

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18
Q

Long arm

A

q

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19
Q

Centromere at the end. Only genes in p arm are for rRNA (non-coding)

A

Acrocentric

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20
Q

Centromere in center

A

Metacentric

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21
Q

Centromere off-center

A

Sub-metacentric

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22
Q

What determines how many bands you will see?

A

How compressed DNA at the time
Resolution
-Landmarks can show up at different resolutions
-Can appreciate smaller abnormalities with higher resolution

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23
Q

________ is the organized image of an individual’s chromosomes. ________ is how you would describe it.

A

Karyogram

Karyotype

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24
Q

Loss/gain of entire chromosome set

A

Euploidy

Haploid, diploid, triploid, tetraploid

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25
Q

Loss/gain of entire less than an entire chromosome set

A

Aneuploidy

Monosomy, Trisomy

26
Q

Presence of more than one cell line

A

Mosaicism

Often function of trisomy rescue (some cells have 3, some have normal 2)

27
Q

Triploidy often results in:

A

Spontaneous abortions

28
Q

Possible origins of triploidy

A

Egg has 46 - didn’t release polar body
Sperm has 46
Two sperm fertilize one egg (most common)

29
Q

Protein structure that forms mediating chromosome pairing

A

synaptonemal complex

30
Q

Physical points along chromosome where crossing over has occurred

A

chiasma

at least one per chromosome arm is required for normal segregation

31
Q

Where is recombination more likely to occur?

A

Increased near telomeres, decreased near centromeres

More in females

32
Q

Two causes of aneuploidy in meiosis and mitosis

A

Nondisjunction

Anaphase lag

33
Q

Failure of chromatids (mitosis or meiosis II) or chromosomes (meiosis I) to separate at anaphase

A

Nondisjunction

34
Q

Failure of a chromatid of chromosome to attach to the spindle and segregate into a daughter cell

A

Anaphase lag

35
Q

Contributing factor in all human trisomies

A

Abnormal recombination

36
Q

Tips of the X and Y chromosomes - identical regions

Only place where X and Y can pair to each other for recombination

A

Pseudoautosomal regions

37
Q

How is incidence of aneuploidy related with maternal age?

A

Advanced maternal age (33-34) is correlated with increased risk of abnormal oocytes and Down syndrome
-associated with most human trisomies

38
Q

What is the two hit theory for why aneuploidy increases with maternal age?

A
  1. Some eggs are produced with missing or mislocated chiasma (this happens during prenatal development)
  2. As women age, meiotic proteins lose the ability to resolve these mishaps
39
Q

Small, cell free fetal DNA sample from maternal blood compared to control chromosome
Very sensitive
Postive predictive value depends on a priori risk
Positive results should be followed by diagnostic testing

A

NIPS

Non Invasive Prenatal Screening

40
Q

Labeling of probe DNA with fluorescent dye, denature and hybridize
Can show copy number, position
Dual color dual fusion design for malignant translocation s

A

FISH

Fluorescence in situ hybridization

41
Q

High resolution tool for copy number analysis
Pieces of DNA hybridized to chip
Quantitative - Is the amount of DNA more or less than expected? (compare pt to reference)

A

Microarray

Yellow if hybridized equally
red or green if unequal

42
Q

What are some limitations of microarray CGH (Comparative Genomic Hybridization)?

A

Doesn’t tell you policy, location of rearranged sequences responsible for copy number change
Can be of unknown clinical significance
Mosaicism can be difficult to ditch if

43
Q

phenotype is result of inappropriate dosage for a critical gene with a genomic segment

  • interstitial (low copy number repeats, more consistent breakpoints)
  • terminal (may not have breakpoints)
A

segmental aneusomy syndromes

44
Q

Balanced rearrangement of chromosomes
de novo carry a 5-10% chance of abnormal phenotype
Carrier risk of unbalanced offspring related to size of segments

A

Reciprocal translocation

45
Q

Fusion of the long arms of two acrocentric chromosomes
Lose two p arms
Increased risk of +13, +21 conceptions

A

Robertsonian translocation

46
Q

Individual with only one representative of a chromosome or chromosome segment

A

Hemizygous

47
Q

Single gene disorder

Simple

A

Mendelian

48
Q

Mechanism is through haploinsufficiency or a gain of function

A

Autosomal dominant

49
Q

Mechanism is typically loss of function (but could also be gain of function)
Haplosufficient

A

Autosomal recessive

50
Q

Pedigree includes mating between individuals with common ancestors

A

Consanguinity

51
Q

Males express phenotype because they are hemizygous

A

X-linked

52
Q

Both alleles at a given locus, when in heterozygous state, are expressed

A

Co-dominance

53
Q

Expression/severity of mitochondrial disease may be extremely variable because of ______________, which is the concept that not every mitochondrial genome is the same with a cell.

A

Heteroplasmy

54
Q

Proposed mechanism of expansion of triplet repeats

A

Replicative slipping

55
Q

Multiple genes + environment

A

Complex disease

56
Q

Proportion of population with a particular genotype that express a phenotype

A

Penetrance

57
Q

What classification of disease has low frequency, high penetrance, and causative alleles?

A

Mendelian

58
Q

What classification of disease has high frequency, low penetrance, and susceptibility alleles?

A

Complex

59
Q

Two disease patients with indistinguishable disease phenotype, even within a single pedigree, but the underlying cause of disease is different

A

Phenocopies

60
Q

Susceptibility genes: Ch 1 complement factor H, ch. 10 ser peptidase HTRA1
Risk increased with smoking
Vision loss

A

Macular degeneration

61
Q

Sequencing only the coding regions of genes

A

Exome sequencing

62
Q

Very distinct phenotype
Autosomal recessive
Extremely rare
Was able to determine cause through exome sequencing

A

Miller syndrome

more realistic, but complicated for Dominant Muscular Dystrophy

MCT (13 decks)

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