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The Dynamic Genome > The Genome's Content > Flashcards

The Genome's Content Flashcards

1
Q

Name the four types of chromosome map from low to high resolution

A

Karyotypic
Linkage
Physical
Sequence

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2
Q

What is the scale of Linkage maps?

A

cM

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3
Q

What is another name given to “linkage maps” and how are they derived?

A

“genetic map”
via monitoring recombination frequencies between markers

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4
Q

What is the scale of physical chromosome maps?

A

bp or kp

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5
Q

How are karyotypic maps derived?

A

From microscopic observation of chromosomal spreads

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6
Q

What is the main end goal of all sequence projects?

A

To sequences all the bases along the chromosome in a sequence map

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7
Q

What is 1% recombination frequency equivalent to?

A

1cM

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8
Q

Why do we need lower resolution maps if higher resolution maps are the main end goal?

A

SOmetimes lower resolution maps are needed to generate the higher resolution maps

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9
Q

What is exome sequencing? Does this type of sequence follow the main goal seen in sequencing today?

A

Sequencing just coding DNA
No, the goal is to sequence entire genomes

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10
Q

Why were the first genomes sequenced from relatively simple model organisms? Name 3 of these model organisms

A

Relatively small genome size and genetic tractability ( easy to control)
E.coli, S.cerivisiae, C.elegans

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11
Q

When was the Human Genome Project initiated and when was it completed?

A

1990
2003

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12
Q

What era of genomic are we currently living in? What types of genomics has this led to?

A

the ‘post-genomics’ era
Large scale approaches which analyse large data sets to investigate gene function (functional genomics) and genome evolution/structure (comparative genomics)

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13
Q

What is forward genetics?

A

Phenotype to genotype
Identifying the gene mutations that are the cause of a specified phenotype

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14
Q

What is reverse genetics?

A

Genotype to Phenotype
Identifying the phenotype caused by a specific mutation

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15
Q

What is functional genomics?

A

The analysis of a gene’s function (this includes the protein’s function that is formed form the protein)

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16
Q

What is Comparative genomics?

A

Comparison of genome sequences and organisation between different organisms and how similarities/differences can show us their evolutionary relationship

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17
Q

WHat was the name of the privately funded genome sequence project and who established it?

A

Celera genomics
Craig Venter and Perkin Elma

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18
Q

What was Celera Genomics’ aim?

A

To sequence genomes quickly, control access of genes and patent them

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19
Q

What is the name of the genome sequencing method used by Celera genomics?

A

Whole genome shotgun

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20
Q

What is the name of the genome sequencing method used by the publicly funded project?

A

Hierarchical shotgun

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21
Q

What was the difference in cost of the public vs celera genome sequencing projects?

A

public = $3 billion
Celera = $300 billion

22
Q

When did the publicly funded genome sequencing project announce its completition and when was it published in Nature?

A

2003 announced
2004 published (Nature)

23
Q

What is another name given to Sanger sequencing?

A

(conventional) dideoxy DNA sequencing

24
Q

Why is Sanger sequencing impractical for large projec that require the sequencing of large or multiple genomes?

A

It has a low throughput (only sequence a small number of bases at once) which therefore makes it expensive and impractical for large projects

25
Q

What does NGS stand for?

A

Next Generation Sequencing

26
Q

What is the benefit of using Next Generation Sequencing over Sanger sequencing?

A

NGS = high throughput low cost (by increasing speed to reduce cost)
Sanger = low throughput high cost

27
Q

How does Next Generation Sequencing (NGS) technologies increase speed and reduce costs?

A

Undergoes “parallel sequencing” of millions of different fragments of DNA at the same time

28
Q

What is Moore’s Law?

A

A prediction in historical trend that the number of transistors on a microchip doubles every two years (offering performance benefits over time) even though the cost of computers is halved

29
Q

What is the difference seen when comparing Moore’s law with the change in cost per raw Megabase of DNA Sequence over time?

A

The decrease in cost of DNA sequencing is much faster than Moore’s law would predict

30
Q

What is the importance of comparing Moore’s law to the change in cost per raw Megabase of DNA sequencing over time?

A

Cost of DNA sequencing is falling at an even faster rater than Moore’s law which highlights the rate of improvement in DNA sequencing technology

31
Q

What was the name of the company that unveiled the first Next Generation Sequencing machine and in what year?

A

454 Life Sciences
in 2005

32
Q

What is the name of the DNA sequencing method used by the first NGS machine by 454 Life Sciences?

A

‘454’ pyrosequencing

33
Q

What molecule released upon nucleotide incorporation by DNA polymerase, is used in pyrosequencing?

A

Pyrophosphate (PPi)

34
Q

How can pyrophosphate (released upon nucleotide incorporation by DNA polymerase) be utlised in pyrosequencing?

A

PPi is used as a fuel for a downstream set of reactions that ultimately produce light (by the action of luciferase of luciferin)

35
Q

What are the 3 overall stages involved in the process of ‘454’ pyrosequencing?

A

library preparation
emulsion PCR
pyrosequencing

36
Q

Roughly how many wells are there is pyrosequencing and how many beads are there per well?

A

1.6 million wells
1 bead per well

37
Q

What’s added to pyrosequencing wells before dNTPs are added?

A

smaller enzyme beads
sequencing primer
DNA polymerase
the two substrates APS and Luciferin

38
Q

What is important about how dNTPs are added to pyrosequencing wells?

A

they are added sequentially and in repeat cycles

39
Q

Why is it important that dNTPs are added sequentially and in repeat cycles during pyrosequencing?

A

incorporation of a nucleotide results in light emission and the intensity is proportionally greater if there are 2 or more consecutive bases of the same type

40
Q

What is a ‘homopolymer error’?

A

An error in the stated number of bases when a single nucleotide occurs more than once in a sequence (i.e because the sequence contains homopolymeric regions)

41
Q

What type of error is pyrosequencing prone to and why is this?

A

Prone to homopolymer error
because it is difficult to measure the proportional increase in light intensity when there are 2 or more consecutive bases of the same type in the sequence

42
Q

What is the name of the sequencing technology developed by Cambridge and was launched commercially in 2006 (it now has about a 70% market share)?

A

Illumina sequencing

43
Q

Illumina sequencing is similar in principle to which other type of DNA sequencing method?

A

Sanger dideoxy sequencing

44
Q

What is the key difference between Illumina and Sanger sequencing methods?

A

Illumina has reversible terminator sequencing which means the terminator can be removed

45
Q

Name a type of third generation sequencing technology

A

PacBio single molecule rear-time (SMRT)

46
Q

What process required in next generation sequencing technology does third generation sequencing technology bypass?

A

bypasses the need for DNA amplification by PCR

47
Q

What is the desired advantage of using third generation sequencing technologies over other sequencing methods?

A

Designed to achieve longer read lengths from single molecules of DNA

48
Q

Third generation sequencing allows for longer read lengths, what are the two key implications of this (compared to low read sequencing methods)?

A

Gets around problems with shorter reads such as assembly of repetitive DNA regions
and helps the analysis of a genome from low yield sources (e.g. if you wanted to genotype a single cell)

49
Q

Name 3 databases that are publicly available to share and store information on genomes/genes.

A

National Centre for Biotechnology Information (NCBI)
European Bioinformatics Institute (EBI)
Universal Protein Resource (Uniprot)

50
Q

Give an example of how it can be useful to sequence genes and have this information publicly available?

A

finding conserved genes in multiple organisms to provide clues on function

51
Q

Describe an innovative application on the use of genome sequencing technologies.

A

Comparison of multiple genomes from different biopsies within a tumour to help identify shared mutations that are initial ‘driver’ mutations that could hopefully one day create personalised cancer treatment

The Dynamic Genome (2 decks)

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