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eleventh edition

Human Genetics Concepts and Applications

Ricki Lewis Genetic Counselor CareNet Medical Group Schenectady, New York

Adjunct Assistant Professor of Medical Education Alden March Bioethics Institute Albany Medical College

Writer, Medscape Medical News

Blogger, Public Library of Science

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HUMAN GENETICS: CONCEPTS AND APPLICATIONS, ELEVENTH EDITION

Published by McGraw-Hill Education, 2 Penn Plaza, New York, NY 10121. Copyright © 2015 by McGraw-Hill Education. All rights reserved. Printed in the United States of America. Previous editions © 2012, 2010, and 2008. No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without the prior written consent of McGraw-Hill Education, including, but not limited to, in any network or other electronic storage or transmission, or broadcast for distance learning.

Some ancillaries, including electronic and print components, may not be available to customers outside the United States.

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Library of Congress Cataloging-in-Publication Data Lewis, Ricki. Human genetics : concepts and applications/Ricki Lewis, Genetic Counselor, CareNet Medical Group, Sche- nectady, New York, Adjunct Assistant Professor of medical education, Alden March Bioethics Institute, Albany Medical College, writer, Medscape Medical News, blogger, Public Library of Science.—Eleventh edition. pages cm ISBN 978-0-07-352536-5 (alk. paper) 1. Human genetics—Textbooks. I. Title. QH431.L41855 2015 599.93’5—dc23

2014020906

The Internet addresses listed in the text were accurate at the time of publication. The inclusion of a website does not indicate an endorsement by the authors or McGraw-Hill Education, and McGraw-Hill Education does not guarantee the accuracy of the information presented at these sites.

www.mhhe.com

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iii

About the Author Ricki Lewis has built an eclectic career in communicating the excitement of genetics

and genomics. She earned her Ph.D. in genetics in 1980 from Indiana University.

It was the dawn of the modern biotechnology era, which Ricki chronicled in many

magazines and journals. She published one of the first articles on DNA fingerprinting

in Discover magazine in 1988, and a decade later one of the first articles on human

stem cells in The Scientist.

Ricki has taught a variety of life science courses at Miami University, the University

at Albany, Empire State College, and community colleges. She has authored or

co-authored several university-level textbooks and is the author of The Forever Fix:

Gene Therapy and the Boy Who Saved It, as well as an essay collection and a novel .

Ricki has been a genetic counselor for a private medical practice since 1984 and is

a frequent public speaker. Since 2012, Ricki has written hundreds of news stories

for Medscape Medical News, articles for Scientific American and for several genetic

disease organizations, and originated and writes the popular weekly DNA Science

blog at Public Library of Science.

Ricki teaches an online course on “Genethics” for the Alden March Bioethics Institute

of Albany Medical College. She lives in upstate New York and sometimes Martha’s

Vineyard, with husband Larry and several felines. Contact Ricki at rickilewis54@gmail.

com , or join the discussion on DNA Science at http://blogs.plos.org/dnascience/ .

Dedicated to the

families who live with genetic diseases, the

health care providers who help them, and

the researchers who develop new tests

and treatments.

Dedicated to the

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iv

C H A P T E R 12 Gene Mutation 212

C H A P T E R 13 Chromosomes 237

P A R T 4 PP A Population Genetics 263

C H A P T E R 14 Constant Allele Frequencies 263

C H A P T E R 15 Changing Allele Frequencies 279

C H A P T E R 16 Human Ancestry and Evolution 302

P A R T 5 PP A Immunity and

Cancer 326 C H A P T E R 17 Genetics of Immunity 326

C H A P T E R 18 Cancer Genetics and Genomics 351

P A R T 6 P AAP Genetic Technology 374

C H A P T E R 19 Genetic Technologies: Patenting, Modifying, and Monitoring DNA 374

C H A P T E R 20 Genetic Testing and Treatment 389

C H A P T E R 21 Reproductive Technologies 407

C H A P T E R 22 Genomics 425

P A R T 1 PP A Introduction 1

C H A P T E R 1 What Is in a Human Genome? 1

C H A P T E R 2 Cells 15

C H A P T E R 3 Meiosis, Development, and Aging 42

P A R T 2 PP A Transmission

Genetics 68 C H A P T E R 4 Single-Gene Inheritance 68

C H A P T E R 5 Beyond Mendel’s Laws 89

C H A P T E R 6 Matters of Sex 110

C H A P T E R 7 Multifactorial Traits 130

C H A P T E R 8 Genetics of Behavior 148

P A R T 3 PP A DNA and

Chromosomes 163 C H A P T E R 9 DNA Structure and Replication 163

C H A P T E R 10 Gene Action: From DNA to Protein 180

C H A P T E R 11 Gene Expression and Epigenetics 199

Brief Contents

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v

Contents About the Author iii

Preface ix

Applying Human Genetics xiii

The Human Touch xiv

The Lewis Guided Learning System xv

P A R T 1 Introduction 1 C H A P T E R 1 CC HH

What Is in a Human Genome? 1 1.1 Introducing Genes and Genomes 2

1.2 Levels of Genetics and Genomics 3

1.3 Applications of Genetics and Genomics 7

1.4 A Global Perspective on Genomes 9

C H A P T E R 2 CC HHC Cells 15

2.1 Introducing Cells 16

2.2 Cell Components 16

2.3 Cell Division and Death 28

2.4 Stem Cells 33

2.5 The Human Microbiome 37

C H A P T E R 3 CC HH Meiosis, Development,

and Aging 42 3.1 The Reproductive System 43

3.2 Meiosis 44

3.3 Gametes Mature 47

3.4 Prenatal Development 51

3.5 Birth Defects 59

3.6 Maturation and Aging 62

P A R T 2 Transmission Genetics 68 C H A P T E R 4

CC HH

Single-Gene Inheritance 68 4.1 Following the Inheritance of One Gene 69

4.2 Single-Gene Inheritance Is Rare 72

4.3 Following the Inheritance of More Than One Gene 77

4.4 Pedigree Analysis 79

4.5 Family Exome Analysis 83

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vi Contents

C H A P T E R 5 CC HH Beyond Mendel’s

Laws 89 5.1 When Gene Expression Appears to Alter

Mendelian Ratios 90

5.2 Mitochondrial Genes 98

5.3 Linkage 100

C H A P T E R 6 CC HH1 21 2 1 2

3

3 4 5 6 7 8 9 10 11

4

I

II

III

IV

V

21 3 4 5

1 2 Matters of Sex 110 6.1 Our Sexual Selves 111

6.2 Traits Inherited on Sex Chromosomes 117

6.3 Sex-Limited and Sex-Influenced Traits 122

6.4 X Inactivation 122

6.5 Parent-of-Origin Effects 124

C H A P T E R 7 CC HH Multifactorial Traits 130

7.1 Genes and the Environment Mold Traits 131

7.2 Polygenic Traits Are Continuously Varying 133

7.3 Methods to Investigate Multifactorial Traits 135

7.4 A Closer Look: Body Weight 142

C H A P T E R 8 CC HH Genetics of Behavior 148

8.1 Genes and Behavior 149

8.2 Sleep 150

8.3 Intelligence and Intellectual Disability 151

8.4 Drug Addiction 152

8.5 Mood Disorders 154

8.6 Schizophrenia 155

8.7 Autism 157

P A R T 3 DNA and Chromosomes 163 C H A P T E R 9 CC HH

DNA Structure and Replication 163 9.1 Experiments Identify and Describe the

Genetic Material 164

9.2 DNA Structure 168

9.3 DNA Replication—Maintaining Genetic Information 170

9.4 Sequencing DNA 176

C H A P T E R 10 CC HH H

C C

CH2

CH2

CH2

H2N NH

NH

C

H O

OHH

mino oup

Ac gro

Arginine R

group

N

Gene Action: From DNA to Protein 180 10.1 Transcription Copies the Information in

DNA 181

10.2 Translation of a Protein 186

10.3 Processing a Protein 192

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Contents vii

12.4 Causes of Mutation 218

12.5 Types of Mutations 221

12.6 The Importance of Position 227

12.7 DNA Repair 229

C H A P T E R 13 CC HH Chromosomes 237

13.1 Portrait of a Chromosome 238

13.2 Detecting Chromosomes 240

13.3 Atypical Chromosome Number 244

13.4 Atypical Chromosome Structure 253

13.5 Uniparental Disomy—A Double Dose from One Parent 258

C H A P T E R 11 CC HH Gene Expression

and Epigenetics 199 11.1 Gene Expression Through Time

and Tissue 200

11.2 Control of Gene Expression 203

11.3 Maximizing Genetic Information 205

11.4 Most of the Human Genome Does Not Encode Protein 206

C H A P T E R 12 CC HH Gene Mutation 212

12.1 The Nature of Mutations 213

12.2 A Closer Look at Two Mutations 214

12.3 Allelic Disorders 217

P A R T 4 Population Genetics 263 C H A P T E R 14 CC HH

Constant Allele Frequencies 263 14.1 Population Genetics Underlies

Evolution 264

14.2 Constant Allele Frequencies 265

14.3 Applying Hardy-Weinberg Equilibrium 267

14.4 DNA Profiling Uses Hardy-Weinberg Assumptions 268

C H A P T E R 15 CC HH Changing Allele

Frequencies 279 15.1 Nonrandom Mating 280

15.2 Migration 281

15.3 Genetic Drift 282

15.4 Mutation 286

15.5 Natural Selection 287

15.6 Eugenics 295

C H A P T E R 16 CC HH Human Ancestry

and Evolution 302 16.1 Human Origins 303

16.2 Methods to Study Molecular Evolution 311

16.3 The Peopling of the Planet 314

16.4 What Makes Us Human? 318

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viii Contents

P A R T 5 Immunity and Cancer 326

P A R T 6 Genetic Technology 374

C H A P T E R 17 CC HH Genetics of

Immunity 326 17.1 The Importance of Cell Surfaces 327

17.2 The Human Immune System 330

17.3 Abnormal Immunity 335

17.4 Altering Immunity 341

17.5 Using Genomics to Fight Infection 345

C H A P T E R 19 C HHC Genetic Technologies:

Patenting, Modifying, and Monitoring DNA 374 19.1 Patenting DNA 375

19.2 Modifying DNA 376

19.3 Monitoring Gene Function 382

19.4 Gene Silencing and Genome Editing 384

C H A P T E R 20 CC HH Genetic Testing and

Treatment 389 20.1 Genetic Counseling 390

20.2 Genetic Testing 392

20.3 Treating Genetic Disease 397

C H A P T E R 18 CC HH Cancer Genetics

and Genomics 351 18.1 Cancer Is an Abnormal Growth That Invades

and Spreads 352

18.2 Cancer at the Cellular Level 356

18.3 Cancer Genes and Genomes 360

18.4 The Challenges of Diagnosing and Treating Cancer 369

C H A P T E R 21 CC HHCellMitochondriaMitochondrialDNA Mitochondrion

Mitochondrial DNA = 37 genes

Reproductive Technologies 407 21.1 Savior Siblings and More 408

21.2 Infertility and Subfertility 409

21.3 Assisted Reproductive Technologies 411

21.4 Extra Embryos 419

C H A P T E R 22 CC HH Genomics 425

22.1 From Genetics to Genomics 426

22.2 Analysis of the Human Genome 430

22.3 Personal Genome Sequencing 435

Glossary G-1 Credits C-1 Index I-1

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Typewritten Text
ix

Human Genetics Touches Us All

When I wrote the first edition of this book, in 1992, I could never have imagined that today, thousands of people would have had their genomes sequenced. Nor could I have imagined, when the first genomes were sequenced a decade later, that the process could take under a day, for less than $1,000. Of course, under- standing all the information in a human genome will take much longer.

Each subsequent edition opened with a scenario of two students taking genetic tests, which grew less hypothetical and more real over time, even reaching the direct-to-consumer level. This new edition reflects the translation of gene and genome testing and manipulation from the research lab to the clinic.

The eleventh edition opens with “ Eve’s Genome ” and ends with “ Do You Want Your Genome Sequenced? ” In between, the text touches on what exome and genome sequencing have revealed about single-gene diseases so rare that they affect only a sin- gle family, to clues to such common and complex condi- tions as intellectual disability and autism. Exome and genome sequencing are also important in such varied areas as understanding our origins, solving crimes, and tracking epidemics. In short, DNA sequencing will affect most of us.

As the cost of genome sequencing plummets, we all may be able to look to our genomes for echoes of our pasts and hints of our futures—if we so choose. We may also learn what we can do to counter our inherited tendencies and susceptibilities. Genetic knowledge is informative and empowering. This book shows you how and why this is true.

Ricki Lewis

Today, human genetics is for everyone. It is about our variation more than about our illnesses, and about the common as well as the rare. Once an obscure science or an explanation for an odd collection of symptoms, human genetics is now part of everyday conversation. At the same time, it is finally being recognized as the basis of medical science, and health care professionals must be fluent in the field’s language and concepts. Despite the popu- lar tendency to talk of “a gene for” this or that, we now know that for most traits and illnesses, several genes interact with each other and environmental influences to mold who we are.

What Sets This Book Apart Current Content The exciting narrative writing style, with clear explanations of concepts and mechanisms propelled by stories, reflects Dr. Lewis’s eclectic experience as a medical news writer, blog- ger, professor, and genetic counselor, along with her expertise in genetics. Updates to this edition include

■ Genetic tests, from preconception to old age ■ Disease-in-a-dish stem cell technology ■ From Mendel to molecules: family exome analysis ■ Allelic diseases: one gene, more than one disease ■ Admixture of archaic and modern humans ■ Gene silencing and genome editing ■ Cancer genomes guide treatment ■ The reemergence of gene therapy ■ Personal genome sequencing: promises and limitations

The transition of genetics to genomics catalyzed slight reorga- nization of the book. The order of topics remains, but material that had been boxed or discussed in later chapters because it was once new technology has been moved up as the “applica- tions” become more integrated with the “concepts.” The book has evolved with the science.

The Human Touch Human genetics is about people, and their voices echo through- out these pages. They speak in the narrative as well as in many new chapter introductions, boxes, stories, and end-of-chapter questions and cases.

Compelling Stories and Cases When the parents of children with visual loss stood up at a conference to meet other families with the same very rare inherited disease, Dr. Lewis was there, already composing the opening essay to chapter 5. She knows the little girl in the “ In Their Own Words ” essay in chapter 2 and on the cover with her dog, who is 1 of about 70 people in the world with giant axonal neuropathy. Perhaps there is no more heart-wrenching image of Mendelian inheritance than the chapter 4 opening photo of a daughter and father, who died from Huntington disease within weeks of each other.

Clinical Application of Human Genetics A working knowl- edge of the principles and applications of human genetics is critical to being an informed citizen and health care consumer. Broad topics of particular interest include

■ The roles that genes play in disease risk, physical characteristics, and behavior, with an eye toward the dangers of genetic determinism

Preface

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x Preface

■ Biotechnologies, including next-generation DNA sequencing, genetic testing, stem cell technology, archaic human genome sequencing, gene therapy, familial DNA searches, exome sequencing, cell-free fetal DNA testing, and personal genome sequencing

■ Ethical concerns that arise from the interface of genetic and genomic information and privacy.

The Lewis Guided Learning System Each chapter begins with two views of the content. “ Learning Outcomes ” embedded in the table of contents guide the stu- dent in mastering material. “ The Big Picture ” encapsulates the overall theme of the chapter. The chapter opening essay and figure grab attention. Content flows logically through three to

five major sections per chapter that are peppered with high- interest boxed readings (“ In Their Own Words, ” “ Clinical Con- nections, ” “ Bioethics: Choices for the Future, ” “A Glimpse of History,” and “ Technology Timelines” ). End-of-chapter peda- gogy progresses from straight recall to applied and creative questions and challenges.

Dynamic Art Outstanding photographs and dimensional illustrations, vibrantly colored, are featured throughout Human Genetics: Concepts and Applications. Figure types include process figures with numbered steps, micro to macro representations, and the combination of art and photos to relate stylized draw- ings to real-life structures.

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New to This Edition!

The genomics of today evolved from the genetics of the twen- tieth century. A Glimpse of History features throughout the book capture key moments in time. Clinical Connections bring chapter concepts to patients and health care providers, with thought-provoking questions for discussion. Key Concepts after all major sections are now questions.

Highlights in the new edition include the following:

Chapter 1 What Is in a Human Genome? ■ The story of young Nicholas Volker, near death when

exome sequencing led to a diagnosis—and a treatment

Chapter 2 Cells ■ The human microbiome

Chapter 3 Meiosis, Development, and Aging ■ Progress for progeria ■ Maternal and paternal age effects on gametes

Chapter 4 Single-Gene Inheritance ■ Family exome analysis solves a medical mystery

Chapter 7 Multifactorial Traits ■ Blond hair among the Melanesians ■ Smoking-related lung cancer

Chapter 8 Genetics of Behavior ■ Genetic risks for posttraumatic stress disorder,

depression, autism ■ Heritability of intelligence at different ages

Chapter 11 Gene Expression and Epigenetics ■ Long noncoding RNAs

Chapter 12 Gene Mutation ■ Gonadal mosaicism ■ Allelic disease—more common than we thought ■ Exon skipping causes and treats disease

Chapter 13 Chromosomes ■ Harnessing XIST to silence trisomy 21 ■ Cell-free fetal DNA for noninvasive prenatal diagnosis

Chapter 15 Changing Allele Frequencies ■ The Clinic for Special Children treats the Amish

Chapter 16 Human Ancestry and Evolution ■ Updated terminology and evolutionary trees ■ Admixture, the Neanderthals, Denisovans, and us ■ What makes us human?

Chapter 17 Genetics of Immunity ■ Genomic epidemiology tracks an outbreak ■ Reverse vaccinology ■ Mimicking CCR5 mutations to prevent HIV infection

Chapter 18 Cancer Genetics and Genomics ■ Summary figure of cancer at different levels

■ Driver and passenger mutations ■ Cancer genomes ■ Cell-free tumor DNA ■ How BRCA1 causes cancer

Chapter 19 Genetic Technologies: Patenting, Modifying, and Monitoring DNA

■ The Supreme court and DNA patents ■ Gene silencing and genome editing

Chapter 22 Genomics ■ Genome sequencing and annotation ■ Practical medical matters ■ Types of information in human genomes ■ A gallery of genomes ■ Comparative genomics ■ Do you want your genome sequenced?

NEW FIGURES

4.6 Eye color 4.8 Loss-of-function and gain-of-function mutations 7.10 Copy number variants 8.6 Nicotine’s effects at the cellular level 8.9 Exome sequencing and autism 9.17 Replication bubbles 12.5 Allelic disease of connective tissue 12.10 Exon skipping and Duchenne muscular dystrophy 13.14 XIST silences trisomy 21 14.11 Several steps identify STRs 15.13 Antibiotic resistance 16.13 Admixture of haplotypes 16.18 What makes us human? 17.14 Filaggrin and allergy 17.18 Genome sequencing to track outbreaks 18.1 Levels of cancer 18.12 Evolution of a cancer 18.13 Cancer chromosomes 19.7 Gene silencing and genome editing

NEW TABLES

2.2 Stem Cell Sources 3.4 Longevity Genes 7.6 Study Designs for Multifactorial Traits 13.2 Maternal Serum Markers 15.1 Clinical Connection: Genetic Disorders among the Amish 19.2 Genetically Modified Foods 22.1 Selected Projects to Analyze Human Genomes 22.2 Cost of Sequencing Human Genomes 22.3 A Gallery of Genomes

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xii Preface

ACKNOWLEDGMENTS

Human Genetics: Concepts and Applications, Eleventh Edition, would not have been possible without the editorial and pro- duction dream team: senior brand manager Rebecca Olson, product development director Rose Koos, executive marketing manager Patrick Reidy, lead content licensing specialist Car- rie Burger, designer Tara McDermott, developmental editors Anne Winch, Erin Guendelsberger, and Emily Nesheim, proj- ect manager Sheila Frank, copyeditor Beatrice Sussman, and photo editor extraordinaire, Toni Michaels. Many thanks to the fabulous reviewers. Special thanks to my friends in the rare dis- ease community who have shared their stories, and to Jonathan Monkemeyer and David Bachinsky for helpful Facebook posts. As always, many thanks to my wonderful husband Larry for his support and encouragement and to my three daughters, my cats, and Cliff the hippo.

Eleventh Edition Reviewers Andy Andres

Boston University Elizabeth Alter

York College Ann Blakey

Ball State University Bruce Bowerman

University of Oregon James Bradshaw

Utah Valley University Dean Bratis

Villanova University Susan Brown

Kansas State University Michelle Coach

Asnuntuck Community College Jonathon S. Coren

Elizabethtown College Tracie Delgado

Northwest University

Dan Dixon University of Kansas Medical Center

Jennifer Drew University of Florida

Gregory Filatov University of California Riverside

Yvette Gardner Clayton State University

Ricki Glaser Stevenson University

Debra Han Palomar Community College

Bradley J. Isler Ferris State University

Bridget Joubert Northwestern State University

Patricia Matthews Grand Valley State University

Gemma Niermann University of California, Berkeley and Saint Mary’s College

Ruth S. Phillips North Carolina Central University

Mabel O. Royal North Carolina Central University

Mark Sanders University of California, Davis

Jennifer Smith Triton College

Michael Torres Warren Wilson College

Jo Ann Wilson Florida Gulf Coast University

Erin Zimmer Lewis University

This book continually evolves thanks to input from instructors and students. Please let me know your thoughts and sugges- tions for improvement. ( rickilewis54@gmail.com )

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xiii

Chapter Openers 1 Eve’s Genome 1

2 Diagnosis From a Tooth 15

3 Progress for Progeria 42

4 Juvenile Huntington Disease: The Cruel Mutation 68

5 Mutations in Different Genes Cause Blindness 89

6 Stem Cell and Gene Therapies Save Boys’ Lives 110

7 The Complex Genetics of Athletics 130

8 Genetic Predisposition to Posttraumatic Stress Disorder 148

9 On the Meaning of Gene 163

10 An Inborn Error of Arginine Production 180

11 The Dutch Hunger Winter 199

12 One Mutation, Multiple Effects: Osteogenesis Imperfecta 212

13 The Curious Chromosomes of Werewolves 237

14 Postconviction DNA Testing 263

15 The Evolution of Lactose Tolerance 279

16 The Little Lady of Flores 302

17 Mimicking a Mutation to Protect Against HIV 326

18 A Genetic Journey to a Blockbuster Cancer Drug 351

19 Improving Pig Manure 374

20 Fighting Canavan Disease 389

21 Replacing Mitochondria 407

22 100,000 Genomes and Counting 425

Applying Human Genetics

A GLIMPSE OF HISTORY Chapter 3 The first view of sperm Chapter 4 Gregor Mendel Chapter 5 The murdered Romanovs and mitochondrial DNA Chapter 9 Kary Mullis invents PCR Chapter 10 The RNA tie club Chapter 12 The discovery of sickled cells Chapter 13 Determining the human chromosome number Chapter 14 Famous forensics cases Chapter 15 Malaria in the United States Chapter 18 Retinoblastoma Chapter 20 Treating PKU Chapter 22 Comparative genomics

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Clinical Connections 1.1 Exome Sequencing Saves a Boy’s Life 10

2.1 Inborn Errors of Metabolism Affect the Major Biomolecules 19

2.2 Faulty Ion Channels Cause Inherited Disease 26

3.1 When an Arm Is Really a Leg: Homeotic Mutations 55

4.1 It’s All in the Genes 73

4.2 “65 Roses”: Progress in Treating Cystic Fibrosis 76

5.1 The Genetic Roots of Alzheimer Disease 96

6.1 Colorblindness 119

7.1 Many Genes Control Heart Health 132

12.1 Fragile X Mutations Affect Boys and Their Grandfathers 226

14.1 DNA Profiling: Molecular Genetics Meets Population Genetics 270

15.1 The Clinic for Special Children: The Founder Effect and “Plain” Populations 284

17.1 Viruses 328

17.2 A Special Immunological Relationship: Mother-to-Be and Fetus 339

18.1 The Story of Gleevec 364

21.1 The Case of the Round-Headed Sperm 410

In Their Own Words A Little Girl with Giant Axons 28

Growing Human Mini-Brains 58

The Y Wars 113

Familial Dysautonomia: Rebekah’s Story 223

Some Individuals With Trisomies Survive Childhood 251

Bioethics: Choices for the Future Genetic Testing and Privacy 11

Banking Stem Cells: When Is It Necessary? 37