How do we know which contigs are part of the same chromosome?

How do we know if a genomic DNA sequence contains a protein-coding gene?

What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms?

How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome?

How has the concept of a reference genome evolved to encompass a broader understanding of genomic variation in humans?

In the discussion we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?

How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show cell- and tissue-specific expression?

Write a short essay that explains how recombinant DNA techniques were used to identify and study genes compared to how modern genomic techniques have revolutionized the cloning and analysis of genes.

What is functional genomics? How does it differ from comparative genomics?

Compare and contrast WGS to a map-based cloning approach.

What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.

Annotation involves identifying genes and gene-regulatory sequences in a genome. List and describe characteristics of a genome that are hallmarks for identifying genes in an unknown sequence. What characteristics would you look for in a bacterial genome? A eukaryotic genome?

How do high-throughput techniques such as computer-automated, next-generation sequencing, and mass spectrometry facilitate research in genomics and proteomics? Explain.

BLAST searches and related applications are essential for analyzing gene and protein sequences. Define BLAST, describe basic features of this bioinformatics tool, and give an example of information provided by a BLAST search.

Describe three major goals of the Human Genome Project.

Describe the human genome in terms of genome size, the percentage of the genome that codes for proteins, how much is composed of repetitive sequences, and how many genes it contains. Describe two other features of the human genome.

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?

The Human Genome Project has demonstrated that in humans of all races and nationalities approximately 99.9 percent of the genome sequence is the same, yet different individuals can be identified by DNA fingerprinting techniques. What is one primary variation in the human genome that can be used to distinguish different individuals? Briefly explain your answer.

Through the Human Genome Project (HGP), a relatively accurate human genome sequence was published from combined samples from multiple individuals. It serves as a reference for a haploid genome. How do results from personal genome projects (PGP) differ from those of the HGP?

Explain differences between whole-genome sequencing (WGS) and whole-exome sequencing (WES), and describe advantages and disadvantages of each approach for identifying disease-causing mutations in a genome. Which approach was used for the Human Genome Project?

Describe the significance of the Genome 10K project.

It can be said that modern biology is experiencing an 'omics' revolution. What does this mean? Explain your answer.

Metagenomics studies generate very large amounts of sequence data. Provide examples of genetic insight that can be learned from metagenomics.

What are DNA microarrays? How are they used?

Annotation of the human genome sequence reveals a discrepancy between the number of protein-coding genes and the number of predicted proteins actually expressed by the genome. Proteomic analysis indicates that human cells are capable of synthesizing more than 100,000 different proteins and perhaps three times this number. What is the discrepancy, and how can it be reconciled?

An interactive Web site for the Human Proteome Map (HPM) is available at http://www.humanproteomemap.org. Visit this site, and then answer the question.

How many proteins were identified in this project?

An interactive Web site for the Human Proteome Map (HPM) is available at http://www.humanproteomemap.org. Visit this site, and then answer the question.

How many fetal tissues were analyzed?

An interactive Web site for the Human Proteome Map (HPM) is available at http://www.humanproteomemap.org. Visit this site, and then answer the question.

Use the 'Query' tab and select the 'Gene family' dropdown menu to do a search on the distribution of proteins encoded by a pathway of interest to you. Search in fetal tissues, adult tissues, or both.

Researchers have compared candidate loci in humans and rats in search of loci in the human genome that are likely to contribute to the constellation of factors leading to hypertension [Stoll, M., et al. (2000). Genome Res. 10:473–482]. Through this research, they identified 26 chromosomal regions that they consider likely to contain hypertension genes. How can comparative genomics aid in the identification of genes responsible for such a complex human disease? The researchers state that comparisons of rat and human candidate loci to those in the mouse may help validate their studies. Why might this be so?

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?

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?