Cleo Osterloh

Database is absolutely an integral part of software systems. To fully utilize ER Diagram in database engineering guarantees you to produce high-quality database design to use in database creation, management, and maintenance. An ER model also provides a means for communication.

Today we're going to walk you through everything you need to know about ER Diagramming. By reading this ERD guide, you will get the essential knowledge and skills about ER Diagrams and database design. You will learn things like what is ERD, why ERD, ERD notations, how to draw ERD, etc. along with a bunch of ERD examples.

What is an ER diagram (ERD)?

First of all, what is an Entity Relationship Diagram?

Entity Relationship Diagram, also known as ERD, ER Diagram or ER model, is a type of structural diagram for use in database design. An ERD contains different symbols and connectors that visualize two important information: The major entities within the system scope, and the inter-relationships among these entities.

And that's why it's called "Entity" "Relationship" diagram (ERD)!

When we talk about entities in ERD, very often we are referring to business objects such as people/roles (e.g. Student), tangible business objects (e.g. Product), intangible business objects (e.g. Log), etc. "Relationship" is about how these entities relate to each other within the system.

In a typical ER design, you can find symbols such as rounded rectangles and connectors (with different styles of their ends) that depict the entities, their attributes, and inter-relationships.

When to draw ER Diagrams?

So, when do we draw ERDs? While ER models are mostly developed for designing relational databases in terms of concept visualization and in terms of physical database design, there are still other situations when ER diagrams can help. Here are some typical use cases.

• Database design - Depending on the scale of change, it can be risky to alter a database structure directly in a DBMS. To avoid ruining the data in a production database, it is important to plan out the changes carefully. ERD is a tool that helps. By drawing ER diagrams to visualize database design ideas, you have a chance to identify the mistakes and design flaws, and to make corrections before executing the changes in the database.
• Database debugging - To debug database issues can be challenging, especially when the database contains many tables, which require writing complex SQL in getting the information you need. By visualizing a database schema with an ERD, you have a full picture of the entire database schema. You can easily locate entities, view their attributes and identify the relationships they have with others. All these allow you to analyze an existing database and to reveal database problems easier.
• Database creation and patching - Visual Paradigm, an ERD tool, supports a database generation tool that can automate the database creation and patching process by means of ER diagrams. So, with this ER Diagram tool, your ER design is no longer just a static diagram but a mirror that reflects truly the physical database structure.
• Aid in requirements gathering - Determine the requirements of an information system by drawing a conceptual ERD that depicts the high-level business objects of the system. Such an initial model can also be evolved into a physical database model that aids the creation of a relational database, or aids in the creation of process maps and data flow modes.

ERD notations guide

An ER Diagram contains entities, attributes, and relationships. In this section, we will go through the ERD symbols in detail.

Entity

An ERD entity is a definable thing or concept within a system, such as a person/role (e.g. Student), object (e.g. Invoice), concept (e.g. Profile) or event (e.g. Transaction) (note: In ERD, the term "entity" is often used instead of "table", but they are the same). When determining entities, think of them as nouns. In ER models, an entity is shown as a rounded rectangle, with its name on top and its attributes listed in the body of the entity shape. The ERD example below shows an example of an ER entity.

Entity Attributes

Also known as a column, an attribute is a property or characteristic of the entity that holds it.

An attribute has a name that describes the property and a type that describes the kind of attribute it is, such as varchar for a string, and int for integer. When an ERD is drawn for physical database development, it is important to ensure the use of types that are supported by the target RDBMS.

The ER diagram example below shows an entity with some attributes in it.

Primary Key

Also known as PK, a primary key is a special kind of entity attribute that uniquely defines a record in a database table. In other words, there must not be two (or more) records that share the same value for the primary key attribute. The ERD example below shows an entity 'Product' with a primary key attribute 'ID', and a preview of table records in the database. The third record is invalid because the value of ID 'PDT-0002' is already used by another record.

Foreign Key

Also known as FK, a foreign key is a reference to a primary key in a table. It is used to identify the relationships between entities. Note that foreign keys need not be unique. Multiple records can share the same values. The ER Diagram example below shows an entity with some columns, among which a foreign key is used in referencing another entity.

Relationship

A relationship between two entities signifies that the two entities are associated with each other somehow. For example, a student might enroll in a course. The entity Student is therefore related to Course, and a relationship is presented as a connector connecting between them.

Cardinality

Cardinality defines the possible number of occurrences in one entity which is associated with the number of occurrences in another. For example, ONE team has MANY players. When present in an ERD, the entity Team and Player are inter-connected with a one-to-many relationship.

In an ER diagram, cardinality is represented as a crow's foot at the connector's ends. The three common cardinal relationships are one-to-one, one-to-many, and many-to-many.

One-to-One cardinality example

A one-to-one relationship is mostly used to split an entity in two to provide information concisely and make it more understandable. The figure below shows an example of a one-to-one relationship.

One-to-Many cardinality example

A one-to-many relationship refers to the relationship between two entities X and Y in which an instance of X may be linked to many instances of Y, but an instance of Y is linked to only one instance of X. The figure below shows an example of a one-to-many relationship.

Many-to-Many cardinality example

A many-to-many relationship refers to the relationship between two entities X and Y in which X may be linked to many instances of Y and vice versa. The figure below shows an example of a many-to-many relationship. Note that a many-to-many relationship is split into a pair of one-to-many relationships in a physical ERD. You will know what a physical ERD is in the next section.

Conceptual, Logical and Physical data models

An ER model is typically drawn at up to three levels of abstraction:

• Conceptual ERD / Conceptual data model
• Logical ERD / Logical data model
• Physical ERD / Physical data model

While all the three levels of an ER model contain entities with attributes and relationships, they differ in the purposes they are created for and the audiences they are meant to target.

A general understanding to the three data models is that business analyst uses a conceptual and logical model to model the business objects exist in the system, while database designer or database engineer elaborates the conceptual and logical ER model to produce the physical model that presents the physical database structure ready for database creation. The table below shows the difference between the three data models.

Conceptual model vs Logical model vs Data model:

ERD features	Conceptual	Logical	Physical
Entity (Name)	Yes	Yes	Yes
Relationship	Yes	Yes	Yes
Columns		Yes	Yes
Column's Types		Optional	Yes
Primary Key			Yes
Foreign Key			Yes

Conceptual data model

Conceptual ERD models the business objects that should exist in a system and the relationships between them. A conceptual model is developed to present an overall picture of the system by recognizing the business objects involved. It defines what entities exist, NOT which tables. For example, 'many to many' tables may exist in a logical or physical data model but they are just shown as a relationship with no cardinality under the conceptual data model.

Conceptual data model example

NOTE: Conceptual ERD supports the use of generalization in modeling the 'a kind of' relationship between two entities, for instance, Triangle, is a kind of Shape. The usage is like generalization in UML. Notice that only conceptual ERD supports generalization.

Logical data model

Logical ERD is a detailed version of a Conceptual ERD. A logical ER model is developed to enrich a conceptual model by defining explicitly the columns in each entity and introducing operational and transactional entities. Although a logical data model is still independent of the actual database system in which the database will be created, you can still take that into consideration if it affects the design.

Logical data model example

Physical data model

Physical ERD represents the actual design blueprint of a relational database. A physical data model elaborates on the logical data model by assigning each column with type, length, nullable, etc. Since a physical ERD represents how data should be structured and related in a specific DBMS it is important to consider the convention and restriction of the actual database system in which the database will be created. Make sure the column types are supported by the DBMS and reserved words are not used in naming entities and columns.

Physical data model example

How to draw an ER diagram?

If you find it difficult to get started with drawing an ER diagram, don't worry. In this section, we will give you some ERD tips. Try to follow the steps below to understand how to draw an ER diagram effectively.

1. Make sure you are clear about the purpose of drawing the ERD. Are you trying to present an overall system architecture that involves the definition of business objects? Or are you developing an ER model ready for database creation? You must be clear about the purpose to develop an ER diagram at the right level of detail (Read the section Conceptual, Logical and Physical Data Models for more details)
2. Make sure you are clear about the scope to model. Knowing the modeling scope prevents you from including redundant entities and relationships in your design.
3. Draw the major entities involved in the scope.
4. Define the properties of entities by adding columns.
5. Review the ERD carefully and check if the entities and columns are enough to store the data of the system. If not, consider adding additional entities and columns. Usually, you can identify some transactional, operational and event entities in this step.
6. Consider the relationships between all entities and relate them with proper cardinality (e.g A one-to-many between entity Customer and Order). Don't worry if there are orphan entities. Although it's not common, it's legit.
7. Apply the technique of database normalization to re-structure the entities in a way that can reduce data redundancy and improve data integrity. For example, the details of the manufacturer might be stored under the Product entity initially. During the process of normalization, you may find that the detail keeps repeating records over records, then you can split it as a separate entity Manufacturer, and with a foreign key that links between Product and Manufacturer.

Data model examples

ERD example - Movie Rental System

ERD example - Loan System

ERD example - Online Shop

Using ERD with Data Flow Diagram (DFD)

In system analysis and design, Data Flow Diagram (DFD) can be drawn to visualize the flow of information within system processes. In a Data Flow Diagram, there is a symbol called Data Store, which represents a database table that provides the information needed by the system.

Since a physical ER Diagram provides a blueprint of an actual database, the entities in such an ERD are aligned with datastores in a DFD. You can draw ERD as a complement to DFD by representing the structure of information that flows within a system, or, on the contrary, to draw DFD in complementing an ERD by showing how the data will be utilized by the system in runtime.

Using ERD with BPMN Business Process Diagram (BPD)

In business process mapping, BPMN Business Process Diagram (BPD) can be drawn to visualize business workflows. In a Business Process Diagram, there is a symbol called Data Object, which represents the data input into / output from process activities.

Since a conceptual and logical data model provides a high-level view of business objects within a system, the entities in such ERDs are aligned with data objects in BPD. You can draw ERD as a complement to BPD by representing the structure of data objects needed by a business workflow, or, on the contrary, to draw BPD in complementing an ERD by showing how the data will be utilized throughout a business process.

Choosing an ERD tool

It takes time and effort to develop a data model with ERD. A helpful database design tool should be able to reduce your time and effort spent. Visual Paradigm provides you with not only an ERD tool but also a set of visual modeling features that helps you draw faster and easier. It supports most of the popular relational database management systems in the market today both in terms of database design, database generation, and ERD reversal.

The ERD designer is available in Visual Paradigm Modeler, which costs only US $6 per month. We would recommend you download and have a try. 30 days of FREE evaluation is offered. No credit card required.

Vacuum Diagram for MK4 1.6 motor

Thompson & Thompson Genetics in Medicine, 8th Edition

Answers to Problems

Chapter 2 Introduction to the Human Genome

1. (a)A ora.

(b) i. At meiosis I. ii. At meiosis II.

2. Meiotic nondisjunction.

3. ()²³ × ()²³; you would be female.

4. (a) 23; 46.

(b) 23; 23.

(c) At fertilization; at S phase of the next cell cycle.

5. Chromosome 1, ≈9 genes/Mb; chromosome 13, ≈3-4 genes/Mb; chromosome 18, ≈4 genes/Mb; chromosome 19, ≈19 genes/Mb; chromosome 21, ≈5 genes/Mb; chromosome 22, ≈10 genes/Mb. Because of the higher density of genes, one would expect that a chromosome abnormality of chromosome 19 would have a greater impact on phenotype than an abnormality of chromosome 18. Similarly, chromosome 22 defects are expected to be more deleterious than those of chromosome 21.

Chapter 3 The Human Genome: Gene Structure and Function

1. There are several possible sequences because of the degeneracy of the genetic code. One possible sequence of the double-stranded DNA is

Mutant 1: single-nucleotide substitution in fifth codon; for example, UAU → UGU.

Mutant 2: frameshift mutation, deletion in first nucleotide of third codon.

Mutant 3: frameshift mutation, insertion of G between first and second codons.

Mutant 4: in-frame deletion of three codons (nine nucleotides), beginning at the third base.

2. The sequence of the haploid human genome consists of nearly 3 billion nucleotides, organized into 24 types of human chromosome. Chromosomes contain chromatin, consisting of nucleosomes. Chromosomes contain G bands that contain several thousand kilobase pairs of DNA (or several million base pairs) and hundreds of genes, each containing (usually) both introns and exons. The exons are a series of codons, each of which is three base pairs in length. Each gene contains a promoter at its 5′ end that directs transcription of the gene under appropriate conditions.

3. A mutation in a promoter could interfere with or eliminate transcription of the gene. Mutation of the initiator codon would prevent normal translation. Mutations at splice sites can interfere with the normal process of RNA splicing, leading to abnormal mRNAs. A 1-bp deletion in the coding sequence would lead to a frameshift mutation, thus changing the frame in which the genetic code is read; this would alter the encoded amino acids and change the sequence of the protein. (See examples inChapter 11.) A mutation in the stop codon would allow translation to continue beyond its normal stopping point, thus adding new, incorrect amino acids to the end of the encoded protein.

4. Mutations in introns can influence RNA splicing, thus leading to an abnormally spliced mRNA (seeChapter 11).Alu or L1 sequences can be involved in abnormal recombination events between different copies of the repeat, thus deleting or rearranging genes. L1 repeats can also actively transpose around the genome, potentially inserting into a functional gene and disrupting its normal function. Locus control regions influence the proper expression of genes in time and space; deletion of a locus control region can thus disrupt normal expression of a gene (seeChapter 11). Pseudogenes are, generally, nonfunctional copies of genes; thus, in most instances, mutations in a pseudogene would not be expected to contribute to disease, although there are rare exceptions.

5. RNA splicing generates a mature RNA from the primary RNA transcript by combining segments of exonic RNA and eliminating RNA from introns. RNA splicing is a critical step in normal gene expression in all tissues of the body and operates at the level of RNA. Thus the genomic DNA is unchanged. In contrast, in somatic rearrangement, segments of genomic DNA are rearranged to eliminate certain sequences and generate mature genes during lymphocyte precursor cell development as part of the normal process of generating immunoglobulin and T-cell receptor diversity. Somatic rearrangement is a highly specialized process, specific only to these genes and specific cell types.

6. Variation in epigenetic modifications might lead to overexpression or underexpression of a gene or genes. DNA methylation might lead to epigenetic silencing of a gene. miRNAs can be involved in regulating the expression of other genes, and mutations in such an miRNA might be expected to alter gene expression patterns. The product of lncRNA genes are RNAs that can be involved in epigenetic regulation or other regulatory pathways; deletion or improper expression of such an miRNA might therefore lead to abnormalities of developmental pathways.

7. Genomic imprinting involves epigenetic silencing of an allele (or alleles at a number of closely located genes) based solely on parental origin due to epigenetic marks inherited through the germline. X inactivation involves epigenetic silencing of alleles along much of an entire chromosome based not on parental origin, but rather on a random choice of one or the other X chromosome at the time of initiation of the process in early embryonic development.

Chapter 4 Human Genetic Diversity: Mutation and Polymorphism

1. (a) CNV.

(b) Indel.

(c) A mutation in a splice site.

(d) An inversion.

(e) A SNP (or in/del) in a noncoding region or intron, or a SNP that leads to a synonymous substitution.

2. Assuming 20 years is one generation, 41 mutations/9 million alleles/2 generations = ≈2.3 × 10⁻⁶ mutations/generation at the aniridia locus. The estimate is based on assumptions that ascertained cases result from new mutation, that the disease is fully penetrant, that all new mutants are liveborn (and ascertained), and that there is only a single locus at which mutations can lead to aniridia. If there are multiple loci, the estimated rate is too high. If some mutations are not ascertained (because of lack of penetrance or death in utero), the estimated rate might be too low.

3. A microsatellite polymorphism, because microsatellite polymorphisms typically have more alleles, which provides greater capacity to distinguish genomes. A single SNP or indel would only have two alleles.

4. Based on information in this chapter, each cell division leads to less than one new single-bp mutation per genome. Rounding this up a bit to be one mutation per cell division, then one would expect at most 100 single-bp differences between cells at the end points of the two lineages mentioned. The rate of CNV de novo changes is much higher, and thus one would expect many, many such differences between the two lineages. Improved technologies now allow sequencing of single-cell genomes (i.e., rather than sequencing DNA from a collection of millions of cells). Thus it will now be possible to determine the answer to this question experimentally, rather than just theoretically.

5. Different types of mutations are sensitive to maternal or paternal age. Both single-bp mutations and CNVs show an increase in frequency with increasing age of the father. In contrast, meiotic nondisjunction for many chromosomes (including chromosome 21) shows an increase with increasing age of the mother. The rate of mutation (per bp) varies greatly in different locations around the genome; hot spots of mutation show much higher rates, although the basis for this is poorly understood. Intrachromosomal homologous recombination can lead to copy number variation in gene families or to deletion/duplications for regions flanked by homologous sequences (e.g., segmental duplications). Overall, the rate of mutation can be influenced also by genetic variation, both at a population level and in specific parental genomes. In any individual genome, this may influence where one falls in the ranges observed in typical genomes, as summarized in the Box on page 55.

Chapter 5 Principles of Clinical Cytogenetics and Genome Analysis

1. (a) Forty-six chromosomes, male; one of the chromosome 18s has a shorter long arm than is normal.

(b) To determine whether the abnormality is de novo or inherited from a balanced carrier parent.

(c) Forty-six chromosomes, male, only one normal 7 and one normal 18, plus a reciprocal translocation between chromosomes 7 and 18. This is a balanced karyotype. For meiotic pairing and segregation, see text, particularlyFigure 5-12.

(d) The del(18q) chromosome is the der(18) translocation chromosome, 18pter → 18q12::7q35 → 7qter. The boy's karyotype is unbalanced; he is monosomic for the distal long arm of 18 and trisomic for the distal long arm of 7. Given the number of genes on chromosomes 7 and 18 (seeFig. 2-7), one would predict that the boy is monosomic for approximately 100 genes on chromosome 18 and trisomic for approximately 100 genes on chromosome 7.

2. (a) Approximately 95%.

(b) No increased risk, but prenatal diagnosis may be offered.

3. Postzygotic nondisjunction, in an early mitotic division. Although the clinical course cannot be predicted with complete accuracy, it is likely that she will be somewhat less severely affected than would a nonmosaic trisomy 21 child.

4. (a) Abnormal phenotype, unless the marker is exceptionally small and restricted only to the centromeric sequences themselves. Gametes may be normal or abnormal; prenatal diagnosis indicated.

(b) Abnormal phenotype (trisomy 13; seeChapter 6); will not reproduce.

(c) Abnormal phenotype in proband and approximately 50% of offspring.

(d) Normal phenotype, but risk for unbalanced offspring (see text).

(e) Normal phenotype, but risk for unbalanced offspring, depending on the size of the inverted segment (see text).

5. (a) Not indicated.

(b) Fetal karyotyping indicated; at risk for trisomy 21, in particular.

(c) Karyotype indicated for the child to determine whether it is trisomy 21 or translocation Down syndrome. If it is translocation, parental karyotypes are indicated.

(d) Not indicated, unless other clinical findings might suggest a contiguous gene syndrome (seeChapter 6).

(e) Karyotype indicated for the boys to rule out deletion or other chromosomal abnormality. If clinical findings indicate possibility of fragile X syndrome, a specific DNA diagnostic test would be indicated.

6. (a) Paracentric inversion of the X chromosome, between bands Xq21 and Xq26, determined by karyotyping.

(b) Terminal deletion of 1p in a female, determined by karyotyping.

(c) Female with deletion within band q11.2 of chromosome 15, determined by in situ hybridization with probes for theSNRPN gene and D15S10 locus.

(d) Female with interstitial deletion of chromosome 15, between bands q11 and q13, determined by karyotyping. In situ hybridization analysis confirmed deletion of sequences within 15q11.2, with use of probes for theSNRPN gene and D15S10 locus.

(e) Female with deletion of sequences in band 1q36.3, determined by array CGH with the three BAC probes indicated.

(f) Male with an extra marker chromosome, determined by karyotyping. Marker was identified as an r(8) chromosome by in situ hybridization with a probe for D8Z1 at the centromere.

(g) Female with Down syndrome, with a 13q;21q Robertsonian translocation in addition to two normal chromosome 21s, determined by karyotyping.

(h) Presumably normal male carrier of a 13q;21q Robertsonian translocation, in addition to a single normal chromosome 21 (and a single normal chromosome 13), as determined by karyotyping.

7. (a) ForFigure 5-6C: 46,XY,dup(X)(q28). The increased ratio of sequences in Xq28 indicates a duplication.

(b) ForFigure 5-9C: 47,XX,+21. The individual is a female, because the intensity of sequences on the X are equivalent to all of the autosomes (other than 21). (The scattering of very low-intensity signals from the Y sequences is simply background noise.)

Chapter 6 The Chromosomal and Genomic Basis of Disease: Disorders of the Autosomes and the Sex Chromosomes

1. Theoretically, X and XX gametes in equal proportions; expected XX, XY, XXX, and XXY offspring (25% each). In actuality, XXX women have virtually all chromosomally normal offspring, XX and XY, implying that XX gametes are at a significant disadvantage or are lost.

2. It is possible that the relevant region of chromosome 9 has very few genes and that the inversion does not interfere with gene structure or function. Carriers are not genetically imbalanced. Their potential risk might be to the offspring, as seen with other pericentric inversions. However, the flanking regions of 9p and 9q are so large (i.e., most of those chromosome arms) that duplication or deletion resulting from meiotic crossing over may be incompatible with life. Alternatively, centromeric regions of chromosomes are relatively poor in recombination; thus there may be very few crossovers in this region, and the inv(9) could pass to the next generation unchanged.

3. No. XYY can result only from meiosis II nondisjunction in the male, whereas XXY can result from nondisjunction at meiosis I in the male or at either division in the female.

4. Translocation of Y chromosome material containing the sex-determining region (and theSRY gene) to the X chromosome or to an autosome.

6. 46,XX; autosomal recessive; prenatal diagnosis possible; need for clinical attention in neonatal period to determine sex and to forestall salt-losing crises.

7. (a) None; the short arms of all acrocentric chromosomes are believed to be identical and contain multiple copies of rRNA genes.

(b) None if the deletion involves only heterochromatin (Yq12). A more proximal deletion might delete genes important in spermatogenesis (seeFig. 6-9).

(c) Cri du chat syndrome, severity depending on the amount of DNA deleted (seeFig. 6-6).

8. Question for discussion. See text for possible explanations.

9. (a) A 1% risk is often quoted, but the risk is probably not greater than the population age-related risk.

(b) Age-related risk is greater than 1%.

(c) No increased risk if the niece with Down syndrome has trisomy 21, but if the niece carries a Robertsonian translocation, the consultand may be a carrier and at high risk.

(d) 10% to 15%; see text.

(e) Only a few percent; see text. The woman's age-related risk may be relevant.

10. 46,XX,rob(21;21)(q10;q10) or 46,XX,der(21;21)(q10;q10). (There is no need to add +21 to the karyotype because the 46 designates that she must have a normal 21 in addition to the translocation.)

11. Crossing over leads to either balanced gametes or nonviable gametes (seeFig. 5-13). Thus liveborn offspring are genomically balanced.

Chapter 7 Patterns of Single-Gene Inheritance

1. (b) Autosomal recessive; 1 in 4, assuming same paternity as her first child.

(c) Calvin and Cathy are obligate heterozygotes. Given that Calvin and Cathy are first cousins, it is also very likely that they inherited their mutant allele through Betty and Barbara from the same grandparent. Thus Betty and Barbara are very likely to be carriers, but it is not obligatory. It is theoretically possible that Cathy inherited her CF allele from Bob and that Calvin inherited his from his father, Barbara's husband. DNA-based carrier testing will answer the question definitively.

2. (a) Heterozygous at each of two loci; for example,A/a B/b.

(b) George and Grace are likely carriers for an autosomal recessive form of deafness; Horace is either a homozygote or compound heterozygote at this same deafness locus. Gilbert and Gisele are both homozygotes or compound heterozygotes for deafness due to mutations at a deafness locus as well. The fact that all of Horace and Hedy's children are deaf suggests that the deafness locus in Gilbert and Gisele's family and the locus in George and Grace's family are the same locus. Isaac and Ingrid, however, although deaf, are deaf due to each being homozygous or compound heterozygote at two different deafness loci, so all of their children are double heterozygotes (as shown in part a of this question).

3. Variable expressivity—d; uniparental disomy—i; consanguinity—j; inbreeding—c; X-linked dominant inheritance—g; new mutation—e; allelic heterogeneity—h; locus heterogeneity—a; homozygosity for an autosomal dominant trait—b; pleiotropy—f.

4. (b) They are homozygous.

(c) 100% for a son of Elise; virtually zero for a daughter unless Elise's partner has hemophilia A.

(d) Enid is an obligatory carrier (heterozygote for hemophilia A mutation) because she has an affected father but is herself not affected, so the chance a son will be affected is 50%. The probability a daughter will be a carrier is 50%, but the daughter's chance of being affected is virtually zero unless Enid's partner is himself affected with hemophilia A, which would give a 50% chance of being affected, or if there is some very unusual circumstance of highly skewed X inactivation or if her daughter has Turner syndrome with a single maternal X carrying the mutant hemophilia A gene.

5. All are possible except (c), which is unlikely if the parents are completely unaffected.

6. (a) New mutation or germline mosaicism in one of the parents.

(b) Mutation rate at theNF1 locus if truly a new mutation; if one of the parents is a germline mosaic, the risk in the next pregnancy is a function of the fraction of gametes carrying the mutation, which is unknown.

(c) Mutation rate at theNF1 locus if truly a new mutation; if the father is a germline mosaic for NF1, the risk in the next pregnancy is a function of the fraction of sperm carrying the mutation, which is unknown.

(d) 50%.

Figure forChapter 7, question 7.

Form all the paths connecting all the pertinent individuals in this pedigree (see Figure). Each path that gives a closed loop is a consanguineous path. There are two closed loops: A-D-H-K-L-I-E-A and B-D-H-K-L-I-E-B. To calculate F, count all the "nodes" (the dots representing each of the individuals) in each of the closed loops, counting each node only once. Call that n. The coefficient of inbreeding due to that loop is then given by ()ⁿ⁻¹. So, in this example, the loop A-D-H-K-L-I-E-A contains seven unique nodes, n = 7. Add all the coefficients for each loop together to find F. For the pedigree, then:

Chapter 8 Complex Inheritance of Common Multifactorial Disorders

1. (a) Autosomal dominant with reduced penetrance. If it were truly multifactorial, the risk for more distantly related relatives would drop by more than 50% with each increase in the degree of relatedness.

(b) In dominant disease, a study of multiple families with the condition would reveal the expected 50% ratio of affected to unaffected in the children of an affected individual (after correcting for bias of ascertainment of the families). In multifactorial inheritance, there would be fewer than the expected 50% affected in the children of an affected individual.

2. Male to male transmission can disprove X-linkage; other criteria of multifactorial inheritance can be examined, as in the text.

3. For autosomal recessive but not for multifactorial inheritance, all of the affected individuals in a family tend to be in the same sibship, with unaffected parents, whereas diseases with multifactorial inheritance can present as affected parents with affected children. It is generally rare for a parent of children with an autosomal recessive disorder to be himself or herself affected because it would require a homozygote or compound heterozygote–affected parent to mate with a carrier of a mutant allele at that same locus. There can be an increased incidence of such rare matings, however, when thereis assortative mating or if the couple isconsanguineous or comes from aninbred population.

Chapter 9 Genetic Variation in Populations

1. One way of determining this is to reverse the question and ask instead what proportion of individuals would behomozygous. Then the proportion that is heterozygous is 1 minus the proportion that is homozygous. The frequency of homozygotes for the first allele would be 0.40 × 0.40 = 0.16, 0.30 × 0.30 = 0.09 for the second allele, 0.15 × 0.15 = 0.0225 for allele three, etc. Adding these up for the five alleles (0.16 + 0.09 + 0.0225 + 0.01 + 0.0025 = 0.285) means 28.5% of individuals would be homozygous for allele 1or allele 2or … allele 5. Therefore 71.5% of individuals would be heterozygous at this locus.

2.q = 0.26,p = ≈0.74,p ² = ≈0.55, 2pq = ≈0.38,q ² = ≈0.07

Frequency ofRh−/− genotype in mother = 0.07. Frequency ofRh+/+ in father = 0.55. Frequency ofRh+/− in father = 0.38.

First pregnancy:

Probability ofRh−/− mother ×Rh+/+ father mating = 0.07 × 0.55 = 3.8%.

Probability ofRh−/− mother ×Rh+/− father mating = 0.07 × 0.38 = 2.66%.

Second pregnancy:

All second pregnancies ofRh−/− mother ×Rh+/+ father will be sensitized by the first pregnancy = 3.8%, and all are at risk for Rh incompatibility in the next pregnancy.

Only half of the first pregnancies of anRh−/− mother byRh+/− father will have sensitized the mother (Rh+/−), so the risk for a sensitizedRh−/− mother with anRh+/− partner in the second pregnancy = × 2.66% = 1.33% and the chance a sensitizedRh−/− mother will have aRh+/− child when her mate isRh+/− = × 1.33% = 0.66%.

Total at risk for incompatibility 3.8% + 0.66% ≈ 4.5% in the population at the time of a second pregnancy in the absence of any prophylaxis.

3. (a) Assume there are 100 individuals in the population, carrying 200 alleles at a particular locus. The frequency ofA is (2 ×) + () = 0.9 and frequency ofa = 0.1

(b) The genotype frequencies will be the same as in this generation, assuming Hardy-Weinberg equilibrium.

(c) Frequency ofA/a byA/a matings = 0.18 × 0.18 = ≈0.0324.

4. (a) When q is small, p = ≈1, and so 2pq = ≈2q. Therefore, if 2pq = 0.04, then the allele frequency of β-thalassemia q = ≈0.02. (You can also calculate q exactly by letting 2pq = 2 (1 − q)q = 0.04, or q² − q + 0.02 = 0 and solve the quadratic equation.)

(b) Assuming only heterozygotes for β-thalassemia are likely to reproduce (a reasonable assumption because the fitness in β-thalassemia is quite low), then 0.04 × 0.04 = 0.0016 = 0.16% of matings will be between heterozygotes.

(c) Incidence of affected fetuses or newborns = 0.04% assuming no increased fetal losses in β-thalassemia, which is a reasonable assumption because the disorder has a postnatal onset.

(d) Incidence of carriers among the offspring of couples both found to be heterozygous is 50%.

5. Only (d) is in equilibrium. Possible explanations include selection for or against particular genotypes, nonrandom mating, and recent migration.

6. (a) Abby has a chance of being a carrier. Andrew has approximately a chance of being a carrier. Therefore their risk for having an affected child is × ×, or.

(b) × × =.

(c) × × =; × × =.

7. (a) Facioscapulohumeral muscular dystrophy:q =, 2pq =. Friedreich ataxia:q =, 2pq =. Duchenne muscular dystrophy is X-linked recessive and occurs mostly in males, so we will ignore any of the rare females affected. If it occurs in the population at a frequency of 1 in 25,000, then, assuming half of the population is male, the frequency in males must be 1 in 12,500, soq =, 2pq =.

(b) The autosomal dominant and X-linked disorders would increase rapidly, within one generation, to reach a new balance. The autosomal recessive disorders would increase also, but only very slowly, because the majority of the mutant alleles are not subject to selection.

8. Mutant allele frequencies are approximately and. Two possible explanations for the difference in allele frequency could be (1) founder effect (or more generally genetic drift) in the early Quebec population when it was very small and inbred, resulting in an increased mutant allele frequency, or (2) environmental conditions of unknown type that provided a heterozygote advantage in Quebec that raised the allele frequency through increased fitness of heterozygote carriers.

Chapter 10 Identifying the Genetic Basis for Human Disease

1. The HD and MNSs loci map far enough apart on chromosome 4 to be unlinked, even though they are syntenic.

2. The LOD scores indicate that this polymorphism in the α-globin gene locus is closely linked to the polycystic kidney disease gene. The peak LOD score, 25.85, occurs at 5 cM. The odds in favor of linkage at this distance compared with no linkage at all are 10^25.85 : 1 (i.e., almost 10²⁶ : 1). The data in the second study indicate that there isno linkage between the disease gene and the polymorphism in this family. Thus there is genetic heterogeneity in this disorder, and linkage information can therefore be used for diagnosis only if there is previous evidence that the disease in that particular family is linked to the polymorphism.

3. Every parent who passed on the cataract was also informative at the γ-crystallin locus, that is, was heterozygous for the polymorphic alleles at this locus. The phase is known by inspecting the pedigree in individuals IV-7 and IV-8 because these two individuals received both the cataract allele and theA allele at the γ-crystallin locus from their father (but note, we do not know what the phase was in the father simply by inspection). We do not know the phase in individuals IV-3 or IV-4 because we do not know if they inherited the cataract mutation along with theA or theB allele at the γ-crystallin locus from their mother. Phase is also known in individuals V-1, V-2, V-6, and V-7. The cataract seems to cosegregate with the "A" allele. There are no crossovers. A complete LOD score analysis should be performed. In addition, one might examine the γ-crystallin gene itself for mutations in affected persons because it would be a reasonable candidate for being the gene in which mutations could cause cataracts.

4. (a) The phase in the mother is probablyB-WAS (whereWAS is the disease-causing allele), according to the genotype of the affected boy. This phase can be determined with only 95% certainty because there is a 5% chance that a crossover occurred in the meiosis leading to the affected boy. On the basis of this information, there is a (0.95 × 0.95) + (0.05 × 0.05) = 0.905 chance that the fetus (who is male) will beunaffected.

(b) This surprising result (assuming paternity is as stated) indicates that the mother has inherited theA allele (and theWAS allele) from her mother and her phase is thereforeA-WAS, notB-WAS. Thus there must have been a crossover in the meiosis leading to the affected boy. To confirm this, one should examine polymorphisms on either side of this one on the X chromosome to make sure that the segregation patterns are consistent with a crossover. On the basis of this new information, there is now a 95% chance that the fetus in the current pregnancy isaffected.

5. No, because you would not know if II-2 inherited the mutant alleleD along with theA from her father or theA from her mother. Phase becomes unknown again, as inFigure 10-10A.

6. Yes, phase is known in the mother of the two affected boys because she must have received the mutant factor VIII allele (h) and theM allele at the polymorphic locus on the X she received from her father.

7. In 10-7A, D = 0, so D′ = 0.

In 10-7B, D= −0.05, and because D < 0, F = smaller of freq(A)freq(S) versus freq (a)freq(s), so F = (0.5)(0.1) = 0.05 versus (0.5)(0.9) = 0.45, so F = 0.05 and D′ = −0.05/0.05 = −1, reflecting the complete linkage disequilibrium.

In 10-7C, D = −0.04, F = 0.05 again, and D′ = −0.8, reflecting a high degree but not perfect LD.

8. Odds ratio for the variant and disease = (a/b)/(c/d) = ad/bc.

Relative risk = [a/(a + b)]/[c/(c + d)] = a(c + d)/c(a + b).

With three times as many controls, the odds ratio = a(3b)/c(3d) = 3ad/3bc = ad/bc, which is unchanged from the previous odds ratio.

Relative risk = [a/(a + 3b)]/[c/(c + 3d)] = a(c + 3d)/c(a + 3b) which isnot the same as the previously calculated relative risk.

Chapter 11 The Molecular Basis of Genetic Disease

1. The pedigree should contain the following information: Hydrops fetalis is due to a total absence of α chains. The parents each must have the genotype αα/−−. The α− genotype is common in some populations, including Melanesians. Parents with this genotype cannot transmit a −−/−− genotype to their offspring.

2. Except in isolated populations, patients with β-thalassemia will often be genetic compounds because there are usually many alleles present in a population in which β-thalassemia is common. In isolated populations, the chance that a patient is a true homozygote of a single allele is greater than it would be in a population in which thalassemia is rare. In the latter group, more "private mutations" might be expected (ones found solely or almost solely in a single pedigree). A patient is more likely to have identical alleles if he or she belongs to a geographical isolate with a high frequency of a single allele or a few alleles, or if his or her parents are consanguineous. See text inChapter 7.

4. These two mutations affect different globin chains. The expected offspring are normal, Hb M Saskatoon heterozygotes with methemoglobinemia, Hb M Boston heterozygotes with methemoglobinemia, and double heterozygotes with four hemoglobin types: normal, both types of Hb M, and a type with abnormalities in both chains. In the double heterozygotes, the clinical consequences are unknown—probably more severe methemoglobinemia.

5. × × =.

6..

7. 8, 1, 2, 7, 10, 4, 9, 5, 6, and 3.

8. Exceptions to this rule can arise, for example, from splice site mutations that lead to the mis-splicing of an exon. The exon may be excluded from the mRNA, generating an in-frame deletion of the protein sequence or causing a change in the reading frame, leading to the inclusion of different amino acids in the protein sequence.

9. Approximately two thirds of the couples to whom such infants were born did not know about thalassemia or the prevention programs. Approximately 20% refused abortion, and false paternity was identified in 13% of cases.

Chapter 12 The Molecular, Biochemical, and Cellular Basis of Genetic Disease

2. Autosomal dominantPCSK9 gain-of-function mutations that cause familial hypercholesterolemia are genocopies of autosomal dominant loss-of-function mutations in the LDL receptor gene (LDLR), because a genocopy is a genotype that determines a phenotype closely similar to that determined by a different genotype (for comparison, see Glossary  for the definition of phenocopy).

4. If Johnny has CF, the chances are approximately 0.85 × 0.85, or 70%, that he has a previously described mutation that could be readily identified by DNA analysis. His parents are from northern Europe; therefore the probability that he is homozygous for the ΔF508 mutation is 0.7 × 0.7, or 50%, because approximately 70% of CF carriers in northern Europe have this mutation. If he does not have the ΔF508 mutation, he could certainly still have CF, because approximately 30% of the alleles (in the northern European population, at least) are not ΔF508. Steps to DNA diagnosis for CF include the following: (1) look directly for the ΔF508 mutation; if it is not present, (2) look for other mutations common in the specific population; (3) then look directly for other mutations based on probabilities suggested by the haplotype data; (4) if all efforts to identify a mutation fail (or if time does not allow), perform linkage analysis with polymorphic DNA markers closely linked to CF.

5. James may have a new mutation on the X chromosome because Joe inherited the same X chromosome from his mother, and the deletion was present in neither Joe nor his mother. If this is the case, there is no risk for recurrence. Alternatively, the mother may be a mosaic, and the mosaicism includes her germline. In this case, there is a definite risk that the mutant X could be inherited by another son or passed to a carrier daughter. Approximately 5% to 15% of cases of this type appear to be due to maternal germline mosaicism. Thus the risk is half of this figure for her male offspring because the chance that a son will inherit the mutant X is × 5% to 15% = 2.5% to 7.5%.

6. For DMD, as a classic X-linked recessive disease that is lethal in males, one third of cases are predicted to be new mutations. The large size of the gene is likely to account for the high mutation rate at this locus (i.e., it is a large target for mutation). The ethnic origin of the patient will have no effect on either of these phenomena.

7. A DMD female like T.N. might have the disease because she carries aDMD gene mutation on the X chromosome inherited from her mother. T.N. could show clinical symptoms if her paternal X (carrying a normal allele at this locus) was subject to nonrandom inactivation in most or all cells. An alternative explanation would be that she has Turner syndrome and that her only X chromosome (inherited from her mother) carries a DMD gene mutation. A third explanation would be that she has a balanced X;autosome translocation that disrupts theDMD gene on the translocated X chromosome. Although her normal X chromosome carries a normal allele at theDMD locus, balanced X;autosome translocations show nonrandom inactivation of the structurally normal X due to secondary cell selection (seeChapter 6).

8. The limited number of amino acids that have been observed to substitute for glycine in collagen mutants reflects the nature of the genetic code. Single-nucleotide substitutions at the three positions of the glycine codons allow only a limited number of missense mutations (seeTable 3-1).

9. Two bands ofG6PD on electrophoresis of a red cell lysate indicate that the woman has a differentG6PD allele on each X chromosome and that each allele is being expressed in her red cell population. However, no single cell expresses both alleles because of X inactivation. Males have only a single X chromosome and thus express only oneG6PD allele. A female with two bands could have two normal alleles with different electrophoretic mobility, one normal allele and one mutant allele with different electrophoretic mobility, or two mutant alleles with different electrophoretic mobility. Because the two common deficiency alleles (A ⁻ andB ⁻) migrate to the same position as the common normal-activity alleles (A andB), the woman is unlikely to have a common deficiency allele at both loci. Apart from that, one cannot say much about the possible pathological significance of the two bands without measuring the enzymatic activity. If one of the alleles has low activity, she would be at risk for hemolysis to the extent that the high-activity allele is inactivated as a result of X inactivation.

10. The box inChapter 12 entitled "Mutant Enzymes and Disease: General Concepts" lists the possible causes of loss of multiple enzyme activities: they may share a cofactor whose synthesis or transport is defective; they may share a subunit encoded by the mutant gene; they may be processed by a common enzyme whose activity is critical to their becoming active; or they may normally be located in the same organelle, and a defect in biological processes of the organelle can affect all four enzymes. For example, they may not be imported normally into the organelle and may be degraded in the cytoplasm. Almost all enzymopathies are recessive (see text), and most genes are autosomal.

11. Haploinsufficiency. Thus, in some situations, the contributions of both alleles are required to provide a sufficient amount of protein to prevent disease. An example of haploinsufficiency is provided by heterozygous carriers of LDL receptor deficiency.

12. This situation is well illustrated by diseases due to mutations in mtDNA or in the nuclear genome that impair the function of the oxidative phosphorylation complex. Nearly all cells have mitochondria, and therefore oxidative phosphorylation occurs in nearly all cells, yet the phenotypes associated with defects in oxidative phosphorylation damage only a subset of organs, particularly the neuromuscular system with its high energy requirements.

13. One example is phenylketonuria, in which intellectual disability is the only significant pathological effect of deficiency of phenylalanine hydroxylase, which is found not in the brain but solely in the liver and kidneys, organs that are unaffected by this biochemical defect. Hypercholesterolemia due to deficiency of the LDL receptor is another example. Although the LDL receptor is found in many cell types, its hepatic deficiency is primarily responsible for the increase in LDL cholesterol levels in blood.

14. There are two defining characteristics of these alleles: the hex A activity that they encode is sufficiently reduced to allow their detection in screening assays (when the other allele is a common Tay-Sachs mutation with virtually no activity), and their hex A activity is nevertheless adequate to prevent the accumulation of the natural substrate (GM₂ ganglioside). There are probably only a few substitutions in the hex A protein that would reduce activity to only a modest degree (i.e., without crippling the protein more substantially). Thus the region of residues 247 to 249 appears to be relatively tolerant of substitutions, at least of Trp for Arg. Substitutions that more dramatically alter the charge or bulk of the residues at these positions may well be disease-causing alleles.

15. A gain-of-function mutation leads to an abnormal increase in the activities performed by the wild-type protein. Consequently, the overall integrity of the protein and each of its functional domains must remain intact despite the gain-of-function mutation. In addition, of course, the mutation must confer the gain of function. Consequently, the mutation must do nothing to disturb the normal properties of the protein and must enhance at least one of them, if not more, to confer the gain of function. Mutations other than missense mutations (e.g., deletions, insertions, premature stops) are almost uniformly highly disruptive to protein structure.

16. The presence of three common alleles for Tay-Sachs disease in the Ashkenazi population seems likely to be due either to a heterozygote advantage or to genetic drift (one form of which is the founder effect, as explained inChapter 9). The high frequency of these alleles might also be due to gene flow, although the population of origin of the three common mutations is not apparent, making this explanation seem less likely (in contrast, say, to the evidence indicating that the most common PKU alleles in many populations around the world are of Celtic origin).

17. As with any genetically complex disorder, the other sources of genetic variation in Alzheimer disease (AD) may include the following: (1) additional AD loci, with lower effect sizes, that have not yet been identified; (2) synergistic effects between known AD genes (or between known genes and environmental risks) that may have a bigger effect than each of the genes or environments individually; (3) genes that harbor multiple very rare mutations of large effect, but which are undetectable by genome-wide association studies methods because each mutation occurs on a different SNP background.

18. The two forms of myotonic dystrophy are characterized by an expansion of a CUG trinucleotide in the RNA, which is thought to lead to an RNA-mediated pathogenesis. According to this model, the greatly enhanced number of CUG repeats binds an abnormally large fraction of RNA-binding proteins, including, for example, regulators of splicing, thereby depleting the cell of these critical proteins. One approach to therapy might be to prevent this binding. This might be achieved by introducing, perhaps by gene transfer (seeChapter 13), a viral vector that expresses a GAC trinucleotide repeat, which would bind to the CUG repeat sequences in the RNA and block the binding of the RNA-binding proteins to the expanded CUG repeats. Expression of too large a number of GAC repeat–containing molecules might itself have undesirable side effects, however, including binding to CUG codons that encode leucine, blocking their translation.

Chapter 13 The Treatment of Genetic Disease

1. Unresponsive patients may have mutations that drastically impair the synthesis of a functional gene product. Responsive patients may have mutations in the regulatory region of the gene. The effects of these mutations may be counteracted by the administration of IFN-γ. These mutations could be in the DNA-binding site that responds to the interferon stimulus or in some other regulatory element that participates in the response to IFN-γ. Alternatively, responsive patients may produce a defective cytochromeb polypeptide that retains a small degree of residual function. The production of more of this mutant protein, in response to IFN-γ, increases the oxidase activity slightly but significantly.

2. An enzyme that is normally intracellular can function extracellularly if the substrate is in equilibrium between the intracellular and extracellular fluids and if the product is either nonessential inside the cell or in a similar equilibrium state. Thus enzymes with substrates and products that do not fit these criteria would not be suitable for this strategy. This approach may not work for phenylalanine hydroxylase because of its need for tetrahydrobiopterin. However, if tetrahydrobiopterin could diffuse freely across the polyethylene glycol layer around the enzyme, the administration of tetrahydrobiopterin orally may suffice. This strategy would not work for storage diseases because the substrate of the enzyme is trapped inside the lysosome. In Lesch-Nyhan syndrome, the most important pathological process is in the brain, and the enzyme in the extracellular fluid would not be able to cross the blood-brain barrier. Tay-Sachs disease could not be treated in this way because of the nondiffusibility of the substrate from the lysosome.

3. Rhonda's mutations prevent the production of any LDL receptor. Thus the combination of a bile acid–binding resin and a drug (e.g., lovastatin) to inhibit cholesterol synthesis would have no effect on increasing the synthesis of LDL receptors. The boy must have one or two mutant alleles that produce a receptor with some residual function, and the increased expression of these mutant receptors on the surface of the hepatocyte reduces the plasma LDL-bound cholesterol.

4. Unresponsive patients probably have alleles that do not make any protein, that decrease its cellular abundance in some other way (e.g., make an unstable protein), or that disrupt the conformation of the protein so extensively that its pyridoxal-phosphate binding site has no affinity for the cofactor, even at high concentrations. The answer to the second part of this question is less straightforward. The answer given here is based on the generalization that most patients with a rare autosomal recessive disease are likely to have two different alleles, which assumes that there is no mutational hot spot in the gene and that the patients are not descended from a "founder" and are not members of an ethnic group in which the disease has a high frequency. In this context, Tom is likely to have two alleles that are responsive; first cousins with the same recessive disease are likely to share only one allele, so that Allan is likely to have one responsive allele that he shares with Tom and another allele that is either unresponsive or that responds more poorly to the cofactor than Tom's other allele.

5. (a) You need both a promoter that will allow the synthesis of sufficient levels of the mRNA in the target tissue of choice and the phenylalanine hydroxylase cDNA. In reality, you also need a vector to deliver the "gene" into the cell, but this aspect of the problem has not been dealt with much in the text.

(b) A phenylalanine hydroxylase "gene" will probably be effective in any tissue that has a good blood supply for the delivery of phenylalanine and an adequate source of the cofactor of the enzyme, tetrahydrobiopterin. The promoter would have to be capable of driving transcription in the target tissue chosen for the treatment.

(c) Any mutation that severely reduces the abundance of the protein in the cell but has no effect on transcription. This group includes those mutations that impair translation or that render the protein highly unstable. The thalassemias include examples of all these types.

(d) Liver cells are capable of making tetrahydrobiopterin, whereas other cells may not be. The target cell for the gene transfer should thus be capable of making this cofactor; otherwise, the enzyme will not function unless the cofactor is administered in large amounts.

(e) Human phenylalanine hydroxylase probably exists as a homodimer or homotrimer. In patients whose alleles produce a mutant polypeptide (versus none at all), these alleles may manifest a dominant negative effect on the product of the transferred gene. This effect could be overcome by making a gene construct that produces more of the normal phenylalanine hydroxylase protein (thus diluting out the effect of the mutant polypeptide) or by transferring the gene into a cell type that does not normally express phenylalanine hydroxylase and that would therefore not be subject to the dominant negative effect.

6. One must consider the kinds of mutations that decrease the abundance of a protein but that are associated with residual function. One class of such mutations are those that decrease the abundance of the mRNA but do not alter the protein sequence (i.e., each protein molecule produced has normal activity, but there are fewer molecules). Mutations of this type might include enhancer or promoter mutations, splice mutations, or others that destabilize the mRNA. In this case, one could consider strategies to increase expression from the normal allele and perhaps also the mutant allele, as is done with hereditary angioedema, in which danazol administration increases the expression of the product from both the wild-type and mutant alleles. A second class of such mutations are those within the coding sequence that destabilize the protein but still allow some residual function. Here, a strategy to increase the stability or the function of the mutant protein should be considered. For example, if the affected protein has a cofactor, one could administer increased amounts of the cofactor, provided such an approach would not have unacceptable side effects.

7. The drug can facilitate the skipping of a premature stop codon, allowing the translational apparatus to misincorporate an amino acid that has a codon comparable to that of the mutant termination codon. This treatment might allow the synthesis of a protein of normal size in both patients. In the responsive patient, the nonsense codon is located in a functionally "neutral" part of the protein, and the amino acid that is substituted in place of the nonsense codon allowed normal folding, processing, and function of the "corrected" protein. In the nonresponsive patient, however, the nonsense mutation is located in codon 117, which in wild-type CFTR is an Arg residue (seeFig. 12-15). This Arg residue contributes to the Cl ⁻  channel of CFTR. In this unresponsive patient, the drug did not lead to incorporation of Arg at this position, and the Cl ⁻  channel had defective conduction as a result.

Chapter 14 Developmental Genetics and Birth Defects

1. Before determination, an embryo can lose one or more cells, and the remaining cells can undergo specification and ultimately develop into a complete embryo. Once cells are determined, however, mosaic development takes place—an embryonic tissue will follow its developmental program regardless of what happens elsewhere in the embryo. Regulative development means that an embryonic cell can be removed by blastomere biopsy for the purpose of preimplantation diagnosis without harming the rest of the embryo.

2. a–3, b–2, c–4, d–1.

3. a–4, b–3, c–5, d–2, e–1.

4. Mature T or B cells that have somatically rearranged their T-cell receptor or immunoglobulin loci would not be appropriate. This change is not epigenetic; it is a permanent alteration of the DNA sequence itself. Animals derived from a single nucleus from a mature T or B cell are incapable of mounting an appropriately broad immune response.

5. Consider issues of regulation versus simple capacity to carry out a biochemical reaction. Also, consider dominant negative effects of transcription factors, taking into account the frequent binary nature of such factors (DNA-binding and activation domains).

Chapter 15 Cancer Genetics and Genomics

2. Colorectal cancer seems to require a number of sequential mutations in several genes, a process that may take longer than one (in hereditary) or two (in sporadic) mutations in the retinoblastoma gene. Age dependence may also reflect the number, timing, and rate of cell divisions in colon cells and in retinoblasts.

3. A cell line with i(17q) is monosomic for 17p and trisomic for 17q. Thus formation of the isochromosome leads to loss of heterozygosity for genes on 17p. This may be particularly important because one or more tumor suppressor genes (such asTP53) are present on 17p; a "second hit" on the other copy ofTP53 would lead to complete loss of the p53 protein function. In addition, a number of proto-oncogenes map to 17q. It is possible that increasing their dosage may confer a growth advantage on cells containing the i(17q).

4. The chief concern is the need to reduce radiation exposure to the lowest possible level because of the risk for cancer in children with this genetic defect.

5. Although most (>95%) breast cancer appears to follow multifactorial inheritance, there are two known genes (BRCA1 andBRCA2) in which mutations confer a substantial increased lifetime risk for breast cancer (fivefold to sevenfold) inherited in an autosomal dominant manner. Certain mutations in certain other genes, such asATM,BARD1,BRIP1,CDH1,CHEK2,PALB2,PTEN, andTP53, among others, increase the lifetime breast cancer risk significantly over the 12% background risk in the population as well, but generally not to the extent seen with mutations inBRCA1 orBRCA2. In the absence of a gene mutation in a hereditary breast cancer gene, the empirical risk figures are consistent with an overall multifactorial model with admixture of dominant forms of the disease with somewhat reduced lifetime penetrance; thus there is an approximately twofold increased risk for breast cancer in any woman with a first-degree female relative with breast cancer. Direct mutation detection could be performed if desired by the probands in Wanda's and Wilma's families, and if a mutation were found inBRCA1, BRCA2, or one of the other genes that cause substantial increased risk for breast cancer, a direct test for cancer risk could be offered to their relatives. More recently, one leading breast cancer researcher suggested that population-wide screening for disease-causing mutations inBRCA1 orBRCA2 should be initiated independent of family history, either restricted to high-risk ethnic groups or, more widely, to the entire population.

6. It is likely that many activated oncogenes, if inherited in the germline, would disrupt normal development and be incompatible with survival. There are a few exceptions, such as activatingRET mutations in MEN2 and activatingMET mutations in hereditary papillary kidney cancer. These activated oncogenes must have tissue-specific oncogenic effects without affecting development. Although it is not known why such specific types of cancers occur in individuals who inherit germline mutations in these oncogenes, one plausible theory is that other genes expressed in most of the tissues of the body counteract the effect of these activating mutations, thereby allowing normal development and suppressing oncogenic effects in most of the tissues in heterozygotes.

Chapter 16 Risk Assessment and Genetic Counseling

1. (a) Prior risk,; posterior risk (two normal brothers),.

(b) Zero, unless the autosomal dominant form can show nonpenetrance, in which case there is a very small probability that Rosemary, Dorothy, and Elsie would all be nonpenetrant carriers. Without knowing the penetrance, we cannot calculate the exact risk that Elsie is heterozygous.

Figure forChapter 16, question 2.

Similarly, Molly's mother, Lucy, 5/21; Norma and Nancy, 13/42; Olive and Odette, 13/84; Martha, 1/21; Nora and Nellie, 1/42; Maud, 5/42; Naomi, 5/84.

(b) To have a 2% risk for having an affected son, a woman must have an 8% chance of being a carrier; thus Martha, Nora, and Nellie would not be obvious candidates for prenatal diagnosis by DNA analysis because their carrier risk is less than 8%.

4. (a) Use the first equation,I = µ +. To solve forH and substitute it forH in the second equation,H = 2µ + +If. Solve forI, I = 3µ/(1 −f). Substituting 0.7 forf gives:

The incidence of affected malesI = 10µ.

The incidence of carrier femalesH = 18µ.

Chance next son will be affected is × 0.9 = 0.45.

(b) Substitutef = 0 into the equations and you getI = 3µ andH = 4µ.

(c) 0.147.

Figure forChapter 16, question 4.

5. (a) The prior risk that either Ira or Margie is a cystic fibrosis carrier is; therefore the probability that both are carriers is × =.

(b) Their risk for having an affected child in any pregnancy is × =.

(c) Bayesian analysis is carried out.

Thus the chance that Ira's and Margie's next child will be affected is × =.

	Both Carriers	Not Both Carriers
Prior
Conditional  (3 normal children)	()3	1
Joint	× ()3 = 0.19	= 0.56
Posterior	0.19/(0.19 + 0.56) =	0.56/0.75 = ≈

6. The child's prior probability of carrying a mutant myotonic dystrophy gene is. If it is assumed that he has a chance of being asymptomatic, even if he carries the mutant gene, then his chance of carrying it and showing no symptoms is. Testing is a complex issue. Many would think that testing an asymptomatic child for an incurable illness with adult onset is improper because the child should be allowed to make that decision for himself or herself (seeChapter 19).

7. (a) Yes; autosomal recessive, autosomal dominant (new mutation), X-linked recessive, and multifactorial inheritance and a chromosome disorder all need to be considered, as would nongenetic factors such as prenatal teratogen exposure and intrauterine infection. A careful physical examination and laboratory testing are required for a proper assessment of risks for this couple.

(b) This increases suspicion that the disorder is autosomal recessive, but the possibility of consanguinity does not prove autosomal recessive inheritance, and all other causes must still be investigated thoroughly.

(c) This fact certainly supports the likelihood that the problem has a genetic explanation. The pedigree pattern would be consistent with autosomal recessive inheritance only if the sister's husband were carrying the same defect (possible if he is from the same village, for example). An X-linked recessive pattern (particularly if the affected children are all boys) or a chromosome defect (e.g., the mothers of the affected children having balanced translocations with unbalanced karyotypes in the affected children) ought to be considered. The mother and her son should receive a genetic evaluation appropriate to the clinical findings, such as karyotyping and fragile X analysis.

8. The woman needs genetic counseling. She has a 50% risk for passing the mutantNF1 gene to her offspring. The fact that she carries a new mutation only reduces the recurrence risk elsewhere in the family.

9. The seven scenarios are shown in the table.

Conditional Probability Calculation

^* The joint probabilities for the core individuals in the pedigree (I-1, II-1, and III-1) are enclosed in curly brackets { }, and the probabilities for individuals II-3 and III-2 are shown in square brackets [ ]. See Figure 19-7.

The scenarios in which III-2 is a carrier are B2, C3, and C4. Her posterior probability of being a carrier is therefore

10. Make II-1 the dummy consultand. Proceeding as if III-2 and her two unaffected children were not present, the risk that II-1 is a carrier is covered in situations B, C1, and C2 in the accompanying table, giving a posterior probability of

Step One of Dummy Consultand Method

One can then use this calculation as a starting point to determine that the prior probability that III-2 is a carrier, ignoring her two unaffected sons, is the probability that her mother, II-1, is a carrier = ×=; the prior probability that she is not a carrier is 1 − () = (see Table for step two). Then we use another round of conditional probability to see what effect the two unaffected sons of III-2 have, to determine the posterior risk that III-2 is a carrier.

Step Two of Dummy Consultand Method

	III-2 Carrier	III-2 Not a Carrier
Prior probability
Conditional (2 unaffected sons)	()2	1
Joint probability
Posterior probability

Chapter 17 Prenatal Diagnosis and Screening

1. c, e, f, i and j, d, h, g, b, i (and, in part, j), and a.

2. The child can have only Down syndrome or monosomy 21, which is almost always lethal. Thus they should receive counseling and consider other alternatives for having children.

3. No, not necessarily; the problem could be maternal cell contamination.

4. The level of maternal serum alpha-fetoprotein (MSAFP) is typically elevated when the fetus has an open neural tube defect. The levels of MSAFP and unconjugated estriol are usually reduced and the human chorionic gonadotropin level is usually elevated when the fetus has Down syndrome.

5. (a) Approximately 15% (seeTable 5-2).

(b) At least 50% are chromosomally abnormal.

(c) Prenatal diagnosis or karyotyping of the parents is usually not indicated after a single miscarriage; most practitioners would offer parental chromosome analysis and prenatal diagnosis after three spontaneous unexplained miscarriages (although some practitioners suggest offering testing after only two), provided there are no other indications.

6. (a) Yes. Given that her CPK levels indicate she is a carrier of DMD and she had an affected brother, she must have inherited the mutation from her mother because her brother could not have received the mutation from her father. The phase can be determined from analysis of her father, who has to have transmitted a normal X chromosome to his daughter, the consultand.

(b) Yes. A male fetus that receives her father's allele linked to theDMD locus will be unaffected. If a male fetus receives her mother's allele linked toDMD, it will be affected. This, of course, assumes no recombination between the microsatellite marker and the mutation in the DMD gene in the transmitted chromosome.

(c) First, the consultand should have DMD gene testing. The most common mutations in DMD are deletions (and less commonly duplications), although point mutations are also possible (seeChapter 12). The advent of powerful new sequencing technologies and new methods for determining deletions and duplications, such as the multiplex ligation-dependent polymerase assay (MLPA) or copy number measurements by comparative genome hybridization, has made carrier detection for DMD much more sensitive than in the past, when it was limited by the very large size of the gene and difficulties determining a partial gene deletion in a female with two copies of the gene.

7. Question for discussion. Consider issues of sensitivity and specificity of each of the different forms of testing, the psychosocial issues of prenatal diagnosis and termination at different stages of pregnancy, and risk for complications of the two invasive methods.

Chapter 18 Application of Genomics to Medicine and Personalized Health Care

1.

Idiopathic Cerebral Vein Thrombosis and Factor V Leiden

FVL, Factor V Leiden; iCVT, idiopathic cerebral vein thrombosis.

You would expect 625 FVL homozygotes and 48,750 heterozygotes.

Relative risk for iCVT in FVL homozygotes = (1/625)/(15/950,625) = ≈101.

Relative risk for iCVT in FVL heterozygotes = (2/48,750)/(15/950,625) = ≈3.

Sensitivity of testing positive for either one or two FVL alleles = 3/18 = 17%.

Positive predictive value for homozygotes = 1/625 = 0.16%.

Positive predictive value for heterozygotes = 2/48,748 = 0.004%.

Although the relative risks are elevated with FVL, particularly when the individual is homozygous for the allele, the disorder itself is very rare and thus the PPV is low.

This example highlights the concept that a relative risk is always a comparison to people who do not carry a particular marker whereas a PPV is the actual (or absolute) risk for someone who carries the marker.

2.

Deep Venous Thrombosis in the Legs, Oral Contraceptive Use, and Factor V Leiden

DVT, Deep venous thrombosis; FVL, factor V Leiden.

You would expect ≈62 FVL homozygotes and 4875 heterozygotes.

Relative risk for DVT in FVL homozygotes taking oral contraceptives (OCs) = ≈118.

Relative risk for DVT in FVL heterozygotes taking OCs = ≈30.

Sensitivity of testing positive for either one or two FVL alleles = 62%.

Positive predictive value for homozygotes = 3/62 = ≈5%.

Positive predictive value for heterozygotes = 58/4875 = 1.2%.

Note that DVT is more common than the example of idiopathic cerebral vein thrombosis given in question 1, whereas the relative risks for homozygotes are of similar magnitude (101 vs. 118); thus the PPV of testing homozygotes is accordingly much higher but is still only 5%.

3. You should first explain to the parents that the test is a routine one performed on all newborns and that the results, as in many screening tests, are often falsely positive. The parents should also be told that the test result may be a true positive, and if it is, a more accurate and definitive test needs to be done before we will know what the child's condition really is and what treatment will be required. The child should be brought in as soon as possible for examination and the appropriate samples obtained to confirm the elevated phenylalanine level to determine if the child has classic or variant PKU or hyperphenylalaninemia, and to test for abnormalities in tetrabiopterin metabolism. Once a diagnosis is made, dietary phenylalanine restriction is instituted to bring blood phenylalanine levels down below the range considered toxic (>300 µmol/L). The child must then be observed for dietary adjustments to be made to keep the blood phenylalanine levels under control.

5.

Carbamazepine-Induced TEN or SJS

SJS, Stevens-Johnson syndrome; TEN, toxic epidermal necrolysis.

Sensitivity = 44/44 = 100%.

Specificity = 98/101 = 97%.

Positive predictive value = 44/47 = 94%.

Chapter 19 Ethical and Social Issues in Genetics and Genomics

1. The first consideration is testing the boy for an incurable disease. Because the boy has symptoms and the family is seeking a diagnosis, this isnot the same situation as if an asymptomatic child is being considered for predictive testing for an adult-onset disorder, such as classic myotonic dystrophy. However, because Huntington disease in a child is overwhelmingly the result of an expansion of an enlarged triplet repeat in one of the parents, usually the father, finding a markedly enlarged expansion in the child will automatically raise the possibility that one of the parents, probably the father, is a carrier of a repeat that is enlarged enough to cause adult-onset Huntington disease in him. Thus, by testing the child, one might inadvertently discover something about a parent's risk. Testing should therefore be carried out with informed consent from the parents. Other issues: If one of the parents carries theHD gene, what do you do about testing the asymptomatic older sib?

3. You must consider the extent to which withholding information constitutes "a serious threat to another person's health or safety." In these different disorders, consider how serious the threat is and whether there is any effective intervention if the relative were informed of his or her risk.