Blog from November, 2018

In July of 2018, 23andMe announced that GlaxoSmithKline- a large pharmaceutical corporation- purchased a $300 million stake in the genetic testing company. The pharmaceutical company hopes to collaborate with 23andMe and use their genetic data to develop new drugs. Privacy is one of the biggest concerns for consumers. Peter Pitts, president of the Center for Medicine in the Public Interest, was quoted in a TIME article stating, “This information is never 100% safe. The risk is magnified when one organization shares it with a second organization. When information moves from one place to another, there’s always a chance for it to be intercepted by unintended third parties.” Not only should the people who completed the DNA test be concerned, but blood relatives could also be identified with the right information. 23andMe commented in the article assuring consumers that data privacy is a top priority for the company and data from customers is never used for research without consent. However, some critics believe that users who allow their data to be used in research should be compensated in some way or be able to take the test for free since the company will be profiting off their data. In my opinion, customers should be told who will have access to their data and what it will be used for before they take the test. I also think it is a good idea to offer free tests for customers who are willing to allow their sample to be used in research since they will essentially be profiting off of it.

 

Source 

Ducharme, Jamie. “23andMe's GlaxoSmithKline Partership Raises Privacy Concerns.” Time, Time, 26 July 2018, time.com/5349896/23andme-glaxo-smith-kline/.

On Monday, the FDA approved a drug that targets cancer through genetics and DNA rather than the tumor. This drug is called Vitrakvi and was developed by a company named Loxo Oncology. This company's approach is to develop drugs that act on cancerous genetic mutations rather than the type of cancer/tumor the person has and Vitrakvi was the first one that the company has gotten approved. Although, this treatment does come with a big price tag. This drug costs $393,000 a year for adults. For pediatric patients the drug costs around $132,000. This whole topic interests me because this company is targeting the specific genetic mutation rather than the type of cancer. It is more specific and is a new way to approach a cancer treatment. This whole idea of research targeted on the genetic mutation started after the attention in 2013 when it was discovered that endometrial cancer was genetically similar to forms of ovarian and breast cancer. This company has said to have promising results with a 81% response rate, meaning their tumor shrank. This is only the second time the FDA approved a drug for cancer that is based on a specific mutation rather than the cancer's tumor type. 

Recently a Chinese scientist, Dr. He, allegedly created genetically altered human twins that are resistant to HIV. Dr. He managed to do this by using a CRSPR Cas-9 protein, which essentially cut out the CCR5 gene. The CCR5 gene is responsible for creating a protein that allows HIV to enter cells, so by cutting out this gene Dr. He seemingly made the twins HIV resistant.

When Dr.He and his team shared their experiment at a conference in Hong Kong, where it received a lot of criticism and backlash for a couple of reasons. The first reason being that in most places in the world using humans as test subjects in experiments is illegal, and can lead to time in prison. Another reason for the backlash is that using humans as test subjects goes against an agreed upon code of ethics in the field. A third reason for the extreme backlash is that the technology used to edit genes is nowhere near perfect, and when used can lead to a multitude of life threatening problems from birth defects to never before seen diseases. These diseases may be caused, because the protein CRSPR used could have possibly cut the wrong part of the gene sequence. The opinion of many scientists at the conference was that Dr.He recklessly endangered the lives of babies for a reason that was nowhere near good enough. 

To try and ease some of the tension Dr. He told fellow scientists that after testing cells of the newborn babies nothing harmful was found, which provides evidence that his gene editing worked correctly. Even though Dr. He is though to be ethically in the wrong, his experiment may have opened a whole new realm of possibilities in the future of gene editing. 


Source: 

“Chinese Scientist Creates Genetically Edited HIV Resistant Babies.” IAfrica.com, 27 Nov. 2018, www.iafrica.com/chinese-scientist-creates-genetically-edited-hiv-resistant-babies/.

Cancer Risk and Height

Leonard Nunney is an evolutionary biologist at the University of California, Riverside. He recently decided to start exploring the idea that cancer risk may be correlated to a person's height. He conducted four large studies that included hundreds of thousands of cancer patients. “He found that every additional 10 centimeters in height was associated with a 10% increase in cancer risk” (Pultarova). This study was published October 24, in the Proceedings of the Royal Society Journal. His research did not necessarily prove that being tall increases your risk of cancer, but rather, the two factors might be associated. In an interview with LiveScience, Nunny stated that these findings could have a very simple explanation- “Taller people have more cells in their bodies” (Pultarova). Cancer is often a result of mutations in a single cell’s DNA that occurs when the cell divides. Ultimately, Nunney concluded that “The more cells, the higher rates of mutations and the higher odds that one of these mutations will lead to cancer” (Pultarova). The study focused on 23 different types of cancer and found that 14 of the illnesses can be traced back to a person’s height. There are many other influences and genetic factors that are correlated with cancer, however, it is interesting to think that height might be one of them. 


Source: 
Pultarova, Tereza. “Cancer Risk May Increase with Height for a Simple Reason.” LiveScience, Purch, 1 Nov. 2018, www.livescience.com/63990-cancer-risk-height.html.

According to a study done at NASA's national jet propulsion laboratory, bacteria found on the International Space Station (ISS) have been found to be resistant to multiple antibiotics tested against them. Inevitably, where there are humans, there are bacteria, even up in space. Continuing research done prior, scientists at the NASA lab identified a strain of Enterobacter bugandensis, that was resistant to all nine antibiotics tested against them. The scientists compared the genetics of the ISS strains to three strains of E. bugandensis collected back on Earth that were found to be pathogenic. The ISS strains were similar in many ways to strains found on Earth, including genes associated with antimicrobial resistance and potential virulence . Based on the genetic findings, it is estimated that the ISS strains were around 79 percent likely to be pathogenic and cause disease. Although the astronauts have not been sickened because of the bacteria, the news will certainly impact the planning of future missions. E. Bugandensis is a common bacteria that can cause disease on people with weakened immune systems and can even cause sepsis. Given the limited medical support on the ISS, this is something else to take into consideration.

I find the genetic connections to this case very interesting. How exactly do the strains differ genetically? How does space play a factor in the genetics? How will this effect future planning? Bacteria in space have been know to exist, especially coming from humans on the ISS. Even with no known diseases caused as of yet, the emergence of antibiotic resistance would make the treatment of any bacterial infections caught much more difficult. If an astronaut would get sepsis, they would need to be sent back to Earth, but that would be a very dangerous option. More investigation is definitely needed to look into the danger posed. But another interesting though posed earlier is how these strains compare to those on Earth. I wonder which astronauts brought the specific strains up, and what their history of antibiotic use is. Additionally, what is the capability to treat an infection in house on the ISS, and has antibiotic use their contributed to the problem. Certainly isolation from Earth for some time would limit the amount of antibiotic exposure they had, but there has been interesting research in the last few years on evolutionary pressures creating resistance in bacteria. Would space have an effect on this?



Source: https://gizmodo.com/nasa-scientists-find-possibly-infectious-superbugs-on-b-1830664400

In the 1970's scientists discovered that certain cells can shuffle and edit DNA which is known as somatic recombination. Some of these cells include immune cells and B cells. Scientists have also seen hints that it could also be occuring in our brains in neurons. Neurons can differ dramatically from one another with some having more DNA than neighboring cells. Neuroscientist Jerold Chun and his colleagues aim to find definite evidence of somatic recombination in the brain. They conducted research on donated brains of healthy elderly people and patients who had non-inherited Alzheimer's disease. They tested to see if the cells had different versions of the gene for the amyloid precursor protein (APP), the source of the plaques in brains of those with Alzheimer's. They wanted to do it on APP because other studies have shown that neurons of patients with Alzheimer's can have extra copies of the gene which could possibly come from somatic recombination. The researchers were able to identify that neurons seem to carry thousands of APP gene variants. From the study they also discovered that neurons from the Alzheimer patients had about six times as many varieties of the APP gene as did the cells from the healthy people. His team thinks that reshuffling depends on an enzyme called reverse transcriptase that makes DNA copies from RNA molecules. They believe that a new variant could arise when the enzyme duplicates the APP gene and slips it back into the genome. This can create a sloppy copy that may not match the original and code for a different variant of APP. If more studies occur that confirm what they think then we can block the enzyme like treatment for HIV and work against Alzheimer's disease. 

http://www.sciencemag.org/news/2018/11/landmark-study-shows-brain-cells-revamp-their-dna-make-new-proteins-perhaps-sparking

The first human genome sequence was published in 2001. The reference genome has since had constant additions to it so that it can better represent the range of variations between us humans. The current version is called GRCh38. A group of researchers, led by Rachel Sherman, set out to create a pan-genome for Africa. Of the tested DNA they discovered some sections, longer than 1,000 base pairs, did not match the reference, GRCh38. They found nearly 300 million base pairs or about 10% of the reference genome. The big problem with this new information is that it can have medical consequences. Since the reference genome doesn't adequately represent certain populations, when looking for genome variations linked to conditions you are going to want a reference that's more representative of the tested DNA. By creating a pan-African genome they plan to help with this problem. 

https://arstechnica.com/science/2018/11/our-human-reference-genome-is-missing-a-lot-of-material/

Long life spans tend to run in families, its believed to be attributed through genes. But now, a large new study of data from the genealogy website Ancestry reveals that genetics may play less of a role in life span than previously thought. Previous studies failed to take into account a pattern of human relationships: that people tend select romantic partners with similar traits to their own. The findings mean that previous studies may have overestimated the heritability of life span, the researchers said.researchers analyzed information from more than 400 million people using publicly available family trees from Ancestry. Because the researchers needed to know the life span of these individuals, the study looked at only those who were born in the 1800s or early 1900s and were deceased. With the data they found that it doesn't have to do with family history or similar living environments, they looked at assortative mating. The large data set allowed researchers to examine the effect of what's called assortative mating, the phenomenon in which people tend to select spouses who are similar to themselves. If assortative mating was what they did, it would mean that factors that are important for life span tend to be similar among spouses. So, spouses tend to have the same life span because they picked a spouse that was like them. 

Recently, California has been plagued with intense wildfires that have taken more than forty lives. Officials are now using advanced DNA technology in order to identify victims of the wildfires. The new technology medical examiners are using is called Rapid DNA which “is a term for portable devices that can identify someone's genetic material in hours, rather than days or weeks and more extensive equipment it can take to test samples in labs.” This technology makes it easier to identify the deceased, and takes significantly less time. In order to use the machine DNA from when the person was alive is needed as well as viable remains, which are sometimes not found in cases of burning. Due to the rarity of having DNA tests, sometimes it is often easier for officials to use medical records such as dental x-rays or history of bone fractures to identify the deceased.


https://www.14news.com/2018/11/14/identifying-wildfire-dead-dna-likely-older-methods-too/


Scientists are using DNA from a 9,000 year old mummy found in Alaska along with the DNA of ancient Brazilians in order to theorize how humans migrated from Asia down to South America. Researchers have found that migration occurred from North America to South America in three major waves. By using DNA analysis, researchers have been able to find similarities in human remains found in North and South America. After finding similarities, scientists are able to see which groups from North America populated South America due to their similar genetics. This study is important because it shows that there were many levels of genetic diversity in the Americas, due to the different waves of migration. Analyzing ancient DNA discovered in  10,000 year old remains that Amazonians and indigenous Australians share DNA. Finding Australian DNA has raised many questions about how people crossed from Australia over the Pacific to reach the Americas. It is theorized that the ancestors of the two groups once lived in Asia and migrated to Australia and North America separately.


https://www.sciencenews.org/article/ancient-dna-fossils-south-america-populated

Many people have a great fear of loosing hair, for some this fear becomes a reality a soon as childhood.  This is called hypotrichinosis complex.  Those who have hyporichinosis complex will have hair as in infant, but their hair will begin to thin out early into childhood.  Researchers have known that this is a hereditary trait, but they have now discovered the gene responsible for this type of hair loss.  Those at the University Hospital of Bonn in Germany discovered that mutations is the LSS gene drive this defect.  Lanosterol Synthase (LSS) is a gene that impacts the metabolic pathway to the health of hair follicles.   

Image result for hair genetics

Researchers evaluated the DNA of three different families with no relation, of all the members eight of them experienced hair loss.  All eight of those members had mutations in the LSS gene.  Researchers continued their study from there.  They collected and analyzed tissue samples from those with and without the mutation in the LSS gene in attempt to find out exactly where the lanosterol sythase is located in the hair follicle.  They found that in the normal LSS gene enzymes of LSS where found in the endoplasmic reticulum.  Those with the mutation in the LSS gene where found to have the enzyme spread outside of the endoplasmic reticulum and into the cytosol.  This still doesn't fully explain why the hair falls out, but researchers have a theory.  

They believe that the leakage of the LSS into the cytosol confuses the follicle and cause it to get rid of the hair.  Although they don't fully understand the hair loss, this discovery broadens the picture behind the cause of this disease.  There is still a while until they find a cure for this hair loss, but thankfully there is no other effect besides hair loss. 




Cohut, Maria. “New Genetic Culprit Found for Early Progressive Hair Loss.” Medical News Today, MediLexicon International, 10 Nov. 2018, www.medicalnewstoday.com/articles/323635.php.




GDF15 Protein

Scientists engineer proteins that can now make obese mice to exponentially lose weight and lower their cholesterol. This is somewhat crucial now that almost 40% of Americans are now considered obese; can these findings create a pill for humans that can have the same effect? Scientists from a biotechnology company called Amgen Inc. have found a naturally occurring protein within both monkeys and rats that have brought about significant changes in obesity in both animals. These protein provided healthy weight loss and rapid improvements on measures of their metabolism and heart health.

In mice who received a bioengineered version of their GDF15 protein, researchers observed that these mice would opt out of the extra-rich condensed milk, that they normally go crazy about, for their standard mouse food. After 35 days, these mice who were bioengineered lost approximately 20% of their body weight, while the placebo mice gained 6% of their starting weight. Insulin levels and total cholesterol readings were distinctly improved in the treated animals as well.

Chromosome 19 (human)

This reengineering is suggested to have the power to decrease or turn off the urge of reward-driven eating that drive many people to becoming obese, or inhibiting others from losing weight. Foods such as doughnuts, milkshakes, or bacon cheeseburgers seemed less enticing. Some of the weight-loss medications approved by the FDA similar to this reengineering appeared to nudge food preferences of obese patients into healthier directions, further leading to better health conditions. The GDF15 protein fidgets with the chemical signaling systems of humans, so scientists have been working to find equal options with similar benefits that can work together to activate many different systems that work together to increase weight loss.  



http://www.latimes.com/science/sciencenow/la-sci-sn-weight-loss-protein-20171019-story.html

At the Institute for Equine Genomics at Bingham University researchers worked to better understand the genetics behind breeding success in horses. Gene variants are one component they look at to determine if a horse could be a great racehorse. Seabiscuit is a legendary racehorse that does not fit the typical characteristics of a great thoroughbred. He was small, “lazy”, and completely written off after losing his first 17 races. However, after beating Triple Crown winner War Admiral as an underdog, he was voted 1938 Horse of the Year. 

A few years ago, Jacqueline Cooper from the Seabiscuit Heritage Foundation got in touch with the Institute, asking if they could test a fifth-generation of Seabiscuit for breeding purposes as well as learning more about the ancestor’s genetics. Because the relationship was so distant, this wasn’t possible. Instead, they extracted a DNA sample from Seabiscuit’s silvered hooves. Removing and preserving a champion racehorse’s hooves was once customary. The owner kept them as keepsakes and decorative mementos.

seabiscuit silver hoof.jpg

Student Kate DeRosa and Andy Merriweather, director of the campus Ancient DNA and Forensic Laboratory, drilled into the coffin bone of the hooves. The coffin bone is the bottommost bone in a horse’s hoof. After extraction they found that the mitochondrial DNA was still intact. This DNA allowed the researchers to verify the maternal lineage and prove that the hooves did, in fact, belong to Seabiscuit. They also found that the nuclear DNA had been degraded due to its age and the chemical treatment it underwent while being silvered. Despite this, Kate was still able to sequence genes associated with optimal racing distance. They found that Seabiscuit had variants that are found in successful distance runners. Most interesting was that his genes also included minor variants found in good sprinting horses. This rare combination explains Seabiscuit’s record. He won races by both very short and extremely long distances. 



Kate DeRosa.jpg

seabiscuit hoof2.jpg

When looking at successful racehorses today that have a genotype similar to Seabiscuit’s, they tend to be late bloomers when compared to other genotypes. This is much like Seabiscuit’s career; he didn’t begin winning until he was 4. The Institute will continue sequencing Seabiscuit’s genes looking for links to physical attributes as well as temperament traits. They theorize that Seabiscuit could have had behavioral genes that filled him with such a desire to win that it overpowered his less than ideal physical traits. They are interested to see how his DNA differs from modern racehorses knowing how different thoroughbreds looked in the past. The researchers also mention that it is not currently possible to clone Seabiscuit due to the low quality of nuclear DNA.

Tammariello, Steven. “Scientists Extract DNA From Seabiscuit's Hooves To Figure Out How He Was So Fast.” Smithsonian.com, Smithsonian Institution, 29 Oct. 2018, www.smithsonianmag.com/history/scientists-extract-dna-from-seabiscuits-hooves-to-figure-out-how-he-was-so-fast-180970649/.


The DNA from one person yielded different results from different companies

One man sent nine samples of his DNA to three different companies and he received six different results. Rafi Letzter, a writer from Live Science, sent his DNA to AncestryDNA, 23andMe and Nat Geo, which uses Helix to process the raw DNA while Nat Geo interprets the DNA. Letzter knows he comes from a family with strong Jewish ties but he has never taken a test before. 

AncestryDNA samples:

Three samples were sent, all under different names but only two got processed, as one resulted in an error preventing him from accessing his results. 

First sample:

Second sample:


23andMe Samples:

Letzter sent three samples to 23andMe. At first, two samples both reported low 90s (percent) in the Ashkenazi Jewish origin. The third sample was sent under a female name and was labelled as female, even though Letzter is a male. The sample was processed fine but 23andMe asked for more personal information since the sample came from someone with "unexpected chromosomes." However, while reporting on this story, 23andMe updated its DNA interpreting system, meaning it reassessed all of the DNA already in it system. After the update, the reports came back as 100 percent Ashenazi Jewish. 

Nat Geo and Helix:

Again, three DNA samples were sent to this company for testing, but only two were successful in retrieving results. 

First sample:

Second sample:

As you can see, this company found that Letzter was significantly less Ashkenazi Jewish than the previous two companies.


Why does this matter? And how does this happen?

Well, it kind of doesn't matter, and it happens for a number of reasons. The reason for population genetics is to focus more on where groups of people moved and when. Ancestry isn't an exact science since humans have never been exact/hyper-distinct groups of people. According to the article, "To divide people into groups, Platt told Live Science, researchers make decisions: For example, they'll say, the members of this group of people have all lived in Morocco for at least several generations, so we'll add their DNA to the reference libraries for Moroccans. And people who had one grandparent with that sort of DNA will hear that they're 25 percent Moroccan. But that boundary, Platt said, is fundamentally 'imaginary.' 'There is structure to history,' he said. 'Certain peoples are more closely related to each other than to other peoples. And [commercial DNA companies] are trying to create boundaries within those clusters. But those boundaries never really existed, and they aren't real things.'"

What could this mean for the future of commercial DNA testing companies?

This lack of certainty could cause a drop in consumer faith in the products. If you can send in nine different samples and get six different results, it'd be hard to be sure which report, if any, you should believe. Also, as we heard in class, 23andMe is now going to test how you respond to certain medications. Well, if their ancestry data is so subject to error, how can the reports on medication response be trusted? That's certainly something 23andMe can't afford to be wrong about. 



This article talks about a recent development that a team of scientists have recently uncovered. This development is that based on genetic markers the scientists have created a test to help predict the lifespan of humans. The test shows that some people are genetically predisposed to live 5-10 years longer than some of their counterparts. The test is based on 21 different genetic locations, and how they pertain to getting certain diseases such as Alzheimer's, or Lung cancer. Predisposition to these diseases is thought to be cause of much of the variation in the lifespan predictions. Interestingly, the student didn't find any information about other types of cancers, and is thought to be related to this specific time period(present). This idea came up because in the past even if a person was predisposed to get Lung cancer, there wasn't as great of a chance as there is today, due to the smoking epidemic. In the future, scientists hope to more precisely understand these genetic markers, and eventually try to slow down the aging process. 


https://www.medicalnewstoday.com/articles/323414.php

Sandoiu, Ana. “Scientists Create Genetic Score That Predicts Lifespan.” Medical News Today, MediLexicon International, 22 Oct. 2018, www.medicalnewstoday.com/articles/323414.php.