Week 3 Part 1 Flashcards
What is the definition of a genome?
All the genetic material in the chromosome of a particular organisms
DNA in all cellular life form, RNA in some viruses
Define Genomics
The study of genes and their function
What does the nuclear genome contain and divided into?
Contain - approx 3,200,000,000 nucleotides to form 24 chromosomes
Divided into 24 linear molecules
What is mitochondrial genome?
Circular double-stranded DNA molecule
Contain 16,569 nucleotides
What does the mitochondrial genome give rise to?
- 37 genes coding for 2 rRNAs (12S abs 16S)
- 22 tRNAs
- 13 polypeptides
It is a maternal origin
What is mitochondria?
Central role in cellular energy provision
Organelles Contain their own genome with modified genetic code
Not self supporting entities
Rely heavily for their function on imported nuclear gene products
Where is the mammalian mitochondrial genome transmitted?
Exclusively though the female germ line
What are mt-DNA encoded polypeptides?
All subunits of the enzymes complexes of the oxidative-phosphorylation system
What is a genomic biomarkers?
A measurable DNA and/or RNA characteristic that is an indicator of normal biological process, pathogenic process, and/or response to therapeutic or other intervention
What is the definition of genomic biomarkers used by?
- European Medicines Agency (EMA)
2. Food and Drug Administration (FDA)
What can a genomic biomarker be a measurement of?
- The expression of a gene
- The function of a gene
- The regulation of a gene
What can a genomic biomarker consist of?
One or more deoxyribonucleic acid (DNA)
And/or ribonuclease acid (RNA) characteristics
What do DNA characteristics include?
- Single nucleotide polymorphism (SNP)
- Variability of short sequence repeats
- Haplotypes
- DNA modifications e.g. methylation
- Deletion or insertion of a nucleotide
- Copy number variations
- Cytogenetic rearrangements e.g. translocations, duplications, deletions or inversions
What do RNA characteristics include?
- RNA sequences
- RNA expression levels
- RNA professing e.g. splicing and editing
- MicroRNA levels
What doesn’t the definition of a genomic biomarker include?
Measurement and characterisation of protein or low molecular weight metabolites
What do GWAS use?
Whole genome sequencing
What is whole genome sequencing?
The entire genome being broken up into pieces of 2000, 10,000 and 50,000 base pairs long
What does a huge percentage of the human genome consist of?
Repeated non-coding sequences dispersed throughout the genome
Include:
- LINES
- Minisatellites
Multiple copies of the same sequence that does not appear to have any valid function
Whole exome sequencing
32 million bases
Collect blood Extract and fragment DNA Capture exome DNA with probes Recover only exome DNA fragments Sequence on next generation platform
What is single nucleotide polymorphism?
- Altered single nucleotide (e.g. A,T,C,G) in the genome
- SNP are found in coding and predominantly in non-coding regions
- SNP occur with a very high frequency, hence most common form of genetic variation
- Identify whether a SNP occurs more often in people with a disease than controls
- SNP do not cause disease, but affect chance of developing disease, response to pathogen, drug etc
When do you get Synonymous (silent mutation) of SNP?
If SNP lead to same polypeptide sequence
When do you get non-synonymous (missense & nonsense mutation)
If SNP lead to different polypeptide sequence
Who suggested that ~50% of a persons risk of becoming an addict is due to genome?
Family studies including monozygotic twin, dizygotic twin, adopters and siblings
Who typically smokes more and thus have a greater risk for smoking-induced diseases?
Individuals with fast nicotine metabolism
What is dependent on the rate of nicotine metabolism?
The efficacy of smoking cessation pharmacotherapy
What was the objective of GWAS of a biomarker of nicotine metabolism?
Use nicotine metabolite ratio (NMR) in GWAS to identify novel genetic variants influencing nicotine metabolism
What was the Heritability estimates obtained for NMR using monozygotic and dizygotic twins of the Finn Twin cohort?
0.81
Individuals with fast nicotine metabolism
- Smoke more (finance and health implications)
- Have a greater risk of smoke-related disease
- Poor response to smoking cessation pharmacotherapy
What is a predominant metabolite of nicotine with half life of 15-20 hours?
Continine
Why do you use nicotine ratio?
To measure:
- Nicotine metabolism rate
- Total nicotine clearance
- CYP2A6 activity
What is the equation of NMR?
3-hydroxycotinine/ cotinine
How many smokers were identified from serum samples using liquid chromatography/ tandem mass spectrometry?
1518
What are some of the various demographic and hormonal factors that NMR is influenced by?
- Ethnicity
- Sex
- Hormone replacement therapy
- Use of oestrogen containing contraceptive pills
- Body mass index
- Alcohol consumption
- Cigarette consumption
What was the method for study for GWAS of a biomarker of Nicotine metabolism
- Written informed consent
- GWAS used to identify novel genetic variants influencing nicotine metabolism in whole blood DNA
- Compare data against 1000 Genome project data looking for SNP
- FinnTwin12 is a population-based longitudinal study of 5 consecutive birth cohort, examine genetic and environmental determinate of health-related behaviours
What was the results of GWAS of a biomarker in nicotine metabolism?
- At the region 19q13.2, 719 SNPs were identified within CYP2A6 gene
- Strongest association was for CYP2A6 in Intron 4
- At the region 19q13, SNPs were also identified within CYP2B6, CYP2A7 EGLN2 and NUMBL genes
What was the Nicotine Addiction (Discussion)
- Study aim was to identify novel genetic variants affecting nicotine metabolism
- Several members of cytochrome P450 gene family (CYP2A6, CYP2B6, CYP2A7, CYP2F1) involved
- Top SNP, rs56113850, was located in intron 4 of CYP2A6 accounts for 14-23%
- 2nd SNP, rs113388603, was located in 5.9kb upstream of CYP2A6 accounts for < 1% in NMR
What are the reasons for the SNP involvement in NMR does not account for 81% heritability based on the twins modelling?
- Lack of CYP2A6 coverage on duplications, translocations and rare variants
- High sequence Homology between between CYP2A6, CYP2A7 and CYP2A13 prohibit variant detection
- Analysis can not detect rare SNP that have low effect size
- Relatively small sample size
Genomic Mitochondrisl DNA biomarker?
- Mitochondria are currently believed to play important role in the neurodysfunction and neurodegeneration that underlie PD
- Mitochondrial dysfunction has been considered a common feature of PD