Genomics

Question 1

Before we had physical sequence maps, we had…

Answer 1

Genetic/trait maps.

Question 2

What does 1 centimorgan correlate to?

Answer 2

1% chance of recombination.

Question 3

Nowadays, do we use real or relative distances between genes?

Answer 3

Real, physical distances.

Question 4

What genome fragmentation approach creates a random library?

Answer 4

Shotgun approach.

Question 5

What genome fragmentation approach is less common and more methodical?

Answer 5

Top-down approach.

Question 6

What comes first, scaffolds or contigs?

Answer 6

Contigs.

Question 7

For the Human Genome Project, how were large regions cloned?

Answer 7

Bacterial artificial chromosome (BAC) libraries.

Question 8

Unique 200-500 bp reference sequences in the genome are known as…

Answer 8

Sequence-tagged sites.

Question 9

Did the Human Genome Project use first- or next-generation sequencing?

Answer 9

First-generation.

Question 10

Define genome coverage.

Answer 10

How many times any given base is sequenced.

Question 11

What are two factors that lead to gaps in the genome?

Answer 11

1. The random nature of shotgun approaches.
2. Repeat sequences.

Question 12

Third-generation sequencing is also known as…

Answer 12

Long-read DNA sequencing.

Question 13

Which generation required cloning and PCR of target DNA?

Answer 13

First-generation.

Question 14

Which generation reads the sequence of one molecule in real-time?

Answer 14

Third-generation.

Question 15

Which generation does not require amplification?

Answer 15

Third-generation.

Question 16

Which generation requires the generation of fragment ladders?

Answer 16

First-generation.

Question 17

Which generation reads multiple templates in parallel, in real time?

Answer 17

Second-generation.

Question 18

What is an example of a second-generation technology?

Answer 18

Illumina.

Question 19

What is an example of a third-generation technology, other than Nanopore?

Answer 19

PacBio SMRT.

Question 20

What technology would be useful for error correction (i.e. short reads, high accuracy)?

Answer 20

Illumina.

Question 21

What generation tech would be used for the core assembly of the genome?

Answer 21

Third-generation.

Question 22

Forward genetics starts with a gene to establish phenotype. True or false?

Answer 22

False.

Question 23

If we start with a phenotype, and map it to a chromosomal region, is this forward or backwards genetics?

Answer 23

Forward genetics.

Question 24

What are expressed sequence tags (ESTs)?

Answer 24

Sequenced ends of cDNA that define the boundaries of a transcript.

Question 25

Define open reading frame.

Answer 25

DNA sequence of a gene minus stop codon.

Question 26

What method identifies DNA-binding sites?

Answer 26

ChIP-Seq.

Question 27

What is bigger, minisatellites or microsatellites?

Answer 27

Minisatellites (10-50 nt).

Question 28

What two chromosomal regions may we find repeats more commonly?

Answer 28

1. Centromere.
2. Telomere.

Question 29

Studying the genetic material of a community of organisms is:

Answer 29

Metagenomics.

Question 30

Does comparative genomics study individual or community genomes?

Answer 30

Individual.

Question 31

Are conserved regions functionally important?

Answer 31

Yes.

Question 32

What defines an ultraconserved element?

Answer 32

200+ nucleotides of perfect conservation.

Question 33

If mouse and human genes have synteny, this means…

Answer 33

The same genes exist in the same chromosomal order.

Question 34

What are two benefits of exome sequencing?

Answer 34

1. Cheaper than whole genome.
2. Easier to annotate (more functional proteins).

Question 35

What did the ExAC study look at?

Answer 35

Variation between ~60,000 exomes.

Question 36

In the ExAC study, what percentage of SNPs were novel: 54% or 72%?

Answer 36

72%

Question 37

In the ExAC study, why were some ‘disease’ alleles reclassified?

Answer 37

They were too common compared to disease frequency.

Question 38

What are two advantages of long-read sequencing technologies?

Answer 38

1. Can sequence large repeats.
2. Good for de novo sequencing.