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Chapter 1
What Is in a Human Genome?
READINGS
Chapter Opener
What Information Is in a Human Genome?
Clinical Connection 1.1
Exome Sequencing Saves a Boy’s Life
Bioethics: Choices for the Future
Genetic Testing and Privacy
CHAPTER OVERVIEW
Chapter 1 provides a glimpse of the basic concepts of genetics and
genomics, and offers examples of DNA information impacting daily life. In
this new era of genomics, individuals have access to their own genetic
information, and health care providers are learning how to incorporate
DNA data into diagnostic and therapeutic medicine. Bioethics deals with
issues of privacy, discrimination, and justice that arise from use and
misuse of genetic information. DNA, genes, chromosomes, and genomes
are the levels of genetic information, and they impact biology at the cell,
tissue, organ, individual, family, and population levels. Genes encode
proteins, and the exome is the small part of the genome that does so.
Most traits arise from interactions of genes and environmental factors.
Genetic information is in health care to identify individuals, in investigating
the environment, and in understanding evolution.
CHAPTER OUTLINE
1.1 Introducing Genes and Genomes
1. Genetics is a branch of biology concerned with inherited traits and their variation,
and how these traits are passed from one generation to the next (heredity).
2. With continuing analysis of human genome sequences, human genetics has grown
from a largely academic science to touch many areas of medicine, with practical and
societal implications.
3. Genes are the unit of inheritance and are composed of DNA.
4. An organism’s genome is its complete set of genetic information.
5. Genomics is a field of study that reveals how closely related we are to each other
and to other species.
6. Bioethics is a field of study concerned with issues of privacy, confidentiality, and
discrimination that arise from knowledge of our DNA sequences.
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1.2 Levels of Genetics and Genomics
The Instructions: DNA, Genes, Chromosomes, and Genomes
1. Genetic investigation of the mechanisms of heredity occurs at multiple levels: from
smallest to largest are DNA, gene, chromosome, and genome.
2. A DNA molecule consists of “rails” of alternating sugars and phosphates and “steps”
of adenine-thymine (A-T) and guanine-cytosine (G-C) base pairs. Each three
contiguous base pairs encode one of 20 types of amino acids, which build proteins.
Messenger RNA carries DNA information out of the cell’s headquarters (nucleus) to
where it is used to synthesize proteins.
3. A portion of DNA that encodes a protein is a gene.
4. A DNA molecule replicates as the sides of the double helix part and fill in with new
bases.
5. Different cell types express different subsets of genes.
6. The exome is the 1.5% of the 20,325 or so genes of the human genome that
encodes protein.
7. Mendelian Inheritance in Man (MIM) catalogs disease-related gene variants.
8. Genes can exist in more than one form. Variants (alleles) arise by mutation.
9. Chromosomes consist of genes and associated proteins.
10. The human genome is 22 pairs of autosomes and one pair of sex chromosomes.
11. A karyotype is a photographic chart of an individual’s chromosomes.
12. A Mendelian trait is caused by a single gene. A multifactorial trait is caused by one
or more genes and environmental influences. Most genes do not function alone.
13. Genetic determinism is the idea that our genes control everything about us, with little
or no outside influences.
The Body: Cells, Tissues, and Organs
1. The human body is composed of about 37 trillion cells. All cell types except mature
red blood cells contain the entire genome.
2. Differential gene expression creates more than 290 distinctive cell types, which
combine to form four basic tissue types that interact to form organs and organ
systems.
3. Many organs contain stem cells that “self-renew” as well as produce cells that
specialize. These two properties are essential for growth, development, and healing.
Relationships: From Individuals to Families
1. Genotype is the allelic makeup of an individual; phenotype is the observable or
measureable expression of an individual’s alleles.
2. Dominant alleles are expressed when one copy is present. Recessive alleles require
two copies for expression.
3. Pedigree diagrams follow recessive and dominant traits through generations.
The Bigger Picture: From Populations to Evolution
1. Population genetics concerns allele frequencies in members of the same species in
a specified geographic area.
2. “Gene pool” refers to all of the alleles in a given population.
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3. Population genetics has applications in health care, forensics, and evolution.
4. Comparative genomics explores evolutionary relationships among species.
1.3 Applications of Genetics and Genomics
Establishing Identity
1. DNA profiling compares DNA sequences among individuals.
2. It is used to establish or rule out identity, clarify relationships or ancestry, and to
evaluate crime scenes, probe sites of natural disasters, reunite adopted individuals
with birth parents, test food, and study history.
Health Care
1. Genetic information is being incorporated into diagnosis and treatment.
2. Many diseases are the result of complex interactions among genes and
environmental factors, such as “mossy foot.”
3. Pharmacogenetics predicts responses of individuals to drugs based on genotypes.
4. Single-gene diseases differ from infectious diseases in that recurrence risks are
predictable, pre-symptomatic genetic diagnosis may be possible, characteristic
frequencies are observed in different populations, and correcting or replacing
mutations may be possible.
5. Gene expression commonalities between diseases can reveal new drug targets or
suggest drugs that may be repurposed. A diseasome is a diagram that connects
diseases that share genes with altered expression.
6. Exome sequencing can lead to diagnoses of conditions that are unrecognized from
their symptoms by implicating specific DNA sequences.
A Global Perspective on Genomes
1. Metagenomics considers sequences of all DNA in a particular habitat.
2. Variable DNA sequences are used to “bar-code” species to study biodiversity.
3. Social issues that arise from genetic and genomic technologies include access to,
misuse of, and abuse of DNA information.
4. Nations are individualizing guidelines to maximize benefit from emerging genetic
tests and technologies.
IDEAS FOR CLASSROOM DISCUSSION
1. Bioethics is a field of study concerned with issues of privacy, confidentiality, and
discrimination that arise from access to DNA sequences and their interpretation.
“Bioethics: Choices for the Future” in chapter 1 addresses privacy issues with
collecting personal genetic information, in certain situations and scenarios. Cases
are also presented in the author’s blog, DNA Science (http://blogs.plos.org
/dnascience/). How do students feel about access to their own genetic information?
Does a parent have an obligation to inform a child of a possible mutation, and if so,
under what circumstances?
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2. Students today learn about DNA in grade school. However, coverage of genetics in
the media often deals with cases and emotional issues, rather than the science.
Have students discuss how information is part of the DNA molecule. How does a
DNA polymer differ from a carbohydrate or lipid in terms of information content? How
would a drug that replaces a gene be more effective than a drug that replaces a
protein?
3. The famous case of Nicholas Volker and his dissolving intestines introduced the
world to exome sequencing to diagnose puzzling disorders—the newspaper series
chronicling his early childhood won a Pulitzer. Have students present cases of other
individuals for whom exome sequencing solved medical mysteries. Ask them to
distinguish between the two possible outcomes of family exome sequencing: a de
novo case, or an inherited one. (See last section in chapter 4.)
4. Which genes or inherited traits or conditions would students want to know about in
their future offspring, and which would they not want to know about? Contrast
advantages and dangers of knowing such information. What should be done if
parents disagree?
5. Should students be required to have their exomes or genomes sequenced as part of
a class exercise? Why or why not?
DNA SCIENCE BLOG POSTS (http://blogs.plos.org/dnascience/)
Catching Up with 3 Rare Disease Families
http://blogs.plos.org/dnascience/2014/06/19/catching-3-rare-disease-families/
Clinical Whole Genome Sequencing: Not Quite Ready for Prime Time?
http://blogs.plos.org/dnascience/2014/03/13/clinical-whole-genome-sequencing-quiteready-prime-time/
WEBSITES
Genetic Literacy Project
http://www.geneticliteracyproject.org/
National Organization for Rare Disorders
https://www.rarediseases.org/
Undiagnosed Diseases Program
http://www.rarediseases.info.nih.gov/research/pages/27/undiagnosed-diseases-program
ANSWERS TO REVIEW QUESTIONS
1. Gene pool, genome, chromosome, gene, DNA
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2. a. An autosome does not carry genes that determine sex. A sex chromosome does.
b. Genotype is the allele constitution in an individual for a particular gene.
Phenotype is the physical expression of an allele combination.
c. DNA is a double-stranded nucleic acid that includes deoxyribose and the
nitrogenous bases adenine, guanine, cytosine, and thymine. DNA carries the
genetic information. RNA is a single-stranded nucleic acid that includes ribose
and the nitrogenous bases adenine, guanine, cytosine, and uracil. RNA carries
out gene expression.
d. A recessive allele determines phenotype in two copies. A dominant allele
determines phenotype in one copy.
e. A pedigree is a chart of family relationships and traits. A karyotype is a chart of
chromosomes.
f. A gene is a sequence of DNA that encodes a protein. A genome is all DNA in a
set of genetic instructions. Most human cells have two copies of the genome.
g. An exome is the protein-encoding part of a genome. A genome is all DNA in a
set of genetic instructions.
3. The sequence of DNA nucleotides (A, G, C, T) in a gene comprises a genetic code
that is read three nucleotides at a time to direct the building of proteins.
4. Humans may have the same genes but differ genetically in the alleles they carry.
5. Differential gene expression creates the distinctive cell types.
6. The assumption is that changes in DNA sequence accumulate over time. The closer
the two species, the more recently they descended from a common ancestor and the
more alike their DNA sequences.
7. Answers are in Table 1.2. (a) Risk in people related in certain ways is predictable. (2)
Presymptomatic testing may be possible. (3) Different populations may have different
disease frequencies. (4) It may be possible to correct or compensate for the
underlying genetic abnormality.
ANSWERS TO APPLIED QUESTIONS
1. Answers vary depending on student opinion. A reason to have genetic testing is to
plan for the future based on probabilities of developing particular diseases. A reason
not to have genetic testing is that people die from accidents, injuries, and diseases
that are not inherited.
2. Nutrition is an environmental factor that can influence the severity of an inherited
disease. Gene variants can increase the risk that an individual develops an
environmentally-caused cancer, such as lung cancer.
3. Perhaps a facial image derived from DNA data and displayed in public without the
individual’s permission can be treated as illegal use of any identifying photograph.
The fact that DNA is involved may introduce a greater level of intrusion into one’s
privacy, particularly if it is obtained from garbage, such as discarded gum.
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prior written consent of McGraw-Hill Education.
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ANSWERS TO WEB ACTIVITIES
1. Answers vary depending on website visited and student opinion. FDA has restricted
DTC genetic testing to ancestry.
2. Section 4.5 presents another case of diagnosis from exome sequencing, for a little
girl, Bea Rienhoff. “One of a Kind” is an article in The New Yorker from July 21,
2014, about a boy with mutation in a gene called NGLY1.
3. Disaster victim identification: http://www.dna-worldwide.com/forensic-dnatesting/disaster-victim-identification/
4. Parents might want to know what exactly will be done with their children’s DNA at the
time of collection and going forward; who will have access to the information; and
how the information will be protected.
5. Baylor College of Medicine began one of the first large-scale programs to sequence
exomes and genomes of difficult-to-diagnose cases.
https://www.bcm.edu/research/medical-genetics-labs/test_detail.cfm?testcode=1500
ANSWERS TO FORENSICS FOCUS
1. A difficult question. The repeats do not encode protein so likely do not affect the
phenotype and therefore are likely not subject to natural selection. Therefore the
sequences do not determine traits, health, nor do they reveal anything about
ancestry because the number of repeats can spontaneously change. See chapter 14
for more detail.
2. Genetic information might be useful in a legal case if a particular genotype can
account for a very specific behavior that caused a person to commit a crime.
3. Broaden question beyond TV series—cat and dog hairs used to identify crime
scenes. Here’s a good case: http://sandiegolawlibrary.org/straaaaange-cases-catdna-database-convicts-a-killer/
4. a. Taking part of a dead person’s body is indeed an invasion of privacy.
b. Dr. House is much too quick to diagnose. Appropriately used genetic tests would
help him differentiate among explanations for symptoms and other laboratory test
results.
ANSWERS TO CLINICAL CONNECTION 1.1 QUESTIONS
1. The environment affected Nic’s condition because it was food leaking from his
digestive tract that caused the repeated infections.
2. Section 4.5 presents another case of diagnosis from exome sequencing, for a little
girl, Bea Rienhoff. The author describes the case of Gavin Stevens at Scientific
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American blogs (http://blogs.scientificamerican.com/guest-blog/2012/07/29/rarediseases-5-recent-reasons-to-cheer/). A review article is in The New England Journal
of Medicine (http://www.nejm.org/doi/full/10.1056/NEJMra1312543).
3. Nicholas’s disease had an “atypical presentation.” His symptoms seemed to be
gastrointestinal, not immunological.
ANSWERS TO BIOETHICS: CHOICES FOR THE FUTURE
1. Answers vary and are personal. Key factors are the severity of the illness, how the
disease is inherited (are relatives at risk of disease, or of being a carrier?) and the
relationship of the person with the mutation to family members.
2. Perhaps multiple levels of passwords could be used to access DNA data.
3. Risks: stigmatization, restricting some students from participating in certain sports
and events. Benefits: prevention of health consequences of sickle cell carriers in lowoxygen environments.
4. Answer depends upon how the DNA information would be used. If linked in a
database to records such as passports and driver’s licenses, with appropriate
safeguards for privacy, perhaps this could work.
5. Unsolicited findings are discussed in Chapter 22. Individuals having their exomes or
genomes sequenced are increasingly being asked to declare the types of information
that they do or do not wish to know before the sequencing.
ANSWERS TO KEY CONCEPTS QUESTIONS
1.1
1. Genetics is the study of how traits are transmitted. Heredity considers the
transmission patterns of inherited traits between generations.
2. A gene is a sequence of DNA that encodes a protein. A genome is a complete
set of genetic instructions for an organism.
3. Bioethics combines philosophy, science, and medicine to address controversial
issues. Bioethics applied to genetics largely concerns privacy.
1.2
1. Molecules, cells, tissues, organs, organ systems, individuals, families,
populations, evolution of species
2. In the sequence of nitrogenous bases (A, C, T and G)
3. A gene consists of hundreds of bases. Alteration of the sequences creates a
large number of possible variants.
4. A Mendelian trait is set by inheriting a mutation or mutations in one gene. A
multifactorial trait derives from at least one gene plus environmental influences.
5. Cells specialize by expressing subsets of protein-encoding genes in the genome.
A bone cell expresses a different subset than a blood cell, for example.
6. Genotype is an allele combination; phenotype is the expression of an allele
combination (appearance or health condition). A dominant allele affects the
phenotype in one copy. A recessive allele affects the phenotype in two copies.
7. The more recently two species shared an ancestor (are more closely related), the
more of their DNA sequence they share.
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1.3
1. See how one person is genetically related to another, such as an adopted
individual or remains from a crime or natural disaster scene. Identify components
of food. Reveal causes of past epidemics. Clarify historical relationships.
2. A gene variant combination can make an individual more susceptible to danger
from an environmental factor, such as exposure to a toxin.
3. Answers are in Table 1.2. (a) Risk in people related in certain ways is
predictable. (2) Presymptomatic testing may be possible. (3) Different
populations may have different disease frequencies. (4) It may be possible to
correct or compensate for the underlying genetic abnormality.
4. Identifying gene expression patterns that two diseases share can suggest that a
drug used to treat one condition may be helpful in treating the other. If exome
sequencing reveals a specific mutation combination responsible for a phenotype,
treatments can be developed or repurposed that affect the disease-causing
mechanism at the molecular level.
1.4
1. Metagenomics is the study of all of the DNA in a particular geographic or other
area.
2. Bacteria cause disease in humans and understanding their DNA sequences can
suggest how they infect and how drugs can be used to kill them.
ADDITIONAL QUESTIONS
1. Humans contract the infectious disease leishmaniasis from sandflies that transmit
the microorganism Leishmania braziliensis. The first sign is a skin lesion, followed by
facial disfiguration. The disease is endemic (very common) in Bolivia, where it is
seen more in males, younger people, and those who spend the most time in the
forest. A genetic susceptibility might also influence who becomes infected, as
suggested by highly susceptible strains of mice. What type of evidence in the
Bolivian population, which consists of indigenous and immigrant populations, might
suggest an inherited component to susceptibility of this infection? Cite a disease
mentioned in chapter 1 that is similar to leishmaniasis in terms of whom it affects.
2. Osteoporosis thins bones in millions of people. A much rarer, inherited condition,
osteopetrosis, acts oppositely, increasing bone mass. Osteopetrosis does not affect
health, and is typically discovered on x-rays. Why might studying how osteopetrosis
arises be useful, even though it doesn't cause symptoms?
3. In acute intermittent porphyria, an environmental factor such as abuse of drugs or
alcohol, or fasting, triggers potentially fatal attacks on the nervous system. An
abnormal enzyme causes the condition. Why is this disorder considered genetic if it
only produces symptoms in the presence of a specific environmental trigger?
4. Although seizures are usually not inherited, benign infantile familial convulsions run
in families. How can studying this inherited illness provide information that may help
people with non-inherited seizures?
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5. Due to inherited differences in the way the body processes cholesterol, some people
can eat a fatty diet yet have healthy blood serum cholesterol, and others develop
dangerously high cholesterol levels if they do not eat wisely. Several drugs can lower
blood serum cholesterol level. Researchers found that people with a certain variant
of a gene encoding a protein that transports cholesterol into liver cells (cholesteryl
ester transfer protein, or CETP) are likely to have a cholesterol problem, and are also
more likely to benefit from cholesterol-lowering drugs than people with different
alleles. What information would be important to have before undergoing a CETP
gene test and possibly taking a cholesterol-lowering drug?
6. In Graves disease, the immune system attacks the thyroid gland, which normally
produces hormones controlling energy utilization. Siblings of people with Graves
disease are 15 times as likely to develop the disorder as people whose siblings are
unaffected. Women develop the condition more often than men, and a high
percentage of affected individuals smoke. Do you think that Graves disease is
caused solely by an abnormal gene, solely by an environmental trigger, or might
there be another explanation?
ANSWERS TO ADDITIONAL QUESTIONS
1. An inherited susceptibility to leishmaniasis might be involved if blood relatives who
are separated geographically become sick more often than people who only have in
common where they live. The example of “mossy foot” from Chapter 1 is similar.
2. Studying osteopetrosis can reveal how healthy bone mass is maintained, which
might provide insights into osteoporosis, which has an opposite phenotype and is
more common. Drugs may be developed that mimic osteopetrosis to treat
osteoporosis.
3. The condition is inherited because presence of a particular genetic variant is
necessary for symptoms to occur. The susceptibility is inherited, not the disease.
4. Studying this rare inherited condition can reveal basic brain mechanisms that may
explain how more common seizures occur.
5. Important information includes: the risk of cardiovascular disease to an individual;
side effects of cholesterol-lowering drugs; the role of diet in controlling gene
expression; how often a particular genetic variant is associated with increased
cholesterol level; success of drug treatment.
6. Graves disease might be caused by an inherited susceptibility triggered by an
environmental influence, such as exposure to female sex hormones or cigarette
smoke, or the status of the immune system.
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