10.5 The era of whole-genome sequencing

Question 1

Strategy for high-throughput DNA sequencing:

Answer 1

1. Millions of fragments of single-stranded genomic DNA to which poly-A has been enzymatically added at the 3’ end are hybridized to oligo-dT molecules attached to the surface of a special microarray called a flowcell
   2.Using the genomic fragment as template and the oligo-dT as primer, DNA polymerase synthesizes new DNA containing nucleotides with coloured, base-specific fluorescent tags. These nucleotides are also blocked at their 3’ ends so that only one nucleotide can be added at a time. This chemical block is reversible
   3.After a high-resolution camera photographs the fluorescence, chemicals applied to the flowcell remove the tag and blocking group from just-added nucleotide
   4.Each subsequent cycle begins by infusing the flowcell with a new dose of tagged nucleotides and polymerase, and is followed by an iteration of step (c).

Question 2

What is the point of whole-genome sequencing?

Answer 2

The goal is to find directly a DNA alteration that is the disease allele
Sequencing the whole-exome (limited to expressed parts of the genome) is less expensive.

Question 3

A new technique that are making exome and genome sequencing fast and cheap _____________

Answer 3

high throughput sequencing

Question 4

High-throughput or massively parallel sequencing is like Sanger sequencing with a few modifications:

Answer 4

1.Individual DNA molecules are anchored in place
2.Each base is identified before the next one is added
3.Increased sensitivity eliminates need for cloning or PCR

Question 5

Why is it that genome sequencing reveals a sea of variation?

Answer 5

Because each individual differs at > 3 million locations from the RefSeq human genome

Question 6

What are the three ways in which we can tell which polymorphism causes disease?

Answer 6

1. Transmission pattern
2. Predicted effect on protein function
3. Clues from other genome sequences

Question 7

true or false: Common variants are poor disease candidates

Answer 7

true

Question 8

For SNP patterns in a rare dominant trait, what kind of polymorphism should be expected?

Answer 8

heterozygous

Question 9

What two types of individuals should be expected from SNP patterns in a rare recessive trait?

Answer 9

homozygous or transheterozygous