BMS2062 - W1: Genomic Variation and Disease

What is bioinformatics?

any application where computers are used to process, store or analyse biological data

• can be used to study gene, gene sequence, RNA

What is a genomics?

DNA bioinformatics

Genome: The complete set of genetic information in an organism that is housed in the chromosomes

What is transcriptomics?

RNA bioinformatics

Transcriptome: The sequence of each RNA transcript present in a cell or group of cells at a point in time.

What is proteomics?

Protein bioinformatics

Proteome: The sequence of each protein present in a cell or group of cells at a point in time.

What is Structural Bioinformatics?

Structural bioinformatics of proteins (primarily) and other macromolecules

Biological network analysis

What interactions are occurring inside a cell - understand the relationship between DNA, RNA, protein, and cellular function

Hutchinson-Gliford Progeria Syndrome (HGPS)

very rare disease caused by point mutations in the LMNA gene which encodes for lamin protein

How can bioinformatics help combat disease?

Identify where genetic variants associated with disease are located

• sequence an individual’s genome and compare to find variation

Detect which individuals are susceptible or have a high likelihood of being susceptible to a disease

• check if someone has a known variation in their genes based on their genome sequence

Establish how genetic variants actually cause disease

• compare healthy and disease tissue

• comparative transcriptomics or comparative proteomics

• can see consequences of lost/ damaged proteins

Create treatment and management practices for diseases

• can see effects of treatments on the transcriptomic/ proteomics profile of disease tissue

• precision medicine strategies (by seeing where the variation is, can designing drugs/ treatments to treat the disease)

• personalised medicine

requirements of transcription/ translation

• DNA needs to be accessible (epigenetic mechanisms)

• RNA polymerase binds to promotor region

• Separation of template strand and coding strand

• mRNA leaves nucleus, goes to ribosome (recognised via 5’ cap)

• tRNA recruit specific amino acids

• stop codon, mRNA disengages, translation stops

• protein fold into 3D shape (via chaperones, interactions with amino acids, etc)

Types of mutations (which affects how it is passed on)

Somatic mutations: are not passed onto the next generation, but is passed onto other cells originating from the altered cell (mitosis)

Hereditary mutations: are those passed from the parent to the child via the sperm & egg cells

• Present in all of the parents cells

de novo mutation: Mutations not found in the parents somatic cells but that originate in the child & usually present in all cells

• Mutations can arise in the sperm or egg cells or after fertilisation

• Mosaicism possible where some cells have mutation & some don’t

Non-hereditary mutations: Environmental & spontaneous mutations

• e.g. cigarettes, UV, DNA replication errors

Mutation in how many genes required for proto-oncogenes and tumour suppressor genes to cause cancer?

Single proto-oncogene – mutations cause gain of function – loss of cell cycle control = cancer

Two homologous tumour suppressor genes – loss of cell cycle control = cancer

What can mutations in cis and trans regulatory regions cause?

• enhance gene expression

• reduce gene expression

• have no effect

Can change the amount of protein produce which can cause disease

What can mutations in the untranslated regions (Utrs) cause?

mutations in 5’ UTRs can alter interactions with: (causing these factors to bind more strongly/ weakly)

• silences

• enhancers

• transcription factors

• microRNAs

• can also alter stability of mRNAs produced

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Mutations in 3’ UTRs can alter interactions with microRNAs (increase/ decrease affinity for microRNAs)

What can mutations in the coding regions cause?

Point mutations:

• silent (no change in amino acid)

• nonsense (stop codon)

• missense (change in amino acid)

Frameshift mutations:

• insertions

• deletions

(if nucleotides are inserted/ deleted in groups of 3, then it will not result in a frameshift mutation)

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Can cause protein to be:

• non-functional

• partially functional

• gain a new/ enhanced function

• function normally

What is a neutral mutation?

A mutation that has little or no effect on an organism’s reproductive fitness

• does not alter a protein’s folding, function or stability

Most likely to be a silent mutation, conservative missense mutation, other mutations that don’t alter folding/ function, mutations in 5’ or 3’ UTRs that do not affect amount of protein produced

• can identify a neutral mutation if no individual with the mutation show evidence of disease due to that mutation

What are advantageous mutations?

a mutation that increases the organism’s reproductive fitness

What is a pathogenic mutation?

A mutation where sufficient evidence had been collected to demonstrate the mutation is capable of causing disease

High penetrance = high likelihood of causing disease

Low penetrance = not all people develop the disease/ milder symptoms

• in general, higher degree of protein dysfunction/ folding = higher pentrance

• pathogenic mutation can be masked (recessive vs dominant)

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Which types of mutations can be pathogenic?

• frameshift

• nonsense

• missense

• in the UTRs causing upregulation/ downregulation

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How to determine which mutations are pathogenic?

If a mutation can be correlated with a certain disease (increase risk for a disease)

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Example:

Cystic Fibrosis: deletion of F508 in CTFR gene → CTFR protein become trapped in closed state → chloride cannot pass

In the HEXA gene, the first stop codon in the exon coding sequence occurs at 1588. A mutation 1528 C→T can occur, resulting in CGA → TGA (stop codon).

How many amino acids are lost?

Native: 1587/3 = 529 amino acids

Mutant = 1527/3 = 509 amino acids

Amino acids lost = 20

Sangar Sequencing

• Better for looking at individual or multiple genes rather than the whole genome

• high accuracy (99.99%). The gold standard of DNA sequencing

Steps:

Harvest DNA of interest (usually one or some genes) → create DNA fragments and incorporate chain terminator sequences → use machine to determine which of the 4 nucleotides is positioned at the chain terminator nucleotide for each DNA fragment

Next generation sequencing

• Can be used to look at entire genome or individual/ multiple genes

• faster

• cheaper

• can reveal low frequency DNA variants (mutations in some of the cells but not all of them)

Steps:

Extract genomic DNA → fragment DNA → create many copies of fragmented DNA containing fluorescent nucleotides that can be “read” by sequencing machine → Alignment of sequence reads to create a complete genome sequence

• There are more steps, check W1 lecture 2 last video

what is De novo sequencing?

genome sequence determined for the first time (without a reference sequence)

• time consuming