35 Questions
What is the purpose of a barcode in Illumina workflow?
To enable simultaneous sequencing of multiple samples
What is the function of a flow cell in Illumina sequencing?
To provide a surface for oligos to attach to adapters
What is the content of a FASTQ file in Illumina sequencing?
Four lines per read, including sequence identifier, nucleotide sequence, and quality values
What is the term used to refer to the rapid increase in frequency of a specific genetic variant due to positive natural selection?
Selective sweep
Which enzyme(s) shear DNA at specific sites?
Sbf and ApeKI
Which allele is related to metabolism in bobcats, affecting energy expenditure and obesity?
GPR158
Which measure identifies regions of linkage disequilibrium?
Fst
What refers to the variability in noxious heat detection allele between north and south bobcats?
TRPM
What is the best Phred quality score indicating high consistency in DNA sequencing?
30
What does nucleotide diversity measure?
Genetic variation within a population
Which sequencing method is suitable for de novo bacterial/viral genome assembly and BAC sequencing?
Pac bio (NGS)
What do string graphs in de novo assembly use to construct full sequence contigs?
Edges representing overlaps
What is the primary aim of genome re-sequencing?
To gather data on genetic variation through mapping reads to a known reference sequence
What is a key consideration for cost-saving approaches in genome variation at the population level?
Low coverage whole genome sequencing
How is N50 calculated for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb?
N50 is calculated as 30mb
Which force leads to random fixation of one allele, with the probability of fixation depending on its initial frequency?
Genetic drift
Which process introduces new genetic variation into a population?
Migration
Which mating system is based on an observer able phenotype, leading to an increase in frequency of alleles associated with the phenotype?
Assortative mating
Which mating process results in excessive homozygotes and reduces the number of heterozygotes?
Inbreeding
What is the primary mechanism by which L1 transposons cause genetic variation?
Inserting themselves into different locations in the genome
Which molecular process allows a single gene to produce multiple protein isoforms with distinct properties?
Altered splicing
What is the purpose of adapters in Illumina sequencing workflow?
Facilitate attachment of DNA fragments to the flow cell
What does the Phred quality score of 30 indicate in automated DNA sequencing?
High consistency in nucleobase identification
What is the primary advantage of GWAS?
Its applicability to quantitative and complex traits, and the availability of dense SNP assays covering the entire genome
What is a challenge in GWAS?
The need to genotype thousands of individuals for genes with modest effects
What percentage of the human genome is derived from repetitive elements?
45%
What type of genetic variation actively move around and can cause genetic material rearrangements?
Mobile elements
What is the main difference between de novo sequencing and re-sequencing?
De novo sequencing assembles sequence reads without a reference sequence, while re-sequencing maps reads to a reference sequence to identify genetic variations
What is the purpose of string graph in de novo assembly?
To use overlapping paths to construct full sequence contigs
What is the key factor involved in assessing the quality of de novo assembly?
Number of contigs and contig length
Which approach is used in Illumina sequencing to copy DNA fragments for sequencing?
Bridge amplification
What measure is used to estimate genetic divergence between populations and determine migration?
Fst
What is the nonrandom association of alleles at two or more loci called?
Linkage disequilibrium (LD)
What measures the extent to which alleles on different loci are associated together, relative to that expected by chance?
Coefficient of LD, D
What are segments of chromosomes with strong LD, where alleles on all loci are highly correlated and form haplotypes?
Linkage blocks
Study Notes
Advances in Genomic Sequencing Technologies and Strategies
- Assembly using short reads combined with large mate libraries at different coverages helps assemble larger contigs
- Comparisons between assembly programs should consider speed, error, number of contigs, and contig length
- Velvet is a highly efficient genome assembly program for short DNA sequence reads
- Genome re-sequencing aims to gather data on genetic variation through mapping reads to a known reference sequence
- Structural variation analysis leverages the distance and orientation between paired reads to provide insights on genome structure
- Bridge amplification is used in Illumina sequencing flow cells to amplify DNA fragments for sequencing
- N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb is calculated as 30mb
- Large scaffolds in genomes with many repeats can be generated using mate pair libraries and methods that produce very long reads
- Whole genome sequencing involves sequencing the entire genome, while enrichment targets specific genomic regions
- Cost-saving approaches for genome variation at the population level include low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment
- Considerations for sequencing include capture amount, specificity, variability, reproducibility, cost, and input DNA
- Advantages of low/ultra-low coverage sequencing include data for the entire genome of multiple individuals and increased likelihood of detecting all alleles
Genetic Diversity and Population Structure
- Inbreeding depression is caused by an excess of homozygous genotypes with recessive detrimental alleles in individuals, leading to increased risk of rare genetic disorders.
- Florida Panthers have experienced inbreeding depression, resulting in decreased survival, increased mortality of cubs, reduced offspring numbers, and increased sperm abnormalities.
- Natural selection is driven by hereditary differences among organisms, impacting their ability to survive and reproduce based on fitness.
- Directional selection occurs when individuals homozygous for one allele have greater fitness, leading to a shift in allele frequencies.
- Relative fitness measures the comparative contribution of each parental genotype to the pool of offspring genotypes in each generation.
- Bottleneck events occur when a population is temporarily reduced in size, leading to changes in allele frequencies and loss of genetic variation in future generations.
- The fixation index (Fst) is used to estimate genetic divergence between populations and determines migration, with specific ranges indicating different levels of population structure and migration.
- Fst measures the degree of genetic differentiation among subpopulations within a larger population, providing an estimate of connectivity and assessing population structure.
- Centimorgans (CM) are used as a map unit to measure genetic linkage distance between chromosomes.
- Linkage disequilibrium (LD) is the nonrandom association of alleles at two or more loci, with the likelihood of crossover and inheritance of alleles together on a chromosome.
- Coefficient of LD, D, measures the extent to which alleles on different loci are associated together, relative to that expected by chance.
- Linkage blocks are segments of chromosomes with strong LD, where alleles on all loci are highly correlated and form haplotypes, identified by genotyping single nucleotide polymorphisms (SNPs).
Test your knowledge about recent advances in genomic sequencing technologies and strategies with this quiz. Explore topics such as genome assembly, re-sequencing, structural variation analysis, sequencing platforms, and cost-saving approaches for population-level variation studies.
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