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Genetics and genomes > W11LECT - Genome and environment > Flashcards

W11LECT - Genome and environment Flashcards

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Biology 101 flashcards
1
Q

What is Minor allele frequency (MAF)?

A
  • The frequency at which the less (second most) common allele occurs in a given population.
  • By definition it is < 0.5 (5%).
  • If the MAF of an SNP is >5%, then it is called frequent
    +) if between 0.5-5%, it is low
    +) if it is below 0.5%, it is rare.
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2
Q

What are the features of High penetrant variations?

A
  • Trait it produces will almost always be apparent in an individual carrying the allele
  • The variation significantly influences the function of a gene or its products.
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3
Q

Give examples of diseases/gene that represent High penetrant variations?

A
  1. Xeroderma pigmentosum/DNA repair
  2. Phenylketonuria/PAH
  3. Familial hypercholesterolemia/LDLR
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4
Q

Give examples of Environmental factor/phenotype that represent High penetrant variations?

A

− UV light/skin cancer
− Phenylalanine/mental disorders
− Cholesterol/atherosclerosis

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5
Q

Give examples of Environmental factor/phenotype that represent High penetrant variations?

A

− UV light/skin cancer
− Phenylalanine/mental disorders
− Cholesterol/atherosclerosis

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6
Q

What are the features of Low penetrant variations?

A
  1. Only sometimes produce perceptible phenotype. The variation does not influence significantly the function of the gene or its products, or the intact gene is not essential for the normal phenotype.
  2. But in interactions with other variations or environmental factors its effect may be apparent.
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7
Q

What are the 3 examples of Low penetrant variations?

A
  1. Alpha 1-antitrypsin deficiency
  2. Factor V Leiden
  3. Hereditary haemochromatosis
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8
Q

What is Biological function of the ATM?

A
  • The product of the ATM gene mutated in the human genetic disorder ataxia-telangiectasia (AT)
  • Containing: a C-terminal protein kinase domain DNA binding domain
  • 85% of the mutations reported in A-T patients are predicted to truncate the protein
    Others: missense mutation etc.
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9
Q

What are the symptoms of Ataxia-Teleangiectasia (A-T)?

A

Symptomes:
* progressive cerebellar ataxia of
early childhood
* occulocutaneus teleangiectasia (dilatated vessels in cornea and skin)
* Immundeficiency (hypoplasia of
the thymus)
* strong predisposition to
malignancy

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10
Q

What are the features of Alpha 1-antitrypsin deficiency?

A
  1. Mutation in the SERPINA1 gene (causes defective production of alpha 1-antitrypsin).
  2. Population frequency: 4.9%.
  3. The carriers are sensitive to cigarette smoke and other air-borne particles leading to lung emphysema, COPD, or asthma.
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11
Q

What are the features of Factor V Leiden?

A
  1. Caused by the Leiden mutation in F5 gene (R506Q). In this disorder, the Leiden variant of factor V of the coagulation system cannot be inactivated by activated protein C.
  2. Carrier frequency is 6.5%.
  3. Oral contraceptives, long physical inactivity (air travel), pregnancy increase the risk for development of deep vein thrombosis.
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12
Q

What is the The heritability (h2) of a trait?

A
  • The heritability (h2) of a trait is a measure of the degree of resemblance between relatives.
  • Heritability is a statistic used in the fields of genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population.
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13
Q

How to measure the heritability (h2) of a trait?

A

h2 = additive genetic variance (VA)/ phenotypic variance (VP)
=> h2=VA /VP =VA /(VG+VE)

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14
Q

What is the range of the heritability (h2) of a trait?

A

Heritability ranges from 0 to 1 (traits with no genetic variation have a heritability of 0)

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15
Q

Heritability is a function of the environment (VE)
=> T/F? WHY?

A

TRUE!
Since heritability is a function of the environment (VE), it is a context dependent measure.
It is influenced by both:
− The environment that organisms are raised in
− The environment that they are measured in
h2=VA /VP =VA /(VG+VE)

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16
Q

What are the features of Metagenomics?

A

Metagenomics- it is the study of metagenome:
- Genetic material recovered from environmental samples.
- The term was first used in 1998
- Enables studies of organisms that are not easily cultured in a laboratory

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17
Q

Quantitative Trait Locus (QTL)
1. What is Quantitative Trait Locus (QTL)?

A

A genomic locus that regulates a quantitative trait (i.e., complex trait).

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18
Q

Quantitative Trait Locus (QTL)
2. Depending on the trait under genetic control a QTL can be referred to as ..

A

– eQTL (regulation of gene expression),
– mQTL (regulation of metabolite),
– methQTL (regulation of methylation), histoneQTL (regulation of histone modification), miQTL
(regulation of miRNA),
– pQTL (regulation of protein)
– sQTL (regulation of splicing or relative transcripts abundances).

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19
Q

Quantitative Trait Locus (QTL)
3. What is the purpose of QTL mapping analysis?

A

QTL mapping analysis focuses on finding statistical associations between genomic loci (e.g. DNA sequence variants such as SNVs) and quantitative variation in phenotypic traits.

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20
Q

What is Genome-Wide Association Study (GWAS)?

A
  • An observational study of a genome-wide set of genetic variants in different individual to see if any variant is associated with a trait
  • GWASs typically focus on associations between SNPs and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms
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21
Q

Population distribution of certain genotypes influencing ___

A

the respond to environmental stimuli (e.g. ionising radiation)

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22
Q

What is Morphogene?

A

distribution governs the pattern of tissue development in the process of morphogenesis or pattern formation,

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23
Q

Describe mutation or polymorphism in gene coding for HHIP = hedgehog-interacting protein

A
  • Two SNPs near this gene are significantly associated with risk of chronic obstructive pulmonary disease (COPD).
  • A single nucleotide polymorphism in this gene is also strongly associated with human height
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24
Q

How the environmental factor affect us?

A
  1. Short term effect through EPIGENETIC mechanism
    - E.g, DNA methylation, histone modification, DNA remodeling
  2. Short term effect through mutation
  3. Long-term adaptation by evolution
    - Genetic drift, bottle-neck effect
25
Q

What is Evolution:?

A

The natural evolution of new species is influenced by traits determined by the genetic characteristics of the species and by changes in the living and non-living environment and their continuous interaction.

26
Q

What is Evolution Genetics:

A

The steps of evolution are based on changes in the genetic composition of a population - the frequency of alleles.

27
Q

Micro evolution is happening in human rigth now !
=> How?

A
  • Chromosome-protein-DNA variations
  • A set of intraspecific changes within a species, resulting from changes in the genome of the population due to external and internal forces.
  • the creation of new subspecies or species
28
Q

What are the 4 Potential causes of allele frequency changes?

A
  1. Mutation
  2. Migration
  3. Natural selection
  4. Genetic drift
29
Q

Make a schematic diagram of Evolution factors

A
30
Q

What is Natural Selection?

A

Genetic variation causes certain biological traits to become more common in a population because they confer some sort of selection advantage on their carriers.

31
Q

What are the 3 Genome-shaping selection mechanisms?

A
  1. Natural (or purifying) selection
  2. Positive selection
  3. Balancing selection
32
Q

What is Natural (or purifying) selection?

A

the unfavorable mutation is not passed on

33
Q

What is Positive selection?

A

the beneficial mutation is enriched (e.g. lactase persistence)

34
Q

Give an example of Balancing selection

A

Balancing selection: e.g. heterozygosity may be advantageous over some environmental factor (e.g. Sickle cell anemia)

35
Q

Describe Traces of microorganism-human genome interactions in
the human genome

A
  • More than a hundred of human genes originate from bacteria (145), through horizontal gene transfer.
  • 8% of our genome originates from retroviruses.
  • There are human genes specifically against bacterial or viral infections, like genes for pattern recognition receptors like TLRs, MBL, CD14, NOD2 etc., or for antiviral proteins like APOBC3G, TRIM5, BST2.
  • Infections have one of the largest roles in the formation of human genome!
36
Q

Genetic drift
1. What is genetic drift?

A

Certain alleles may randomly disappear or increase in a population.

37
Q

Genetic drift
2. What is the cause of genetic drift?

A
  1. a small part of the population migrates, with a different allele
    distribution from the population as a whole
  2. Or a large part of the population dies and only a small part reproduces
38
Q

Genetic drift
3. What is the consequence of genetic drift?

A

Small populations and some people have many more offspring, etc.

39
Q

Give definition and example of Population bottleneck

A

random isolation due to environmental impact
- e.g.: disaster

40
Q

What is Founder population (founder effect)?

A

population bottleneck spec. case with few number of ancestors, inbred

41
Q

Amish
1. What are the features of Amish?

A
  • Founded around 1690 by about 200 German and Swiss immigrants
  • Today there is a population of 250,000
  • Ellis-van Creveld syndrome (ectodermal displasia)
  • Locus: 4p16.2
  • Gene: EVC - transmembrane protein
42
Q

Amish
2. What are the symptom and frequency of Amish?

A
  1. Symptoms
    - low stature
    - polydactyly
    - cardiac malformations nail
    - displasia
    - hypodontia
    - Gene: EVC - transmembrane protein
  2. Frequency
    - average 1/60000
    - amis 1/200
43
Q

What are the features of Migration?

A
  • Makes two different populations more similar to each other
  • Population admixture (population admixture)
  • E.g. Homo sapiens + Neanderthal + Genyisovian (Denisovan)
  • USA: The genetic background of African Americans is on average 75% African and 25% European
44
Q

How can Sunlight affect genome?

A

Selection pressures:
- UV radiation. It can cause DNA mutations and cancer in the skin (melanoma). The best defense against it is the melanin produced by melanocytes, which gives the skin dark color.
- D vitamin produced in the skin when exposed to sunlight. But high melanin content decreases this process.

45
Q

What are Major determinants of pigmentation in humans?

A
  • SLC24A5 ( Solute Carrier Family 24 Member 5) gene: A111T
  • SLC45A2 gene: L374F
  • Both are fixed in light-skinned Europeans
46
Q

Describe Light- gene interaction today

A
  • The prevalence of melanoma has been increasing in light- skinned populations due to excess exposure to sunlight (sunbath).
  • 100% of black-skinned individuals of African origin, 93% of Indians and 85% of East-Asians living in Canada suffer from D vitamin deficiency.
47
Q

How can High altitude affect genome?

A
  • Indigenous highlanders living in the Andean Altiplano in South America, in the Tibetan Plateau in Asia, and at the highest elevations of the Ethiopian Highlands in east Africa have evolved three distinctly different biological adaptations for surviving in the oxygen-thin air found at high altitude.
  • Andeans: ability to carry more oxygen in each red blood cell
  • Tibetians: increase their oxygen intake by taking more breaths per minute
48
Q

How can Available food affect the genome?

A
  • AMY1 gene coding for salivary amylase, which digests starch.
  • Extra AMY1 copies endow the individuals carrying them with the capacity to produce more salivary amylase.
  • high-starch-diet populations had more copies of AMY1.
49
Q

What are the features of AMY1 CN?

A
  1. Host genetic variation influences microbiome composition
  2. High AMY1 copy number (CNV) is associated with higher levels
    of Porphyromonas in saliva
  3. High AMY1-CN stool has more resistant starch degraders; drives more adiposity in GF mice
  4. The oral and gut microbiome influenced by AMY1 CN
50
Q

Selection for high fat diet
1. What is the role of CPT1A gene?

A
51
Q

Selection for high fat diet
2. What happen if there is p.Pro479Leu mutation in CPT1A gene?

A
  • hypoketotic hypoglycemia
  • high infant mortality
  • 68% frequency in Northeast Siberians
  • allele protective against overproduction of ketone bodies
    BUT: Migration or change from the traditional diet to a more carbohydrate-based one can lead to diseases.
52
Q

Explain Cohort vs Case-Control study

A
53
Q

Explain Cohort vs Case-Control study

A
  1. Case-Control Populations
    * Homogeneity of Cases and Controls
    * Population Stratification
    * Accurate Diagnosis of the Disease
    * Optimal for Rare Diseases
  2. Cohorts in a Medical Study
    * Better Characterized than Populations
    * Can focus on Subpopulations and Ethnic Subgroups
54
Q

What are the features of Gene-Environment-Wide Interaction Study

A
55
Q

Where is the missing heritability?

A
56
Q

Explain The importance of genetic structure

A
  1. Genetic structure: not everyone in the population is from same genetic background
    - Some people are more genetically similar than others
    - Israel: Ashkenazi Jews, Mizachi Jews, Arabs,…
    - US: Caucasian, Black, Hispanic
  2. Many SNVs in the genome have different distribution between Africans and Europeans
    - Most not due to selection/adaptation but due to random drift
57
Q

Describe Genetic structure in different population

A
  1. Many traits have strong population association
    - In the US, diabetes much more common among blacks
    - In Israel, Crohn’s disease is much more common among Ashkenazi Jews
  2. Every SNV which differs in distribution between Europeans and Africans will be statistically associated with the disease
    - Only because of structure/stratification in our sample!
58
Q

Explain Genetic risk prediction

A

Genetics and genomes (19 decks)

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