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This introductory seminar course and the materials presented here focus on the science underlying personal genome analysis, comparison of tests available from the varied companies that dominate the direct-to-consumer genetic marketplace (e.g., Ancestry DNAFamily Tree DNAThe Genographic Project, and 23andMe), and building the knowledge to navigate the results obtained from the analysis of your own DNA sample. Materials are organized to support this course, aimed at introducing someone with only a basic understanding of biology to The Personal Genome and the discoveries that lie within, but are available to anyone. The site is actively "under construction".

COURSE OBJECTIVES:  In this course you will:

  • Contrast different types of genetic information indicative of ancestral relationships
  • Recognize the existence of genetic structure among human populations across the globe
  • Build proficiency in the conceptual foundation for the methods that underlie tests of human ancestry
  • Navigate the 23andMe web platform to view the various interpretations of genome data
  • Investigate the relationship between genotype and phenotypic characteristics with known genetic basis
  • Evaluate the personal and the potential societal impacts from commercialization of genetic tests
  • Develop skills for contributing to a productive group discussion about science and humanity
Date

Topic

Learning objectives

Week 1

Consequences of DNA Testing

Consider the possible outcomes of DNA testing

Evaluate the value of the results versus potential foreseen and unforeseen consequences

Identify the potential impacts of DNA testing on you and your relatives

Week 2

DNA and the Human Genome

Registering a 23andMe Kit

Relate the molecular structure of DNA to genome sequence

Recognize the presence of a shared genome among cells of your body

Prepare authorization forms and samples for DNA testing

Week 3

Genealogy to Trees: Inheritance and Tracing Ancestry Near and Far

Reading: Genetic Connections Between Organisms from the Tree of Life Project

Integrate parent-offspring relationships into the broader Tree of Life

Apply a ‘tree thinking’ framework to individuals, populations and species

Recognize the utility of shared features, such as SNPs, as indicators of common ancestry

Week 4

Mitochondrial Eve & Y-Chromosome Adam

Reading: The Recent African Genesis of Humans, Cann & Wilson, Scientific American (ICON link)

Trace the uni-parental history of the mitochondrial genome and Y chromosome

Contrast between unique mutations and common SNPs in ancestry analysis

Recognize the geographic patterns and the prevalence of haplogroups

Week 5

Ancestry Composition

Identify your placement within the Y chromosome and/or mtDNA tree of humanity

Interpret the different predictions of the ancestry composition

Recognize the presence of ancient genetic variants revealed by Neanderthal ancestry

Week 6

Geographic Variation Among Humans

Reading: assigned on ICON

Evaluate the importance of reference populations in ancestry analysis

Contrast geographic patterns of shared and private variation in humans

Relate patterns of genetic variation in modern human populations to global colonization

Week 7

Autosomal Inheritance

Contrast different patterns of inheritance; mtDNA, Y, X, and autosomes

Consider the role of recombination in shuffling autosomes and X chromosomes

Calculate degrees of relatedness and expected similarity in autosomal DNA

Week 8

Genetic Genealogy: It’s All Relative(s)!

Evaluate the relationships revealed with other users indicated by shared genome segments

Recognize the value of testing known relatives to partition branches of your family tree

Predict the percent similarity expected based on degree of family relationship

Week 9

Genetic Variation and Phenotypic Diversity

Recognize the influence of the genotype on the appearance of a phenotype

Contrast between traits with simple versus complex genetic causation

Evaluate the association between genetic variants and complex phenotypes

Week 10

Navigating Your Genome

Compare regions of your genome shared with relatives

Use SNPedia to identify variants of interest and explore your genotype

Week 11

Test Results and Health Risk

Interpret the meaning of increased health risks associated with genetic variants

Recognize the impact of genetic variants on the effectiveness of pharmaceuticals

Week 12

FDA Regulation of DTC Genetic Tests

Readings: Green & Farahany Nature 2014 (ICON link), Swan Genetics in Medicine 2010 (ICON link)

Other coverage: The New Yorker, NY Times

Evaluate potential outcomes of learning about disease risks

Recognize the current level of impression in risk assessment from genetic data

Week 13

Downloading and Using Your Genome Data

Download your DNA test results and identify fields of the text file

Identify tools available for further analysis and interpretation of genome data

Week 14

Direct-to-Consumer Genetic Tests; Which Test To Do?

DTC Genetic Testing Companies Compared

Consider the different uses of direct-to-consumer genetic tests

Compare the results and platforms provided by different companies

Identify relatives that can be tested to enhance studies of ancestral relationships

Week 15

The Future of Genetic Testing

Reading: Perfect Genetic Knowledge by Dawn Field

Evaluate the value of personal genetic information relative to its costs

Identify societal impacts of widespread genetic testing

Back in May of 2018 researchers at the University of Oregon developed a computer program that brings us one step closer to understanding the links between genetic mutations and disease. The new software is called bpRNA and has the capability to interpret secondary structures in RNA. This allows for more precise and complete study of structure and sequencing. RNA is responsible for delivering DNA codes. Viewing noncoding RNA caring diseases caused by gene mutation are now more accessible through the invention of this tool. Ribonucleic acids are a fundamental part of life and this new invention unlocks massive potential in unlocking the key to curing or preventing gene related diseases.


https://www.sciencedaily.com/releases/2018/05/180520090916.htm

Vaping is a form of e-cigarette that has become very popular in todays world. It is better than smoking cigarettes because it does not contain tobacco which coats the mouth, throat, and lungs in tar.  Vaping however can increase the risk of mouth cancers, according to a new study, which suggests e-cigarettes lead to the buildup of chemicals known to cause harmful DNA mutations. A research study showed, after a 15 minute vaping session, they found three chemicals known to be carcinogens increased measurably in the saliva. Most of the participants showed signs of DNA damage which was caused by the chemical Acrolein that is found in vape. For this research study, they found five volunteers and looked at the cancer-causing chemicals that built up after vaping, as well as looking into the type of DNA damage they caused They found three chemicals build up in the mouth after vaping: formaldehyde, acrolein, and methylglyoxal,  all of which are known to cause DNA mutations, but there is little information on their effect in combination, Dr Balbo, a researcher said. If the cells are unable to repair the damage or if mutations build up over time, then it can cause cancer. Vaping may be better than smoking a cigarette but it still is not a healthy decision. 

https://www.independent.co.uk/news/health/vaping-ecigarette-cancer-smoking-dna-mutation-tobacco-study-a8499246.html

A Father's Mitochondria

In a recent study by Proceedings of the National Academy of Sciences of the United States of America (PNAS), recent research has concluded that the mitochondria (the powerhouse of our cells) can come from both our parents and not simply our mothers. PNAS concluded that, in multiple families, mitochondria from the father’s sperm was able to pass through children over various generations. This new information could lead to better treatment of mitochondrial disorders and even expand our knowledge over the “mitochondrial Eve”.

The mitochondria are able to power our bodies through converting sugars, fats, and proteins that we eat into molecules our cells can use to function. Knowing this, when something goes wrong the result is often grave, generating lifelong problems or even death of babies that have been affected in the womb. Every person with a mitochondrial disease is affected differently, MELAS syndrome begins in early childhood and causes seizures and dementia. Another, Kearns-Sayre syndrome, can result in problems with sight and hearing which can leave a person blind and deaf.

Mitochondria sit separately inside of cells and have their own DNA, different from the cell’s main DNA in its nucleus. They reproduce themselves and move from each generation by accompanying the egg. During fertilization, the father’s sperm transfers his DNA into an egg, however, only a few or none of the sperm’s mitochondria get in. Even if they did, the egg still has special mechanisms designed to destroy them. This new research that PNAS conducted has concluded that, in a few families, the mitochondria from the father was able to enter the egg without getting destroyed. Sometimes the DNA from the father would be more apparent as the fertilized egg grew into an embryo, even more than that of the mothers. Unfortunately, they are not sure how some father’s mitochondria were permissible in the egg yet.


Since even tiny changes can be fatal when a human’s mitochondrial DNA is altered, this can help us study distant ancestors and other people from our ethnic group (we learned this in class too!). However, all of this work has been based on the fact that the mitochondria were passed down from the female line only, and we now know it could be from either parent.


Considered the most significant implications of these findings, we could now produce better treatments because of this new understanding of how the mitochondria are passed on. It could possibly encourage properly functioning mitochondria to multiply inside a fertilized egg at the expense of broken ones as well. The downfall of all of this is how controversial it is to do any of these treatments. Since these treatments would involve influencing someone’s DNA in a way that would be inherited by further generations. However, a Chinese researcher recently gene edited two babies successfully, so maybe, depending on the outcome, this could allow testing treatment on a person’s mitochondria.


The website used - https://theconversation.com/study-shows-mitochondrial-dna-can-be-passed-through-fathers-what-does-this-mean-for-genetics-107641


LCA in People & Animals

Since she was born, Misty Lovelace struggled with progressively going blind throughout her life. When she was 12, doctors concluded that Misty’s blindness had a genetic cause called Leber Congenital Amaurosis (LCA). For those of you who didn't know, LCA is an eye disorder that mainly afflicts the retina. The retina is the specialized tissue at the back of the eye that recognizes light and color. People with this disorder typically experience severe visual impairment. Although the visual impairment tends to be stable, it could worsen very slowly over time. Fortunately, Jean Bennett and Albert Maguire, a team at the University of Pennsylvania, were testing a potential cure for LCA. The very next day after the surgery, Misty was able to see for the first time in years. After they were home, Misty was in the backyard pool, when she looked up and started to scream. Being a caring mother, she rushed out, with the thought of fear that something was hurting her daughter. Misty was finally able to see the stars.The treatment that Misty was able to undergo, first was performed on a dog named Mercery as well as mice. In Mercery's case, he was born with defective copies of RPE65, the gene affected by LCA, which is crucial for the visual cycle in mammals. This is due to the fact, that when the light hits sensitive pigments in the retina, it launches a series of reactions that make sight possible. For people who have two defective copies of RPE65 aren't able to react to light properly. As time passes, the light-sensing cells, causing the rods and cones die off. Thus creating their vision to disappear. While working with the dogs, scientists altered a small virus that’s harmless to mammals (adeno-associated virus). This virus carries the DNA with normal RPE65. Which they then inject into one eye of each blind dog. Within days, the frightened dogs who once bumped into objects around the house had turned into active, sighted animals.

Source: 

https://www.smithsonianmag.com/science-nature/new-treatment-blindness-ingenuity-180970719/

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