Module 3: Human Molecular Genetics Flashcards
Why was the human genome sequenced?
Identify all human genes and their roles, analyse genetic variation between humans, sequence genomes of several model organisms, develop new sequencing techniques and computational analyses, share genome information with scientists and the general public as fast as possible
What does the human genome consist of
22 autosomes, 2 sex chromosomes (6 billion base pairs, <20000 genes), single circular mitochondrial DNA (16,569 base pairs, 37 genes)
What were the key findings of the human genome?
There are fewer genes than expected (<20000), less than 2% of our genome codes for proteins, the genome is dynamic, we still don’t know what many protein coding genes do, most human genes are related to those of other animals, humans are 99.9% similar at a sequence level
How many genes does the human genome have
<20000
What percentage of the genome is exons
<2%
What percentage of the genome is introns
20%
What percentage of the genome has an unknown function
~20%
SNPs
Single nucleotide polymorphisms: sites in the DNA that commonly vary within populations
How common are SNPs
Around 1 in 300 nucleotides
Where do SNPs come from
Mostly from your parents
Why sequence a genome?
Find out who you’re related to, where some of your ancestors come from, disease risk/association, hair loss risk, muscle type, drug response, crime solving
Causative vs linked SNPs
In vs not in gene
Non-coding vs coding SNP
Non coding changes amount of protein produced, coding may change amino acid sequence
What makes it a SNP not a mutation
If present in more than 1% of the population
STRs
Short tandem repeats: repeats of 2-5 nucleotides found in specific regions of the genome. Inherit a gene from each parents, may be different lengths. E.g could be 3,8 at STR1
InDels
(e.g cystic fibrosis)
Small insertions or deletions, can cause frameshift if not a multiple of 3
What is the second most common variant type in the human genome
InDels
CNVs
(e.g Huntington’s, trisomy 21)
Copy number variations: chunks of DNA >500bp that are present at different amounts or copy numbers relative to a reference genome
How many CNVs do humans have
10000
Many genes found in CNV are associated with ________
Sensory perception and immunity
What are human genomics likely to be used for in the future
Further research into evolution and descent, complex polygenic and rare diseases, drugs and personalised medication
What ethnicity genomes vary the most
African as they have had the most time to evolve
What is comparative genomics
Comparing genomes to examine what is conserved and what is different
Why is it hard to sequence ancient DNA
DNA degrades and is masked by more modern DNA. DNA bases are also modified as they degrade, sometimes changing the sequence
What were the most outstanding findings from sequencing neanderthal genomes
Some of us (Asian and Europeans) carry neanderthal DNA (~2-4%). Africans show no sign of these alleles
Where is Denisovan variation seen in modern humans
4-6% of the genomes of present day Melanesians
How are sequenced genomes compared
Alignment
Mutation definition
Permanent change to the base sequence of a gene
The outcome of a mutation can depend on
Environmental effects (e.g diet, exposure to toxins), other genes (genetic background)
How are mutations classified
Dominant vs recessive and loss vs gain of function
What is a dominant mutation
Causes a phenotype when heterozygous
What is a recessive mutation
Causes a phenotype only when homozygous
A loss of function mutation is often
Recessive, as a normal copy exists on the other chromosome which can replace the lost function
A gain of function mutation is often
Dominant because having an allele that works too well or does something novel will not be replaced by the normal copy of the gene.
Give an example of an autosomal recessive disease
Cystic fibrosis
Give an example of an autosomal dominant disease
Huntington’s
Give an example of an X-linked recessive disease
Haemophilia A and B
Inheritance patterns step 1
Are only males affected and are all sons of fathers affected (Y linked)
Inheritance patterns step 2
Are there any cases where an affected child does not have at least one affected parent (recessive)
If recessive, inheritance patterns step 3
Are all sons of an affected mother affected and are more males than females affected (x-linked vs autosomal)
If dominant, Inheritance patterns step 3
Are all daughters of an affected father affected (x-linked vs autosomal)
How to find a disease causing gene using sequencing
Map to human reference, identify novel variants and whether they’re likely to be harmful, then validate and test
Examples of polygenic disorders
Obesity, diabetes, rheumatoid arthritis, gout, bipolar disorder
How to find genes contributing to polygenic diseases
Identify variations from human reference, identify variations shared in cases not controls, validate and test
Most genetic disorders are probabilistic not deterministic, meaning
Having a disease related genetic variation doesn’t mean you’ll get the disease
How do we get information about the function of a gene from its phenotype
By studying organisms that are naturally mutant for a particular gene we can work out what that gene might do (where no natural mutants exist we make our own)
Variation is common but phenotype causing mutations are
Rare
What is functional molecular genetics
Increase rate of mutation, select for phenotype of interest, take gene you’re interested in, copy and insert into another organism, deliberately break particular gene you’re interested in to see what happens
What are model organisms (e.g mouse, zebra fish, drosophila)
Ones that can be easily raised in a controlled environment and are easy to manipulate genetically
What is transgenesis
Engineering a multicellular organism by adding in foreign DNA (e.g regulatory sequence to turn on production of a protein in an organism)
What is CRISPR/Cas9 used for
Damage or modify gene interested in, examine organism or offspring and work out what gene normally does, i.e targeted mutation
What is needed for CRISPR/Cas9
Short guide RNA to bind to gene of interest, Cas9 protein to cut DNA (double stranded cut at site)
How does CRISPR/Cas9 result in mutation
In the absence of a template DNA repair enzymes try to repair cut, often resulting in errors
What type of mutations usually occur at CRISPR/Cas9 cut site
Small indels
How can CRISPR/Cas9 be used in gene editing
By providing a repair template for the DNA to be fixed based off
Can we fix genetic disease
Yes but only if we know what causes it and have a way to correct the defect
How does gene therapy work with cystic fibrosis (CFTR gene)
Plasmid containing normal gene in liposome fuses into cell, enters nucleus, incorporated into DNA, functional protein for chloride ion channel made
How can germline mutations be fixed if mutation is in mitochondrial DNA (called 3 parent babies)
Remove nucleus of fertilised egg, transplant into donor egg with healthy mitochondrial DNA (and destroyed nucleus)
What is pre-implantation genetic diagnosis
Parents with identified risk create IVF babies, embryos screened for genetic diseases before implantation
What are the 5 stages of embryonic development
8 cell stage, cell polarisation, compaction, inner apolar cells cut off, blastocyst
What is the outer layer of the blastocyst called (formerly polar)
Trophectoderm
What type of cells does an embryo begin as
Totipotent
What type of cells are embryonic stem cells
Pluripotent (give rise to anything except trophectoderm)
Once specific genes have been turned on and off, the cell type is:
Determined
Once the cell has become a certain type it is said to be:
Terminally differentiated
Approximately how many types of cells are there in our body
200
What are iPS cells
Induced pluripotent stem cells, made by reprogramming adult skin cells
Adult tissue stem cells are
Multipotent (give rise to a few types of cells including stem cells: regeneration)
Umbilical cord stem cells are
Multipotent as they are immature blood stem cells
Stem cells are important for what types of tissue
Blood and skin which need constant renewing
Blood stem cells are also called
Hematopoietic stem cells
What is gene therapy
A way to correct single gene disorders
How can viruses be used in gene therapy
Insert RNA version of normal allele into retrovirus or other viral vector, let virus infect bone marrow cells tht have been cultured, viral DNA carrying normal allele inserts into chromosome, cells reinjected
What is regenerative medicine
The idea that pluripotent stem cells can be used to repair or replace damaged organs or tissues by being encouraged to differentiate into needed cell type, then transplanted into patients.
Example of IPSC transplants
Corneal transplants
What kind of variation is captured by commercial genetic sequencing companies?
SNPs
