Human Genome Project

Chapter 9

Central Points (1)

Large, international project analyzing human genome

Information from sequencing and mapping all human genes

Gene mapping to locate human genes

Number of surprises as human genome analyzed

Central Points (2)

Scientists apply information from Human Genome Project (HGP) to medical diagnosis and treatment

Physicians use genome to give better medical care

Gene therapy is a future application of the HGP

Ethical and legal aspects of the HGP discussed

9.1 Goals of HGP (1)

1. Create maps of the human and other creatures’ genomes

2. Find location of all genes

3. Compile lists of expressed genes and nonexpressed sequences

4. Discover function of all genes

9.1 Goals of HGP (2)

5. ID proteins encoded by genes and their functions

6. Compare genes and proteins between species

7. Analyze DNA differences between genomes

8. Set up and manage databases based on genomes discovered

DNA Sequence

HGP Timeline

Chromosome Maps

Map shows where all the genes are located on each chromosome

Methods

Began in 1990, human genome ~3.2 billion nucleotides

Required development of automated methods

Bioinformatics created software, web-based databases, and research tools to collect, analyze, and store information

Genomics: study of genomes

HGP Now

Portion that carries genes was sequenced in 2003

Function of remaining 15% unknown and currently being sequenced

Sequenced portion studied to ID genes and assign functions

Proteomics: study of protein structure and function

9.2 Gene Mapping

Genes close together on same chromosome tend to be inherited together and show linkage

In 1936, hemophilia and color blindness found to be linked, both on X chromosome

Difficult to map genes on autosomes, requires very large families with two specific genetic traits

X-Linked Genes

Autosomal Linkage

ABO blood group and nail-patella syndrome

Linked Genes Separate by Crossing Over

Separation of the two alleles is result of crossing over between two genes

Occurs randomly in meiosis

Frequency of crossing over related to distance between two genes

Linkage map of a chromosome can be constructed

Crossing Over

Linkage or Genetic Map

Order of genes on a chromosome and distance between them

Expressed as percentage of crossing-over events

10% = 10 map units or centimorgans (cM) apart

From this pedigree, frequency of crossing over: 2/16 = 12.5%. or 12.5 cM (actual value ~10cM)

Autosomal Linkage

ABO blood group and nail-patella syndrome

Human Linkage Map

Positional Cloning

Markers identified that show differences in:• Restriction enzyme cutting sites • Number of repeated DNA sequences (i.e., STRs)

Markers assigned to chromosomes

Used to follow genetic disorder in pedigrees

Map one gene at a time, and by late 1980s, more than 3,500 genes and markers

Genes Mapped by Positional Cloning

DNA Sequencing Today

Can rapidly sequence DNA with computer programs

Sequence entire DNA sequence in genome

Uses high-speed sequencers and computers

Allowed HGP to succeed

9.3 Whole Genome Sequencing

Construct a genomic library that contains all sequences in a genome

Fragments of DNA placed in a DNA sequencer

Generates nucleotide sequence (As, Cs, Gs, and Ts)

Assemblers (specialized software) produce sequence of genome

Finding Genes from Sequence

Software programs scan sequences, searching for promoter sequence

Sequences that follow promoter are genes

AA sequence determined by matching the nucleotide triplets to corresponding AA

ID protein encoded by this gene

A DNA Sequence

Animation: Gene Sequencing

9.4 What Have We Learned?

> 3 billion nucleotides of DNA

~5% genes code for proteins

Many remnants of genome’s evolutionary history

> Half the genome is repetitive DNA

Types Repetitive DNA

45%: transposons • New copies can move (or transpose) • Most not functional • Do not replicate and move around

17%: LINE 1 sequence

10%: Alu sequences

Others including short tandem repeats (STRs)

Importance of Alu Sequences

Appeared in primate genomes ~65 million years ago (MYA), important in evolution of our genome

Many associated with genetic diseases

2.8 MYA, Alu sequence moved, may be associated with increased brain size

Other Surprises from HGP

20,000–25,000 genes but > 500,000 known proteins (possibly exceed 2 million)

Possible mechanisms• During processing mRNA, the coding segments

can be rearranged• Proteins modified after synthesis

Human Proteome Project (HUPO): ID proteins, functions, and interactions

9.5 How Can Information Be Used?

1. ID location of gene

2. Function of the protein encoded by this gene

3. How the mutated gene or its protein product results in a disorder

Allow development of treatments and medications

Cystic Fibrosis (CF) Gene

Positional cloning ID gene, long arm of chromosome 7

Isolated nucleotide sequence, ID AA sequence of CF protein

Compared to databases of other organisms,

protein in plasma membrane

Now developing medications

9.6 Future of Genome Sequencing

New technologies to reduce cost and time

Make sequencing routine in medical care

Possible for doctors to monitor your health

Provide:• Information to reduce risks for certain diseases • Early diagnosis of conditions

9.7 Gene Therapy

Recombinant DNA technology to treat genetic disorders

Transfer copies of normal genes into cells (or people) with defective copies of these genes

Normal genes directs synthesis of the normal protein

How Are Genes Transferred?

Cells removed from the body

Normal copies inserted using virus, or vector

Cells grown in the laboratory

Checked that normal gene actively making protein

Cells transferred back into the body

First Gene Therapy Patient (1990)

Ashanti DeSilva had severe combined immunodeficiency disorder (SCID)

No functional immune system, die from infection

Inserted gene for adenosine deaminase (ADA) into her white blood cells

Treated cells injected into her, allowed her to develop an immune system

Problems with Gene Therapy

In many cases, gene therapy has not worked

Few patients developed leukemia

At least two people died

Scientists working to correct problems

Need to develop new approaches to use genes to treatment genetic diseases

Spotlight on Law: Moore v. Regents of the University of California (1)

John Moore treated at UC Hospital for hairy cell leukemia

Spleen removed and over years blood, sperm, serum, bone marrow removed as “part of his treatment”

Signed consent form for doctors to do research on cells and expenses paid for by UCLA

Spotlight on Law: Moore v. Regents of the University of California (2)

Moore’s doctors received patent on cell line and sold cell line for stock options and $330,000

Issues: Informed Consent: Moore did not receive enough

information to make an informed consent

Doctor/patient relationship: Moore treated fraudulently, experienced emotional distress