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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
How similar are humans genetically?
99.9%
26
Chimp and human key similarities
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
27
Chimp and human key differences
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
28
Significance of the human genome project
Sequenced the entire genome Managed to identify all the genes within the genome Improve tools for data analysis
29
How long did the HGP take to complete?
13 years
30
What is the goal of the HAPMAP?
Identify SNPs in disease populations
31
What has the HAPMAP been used for?
Mapping ancestry
32
What is the goal of 1000 genomes project?
NHS organised project Look for germline mutations for common diseases
33
What is the goal of the Cancer Genome Atlas project?
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
34
What is the goal of the 100 000 genome project?
Obtain genomic information from patients and family members with rare diseases and cancers to associate gene mutations with disease phenotype
35
Ways to measure a genome
Microarray Sanger Next generation sequencing Third generation sequencing
36
How much DNA is required for microarrays?
Low DNA input
37
What are the uses of microarrays?
Homozygosity mapping Copy number variation identification GWAS Genome-wide linkage analysis
38
What method of DNA sequencing did the HGP use?
Sanger sequencing
39
How much data can Sanger sequence?
1 Kb
40
Companies who have developed next generation sequencing technologies
Illumina Roche Pacbio
41
How much information can next generation sequencing handle?
2400 GB Read short sequences of 50-500 bases <1000 dollars per human read
42
Example of third generation sequencing
Nanopore
43
What does it mean when a sequencing technology can carry out long reads?
Can push through the entire genome, as supposed to other techniques which require fragmentation
44
What is a SNP?
Normal variation between individuals Not necessarily disease-associated
45
In what percentage of individuals are SNPs found?
More than 1%
46
What is the inheritance of SNPs?
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
On average, how often do SNPs occur?
Once every 300 nucleotides
48
How many SNPs are there in the human genome?
Around 10 million
49
How many personal SNPs are found on average?
400 000
50
What is the importance of SNPs?
Most have no effect on health or development But can be associated with the risk of developing a disease
51
What have mtDNA SNPs been used for?
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
Uses of SNPs
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
What is a MAF?
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
Genetic changes that give rise to SNPs
Substitutions Deletions Insertions
55
Where can SNPs be found?
Coding and non-coding regions of the genome
56
What does GWAS do?
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
What are tag SNPs?
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
Rationale behind tag SNPs
Linkage disequilibrium Some loci are said to be in linkage disequilibrium, because SNPs commonly happen together Therefore, they are not independent events
59
What is a haplotype?
Particular pattern of sequential SNPs found on a single chromosome Different haplotypes = different SNP combinations
60
What is the most common cause of linkage disequilibrium?
Physical linkage
61
What is the main way we differentiate between SNPs and mutations?
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
Common sources of mutations
Errors during DNA replication Damage to the DNA
63
Types of mutations
Synonymouds Non-synonymous CNV Translocations Stop-gain Activating SNVs
64
What are synonymous mutations?
Do not alter the amino acid sequences Silent mutations
65
What are non-synonymous mutations?
Alter the amino acid sequence of a protein
66
What are CNVs?
Gain or loss of genes/part of genes The number of copies for a particular gene varies between individuals
67
What are translocations?
Segment of a genes from one chromosome becomes heritably linked to a gene from another chromosome Example = phiadelphia chromosome
68
What is a stop-gain mutation?
Adds an innapropriate stop codon
69
What is an activating mutation?
Adds a transcription factor binding site in the promoter
70
What are SNVs?
Events less than 1% that are associated with disease
71
What determines the consequence of a mutation?
The gene it affects
72
What happens if tumour suppressor genes become mutated?
Cells grow uncontrollably and may form a mass p53
73
What happens if an oncogene becomes mutated?
Increase in cell proliferation EGFR, KRAS, PIK3CA
74
What are driver genes?
A gene whose mutations increase net cell growth
75
What can gene expression profiles provide us?
Can plot the gene profile of an individual, as well as a cancer genome, and look at the differences in gene expression
76
What can disease association studies provide us with?
Personalised therapies Early diagnosis Targeted intervention
77
What are challenges of gene expression profiles for disease targeting?
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
Are CNVs mostly benign or disease-causing?
Benign
79
How many CNVs are shared across a population?
89%
80
What is CCL3L1?
Increase in copy number confers increased resistance to HIV infection
81
Are SNVs mostly benign or disease-causing?
SNVs change gene products and are specific for diseases/individuals
82
Where do SNVs originate?
In somatic tissues
83
What does personal genomics allow you to do?
Genetically test for rare diseases So you can think about intervention, preventative treatment, lifestyle choices and reproductive decisions
84
Potential drawbacks of personal genomics
Potential for abuse Ethical considerations Cost Regulations

Genomics (9 decks)

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