Updated 03/18/13

Genes, Genomes and Human Disease, Part 1 3/18/13 

 Katherine M. Hyland, PhD 

 BIOGRAPHY:  

Katherine M. Hyland, PhD is a Professor in the Department of Biochemistry and Biophysics, and an affiliate member of the Institute for Human Genetics at UCSF School of Medicine. She received her B.S. in Biochemistry from Virginia Tech, an M.S. in Molecular Cytogenetics from Rutgers University, and a Ph.D. in Molecular and Human Genetics from the Johns Hopkins University. Her PhD thesis focused on chromosome structure and function in budding yeast. She was a postdoctoral fellow at the Centre for Molecular Medicine and Therapeutics at the University of British Columbia in 1998‐99, and a postdoctoral fellow at the UCSF Comprehensive Cancer Center from 1999‐2002. In 2002, she joined the faculty at UCSF. Her primary roles at UCSF are in professional school education and faculty development. She is Course Director of the Mechanisms, Methods and Malignancies Block, an interdisciplinary second year medical school course that focuses on the basic and clinical science of cancer, and directs the Medical Genetics component of the integrated medical school curriculum. She is also a co‐director of the Postdoctoral Teaching Fellowship Program. In 2008, Dr. Hyland was inducted into the Haile T. Debas Academy of Medical Educators, and she currently serves as co‐Chair of the Faculty Development Working Group. She has participated in numerous educational workshops, and has completed the UCSF Teaching Scholars Program and the Harvard Macy Program for Educators in the Health Professions. She has led faculty development workshops at UCSF as well as at national meetings and other medical schools, including the University of Kragujevac, Serbia, and St. George’s University, Grenada. She has developed an online peer‐feedback training program for educators that will be shared with other medical schools, and is involved in several innovative educational projects. She is Chair of the Genetics Course Directors group in the Association of Professors of Human and Medical Genetics (APHMG), and is also an active a member of the International Association of Medical Science Educators (IAMSE), the American Society of Human Genetics (ASHG), the Association of Biochemistry Course Directors (ABCD) and the Western Group on Educational Affairs (WGEA).      

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Genes, Genomes and Human Disease

UCSF Mini Medical School

Katherine Hyland, PhDDepartment of Biochemistry & Biophysics,

Institute of Human Genetics

Common Variable Immune Deficiency (CVID)

“late onset” humoral immune deficiency

Significant % = genetic cause

Heterogeneous: defect in single or multiple genes

75-80% = unknown cause, genetics likely plays a role

Elizabeth

Genetics of CVID

10-20% have known genetic cause

Inherited in either Autosomal Dominant or Autosomal Recessive manner

5 known genes

Different types of mutations in different families/geographic populations

Outline: Genetics Part 1

1. Intro:

Genetics of CVID

Genetic Contribution to Dis-ease

2. The Basics

DNA, Genes, chromosomes, genomes

3. Genetic Variation

Mutations and polymorphisms

Outline: Genetics Part 2

1. Inheritance of genetic disease Inheritance patterns and pedigrees

2. Genetic Testing Methods of analyzing single genes,

chromosomes and whole genomes

Direct to Consumer Testing (TCT)

Learning Goals

1. Describe how genetics contributes to human disease

2. Understand basic genetic terminology

3. Describe the organization of the human genome

4. Describe the types of variation seen in the human genome, and potential phenotypic consequences

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Dis-ease is due to combination of Genetics and Environment

• Measles, lungcancer

• Diabetes, stroke, hypertension, Alzheimer dz

• CVID

• Cystic fibrosis, Down syndrome

• CVID

Examples:

Environmental•Diet, lifestyle, etc.

Genetic

Rare, disease-causing mutation

Common/Rare, susceptibility variants

Medicine through a Genetic Lens

Why this person?

Why this disease?

Why now?

What can we do to restore this person to her/his own unique steady state?

Outline: Genetics Part 1

1. Intro:

Genetics of CVID

Genetic Contribution to Dis-ease

2. The Basics

DNA, Genes, chromosomes, genomes

3. Genetic Variation

Mutations and polymorphisms

?

The ABC’s of Genes and Genomes

DNA = “letters”

Genes = “words”

Chromosomes= “chapters”

Genome = Entire book ~

A manual for creating a living being!!

What do we have in common with every other living thing on earth??

Composed of 4 basic elements :

A = Adenine

T = Thymine

C = Cytosine

G = Guanine

DNA!!

*The 4 letters of the DNA alphabet!

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DNA Structure

Molecular Biology of the Cell, 5th Edition. By Alberts, Johnson, Lewis, Raff, Roberts and Walter. Garland Science Publishing, 2008

Human DNA is packaged into 24 chromosomes

22 autosomes and 2 sex chromosomes, X &Y

Each “somatic” cell has 46 chromosomes:

F 2 copies of each autosome and 2 sex chromosomes, XX (female) or XY (male)

Packaging DNA into Chromosomes

Molecular Biology of the Cell, 5th Edition. By Alberts, Johnson, Lewis, Raff, Roberts and Walter. Garland Science Publishing, 2008

Human DNA is packaged into 24 chromosomes

Chromosomes range in size from 50 million to 250 million base pairs of DNA

Each gene has a specific location on one of the 24 chromosomes (e.g. ‘street address’)

Prophase Prometaphase(nuclear envelope breakdown)

Metaphase Anaphase Cytokinesis

Metaphase spread of human chromosomes

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Human Karyotype: 46,XY Human Karyotype 46,XY

Venter, PLoS Biology 5(10), Oct 2007.

G-banded karyotype Spectral karyotype

What is a GENE? A sequence of DNA that

carries the information to make a specific protein (or functional RNA)

Humans are diploid = 2 copies of every gene

Each gene has a specific location on one of the 24 chromosomes

(e.g. ‘street address’)en.wikipedia.org

AllelesWildtypeMutation 1

Mutation 2

Homozygous wildtype

Homozygous mutant

Heterozygous Compound Heterozygous

Homologous chromosomes

Locus

Alleles

Phenotype

Genotype = Alleles present in an individual at a specific locus

= Physical expression of

genotype; result of interaction of

genotype with the environment

What is a GENOME?

An organism’s complete DNA sequence - a blueprint to make a human being!

Both genes and non-coding regions

Nuclear + Mitochondrial DNA

Every cell in your body contains a complete copy of your genome

Not all genes are turned ‘on’ in every cell - only a subset that are needed to carry out the functions of that cell type

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How big is the Human Genome?

3 billion base pairs of DNA (A/T, C/G)

<20,000 genes = many fewer than anticipated!

CATGCACGTCTCAGTCGCGT

AC

GT

CT

CA

GT

CG

CG

TC

AT

GC

Length of complete DNA sequence

equivalent to 200volumes of a

Manhattan telephone book (1000 pgs each)!

How big is the Human Genome?

~ 2 meters! (> 6 feet)

DNA from all 100 trillion cells of our bodies = over 113 billion miles!

From earth to sun and back 610 times!!!

Alberts et al, Molecular Biology of the Cell, 5th Ed. Fig 4-16, Garland Publishing 20008.

20,000

The function and organization of the human genome

Coding Regions = “gene rich”

Non-coding Regions = “Dark Matter”

• ~1-2% of genome • Actively transcribed• Decondensed during

interphase• Euchromatin

• ~98-99% of genome • Not transcribed - but functional! e.g. maintain chromosome structure

• Condensed throughout cell cycle• Heterochromatin

Human Genome Project

1990

Began ~ planned 15 year project

2000/2001

“Working draft”

published

2003

High quality “finished

sequence”completed

2006

Final sequence

papers published…

2012

ENCODE

Advances in Whole Genome/ExomeSequencing,Genetic Variation

Nature ENCODE Explorer Sept. 2012

http://www.nature.com/encode/

• Encyclopedia of DNA Elements (ENCODE) project

• Goal: characterize all the functional elements in the human genome

• Results: HG is much more “active” than anticipated!

• Non-coding DNA contains genetic switches

• >80% has biological function• Chromatin structure

• Transcription regulators

• Epigenetic regulation

• Huge significance for understanding human disease!

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Outline: Genetics Part 1

1. Intro:

Genetics of CVID

Genetic Contribution to Dis-ease

2. The Basics

DNA, Genes, chromosomes, genomes

3. Genetic Variation

Mutations and polymorphisms

Human Genetic Variation

Human Genome = 3 billion bp DNA = “average sequence”

6 billion human genomes!

Any two humans are 99-99.9% genetically identical

~3.5 million nucleotide differences

~100 structural differences

Rare vs. common variants

Each individual heterozygous at ~20% of all loci

We are all alike, but not the same!!!

Human Genetic VariationWhere does genetic variation

come from?

1. Errors introduced during DNA replication

• ~1 error per 108 base pairs per cell division

• 100’s of new mutations genome-wide!

2. Errors in “homologous recombination” when producing egg and sperm

3. “Mutagens” in environment, e.g. radiation, chemicals, cigarette smoke

4. Failure to repair DNA damage

Mutation = Any change in DNA sequence

Consequences of Genetic Variation Vary

Frequency of variant in population Common, low impact on health

Rare, high impact on health

Genetic Disease

(e.g. cystic fibrosis,

Down syndrome

Common “Multifactorial”

Disease (e.g. diabetes, stroke,

hypertension)

Benign phenotypic differences

(e.g. hair/skin

color, asparagus

smell)

Neutral Variants

1%

“Polymorphisms”“Mutations”

Location of Genetic Variants

In or near gene (coding or regulatory region)

Usually Rare, high impact*

In non-coding regions (intergenic regions or introns)

Usually Common, low impact*

intergenic

Gene 2

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Sequence Variants: single nucleotide

BEER

BEAR

BEER I’d like to drink a beer.

I’d like to drink a bear.

Word Misspelled word

Interpret sentence

Single Nucleotide Polymorphisms (SNPs)

Synonymous SNP (silent)

Non-synonymous SNP

80%

20%

SNPs: How different are we?

Occur every ~300-1000 bps

Account for majority (~90%) of genetic variation

On average, 3-10 million single nucleotide variations between 2 people

Deletions and Duplications

NORMAL:“I LIKE TO SWIM IN THE OCEAN BUT I DO NOT LIKE TO SWIM IN THE POOL.”

DELETION:“I LIKE TO SWIM IN THE POOL.”

DUPLICATION:“I LIKE TO SWIM IN THE OCEAN BUT I DO NOT LIKE TO SWIM IN THE OCEAN BUT I DO NOT LIKE TO SWIM IN THE POOL.”

Copy Number Variants (CNVs)

Large chunks of DNA- repeated or deleted

Consequences vary

Many are neutral or benign

Those that alter gene dosage or expression or disrupt genes may contribute to disease risk

CNVs and Cake Mix:

- Add one egg- Add one egg, egg, egg

Structural Variation

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Key words

DNA

Gene

Allele

Chromosome

Genome

Genotype

Phenotype

Mutation

Polymorphism

Learning Goals

1. Describe how genetics contributes to human disease

2. Understand basic genetic terminology

3. Describe the organization of the human genome

4. Describe the types of variation seen in the human genome, and potential phenotypic consequences

QUESTIONS?