Genetics and Genomics Flashcards

1
Q

What is a haplotype?

A

=an individuals set of alleles at a locus or cluster or loci on a chromosome

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2
Q

What are single gene disorders?

A
  • these disorders are determined primarily by the alleles at a SINGLE locus
  • recurrence risk describes the likelihood of passing on the gene
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3
Q

Mendelian Genetics… what is it concerned with?

A

-monogenetic traits aka single gene traits

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4
Q

Independent assortment

A

is one gene locus is independently transmitted from a gene on a different locus

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5
Q

Autosomal dominant disease

A

seen in every generation
M=F
-structural genes are often seen in this inheritance pattern
-no skipping generations unless new mutation!
-probability to inherit=50%

ex. achondroplasia

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6
Q

Achondroplastics are…

A

rizomyere???

their limbs (humerus and femur) are short but their tib/fib and radius/ulna are normal length

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7
Q

What is the danger with 2 people who have an AD disease mating?

A

-they have more problems in those who will become homozygotes much more severe issues

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8
Q

Autosomal Recessive

A

-rare
-often seen in metabolic disorders
-this is sometimes seen in those who are relatives who mate CONSANGUINITY
-those that are heterozygotes may have reduced enzyme activity and then combine to make no activity
M=F
-probability to inherit from heterozygote parents 25%

Ex.
-Hurler/Hunter

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9
Q

What is hurler syndrome?

A
  • AR disease
  • skeletal abnormalities
  • similar to hunter
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10
Q

Cystic fibrosis

A
  • mutation to CTFR gene
  • Cl transporter mutation
  • pleiotropic: effects more than one organ
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11
Q

Remember that dominant and recessive refer to ___ not ___

A

traits not genes!

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12
Q

Sex linked inheritance

A

types:
X linked dominant
X linked recessive
Y linked

x chromosome: larger so more mutations
-common in men

y linked: much smaller contains less genes

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13
Q

X linked recessive

A

M > F–bc males usually only ones affected

-SONS of heterozygote mothers have 50% chance of being affected

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14
Q

X linked dominant

A

M and F can be affected

-all female offspring of affected father will be affected

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15
Q

Y linked

A

only father to son transmission

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16
Q

Mitochondrial Inheritance

A
  • only given from mother
  • all offspring of affected females show signs of disease
  • not all mitochondria congregate in specific organs… so they effect organs different =heteroplasmy
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17
Q

New mutations

A
  • this can complicate the “normal” pattern of inheritance

- the gene transmitted undergoes a mutation from the normal allele

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18
Q

Achondroplasia and risks and what they have!

A
  • most cases are due to new mutations
  • only 1/8 are transmitted from dwarf parents
  • distinguish this by taking a family hx

remember they are: Rhizomelic—> refers to either a disproportion of the length of the proximal limb, such as the shortened limbs of achondroplasia, or some other disorder of the hip or shoulder.

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19
Q

What is gremlin mosaicism?

A
  • when 2 or more offspring present with an AD disease with no familial hx
  • this is when all parts of the germline cells are affected by the same mutation
  • mutation occurs during the parents embryonic development of the germ cells
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20
Q

Age Dependent Penetrance

A

aka delayed age onset

  • ex. of this is BRCA gene
  • this is when the disease does not present until AFTER patients reach reproductive age or adulthood
  • this can cause a difficulty in detecting the mode of inheritance

other ex.
huntingtons
polycystic kidney disease
alzheimers

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21
Q

Reduced penetrance

A

-this is when those that have the genotype fail to express the appropriate phenotype although they pass it to the next generation

penetrance is the general idea that a phenotype expression is dependent upon the predisposing genotype

ex. retinoblastoma

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22
Q

Variable expression

A

a trait in which the same genotype can produce phenotypes of varying severity or expression

  • penetrance=complete
  • severity is what varies
  • a parent with midl expression may pass on the disease

ex. neurofibroblastoma

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23
Q

What are some causes for variable expression?

A
  1. environmental factors
  2. modifier genes
  3. allelic heterogeneity
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24
Q

What is pleiotropy?

A

-genes that affect multiple aspects of physio or anatomy

ex. sickle cell
OI
CF

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25
Marfan syndrome
- mutation to fibrillar | ex. of pleiotropy
26
Locus heterogeneity
=single disease phenotype caused by mutations at different loci in different families a risk of this is testing for the wrong mutation -ex. OI
27
Genomic Imprinting... ex. of this
=process by which genetic material is expressed differently when inherited from the mother than when inherited from the father - methylation ex. prader will an anglemans Prader willi is inherited from the PATERNAL side Anglemans is MATERNAL (heavy retardation)
28
Anticipation
=progressivle earlier onset and increased severity of certain diseases in successive generations of a family ex. myotonic dystrophy
29
Population genetics: what factors determines it?
the branch of genetics dealing with genetic variation and genetic evolution of population -it looks at how these frequencies change or are maintained in different populations a. genetic factors b. environmental and societal factors
30
What is the multiplication rule?
probability that BOTH event 1 and 2 will occur together multiply probabilities together
31
What is the addition rule?
probability that EITHER event 1 or 2 will occur together add the probabilities together
32
hardy weinberg
states that population frequencies will stay at a constant from generation to generation p=normal q=mutant p+q=1 *calculates genotype frequencies p^2 +2pq + q^2=1 p^2=homozygous normal
33
what are the assumptions for hardy weinberg to be true? 4
1. large population 2. no mutation 3. no selection 4. no migration
34
when is hardy weinberg used in the clinical setting?
often used for autosomal recessive conditions
35
what is the 2/3 rule?
2/3 for heterozygotes who are carriers and do not have disease. 1/4 chance for child who does not have the disease and multiple these by the population frequency
36
What are some causes in population change frequencies?
1. natural selection 2. genetic drift 3. founder effect 4. gene flow
37
natural selection... ex. of some diseases
-sickle cell: protects from malaria -CF: protects against diarrhea leiden V: entourage coagulation
38
What are some examples of the founder effect?
- the founder effect is a large shift in frequencies in a small population containing little genetic variation - often subsets of populations a. islands b. small towns c. ashkenazi jews
39
Why is knowing the ethnic population of your patient important for genetic testing?
- if you know the ethnic population you can order more specific genetic testing - this can ultimately save cost
40
What is cytogenetics?
=the study of chromosomes and their abnormalities | -uses cytology and genetics
41
What is a karyotype? What criteria are they numbered by?
- chromosomes are extracted from nucleus, stained, and matched according to a. size b. banding patterns c. location of centromere
42
nomenclature for chromosomes
p=petitie small arm q=long arm metacentric: equal on each side of centromere submetacentric: longer on once side acrocentric: very small p arm
43
What is the problem with acrocentric chromosomes?
they often can have robertsonian translocations
44
What is euploid?
a multiple of a haploid number (N=23)
45
What is aneuploid?
trisomy or monosomy =extra or missing chromosomes -it is the state of not having euploidy **most common cause is nondisjunction**
46
When does nondisjunction occur?
it can occur during meiosis 1 or 2. - Often occurs during meiosis 1 in female gametes - it can occur in men but much later in life at about ~60 years old
47
What is polyploidy?
=more than 2 sets of homologous chromosomes ex. 2 sperm--1 egg 1 sperm--diploid egg
48
Down syndrome... what is its MAIN cause?
47 chromosomes (21) - retardation - heart problems - early onset alzheimers main cause: maternal meiosis I
49
Kleinfelter syndrome
XXY | 47
50
XYY syndrome
XYY 47 -very tall -severe acne lots in prison population?
51
Turner Syndrome
45 XO -monosomy X "webbed neck" infertile -could also have mosaic turners which are fertile therefore it is important to know where its full turners or not -this is the SINGLE MOST COMMON ABNORMALITY IN ABORTIONS
52
Edward Syndrome
``` 47 trisomy 18 -mental retardation -overlap of middle and index fingers -only 5% survive to 1 year ```
53
Patau Syndrome
47 trisomy 13 -microcephaly polydactyl
54
Prader Willi
- paternal chromosome - 15 mutation - fat - short stature
55
Angelmans Syndrome
- From maternal side - severe - absence of speech
56
Whats the difference between genetics and genomics?
genetics: study of traits genomics: is the study of genes
57
Inactivating changes in genes
- these are more common that activating changes - mutations which reduce expression - reduce activity of protein - can alter splicing balance
58
What are reasons for gaps in the genome?
1. chromosomes are not continuous 2. some sequences are hard to read high GC 3. some sequence is hard to align--repeats human genome is the ARTIFICIAL reconstruction of chromatin
59
What is some evidence for a genetic contribution to a disease?
1. congenital disorders 2. family hx 3. cross cultural 4. multigenerational 5. GWAS 6. identical twins separated at birth *ideal* 7. expression analysis
60
what is missing heritability?
-we know its heritable but we do not know the gene for it
61
Lamina A mutations
C--> T conversion - mutation is absent in both parents - usually acquired from a gremlin mutation - it is what causes progeria
62
What is the difference between family Hx and Genetic status?
They are often used interchangeably but they are 2 different things Family hx: stress, diet, exercise, infections, drugs/alcohol, exposure level to various things genetic statusL shuffling, mutation to germ line, donor egg, adoption where do they overlap? SNPs, most disease risks
63
What are PROBLEMS with family hx?
- time consuming - not recorded in a usable format - mistakes in recalling cause of death - many know little about health hx due to secrecy, and low privacy rates - adoption or donor eggs - false paternity - health records die with people
64
What are some advantages to multi-generational pedigree analysis?
-families have low genetic noise (they are very similar) -example ashkenazi jews mormons
65
gene--disease replationships
1. gene is perfectly associated with disease * high penetrance- typical of monogenic 2. gene is poorly associated with disease * low penetrance- typical of multi genic diseases 3. gene is strongly associated with disease but at variable levels * high penetrant but variable EXPRESSIVITY
66
What are the steps to test pre-implantation embryos for IVF?
- induct the F to produce multiple oocytes - harvest the embryos by transvaginal aspiration with US - IVF with fathers sperm - Harvest one of the 8 cells - test cells for known mutations that you are looking for - only implant the unaffected embryos