Genomics 1

What method was used to sequence DNA in the HGP?

Sanger sequencing

What were 2 of the major technical challenges the HGP faced?

• Used vertical acrylamide gels > these were very big and therefore difficult to pour

• A lack of genetic markers needed to label the genome - very few were available at the time

What was the general method they employed to carry out the HGP - prior to sequencing?

• First cut the genome into fragments - different sized fragments to ensure overlap so that it can be put back together

• Used genetic markers as there was concern about repeating regions

What is a genetic marker?

A genetic marker is a DNA sequence with a known physical location on a chromosome

How did the HGP discover more known markers?

• Using radiation by hybrid mapping of ESTs (expressed sequence tags)

• Radiation is used to fragment genome

• Clone fragments into rodent cells (hybridization) - Random human DNA fragments are inserted into rodent cells.

• Test for co-occurrence of ESTs - Each cell line is tested for which Expressed Sequence Tags (ESTs) are present together in the same fragment

• FREQUENCY OF CO-OCCURANCE = PROXIMITY

• This method allowed them to use expressed genes as known markers

Who came as a competitor to the HGP?

Craig Venter founded Celera in 1998 - proposing that sequencing could be accomplished much faster by whole genome shotgun sequencing

Main outcomes of HGP:

• The consortium model for tackling large projects

• A reference genome that allowed the identification of genetic variation in humans

• Technological changes have been truly revolutionary. Unleashing the power of genomics

what technology allowed the complete human genome to be published in 2022?

Long-read sequencing - Telomere-to-telomere assembly that is gapless for all chromosomes, except Y

How did Galton suggest that heredity could be studied statistically?

Developed correlation and regression to study resemblance of relatives

What was meant when Mendel described ‘particulate’ inheritance?

• Proposed that traits are passed down through discrete units (now known as genes).

• Law of Segregation (Each individual has two alleles per gene, which separate during gamete formation.)

• Law of Independent assortment (Genes for different traits are inherited independently (assuming no linkage))

When you have traits that don’t fit neatly into categories, what sort of variation do they show?

Continuous - for traits like: height, weight, or disease susceptibility

• these traits are influenced by multiple genes + environmental factors

• PARTICULATE INHERITANCE BUT CONTINUOUS VARIATION

What are mendelian traits called in modern terms?

Genes of major effect - especially when a single mutation (like a knockout or loss-of-function) causes a dramatic change.

What would be the result of blending inheritance?

Would cause variation to be slowly eroded

Non-genetic variation can be due to:

• Non-inherited epigenetic effects

• Phenotypic plasticity

• Genotype-by-environment interactions

What is it that causes a difference in trait value?

Allelic differences at a loci - most genetic variants (alleles) don’t cause a complete loss or gain of function but tend to produce gradual, quantitative differences in how a gene behaves.

How to work out the trait value for an individual?

Is the sum of the effects of the alleles at locus L affecting that trait > there is always deviation due to environmental effects

What is a quantitative trait?

They are polygenic - effected by many genes of small effect

What can a parent-offspring regression line tell us?

The slope provides an estimate of the proportion of variation that is heritable - additive genetic variance

What can narrow sense heritability actually tell us?

The degree to which you can predict offspring phenotype given parental phenotype

What does it mean if an allele is co-dominant/additive?

Where heterozygotes express characteristics of both inherited alleles rather than one masking the other

When each allele increases the trait value by the same amount > means they are co-dominant

Why don’t identical genotypes have identical phenotypes?

• Gene expression and development are imperfect

• Environmental heterogeneity adds noise

What does it mean that genetic variation is invisible?

• Even though individuals differ genetically, their phenotypes blend smoothly.

• There are no sharp jumps or distinct categories—just gradual differences.

• So unless you genotype individuals or use statistical models, the underlying genetic diversity isn’t obvious.

What can broad sense heritability tell us?

How much of trait variation can be attributed to genetic differences

Equations of broad and narrow sense heritability?

h² = VA/VP

H² = VG/VP

How can variation be genetic but non-heritable?

Genetic variation that relies on combinations of alleles may not be heritable if the combinations are not predictable

Why is resemblance of siblings greater than that of parent-offspring?

Siblings can share diploid genotype

What does additive variance assume?

the effect of a genotype is just the sum of the two individual alleles' effects.

What is dominance?

When the interaction between the two alleles at the same locus produces an effect that can't be predicted just by adding them up individually - The dominance effect therefore lives at the level of the diploid genotype pair, not the individual allele.

How can dominance contribute to the resemblance of siblings

because they often share a diploid genotype, not just alleles

What does the dominance effect measure?

This measures how much the heterozygote deviates from what you'd expect if effects were purely additive

What does the midpoint of homozygotes tell you?

If the heterozygote is exactly half way between the two homozygotes meaning it is completely additive - Any deviation from this midpoint means the two alleles are interacting: one is altering the other's effect

Which relatives are affected by dominance and additive effects?

• Additive effects are properties of individual alleles. When a parent reproduces, they pass on one allele at each locus to their offspring. This means any two relatives who share a common ancestor have a chance of carrying the same allele inherited from that ancestor

• Dominance is a property of the diploid genotype - the specific pair of alleles at a locus. For two individuals to share a dominance effect, they need to carry the exact same two-allele combination

What was the first type of genome sequencing?

Edman degradation sequencing - a type of protein sequencing where one amino acid is removed at a time to allow determination of the sequence - developed in 1950s

What is sequencing by synthesis?

A method of determining the order of DNA bases by adding one base at a time and detecting which base was added during DNA synthesis.

Principles of sanger sequencing?

• Genome is fragmented into smaller pieces - these vary in size

• Separate DNA fragments in order of size - uses polyacrylamide gel electrophoresis

• Uses radiolabels to visualise the DNA fragments

• Four separate reactions were run (one for each base), each requiring radioactive isotopes to tag the terminating base.

DONE UP TO FIRST SECTION - SEQUENCING LEC - SANGER SEQUENCING RADIOACTIVITY