Topic 7: Genomics Part 1

Question 1

Genetics vs genomics

Answer 1

Genetics = studying the functions, interactions and inheritance of a small set of related genes
Genomics = studying the structure, function and evolution of an organisms entire genome

Question 2

First virus chromosome sequenced in… Organellar chromosome? (which one)?

Answer 2

Virus = 1977
Human mitochondrial DNA = 1981

Question 3

First prokaryotic genome sequenced in? What technique?

Answer 3

1995 = Haemophilus influenza
Shotgun sequencing

Question 4

Slides 7,8

Answer 4

Shotgun sequencing

Question 5

First eukaryotic genomes sequenced when? What?

Answer 5

1996 = Saccharomyces cerevisiae
2000 = Arabidopsis thaliana

Question 6

What are notoriously difficult to sequence?

Answer 6

Centromeres, p arms of acrocentric chromosomes (repetitive regions)

Question 7

How many protein encoding genes in humans?

Answer 7

Around 20,000

Question 8

Most of human DNA is…

Answer 8

Non coding (99% introns)

Question 9

What percent of human non-coding DNA is unique? Transposable elements?

Answer 9

15%
44%

Question 10

Why is there sequence homology between humans and other species

Answer 10

Reflective of evolutionary ancestry
We can use DNA to reconstruct evolutionary history/relationships (phylogenetics)

Question 11

Forms of next-generation sequencing

Answer 11

Illumina sequencing: short reads, 100-300 bp, billions sequenced at a time
Third-generation sequencing: long reads (10,000+ bp)

Question 12

Why use illumina or third-gen sequencing

Answer 12

Sequence many DNA fragments simultaneously
Provide faster and less expensive determination of DNA base sequence
No prior knowledge needed

Question 13

Five steps to illumina sequencing

Answer 13

1. Cut genome up into small fragments and denature (ssDNA)
2. Attach fragments to glass slide
3. Each fragment is used as template for DNA synthesis
4. Picture taken as each base is added
5. Assembly (computer analyzes image+ does assembly)

Question 14

How does illumina work?

Answer 14

Fluorescent tag associated with each base

Question 15

What is a single-nucleotide polymorphism

Answer 15

A variation at a single position in a DNA sequence among individuals
Most commonly used genetic marker

Question 16

A character or a gene is polymorphic if…

Answer 16

More than one state or version exists in the population

Question 17

SNPs are used in

Answer 17

Population genetics, association studies, phylogenetics

Question 18

Two groups involved in the race to sequence the human genome

Answer 18

1. International human genome sequencing consortium (Francis Collins)
2. Celera genomics (Craig Venter)

Question 19

Is the human genome completely sequenced?

Answer 19

Still many regions of different chromosomes that remain unsequenced