Human genetics

Question 1

1990

Answer 1

• HGP is launched in the US
• Ethical, legal and social implication (ELSI) programs founded at NIH and DOE
• First gene for breast cancer (BRCA1 mapped)

Question 2

1991

Answer 2

First US genome centers established

Question 3

1992

Answer 3

Second-generation human gnetic map developed

Rapid data release guidelines established by NIH and DOE

Question 4

1993

Answer 4

New five-year plan for the HGP in the US published

Sanger Centre founded (later renamed Wellcome Trust Sanger Institute)

Question 5

1994

Answer 5

HGP’s human genetic mapping goal is achieved

Question 6

1995

Answer 6

HGP’s human physical mapping goal achieved

First bacterial genome (H. influenzae) sequenced

US Equal Employment Opportunity Commission issues policy on genetic discrimination in the workplace

Question 7

1996

Answer 7

First human gene map established

Pilot projects for human genome sequencing begin in the US

First archael genome sequenced

Yeast geneome sequenced

HGP’s mouse genetic mapping goad achieved

Question 8

What is genetic mapping?

Answer 8

• based on the recombination frequencies using genetic markers
• 50% = unlinked
• <50% = linked and decreases between closer markers

Question 9

What is physical mapping?

Answer 9

-based on direct DNA analysis

Question 10

What is ordered cloning?

Answer 10

• genomic DNA is cut into smaller pieces (incomplete restriction digest) and all pieces are cloned into vectors
• before you actually start sequencning, you make a physical map of the genome
• this map contains many different markers (restriction cut sites) that you can use to try and order the fragments from your vectors
• sequence all fragments in the vectors, and try to arrange each fragment with the physical map you have created

Question 11

What markers can you use to align your fragments with the physical map?

Answer 11

Sequence tagged sites

Question 12

What is shotgun sequencing?

Answer 12

• genomic DNA is cut into numerous small overlapping fragments and is cloned in bacteria
• each fragment is sequenced
• overlap in sequence is used to order the clones
• entire genomic sequence is assembled with powerful computer programs

Question 13

What is coverage

Answer 13

The average number of times a given nucleotide is sequenced

Question 14

Repetitve sequences in the human genome

Answer 14

• 50% of the human genome is repetitive DNA

- may produce gaps during genome sequencing

Question 15

Gaps during genome sequencing may come from

Answer 15

• tandem repetitive DNA
• centromeres
• highly repetitive to where we do not know how to order them

Question 16

What is next-generation sequencing

Answer 16

• most produce relatively short reads
• very good for re-sequencing a genome
• not very good at sequencing repetitive DNA
• sequencing a genome where a reference is available

Question 17

Sequencing by synthesis

Answer 17

Template preparation
- shear DNA, add adaptors, PCR amplify
Sequencing 
- addition of nucleotides with fluorescent label and blocker 
- prevent the addition of more than one nucleotide 
Data analysis 
- put all of the pieces together 
- achieve sufficient coverage

Question 18

Types of third-generation sequencing

Answer 18

Single-molecule sequencing

Long read sequencing

Question 19

Single-molecule sequencing

Answer 19

• PCR is not needed prior to sequencing
• PCR can include bias into your library
• not all sequences in a gnome amplify efficiently
• information is lost with PCR
• epigenetic modifications

Question 20

Long read sequencing

Answer 20

• up to 2 million bp

- allows sequencing into repetitive regions of genomes