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Test II Flashcards

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1
Q

Ancient DNA (aDNA)

A
  • DNA extracted form ancient specimens

e. g. archaeological/historical skeletal material, mummified tissue

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2
Q

Gene Frequency

A

The ratio of the number of a specified allele in a population to the total of all alleles at its genetic locus

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3
Q

Allele Frequency

A

Proportion of gene copies in a population that are given allele type.

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4
Q

aDNA Information

A
  • Short fragment lengths (<500), usually below 70 bp
  • Extremely low quantities
  • Genetic material undergoes modification soon after death, which results in its fragmentation and damage
  • ->Includes ssDNA breaks, base modifications, due to oxidation and hydrolysis and base loss
  • ->Most common base modification is deamination of cytosine to form uracit
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5
Q

aDNA problems

A
  • Complex mixture of DNA originating from multiple sources, e.g. DNA sample may contain microbial, environmentally introduced DNA to the fossil during deposition
  • Contamination by extraneous genetic material, i.e. outside the organism, pollen
  • PCR fail due to enzymatic inhibitors in the aDNA sample
  • Need dedicated aDNA lab facility
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6
Q

Genetics of Lactose Persistance

A
  • Autosomal dominant trait
  • ->enabling life long digestion of the milk sugar lactose
  • ->Enzyme=LPH
  • ->Lactase persists into adult life in some but not all

-Common genetic trait in many European, African and Middle Eastern popn

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7
Q

Lactase intolerance

A
  • Lactase (LPH) hydrolyses the milk disaccharide lactose into its component monosacharides, galactose and glucose for absorption in the small intestine.
  • If lactase is absent, the lactose cannot be absorbed by the intestinal mucosa
  • Reaches the colon undigested where it is fermented by colonic bacteria

Symptoms: abdominal pain, diarrhoea, blotting

  • C –>T transition
  • Chromosome 2
  • Located upstream of LCT gene
  • SNP prevents down regulation of lactose activity after wearing.
  • Affects binding site of transcription factor
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8
Q

HWE

A

Defines a condition in which the allelic and genotypic frequencies in a population are not changing over time.

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9
Q

Microevolution

A

Changes in a population’s gene pool from generation to generation

(1) Source of new allelic variation: mutation
(2) Mechanisms that alter existing genetic variation: Migration, natural selection, genetic drift, non random mating

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10
Q

Natural Selection

A

The process that progressively eliminates individuals whose fitness is lower.
e.g. mice in regions with light coloured soils/rocks have light coloured fur. Mice in regions with black volcanic rock have dark fur

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11
Q

Fitness

A

Measure of reproductive success

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12
Q

Principles behind HWE

A

To reach equilibrium, 5 strict conditions must be met:

  1. Large population of randomly breeding individuals
  2. No natural selection
  3. No new mutation
  4. No migration
  5. No genetic drift
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13
Q

5 Major Evolutionary Forces Affecting Genetic Variation in Population

A
  1. Source of new allelic variation
    - mutation (low rate, not major)
  2. Mechanisms that alter existing genetic variation
    - Natural selection
    - Genetic drift
    - Migration
    - Non random mating
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14
Q

Selection acts in three ways:

A
  1. Disruptive selection
  2. Stabilizing selection
  3. Directional selection
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15
Q

Disruptive Selection

A

Both extreme forms of the trait have higher fitness than does the average

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16
Q

Disruptive Selection example

A

e. g. Polymorphisms in land snails. A series of alleles determines the ground colour
- brown dominant to pink, brown and pink dominant to yellow
- colouration of the snails is correlated with the specific environment where they are found
- change in frequency is due to change in environment; predation (song thrush bird) and thermoregulation.

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17
Q

Effect of Pesticides on Allele Frequencies

A
  • Diseases persist in all living organisms due to changes in allele frequency tend towards an evolutionary equilibrium in which mutation balances selection
  • The use of pesticides and antibiotics cause pests that were under control to return.
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18
Q

Stabilizing Selection

A

Average form of the trait has higher fitness than does either extreme

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19
Q

Stabilizing Selection example

A

e. g. Sickle cell disease
- SNP causes the disease
- Autosomal recessive disorder

HB^A HB^A and HB^A HB^S

  • makes hemoglobin A
  • biconcave shape
  • RBC survive up to 4 months

HB^s HB^s

  • makes hemoglobin S
  • Altered form, sickle shape, survive a few weeks
  • decrease in RBC –> Anemic, life threatening
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20
Q

Sickle Cell Advantage

A

Heterozygote advantage=higher fitness

  • H^s allele found to be at high frequencies among humans population exposed to malaria
  • H^A H^s red cells are likely to rupture when infected by a parasite, preventing parasite from propagating

Stabilising selection plays a role in maintaining alleles that are beneficial to the heterozygote but harmful to the homozygote

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21
Q

Directional Selection

A

Favours the extreme phenotype. one extreme form of the trait has the highest fitness.

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22
Q

Directional Selection example

A

Peppered moth.

  • Typical form, light colour with small dark spots, camouflage to hide from predatory birds
  • Carbonaria (melanic), black wings, high frequency 18th and 19th Industrial revolution. Due to dark soot air pollution.
  • Carbonaria form decreased when clean air act was introduced.
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23
Q

Pesticide example

A

DDT is an organochloride nerve toxin in insects. Common pesticide.

  • Dominant mutations in a single gene confer resistance through detoxification of DDT
  • In Bangkok, DDT uses resulted in increase in mosquito genotypes RR but these rapidly declined when stopped spraying
  • Genotype RS decreased but then rapidly increased when spraying stopped. More advantage to have both alleles

R-dominant, resistance allele
S-susceptibility allele.

RR genotype confers a fitness cost. In the absence of the insecticide, resistance is subject to negative control

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24
Q

Preimplantation Genetic Diagnosis (PGD)

A

Test an embryo before implantation in the uterus for single gene disorder.

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25
Q

PGD technique

A
  • Technique allows detection of genetic and chromosomal abnormalities prior to implantation
  • One cell or blastomere or an 8 cell embryo can be removed for testing. The remaining cell will complete normal development
  • Accuracy for detecting a mutation or abnormal chromosome is about 97%
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26
Q

Social issues of Genetic Testing

A

Genetic info is personal, powerful, potentially predictive, pedigree sensitive, permanent, and prejudicial.

Social issues are:

a) Education
b) Psychological issues- fear of unknown, coping with uncertainty, guilt, shame, survivor guilt, family dynamic
c) Discrimination risk-by employers, insurers, commercial institutions, school, armed forces etc.
d) Ethical issues-privacy and confidentiality, fairness in use of information, commercialisation/patents, social concepts of health/disease, reproductive rights

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27
Q

Ethical Challenges

A
  • Informed consent of participants
  • Archiving of data and privacy and storage of personal information
  • Minimization of risk e.g. physical, psychological, social or cultural risk, negative consequences, stress, embarrassment etc.
  • Social and cultural sensitivity
    e. g. respect for culture, social and language preferences and sensitivities. When culture is different, consult a qualified person
  • Declaration of conflicts of interest
    e. g. unfair professional, commercial or personal advantage. Direct/indirect money making interest. Declaring is research is commissioned or sponsored.
  • Exploitation of relationships
    e. g. between researcher and participant.
28
Q

Policy Challenges Involved with Genetic testing

Tissue Act 2008

A

Purpose: to help to ensure that collection of human tissue

a) occurs with proper recognition or and respect for-
- the autonomy and dignity of the individual whose tissue it it
- the cultural and spiritual needs, values and beliefs of immediate family
- cultural, ethical and spiritual implications of the collection of use of human tissue
- the public good associated with collection or use of human tissue

b) Does not endanger the health and safety or members of the public.

29
Q

Website to find info regarding Genetic tests

A
  1. ncbi

2. genetest.org.

30
Q

LOD score

A
  • Logarithm of Odds
  • Statistical analysis used to assess the likelihood of linkage between genes from pedigree data

z=log10 linked/not linked

LOD of 3 or higher=linkage

31
Q

SNP

A
  • Single nucleotide polymorphism
  • One base pair change
  • A single nucleotide locus with two naturally existing alleles defined by a single base pair substitution.
32
Q

DIP

A
  • Deletion-insertion polymorphism

- Short insertion or deletions of a single or a few base pairs.

33
Q

DFNA28

DFNB79

A

Deafness, autosomal dominant (A), 28-time it was identified

Deafness, autosomal recessive (B)

34
Q

Genetic Mapping

A

A genetic map is used to locate and identify the gene or group of genes that determines a particular inherited trait.

35
Q

Genetic mapping example

A

Deafness

  1. Ascertain families
    - autosomal dominant, vertical pattern of inheritance
    - late onset progressive
    - informed consent
    - collect DNA samples
  2. Review medical history
    - Audiogram analysis: measures how loud sounds at a range of frequencies before a person can hear them
  3. Screen for known DFNA loci (e.g. DFNA28)
  4. Genome wide scan (e.g chromosome 8q 22)
  5. Develop haplotypes
  6. Physical map
  7. Candidate genes (7 known, 20 predicted)
36
Q

Positional cloning

A

A technique for isolating and cloning a gene

e.g. a disease associated gene. Relies on genetic markers.

37
Q

Positional cloning example

A

Neurofibromatosis (NF)

  • Autosomal dominant
  • Fully penetrant
  • Causes proliferation of nerve tissue, tumours usually benign. Cells grown uncontrollably
  • High blood pressure, bone abnormalities, learning disabilities, larger heads, short stature.
  • Phenotype appears late childhood or adolescence
  • NF gene is on chromosome 17, no cure, but some treatments

Determines whether of not a SNP is linked to the NF gene.
Hypothesis: NF is linked to SNP 1 on chromosome 17.

38
Q

GWAS

A

Genome wide association studies

  • scanning genetic markers (SNPs) across the genomes of many people to find a genetic variation associated with a particular disease.
  • If certain genetic variations are found to be significantly more frequent in people with the disease compare to people without disease, the variation are said to be ‘associated’ with the disease.
39
Q

HRM

A

High resolution melting analysis

40
Q

MAF

A

Minor allele frequency

-frequency at which the less abundant allele of a SNP occurs in a given population

41
Q

Tag SNP

A

SNP that is in strong LD with multiple SNP

LD-linkage disequilibrium

42
Q

Using HRM analysis to identify a SNP

A
  • Used for identifying SNPs in DNA sequences
  • PCR reaction, includes a dsDNA binding dye e.g. SYBR green
  • DYE has a high fluorescence when bound to dsDNA and low fluorescence in the unbound state
  • Amplification is followed by a HRM step using instrumentation
  • When the dsDNA dissociates into single strands, the dye is released, causing a change in fluorescence.

e. g. A low temps, the DNA will be double stranded and the dye will strongly fluoresce. As temp increases, fluorescence will decrease 1000-fold as the dye is released when the two strands denature
- Final result is a melt curve profile characteristic of the amplicon

43
Q

Designing a GWAS study

A
  1. Selection of a large number of individuals
    e. g. Coharts/case control studies
  2. DNA isolation and genotyping
  3. Statistical Test-association between SNP passing quality thresholds and disease traits
  4. Replication of identified associations in an independent population sample

GWAS is based on Linkage Disequilibrium at the Population Level.

44
Q

Coharts study

A

Researchers follow a large group of individuals over time and measure many aspects of their health

45
Q

Case control study

A
  • Pairs of individuals are matched so that they share as many characteristics as possible
    e. g. age, sex, environmental exposures
  • SNP is then associated with the presence or absence of the disorders
46
Q

‘Affected sibling pair’ strategy

A

Scans genomes of siblings for SNPS shared by those with the condition, but not by those who don’t have it

47
Q

Homozygosity mapping

A
  • Performed on families that are consanguineous.
  • Scans stretches of homozygous DNA
  • Children in this case are more likely to inherit two copies of the mutation.
48
Q

Interpreting GWAS Data

A
  • Need 1000s of SNPS for GWAS. Just looking for a single change in the SNP
  • Strength of association between each SNP and disease is calculated on the basis of the prevalence of each SNP in cases and control
  • Frequencies of variants are determined in large samples of control and disease groups
  • Significance of the outcome is based on P values
  • GWAS Null Hypothesis= occurance of a certain SNP and a particular phenotypes is determined by change
  • P value less than 5 x10^-8, indicates the association is not the result of chance. Rejects null hypotheisis
  • Looking at allele frequency, can work out a P value
  • In GWAS, you extract DNA and genotyping the SNP
49
Q

Advantages of GWAS

A
  • Revolutionised the search for genetic influences on complex traits
  • Rapid advances in technology and quality control now permil affordable, reliable genotyping of up to 1 million SNPS in a sinlge scan of a persons DNA
  • Identified SNPS associated with common diseases, related to quantitative traits (e.g. height)
  • Rank relevant importance of previously identified susceptibility genes
  • Demonstrate gene-gene interactions or modifications of the association of one genetic variant by another
  • Detect high risk haplotypes or multiple SNPS within a single gene.
50
Q

Limitations of GWAS

A

-Enormous n# of statistical tests are required.
-The reveal associations between two types of information, not causes
-Bias can be introduced in a way the patient population is selected
-Their accuracy is affected by complicating factors:
Phenocopy= an environmentally caused trait that occurs in a familial pattern e.g. hearing loss due to environmental factors
Epistasis= a gene masks the expression of another

  • They may miss extremely rare SNPS
  • Reproducibility: sometimes are not replicated across studies or populations
51
Q

Phenotype and Genotype frequency

A

Proportion of individuals in a population that have a particular phenotype

Proportion of individuals in a population that carry a particular genotype.

52
Q

Origin of LP

A
  1. Cultural historical hypothesis: LP allele arose from low frequenciy through selection in cultures with a long history of dairying
  2. Reverse cause hypothesis: LP allele may have already been common in certain populations due to genetic drift and only these popn would have adapted the cultural practise of dairying
53
Q

Genetic Drift

A

Change in allele frequency in a population due to random flactuations

  • Result is either loss of an allele of its fixations at 100% in the popn over time
  • Effect is greater in small populations

Two examples: Bottleneck and founder effect

54
Q

Founder and Bottleneck effect

A

Founder: a few individuals separate from a larger population and establish a new population

Bottleneck: Large proportion of individuals die e.g. from environmental disturbances

55
Q

Non Random mating

A
  • Individuals select mates based on their phenotypes or genetic lineage.
  • alters the relative proportion of homogygotes and heterozygotes predicted by HW equation but does not change allele frequencies
  • Interbreeding results in a higher proportion of homozygotes in a population
    e. g. agriculture-desirable trait, recessive genetic trait.
56
Q

Assisted Reproductive Technologies (ART)

A

Method that replaces the source of a male or female gamete, aid fertilisation or provide a uterus
-Developed to treat infertility but are becoming part of genetic screening

57
Q

Advantages of Genetic Testing

A
  • Improve lives with respect to health and standards of living
  • Clarify a diagnosis and direct a physician towards appropriate treatments.
  • Allow families to avoid having children with devastating diseases.
  • Identify people at high risk for conditions that maybe preventable
58
Q

Disadvantages of Genetic testing

A
  • Possibility of lab errors –>sample misidentification, contamination
  • Uncertainties surrounding test interpretation
  • Lack of available medical options
  • Potential for provoking anxiety
  • Risks for discrimination e.g. insurance policies
  • Social stigmatisation.
59
Q

Policy Challenges Involved with Genetic testing

The HSNO Act 1996

A

Purpose: To protect the environment and the health and safety of people and communities by preventing or managing the adverse effects of hazardous substances and new organisms.

60
Q

Syndromic

A

Hearing loss appears with another phenotype

e.g. have a syndrome associated with hearing loss

61
Q

Nonsyndromic

A

Hearing loss is the only phenotype the individual has.

62
Q

Genetic Linkage

A
  • Describes how 2 genes that are closely associated on the same chromosome are frequently inherited together
  • Closer 2 genes are on the chromosome, greater their chances are being inherited together or linked
  • Strength of linkage between 2 genes depends upon the distance between the genes on the chromosome
63
Q

Genetic Markers

A

-Identifiable segments of DNA sequence with a known physical location on a chromosome.

Properties

  • easy identifiable
  • associated with a specific locus
  • highly polymorphic

Purpose: to track the inheritance of a nearby gene that has not yet been identified, but whose approximate location is known. Used in genetic analysis.

64
Q

Haplotypes

A
  • Unique combinations of linked alleles over extended regions of the genome
  • A group of specific alleles at neighbouring genes/markers that tend to be inherited together.
65
Q

Replication Slippage

A

Causes by mismatches between DNA strands while being replicated during meiosis.

66
Q

Linkage Disequilibrium (LD)

A
  • Association between 2 alleles near each other on a chromosome, such that they are inherited together more frequently than expected by chance.
  • The degree to which an allele of one SNP is observed with an allele of another SNP within a popn

Loci that are physically close together exhibit stronger LD than loci that are further apart on a chromosome.

67
Q

Linkage equilibrium

A
  • The haplotypes are present at equal frequencies

- Knowledge of sequence at site 1 provides no information about sequence at site 2.

Advance Genetics (8 decks)

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