Genes and Genomes

H. Winkler

In 1920, he coined the term “genome” which referred to a complete set of chromosomes and its genes

Now, it refers to all the DNA in a haploid set of chromosomes

T.H. Roderick

In 1986, he coined the term “genomics” which indicates the study of genomes

Linkage studies

Genetic research methods used to identify the location of genes on chromosomes by analyzing inheritance patterns within families

Cytogenic map

Distinguishes DNA sequences that are at least 5,000 kilobases apart

Linkage map

Distinguishes genes hundreds of kilobases apart

Physical map

Distinguishes genes tens of kilobases apart

Sequence map

Depicts the order of bases

Most detailed and specific genetic map

Positional cloning

Gene-by-gene approach that matches single genes to specific diseases

Begins with a phenotype, and gradually identifies a causative gene, localizing it to a part of a chromosome

Duchenne muscular dystrophy, cystic fibrosis, and Huntington disease

Diseases discovered through positional cloning

Dystropin

A protein which keeps muscle cells intact

Alterations lead to Duchenne muscular dystrophy

The Human Genome Project

Emerged in the 1980s with several goals, this idea aims to sequence a human genome

A $3 billion, 15-year project directed by the DOE and NIH

1984

The HGP was brought up at a meeting held by the DOE, discussing long-term population genetic defects of exposure to low-level radiation

1985

University of California, Santa Cruz called for an institute to sequence a human genome

1986

Virologist Renato Dulbecco proposed that the origin of cancer lies in the human genome sequence

Scientist packed a room at the Cold Spring Harbor Laboratory on New York’s Long Island to discuss the feasibility of the HGP

1990

Official start of the Human Genome Project with James Watson

2001

First draft of the human genome

2003

Finished sequence of the HGP

ELSI

Recognized the impact of HGP on public policy

Prevents misuse of information and genotypic discrimination

3% of the government-sponsored budget was set aside

Expressed Sequence Tag (EST) technology

Enables researchers to find protein-coding genes (expressed as RNA); cDNAs that are expressed in a particular cell type

DNA microarrays

Display short DNA molecules; important in sequencing and assessing gene expression

Measures expression levels of a large number of genes simultaneously

Clone-by-Clone Approach / Hierarchical Shotgun Sequencing

Used by the US government-funded international consortium which aligned pieces one chromosome at a time

Maps chromosomes before sequencing

Whole Genome Shotgun Approach

Used by Celera Genomics in which the entire genome is shattered then rebuilt

Useful for small genomes

No prior mapping

Sequencing

DNA “shotgunned” into many small fragments, using restriction enzymes

Determines nucleotide sequence

Assembly

Software aligns ends of DNA pieces by recognizing sequence overlaps

Aligning/merging of sequences

Annotation

Software searches for clues to location of protein-encoding genes. Databases from other species’ genomes searched for similarities to identify gene functions

Identifies functional elements

Tiling

Tiling microarrays display genome pieces

Has short fragments of nucleic acids immobilized on a substrate

Comparative genetics

Eases the comparisons and interpretations of the human genome using a reference genome sequence

Reference genome sequence

A digital DNA sequence assembled from the most common base at each point of sequenced genomes

Idealized assembly of DNA from a number of people

Limitations of Exome and Genome Sequencing

• Copy number variants

• Mitochondrial DNA

• Uniparental disomy

• Gene-gene and gene-environment interaction

Uniparental disomy

Both members of chromosome pair are inherited from one parent while the other parent chromosome is missing

Genome Sequence Data Interpretation Considerations

• Incomplete penetrance

• Variable expressivity

• Epistasis

• Genetic heterogeneity

• Environmental influence

Variable expressivity

Series of signs and symptoms

Genetic heterogeneity

Single clinical disorder is caused by several genes

Genome sequencing

Provided information on how crossing over and de novo mutations are connected

De novo sequencing

Sequencing of novel genome without reference sequence