Exam 1 Homework and Quizzes

Question 1

The human genome project was launched in ____, produced the first draft assembly in _____, and was finished in _____

Answer 1

1990
2001
2003

Question 2

Abbreviations in order from smallest to largest

Answer 2

bp Kb Mb Gb Tb Pb

Question 3

approximately how many bases are in a typical diploid mammalian genome

Answer 3

6 million

Question 4

approximately how many bases are in a typical mammalian mitochondrial genome

Answer 4

16,000 bp

Question 5

Approximately what proportion of a mammalian genome codes for proteins

Answer 5

2%

Question 6

Approximately 50% of a mammalian genome is comprised of what type of DNA element

Answer 6

repetitive DNA

Question 7

The polymerase chain reaction has four key ‘ingredients’ necessary to replicate DNA in a tube

Answer 7

DNA template
DNA polymerase
Nucleotides
Primers

Question 8

What are the three stages of the polymerase chain reaction

Answer 8

denaturing
annealing
extending

Question 9

Sanger sequencing differs from PCR in one key element, what is that key element

Answer 9

sanger uses dideoxynucleotides along with the deoxynucleotides

Question 10

Illumina sequencing requires that the library contain fragments in a certain size range. what size range are typical of whole genome sequencing libraries

Answer 10

300-350 bp

Question 11

PacBio and Oxford Nanopore sequencing are very different but share one characteristic in common, and this characteristic differentiates them from Illumina technology. What is that characteristic?

Answer 11

they need a long DNA template strand to start sequencing

Question 12

Five domains of genome research

Answer 12

• understanding the structure of genomes
  -understanding the biology of genomes
  -understanding the biology of disease
  -advancing the science of medicine
  -improving the effectiveness of health care

Question 13

What is the largest current bottleneck in genomics

Answer 13

analyzing the stream of data from technological advances

Question 14

In the Illumina process, the nucleotides are very specialized. they have two key attributes, what are they

Answer 14

flour specific for the identity of the nucleotides
3’ hydroxyl group is blocked with a chemical blocker so next step can be accurately detected

Question 15

____ of reads to the reference sequence is the first step to identify variation of all types

Answer 15

alignment

Question 16

Long read sequencers such as the PacBio instrument are a departure from short read sequencings such as Illumina. What is the first major requirement for these long read technologies that is different from short read technologies

Answer 16

high molecular weight genomic DNA
must be sufficient quality to allow for >30Kb shearing to produce PacBio continuous reads

Question 17

A typical workflow of whole exome sequencing analysis consists of the following steps

Answer 17

-raw data QC
-Pre-processing
-mapping
-post-alignment processing
-variant calling
-annotation
-prioritization

Question 18

standard preprocessing procedure includes

Answer 18

-3’ end adapter removal
-trimming of low quality bases at the ends of the reads

Question 19

many different tools have been developed for short reads mapping. In general, they use two algorithms for aligning sequences

Answer 19

-Burrows-Wheeler transformation- compression technique
-smith-waterman- dynamic programming algorithm

Question 20

Of the sequence aligners they evaluated which two were the fastes

Answer 20

Bowtie 2
BWA

Question 21

After mapping reads to the reference genome, a three-step post-alignment processing procedure is recommended to minimize the artifacts that may affect the quality of downstream variant calling. It consists of

Answer 21

-read duplicate removal
-indel realignment
-base quality score recalibration (BQSR)

Question 22

Variant analysis consists of

Answer 22

genotyping
variant calling
annotation
prioritization