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Questions and Answers
What is the primary source of germline single nucleotide variants (SNVs)?
What is the primary source of germline single nucleotide variants (SNVs)?
What is the approximate frequency of variants in the human genome?
What is the approximate frequency of variants in the human genome?
What determines the amount of DNA shared between individuals?
What determines the amount of DNA shared between individuals?
What is the percentage of gametes carrying a heterozygous germline variant?
What is the percentage of gametes carrying a heterozygous germline variant?
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What is the characteristic of rare germline variants?
What is the characteristic of rare germline variants?
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What is true about the male and female germline lineages?
What is true about the male and female germline lineages?
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What is the main effect of genetic drift on allele frequency?
What is the main effect of genetic drift on allele frequency?
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What is the result of a recessive phenotype?
What is the result of a recessive phenotype?
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What is an example of balancing selection?
What is an example of balancing selection?
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What is the term for a newly arising variant in the germline?
What is the term for a newly arising variant in the germline?
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What is the effect of a genetic bottleneck on a population?
What is the effect of a genetic bottleneck on a population?
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What is the term for a change in the frequency of a variant in a population due to a change in fitness?
What is the term for a change in the frequency of a variant in a population due to a change in fitness?
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What is the result of a frameshift variant?
What is the result of a frameshift variant?
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What is the term for a variant that alters splicing donor or acceptor sites?
What is the term for a variant that alters splicing donor or acceptor sites?
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What is the term for the two inherited copies of each chromosome?
What is the term for the two inherited copies of each chromosome?
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What is the result of positive selection on a phenotype?
What is the result of positive selection on a phenotype?
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What type of variant can occur if a structural variant disrupts a gene, leading to protein truncation?
What type of variant can occur if a structural variant disrupts a gene, leading to protein truncation?
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What is the term for an allele present on one of two homologous chromosomes?
What is the term for an allele present on one of two homologous chromosomes?
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What type of selection acts on a phenotype to increase the frequency of a variant in a population?
What type of selection acts on a phenotype to increase the frequency of a variant in a population?
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What is the term for a phenotype that leads to a non-viable embryo?
What is the term for a phenotype that leads to a non-viable embryo?
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What is the lineage of cells that contributes to the production of gametes?
What is the lineage of cells that contributes to the production of gametes?
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When do PGCs arise in humans?
When do PGCs arise in humans?
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How many cell divisions do male germline cells undergo per year at puberty?
How many cell divisions do male germline cells undergo per year at puberty?
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What percentage of germline SNVs are introduced via the male germline?
What percentage of germline SNVs are introduced via the male germline?
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In what percentage of cases of Down syndrome does the additional copy of chromosome 21 come from the mother?
In what percentage of cases of Down syndrome does the additional copy of chromosome 21 come from the mother?
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What is the term for a variant that does not generate a measurable phenotype?
What is the term for a variant that does not generate a measurable phenotype?
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What is the difference between dominant and recessive variants?
What is the difference between dominant and recessive variants?
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What is an example of a fitness advantage that is caused by human intervention?
What is an example of a fitness advantage that is caused by human intervention?
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What is negative selection, also known as?
What is negative selection, also known as?
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What is an example of balancing selection?
What is an example of balancing selection?
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What determines the relative importance of selection and genetic drift?
What determines the relative importance of selection and genetic drift?
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What is the effect of negative selection on allele frequencies?
What is the effect of negative selection on allele frequencies?
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What is an example of a trait that is under positive selection in one environment but negative selection in another?
What is an example of a trait that is under positive selection in one environment but negative selection in another?
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What is the effect of genetic drift on variants that cause phenotypes?
What is the effect of genetic drift on variants that cause phenotypes?
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What is the primary factor that influences the increase in cytogenetic abnormalities with maternal age?
What is the primary factor that influences the increase in cytogenetic abnormalities with maternal age?
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What is the probability that a de novo germline variant in a spermatogonial stem cell (SSC) will be passed to the next generation?
What is the probability that a de novo germline variant in a spermatogonial stem cell (SSC) will be passed to the next generation?
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How much DNA is shared between an individual and their grandparent?
How much DNA is shared between an individual and their grandparent?
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What is the typical difference in germline DNA between two unrelated individuals?
What is the typical difference in germline DNA between two unrelated individuals?
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What are common variants in the context of germline DNA?
What are common variants in the context of germline DNA?
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What can patterns of allele frequencies help reconstruct?
What can patterns of allele frequencies help reconstruct?
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Which force can cause a newly arising de novo germline variant to become rare or die out?
Which force can cause a newly arising de novo germline variant to become rare or die out?
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What is the probability that a de novo germline variant in a zygote will be present in the gametes of the resulting individual?
What is the probability that a de novo germline variant in a zygote will be present in the gametes of the resulting individual?
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How often does a newly arising de novo germline variant become common?
How often does a newly arising de novo germline variant become common?
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What proportion of DNA do full siblings share with each other?
What proportion of DNA do full siblings share with each other?
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What is a common characteristic of genetic bottlenecks?
What is a common characteristic of genetic bottlenecks?
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What process is described by the phenomenon where disease-causing alleles become common due to chance?
What process is described by the phenomenon where disease-causing alleles become common due to chance?
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Which type of genetic variant involves the introduction of a premature stop codon?
Which type of genetic variant involves the introduction of a premature stop codon?
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How can non-coding variants impact gene expression?
How can non-coding variants impact gene expression?
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What is a primary feature of the founder effect?
What is a primary feature of the founder effect?
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What genetic phenomenon was key to the high frequency of the BRCA1 indel allele in the Ashkenazi population?
What genetic phenomenon was key to the high frequency of the BRCA1 indel allele in the Ashkenazi population?
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How do frameshift mutations exert their impact on proteins?
How do frameshift mutations exert their impact on proteins?
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In the context of genetic drift, why might small populations experience significant shifts in allele frequencies?
In the context of genetic drift, why might small populations experience significant shifts in allele frequencies?
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What type of structural variant leads to gene truncation?
What type of structural variant leads to gene truncation?
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Which example illustrates an impact of genetic drift during breed formation in dogs?
Which example illustrates an impact of genetic drift during breed formation in dogs?
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Study Notes
Germline Lineage
- The germline lineage involves cells that give rise to gametes (sperm and egg cells) and their precursors
- The male germline undergoes many more cell divisions than the female germline
- Germline single nucleotide variants (SNVs) primarily arise in the male germline, and their number depends on the father's age
- Cytogenetic variants frequently arise in the female germline, and are more common in older women
Inheritance
- A heterozygous germline variant is carried by 50% of gametes
- The amount of DNA shared between relatives can be calculated, given that a child inherits 50% DNA from each parent
- Unrelated people in the population on average differ at 3 million positions in the genome, with an average of ~1 variant per 1000 bp
- The amount of DNA shared between individuals depends on their population histories; germline variants allow us to reconstruct population histories
Variants
- Common germline variants are shared by many individuals and may have occurred many generations ago
- Rare germline variants are shared by few individuals, or may be unique to a single individual, and likely occurred in the germline of a recent ancestor
- All germline variants start off as rare, and selection and genetic drift determine if they become common
Selection and Genetic Drift
- Genetic drift is the change in allele frequency due to chance, and is particularly important in small populations
- Selection is the change in allele frequency due to a change in fitness, which acts on phenotypes
- Phenotypes can be dominantly or recessively inherited, and can be conferred by changing the amino acid composition of a protein or by altering the amount of a gene product
Phenotypes
- Coding variants can cause changes in the amino acid composition of a protein, leading to phenotypes
- Non-coding variants and copy number variants can cause changes in the amount of protein product that is produced, leading to phenotypes
- Examples of variants that can cause phenotypes include missense, nonsense, in-frame insertion or deletion, frameshift, splicing, and gene truncation via structural variants or transposable element insertions
Selection
- Positive selection acts on a phenotype to increase the frequency of a variant in a population
- Negative selection acts on a phenotype to decrease the frequency of a variant in a population
- Balancing selection is an interaction between positive and negative selection that acts to maintain several alleles in the population
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Description
Learn about the differences between male and female germline lineages, how genetic variations arise, and their dependence on age. Understand the role of germline variants in gametes and their impact on offspring.
