Summary Oxford University FHS revision notes: Whole Genome Sequencing
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Course
Genetics and Evolution
Institution
Oxford University (OX)
My Oxford University notes for the FHS exam in Genetics and Evolution. Useful for Biology, Biomedical Sciences and Human Sciences. I achieved a first and multiple academic prizes. Includes descriptions of concepts and key references/experiments.
What does society gain by continuing to fund research aimed at sequencing additional human genomes?
Discuss with examples the impact that affordable whole genome sequencing has had on our understanding
of modern humans.
A human genome can be sequenced in a day: how does this contribute to our understanding of human
phenotype differences?
Discuss the technologies needed to sequence human genomes.
SOCIETAL BENEFITS
General
NOTE sequencing is becoming much more affordable -> research is making clear progress
$2.7 billion for the Human Genome Project
$600 to sequence a genome today
Molecular Medicine
See notes on Genomic Studies of Disease.
Increasingly detailed genome maps have aided researchers seeking genes associated with dozens of
genetic conditions, including myotonic dystrophy, fragile X syndrome, neurofibromatosis types 1 and 2,
inherited colon cancer, Alzheimer's disease, and familial breast cancer.
On the horizon is a new era of molecular medicine characterized less by treating symptoms and more by
looking to the most fundamental causes of disease. Rapid and more specific diagnostic tests will make
possible earlier treatment of countless maladies. Medical researchers also will be able to devise novel
therapeutic regimens based on new classes of drugs, immunotherapy techniques, avoidance of
environmental conditions that may trigger disease, and possible augmentation or even replacement of
defective genes through gene therapy.
Risk assessment
Main applications
Assess health damage and risks caused by radiation exposure, including low-dose exposures
Assess health damage and risks caused by exposure to mutagenic chemicals and cancer-causing
toxins
Reduce the likelihood of heritable mutations
Improve ability to assess risks posed to individuals by exposure to toxic agents. Scientists know that genetic
differences make some people more susceptible and others more resistant to such agents. Far more work
must be done to determine the genetic basis of such variability. Understanding informs the need for
possible risk management options.
Example: risk assessment of patients with acute myeloid leukaemia (AML) (cancer of the blood and/or
bone marrow) (KLCO et al. 2015)
Next generation sequencing (NGS) techniques on patients diagnosed with AML to identify
associations between specific mutations and disease outcome
Patients with persistent leukaemia-associated mutations in their bone marrow cells after
chemotherapy had a significantly increased likelihood of relapse and reduced overall survival
, (median 10.5 months) compared to those with successful mutation elimination (median 42.2
months)
The results of this second study demonstrate the important role that genetic mutation plays in AML
and also suggest that targeted NGS techniques can improve risk assessment of patients with AML
Evolution
Main applications
Study evolution through germline mutations in lineages
Study migration of different population groups based on female genetic inheritance
Study mutations on the Y chromosome to trace lineage and migration of males
Compare breakpoints in the evolution of mutations with ages of populations and historical events
Example: Central Africa RHG and AGR example of gender-biased gene flow (HEWLETT 1996):
In the central African rainforest area:
o Baka RHG women married to Bantu-speakers AGR 4.5%-8.6%
o No Baka RHG men married to Bantu AGR women
VERDU et al. (2013): evidence of gene flow between these populations is stronger for the Y
chromosome than mtDNA
o “Male-mediated”: gene flow mostly via RHG brides entering AGR groups, then returning to
RHG with children
o NOTE this pattern is an exception: although most Pygmy populations have patrilocal
customs, their sex-specific genetic patterns resemble those of matrilocal populations
o Sociocultural-driven movements of spouses in a context of patrilocality and social
discriminations against Pygmies
o Recent history and complex sociocultural factors regarding intermarriage customs, mobility
of spouses, and gender-related socioeconomic discriminations can explain highly variable
sex-specific genetic and demographic patterns at a local geographical scale among human
populations
Forensics
Main applications
Identify potential suspects whose DNA may match evidence left at crime scenes
Exonerate persons wrongly accused of crimes
Identify crime and catastrophe victims
Establish paternity and other family relationships
Identify endangered and protected species as an aid to wildlife officials (could be used for
prosecuting poachers)
Detect bacteria and other organisms that may pollute air, water, soil, and food
Match organ donors with recipients in transplant programs
Determine pedigree for seed or livestock breeds
Authenticate consumables such as caviar and wine
Non-coding DNA
e.g. elucidate the importance on non-coding regions of the genome.
LINES: long interspersed nuclear elements (21% of the human genome)
Have a promoter and encode a reverse transcriptase and an integrase
Can cause disease. Examples:
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