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Genomics > Introduction to genomics > Flashcards

Introduction to genomics Flashcards

1
Q

What is genomics?

A

Study of genomes, representing a new era in biology and medicine

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2
Q

How old is genomics?

A

15 years old

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3
Q

What is involved in genomics?

A

Sequencing, mapping, comparison and function of genomes

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4
Q

What is genetics?

A

Looks at single genes

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5
Q

What is genomics?

A

Explores all the genes in an entire system

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6
Q

What is a genome?

A

Amount of DNA in a single cell of an organism

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7
Q

How many genes in the human genome?

A

23 000

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8
Q

How many bases in the human genome?

A

3.2 billion bases

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9
Q

How long is the human genome?

A

6 ft

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10
Q

Describe the hierarchy of the information obtained by the genome

A

Gene -> protein -> phenotype

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11
Q

What information will the sequence information in the genome show?

A

The position of every gene along a chromosome

The regulatory regions that flank each gene

The coding sequence that determine the protein produced by each gene

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12
Q

How many chromosomes in a human?

A

23 pairs

22 are autosomes
1 pair of sex chromosomes

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13
Q

What are the 4 levels of gene expression?

A

Genome

Transcriptome

Proteome

Proteins

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14
Q

Where are introns?

A

Intragenic regions

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15
Q

What are introns?

A

Non-coding pieces of precursor mRNA

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16
Q

What are exons?

A

Coding sections of the gene that are retained in the processed mRNA

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17
Q

How is the distribution of genes along a chromosome?

A

Not even

Some chromosomes are gene poor

Some are dense

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18
Q

What are desert sequences?

A

Regions of chromosomes of longer than 500kb with no genes

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19
Q

What percentage of DNA is repetitive?

A

50%

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20
Q

What is a challenge with repeptitive DNA?

A

They overlap, making it difficult to determine the number of repeats present

Normally, the sequence of repetitive DNA is determined by the non-repetitive DNA before and after these sections

This is sometimes not possible, since we can only sequence 300 bases at a time

If the repetitive sequence is longer than 300 bases, figuring out where this section starts and ends is difficult

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21
Q

Which technologies will help determine the length of repetitive DNA?

A

Nanopore technology

Third generation sequencing

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22
Q

What is the effect of splice variants?

A

Increase the gene number by causing variants in the gene

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23
Q

What are the two types of genomes in the body?

A

Germ-line = born with

Somatic = genome of disease (cancer)

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24
Q

Percentage of DNA that is non-coding

A

98%

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25
Q

How similar are humans genetically?

A

99.9%

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26
Q

Chimp and human key similarities

A

Nucleotide = 98.77% similar

96% identical in terms of the genome

Average protein differs by 2 aa

27% of proteins are identical

Most differences appear to be neutral mutations

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27
Q

Chimp and human key differences

A

2.7% of the genome is inserted or deleted

35X10^6 large insertions or deletions

Various chromosomal rearrangements

Telomeres are specifically affected

585 genes evolving more rapidly, including transcription factors

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28
Q

Significance of the human genome project

A

Sequenced the entire genome

Managed to identify all the genes within the genome

Improve tools for data analysis

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29
Q

How long did the HGP take to complete?

A

13 years

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30
Q

What is the goal of the HAPMAP?

A

Identify SNPs in disease populations

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31
Q

What has the HAPMAP been used for?

A

Mapping ancestry

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32
Q

What is the goal of 1000 genomes project?

A

NHS organised project

Look for germline mutations for common diseases

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33
Q

What is the goal of the Cancer Genome Atlas project?

A

Analyses the genome, transcriptome, epigenome, proteome and clinical phenotype of cancers

Link these to information about the patient to identify disease-causing mechanisms of cancer

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34
Q

What is the goal of the 100 000 genome project?

A

Obtain genomic information from patients and family members with rare diseases and cancers to associate gene mutations with disease phenotype

35
Q

Ways to measure a genome

A

Microarray

Sanger

Next generation sequencing

Third generation sequencing

36
Q

How much DNA is required for microarrays?

A

Low DNA input

37
Q

What are the uses of microarrays?

A

Homozygosity mapping

Copy number variation identification

GWAS

Genome-wide linkage analysis

38
Q

What method of DNA sequencing did the HGP use?

A

Sanger sequencing

39
Q

How much data can Sanger sequence?

A

1 Kb

40
Q

Companies who have developed next generation sequencing technologies

A

Illumina

Roche

Pacbio

41
Q

How much information can next generation sequencing handle?

A

2400 GB

Read short sequences of 50-500 bases

<1000 dollars per human read

42
Q

Example of third generation sequencing

A

Nanopore

43
Q

What does it mean when a sequencing technology can carry out long reads?

A

Can push through the entire genome, as supposed to other techniques which require fragmentation

44
Q

What is a SNP?

A

Normal variation between individuals

Not necessarily disease-associated

45
Q

In what percentage of individuals are SNPs found?

A

More than 1%

46
Q

What is the inheritance of SNPs?

A

Germline and inherited, so present in all the cells of the body

Unless the SNP is present in the somatic genome of a cancer or in gametes

47
Q

On average, how often do SNPs occur?

A

Once every 300 nucleotides

48
Q

How many SNPs are there in the human genome?

A

Around 10 million

49
Q

How many personal SNPs are found on average?

A

400 000

50
Q

What is the importance of SNPs?

A

Most have no effect on health or development

But can be associated with the risk of developing a disease

51
Q

What have mtDNA SNPs been used for?

A

Tracking migration

All modern humans descended from the mitochondrial Eve

The more genetically different an individual is from this, the early the population migrated from the original source of Eve

52
Q

Uses of SNPs

A

Predict an individual’s response to drugs

Susceptibility to environmental factors

Risk of developing a disease

Track the inheritance of disease genes withing families

Association with complex disease such as heart disease, diabetes and cancer

Track human migration

Identify ethnicities

53
Q

What is a MAF?

A

Within a population, SNPs are scored with minor allele frequency

This refers to the frequency at which the second (most common = not be a SNP, the original sequence) most allele occurs in a give population

Third most common = lower than 1% of the population

54
Q

Genetic changes that give rise to SNPs

A

Substitutions

Deletions

Insertions

55
Q

Where can SNPs be found?

A

Coding and non-coding regions of the genome

56
Q

What does GWAS do?

A

Looks at the associations of these SNPs with disease

Manhattan plots

The higher the peak the more significantly the SNP is implicated with disease

57
Q

What are tag SNPs?

A

Scientists analysed 1000s of individuals and found that the presence of a particular SNP at a particular locus can determine the SNPs further down the genome

So if a patient presents with a SNP at position 5, studies show that they are likely to present with a C SNP at position 305

58
Q

Rationale behind tag SNPs

A

Linkage disequilibrium

Some loci are said to be in linkage disequilibrium, because SNPs commonly happen together

Therefore, they are not independent events

59
Q

What is a haplotype?

A

Particular pattern of sequential SNPs found on a single chromosome

Different haplotypes = different SNP combinations

60
Q

What is the most common cause of linkage disequilibrium?

A

Physical linkage

61
Q

What is the main way we differentiate between SNPs and mutations?

A

Difficult to differentiate between them since they result due to similar processes

Mostly we distinguish between them through their prevalence

SNP = >1%, mutation = <1%

Mutations, also have a high penetrance

62
Q

Common sources of mutations

A

Errors during DNA replication

Damage to the DNA

63
Q

Types of mutations

A

Synonymouds

Non-synonymous

CNV

Translocations

Stop-gain

Activating

SNVs

64
Q

What are synonymous mutations?

A

Do not alter the amino acid sequences

Silent mutations

65
Q

What are non-synonymous mutations?

A

Alter the amino acid sequence of a protein

66
Q

What are CNVs?

A

Gain or loss of genes/part of genes

The number of copies for a particular gene varies between individuals

67
Q

What are translocations?

A

Segment of a genes from one chromosome becomes heritably linked to a gene from another chromosome

Example = phiadelphia chromosome

68
Q

What is a stop-gain mutation?

A

Adds an innapropriate stop codon

69
Q

What is an activating mutation?

A

Adds a transcription factor binding site in the promoter

70
Q

What are SNVs?

A

Events less than 1% that are associated with disease

71
Q

What determines the consequence of a mutation?

A

The gene it affects

72
Q

What happens if tumour suppressor genes become mutated?

A

Cells grow uncontrollably and may form a mass

p53

73
Q

What happens if an oncogene becomes mutated?

A

Increase in cell proliferation

EGFR, KRAS, PIK3CA

74
Q

What are driver genes?

A

A gene whose mutations increase net cell growth

75
Q

What can gene expression profiles provide us?

A

Can plot the gene profile of an individual, as well as a cancer genome, and look at the differences in gene expression

76
Q

What can disease association studies provide us with?

A

Personalised therapies

Early diagnosis

Targeted intervention

77
Q

What are challenges of gene expression profiles for disease targeting?

A

Low penetrance means that mutation is there, but does not lead to disease. Targetting these cells may be more harmful than good

Genomic ethics - should researchers inform patients if they find genes correlated with deadly diseases?

78
Q

Are CNVs mostly benign or disease-causing?

A

Benign

79
Q

How many CNVs are shared across a population?

A

89%

80
Q

What is CCL3L1?

A

Increase in copy number confers increased resistance to HIV infection

81
Q

Are SNVs mostly benign or disease-causing?

A

SNVs change gene products and are specific for diseases/individuals

82
Q

Where do SNVs originate?

A

In somatic tissues

83
Q

What does personal genomics allow you to do?

A

Genetically test for rare diseases

So you can think about intervention, preventative treatment, lifestyle choices and reproductive decisions

84
Q

Potential drawbacks of personal genomics

A

Potential for abuse

Ethical considerations

Cost

Regulations

Genomics (9 decks)

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