Lecture 5 - Genomics

Question 1

What is genomics

Answer 1

Study of an organism’s complete DNA
(genome)

Involves sequencing, mapping, and
analysing genes

Genomics differs from genetics in its
broad scope

Exploring the function and evolution of
genomes

Question 2

What is crossover frequency

Answer 2

The frequency at which two
genes on a chromosome
recombine during meiosis
due to cross-over

Question 3

What is linkage

Answer 3

Genes close to
each other on a
chromosome are less likely
to be separated by
crossing over, so they are
linked

Question 4

What are Genetic maps used for

Answer 4

Genetic maps provide a rough
approximation of the location of
known genes relative to the locations
of other know genes.

For linked genes (genes that are close)
the rate of recombination is
proportional to the physical distance
between the loci.

Question 5

What is the Sanger method for sequencing and how is it done

Answer 5

Chain termination

eg. stop chain at As
then Gs etc….

tagged with fluorescence

Question 6

What was the first genome sequence

Answer 6

Bacteriophage Lambda
49000 bp
Completed in 1982

Question 7

What was the Human Genome project

Answer 7

To obtain the entire DNA sequence of a
HAPLOID human genome – 3 billion bp

Began in 1990, was estimated to take 15
years and cost $3 billion.

Completed in 2001

Major milestone in genomics, enabled new
research avenues

Question 8

How long is the human genome

Answer 8

3.1 billion base pairs

Question 9

What is shotgun sequencing

Answer 9

Randomly breaking up DNA into small fragments, sequencing and reassembling

Used for sequencing large genomes

Steps: Copying, Fragmentation (e.g. sonication or digestion), sequencing,
computational assembly

Question 10

What are some challenges in genomic assembly

Answer 10

No sequencing is entirely accurate, so each region needs to be sequenced multiple times to identify errors

Repetitive sequences (eg. transposons, tandem repeats, centromeres etc..)

Genome assembly requires a lot of computer power

Question 11

Human genome project

Answer 11

GOOGLE

Question 12

SANGER FLUORESCENCE

Question 13

What is next generation sampling

Answer 13

Next-generation sequencing (NGS) is a massively parallel sequencing technology that offers ultra-high throughput, scalability, and speed. The technology is used to determine the order of nucleotides in entire genomes or targeted regions of DNA or RNA

Question 14

SLIDE 43 Sanger vs Next gen

Question 15

What are Oxford nanopores

Answer 15

GOOGLE

Question 16

What is a pangenome

Answer 16

The complete set of genes within a species, encompassing both core genes shared by
all individuals and variable genes present in some but not others

Question 17

What is a core genome

Answer 17

Genes present in all individuals of a
species

Question 18

What is an accessory genome

Answer 18

Genes that vary among individuals,
contributing to diversity

Question 19

What does the human pan genome project do

Answer 19

Creates a reference pangenome that represents human diversity

Question 20

What is a transcriptome

Answer 20

All the RNA molecules transcribed from a genome

Question 21

What are the tools of transcriptomics

Answer 21

RNA sequencing (RNA-seq)

DNA microarrays