Genomic Sequencing Advances Quiz

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Questions and Answers

What is the purpose of a barcode in Illumina sequencing?

Enables simultaneous sequencing of multiple samples (correct)

Aids in forming clusters on the flow cell

Acts as a molecular tag for tracking individual DNA fragments

Helps in identifying the base interpreted from the color of a cluster

What is the function of adapters in Illumina workflow?

Known primers added to ends of DNA fragments (correct)

Contain short DNA sequences for tracking individual fragments

Enable simultaneous sequencing of multiple samples

Form clusters on the flow cell

What does a flow cell in Illumina sequencing consist of?

Clusters formed after bridge amplification

Short DNA sequences added to individual fragments

Glass slide with oligos that attach to adapters (correct)

Raw images processed into FASTQ files

What is the role of cluster in Illumina sequencing?

Formed after bridge amplification, multiple copies of the same DNA strand on flow cell Signup and view all the answers

What does base calling from raw data involve in Illumina sequencing?

Interpreting the identity of the base from the color of a cluster Signup and view all the answers

What is the format of FASTQ files in Illumina sequencing?

A txt file with four lines per read Signup and view all the answers

What is the significance of quality values in Illumina sequencing?

Represent the certainty of the base determined by the clarity of the spot on the flow cell Signup and view all the answers

What is the term for the rapid increase in frequency of a specific genetic variant due to positive natural selection?

Selective sweep Signup and view all the answers

Which of the following is a measure of the amount of genetic variation in a population?

Heterozygosity Signup and view all the answers

Which enzyme shears DNA at specific sites?

ApeKI Signup and view all the answers

Which allele is related to metabolism in bobcats, affecting energy expenditure and obesity?

GPR158 Signup and view all the answers

Which allele is related to abdominal fat storage and lipid metabolism in bobcats?

LECT2 Signup and view all the answers

Which allele is related to noxious heat detection in bobcats?

TRPM Signup and view all the answers

What is the term for distinct chromosomal regions where genetic variants are inherited together?

Linkage disequilibrium Signup and view all the answers

What does Fst measure in population genetics?

Divergence between populations Signup and view all the answers

What is the term for the process of identifying structural rearrangements in the genome?

CNVs Signup and view all the answers

What is the best Phred quality score indicating high consistency in DNA sequencing?

30 Signup and view all the answers

Which method is suitable for de novo bacterial/viral genome assembly and BAC sequencing?

Pac bio (NGS) Signup and view all the answers

What does copy number variation (CNV) refer to?

Variation in repeated genome sequences Signup and view all the answers

What do string graphs in de novo assembly use to construct full sequence contigs?

Nodes representing reads Signup and view all the answers

What is the focus of transcriptome analysis?

RNA molecules in cells Signup and view all the answers

What is the method for SNP detection in genomes and can be used in genetic mapping and estimation of allele frequencies?

RADseq Signup and view all the answers

How are consensus sequences obtained from de novo assembly contigs based on?

Weighted voting, incorporating quality scores for accuracy Signup and view all the answers

What is the main purpose of genome re-sequencing?

To gather data on genetic variation through mapping reads to a known reference sequence Signup and view all the answers

What is the calculation of N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb?

30mb Signup and view all the answers

What is the purpose of large scaffolds in genomes with many repeats?

To be generated using mate pair libraries and methods that produce very long reads Signup and view all the answers

What are the cost-saving approaches for genome variation at the population level?

Low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment Signup and view all the answers

What is the main advantage of low/ultra-low coverage sequencing?

Data for the entire genome of multiple individuals and increased likelihood of detecting all alleles Signup and view all the answers

What does whole genome sequencing involve?

Sequencing the entire genome Signup and view all the answers

What should be considered for sequencing?

Capture amount, specificity, variability, reproducibility, cost, and input DNA Signup and view all the answers

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

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Description

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.