Table of contents

1. Introduction to Genetics51m
2. Mendel's Laws of Inheritance3h 37m
3. Extensions to Mendelian Inheritance2h 41m
4. Genetic Mapping and Linkage2h 28m
5. Genetics of Bacteria and Viruses1h 21m
6. Chromosomal Variation1h 48m
7. DNA and Chromosome Structure56m
8. DNA Replication1h 10m
9. Mitosis and Meiosis1h 34m
10. Transcription1h 0m
11. Translation58m
12. Gene Regulation in Prokaryotes1h 19m
13. Gene Regulation in Eukaryotes44m
14. Genetic Control of Development44m
15. Genomes and Genomics1h 50m
16. Transposable Elements47m
17. Mutation, Repair, and Recombination1h 6m
18. Molecular Genetic Tools19m
- Genetic Cloning
  9m
- Methods for Analyzing DNA
  9m
19. Cancer Genetics29m
- Overview of Cancer
  21m
- Cancer Mutations
  7m
20. Quantitative Genetics1h 26m
21. Population Genetics50m
- Hardy Weinberg
  19m
- Allelic Frequency Changes
  31m
22. Evolutionary Genetics29m

15. Genomes and Genomics

Sequencing the Genome

Genetics

15. Genomes and Genomics

Sequencing the Genome

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1:51 minutes

Problem 25a

Textbook Question

Whole-exome sequencing (WES) is helping physicians diagnose a genetic condition that has defied diagnosis by traditional means. The implication here is that exons in the nuclear genome are sequenced in the hopes that, by comparison with the genomes of nonaffected individuals, a diagnosis might be revealed.
What are the strengths and weaknesses of this approach?

Verified step by step guidance

Understand the concept of Whole-Exome Sequencing (WES): WES focuses on sequencing the exons, which are the protein-coding regions of the genome. These regions make up about 1-2% of the genome but are responsible for most known genetic disorders.

Identify the strengths of WES: One major strength is its cost-effectiveness compared to whole-genome sequencing, as it targets only the exons. Additionally, it is highly efficient for diagnosing genetic conditions caused by mutations in protein-coding regions.

Discuss the weaknesses of WES: WES does not capture non-coding regions of the genome, which may also harbor mutations affecting gene regulation or expression. Furthermore, it may miss structural variations or mutations in regions poorly covered by sequencing technology.

Explain the comparison process: In WES, the patient's exome is compared to reference genomes or the exomes of nonaffected individuals to identify potential pathogenic variants. This requires robust bioinformatics tools and databases to interpret the findings accurately.

Highlight the clinical implications: While WES can provide valuable insights into genetic conditions, its success depends on the quality of the reference data, the ability to interpret variants of unknown significance, and the presence of mutations in the targeted regions.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Whole-Exome Sequencing (WES)

Whole-exome sequencing (WES) is a genomic technique that focuses on sequencing all the protein-coding regions, or exons, of the genome. These exons represent about 1-2% of the entire genome but contain approximately 85% of known disease-related variants. WES is particularly useful for identifying genetic mutations associated with various conditions, making it a powerful tool in clinical diagnostics.

Comparative Genomics

Comparative genomics involves comparing the genomic data of affected individuals with that of nonaffected individuals to identify genetic variations that may contribute to disease. This approach helps in pinpointing mutations that are likely pathogenic, as it highlights differences that could be responsible for the observed phenotypes. It is essential for interpreting WES results and understanding the genetic basis of diseases.

Strengths and Weaknesses of WES

The strengths of WES include its ability to uncover rare genetic variants and its efficiency in diagnosing complex genetic disorders that traditional methods may miss. However, its weaknesses involve the potential for incidental findings, the challenge of interpreting variants of uncertain significance, and the fact that it does not capture non-coding regions of the genome, which may also play critical roles in disease.

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Textbook Question

You have just obtained 100 kb of genomic sequence from an as-yet-unsequenced mammalian genome. What are three methods you might use to identify potential genes in the 100 kb? What are the advantages and limitations of each method?

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Textbook Question

When comparing genes from two sequenced genomes, how does one determine whether two genes are orthologous? What pitfalls arise when one or both of the genomes are not sequenced?

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Textbook Question

What is a reference genome? How can it be used to survey genetic variation within a species?

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Textbook Question

Whole-exome sequencing (WES) is helping physicians diagnose a genetic condition that has defied diagnosis by traditional means. The implication here is that exons in the nuclear genome are sequenced in the hopes that, by comparison with the genomes of nonaffected individuals, a diagnosis might be revealed.

If you were ordering WES for a patient, would you also include an analysis of the patient's mitochondrial genome?

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Textbook Question

Recall that when the HGP was completed, more than 40 percent of the genes identified had unknown functions. The PANTHER database provides access to comprehensive and current functional assignments for human genes (and genes from other species).

Go to http://www.pantherdb.org/data/. In the frame on the left side of the screen locate the 'Quick links' and use the 'Whole genome function views' link to a view of a pie chart of current functional classes for human genes. Mouse over the pie chart to answer these questions. What percentage of human genes encode transcription factors? Cytoskeletal proteins? Transmembrane receptor regulatory/adaptor proteins?

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Textbook Question

Describe how enhancer screens can be used to uncover genetic redundancy.

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Multiple Choice

Restriction enzymes are proteins responsible for what?