Drake AMUTUHEIRE
A biomedical engineer looking for a career in Bioinformatics
Location Uganda
Activity
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Drake AMUTUHEIRE made a comment
Thank you so much for the course!
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Drake AMUTUHEIRE made a comment
1.289
2. Illumina 1.9 encoding
3. The quality decreases as we move a long the sequence
4.yes, most of the sequences tend to have a low base quality scores at the end of the sequence -
Thanks for the heads up. I will make Galaxy my daily go to bioinformatics platform.
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Drake AMUTUHEIRE made a comment
I am so mesmerized with how many tools that are encapsulated within one web-based platform, the Galaxy Platform. Also, the ease with which one easily navigates through the platform makes it easy for everyone not just the typical bioinformatician.
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I haven't heard about galaxy before.
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Drake AMUTUHEIRE made a comment
I think Bioinformatics is multidisciplinary filed that involves not just the use of computational tools, but as well as development of the tools to analyze biological data to the biological question at hand.
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Drake AMUTUHEIRE made a comment
In a hospital setting, it is easy to identify what the cause of a certain chronic infection through sequencing e.g. for those patients in ICU whose cause of the infection has not been defined by the intensivist or clinician
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Drake AMUTUHEIRE made a comment
So excited for the coming three weeks
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Drake AMUTUHEIRE made a comment
Hi, I'm Drake from Uganda. I'm a prospective masters student in Bioinformatics. I am excited to see what this course holds for me
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Drake AMUTUHEIRE made a comment
having to know that science, in particular, genomics is not done by scientists with degrees and PhDs. Introducing students to a vast number of careers, not the ancient times when a student knew they were going to become a doctor and no other course of a career.
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Drake AMUTUHEIRE made a comment
Wind and Insects are mediums through which flowers can be pollinated, transferring pollen grains from the anthers of one flower to the stigma of another flower of the same kind. Through this process, we are going to have an embryo created when the pollen meets with the ova after fertilization. The offspring from the two gametes being linked together will have...
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Drake AMUTUHEIRE made a comment
Writing about scientific research requires a lot of precautions because of the increasing risk of making errors. It would be good to have students have a pre-understanding of genomic terms that would help them differentiate between what is wrong and what is right in a genomics sense.
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Drake AMUTUHEIRE made a comment
I would take the test. Some of the issues that would arise would be the cost, safety of the results, interpretation of the results, Variants of uncertain significance, does the recipient get some sort of counseling after receiving their results, etc.
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Drake AMUTUHEIRE made a comment
Very interested to see how genomics is being introduced into different curricula
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So excited about the package the educators have for us.
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Drake AMUTUHEIRE made a comment
Hi, I'm Drake AMUTUHEIRE, a biomedical engineer, with a high interest in bioinformatics. I hope to start my masters in bioinformatics in September of next year. Genomics is a very few fields more so in low and middle-income countries. The introduction of genomics in all biologicals should be encouraged just like IT has been done in all the courses.
I...
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Drake AMUTUHEIRE made a comment
I am always waiting for something new from COG-UK
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Drake AMUTUHEIRE made a comment
Many thanks for this course!
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Drake AMUTUHEIRE made a comment
The fact that institutions that are somewhere in the development of genomic technology and their acceptance to collaborate on surveillance and research is a good thing for global health.
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Drake AMUTUHEIRE made a comment
An international standard just like we have seen on medical technology and health is very important as it would increase the fast-tracking of diseases e.g. during a pandemic by reducing the time taken to discuss issues as per regional ethical considerations for a specific region. During these times and even after a pandemic, our nightmare is always time, and...
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Drake AMUTUHEIRE made a comment
Genomic data is vastly different from general data because of the consequences it poses on an individual, family, or population. The data is something you can't alter and you are going to live with the interpretation of the data like genetic conditions, and mutations in DNA which you will carry with you in your body for as long as you are alive, so protecting...
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Drake AMUTUHEIRE made a comment
Biobanks and the different individual steps involved in the storage of biospecimens. Empowering low and middle-income countries is actually one of the easiest ways to track, control, and prevent the transmission of disease. This was seen by the sequencing manpower that was available for countries like Uganda had developed. The small it was it enabled tracking...
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Drake AMUTUHEIRE made a comment
The vaccination status is the only sure method to control a pandemic like the SARS-CoV-2 pandemic. So, I would get myself interested to know the efficacy of this vaccine in relation to the question at hand during the surveillance.
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Data sharing eases the fast-tracking of an outbreak when it arises. It eases on research e.g. vaccine development through comparison of the different pathogen genomes.
Linking genomic data to clinical data is important, especially for personalized medicine where we can have treatment tailored for a specific individual.
Cloud-based data storage can have...
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Drake AMUTUHEIRE made a comment
When searching for a database I always search for specificity first like drug-related databases, pathogen-related, nutrition-related, Microbial Resistance databases etc. I also go for the credible and most used like National Centre for Biotechnology Information (NCBI), EMBL-EBI which are used and cited in most of recent research mostly COVID-19.
The value...
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Drake AMUTUHEIRE made a comment
The last query has not fully answered the fact that I gave a different answer but which was quite similar by needed to get to the specifics.
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Drake AMUTUHEIRE made a comment
Genomic surveillance helps in determining which population is most affected and is very good at determining the coverage of a given variant, which is good when you are tracking exponentially rising cases, especially in a pandemic.
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Sequencing coverage is the number of reads that align to the reconstructed reference genome. It is important for use in investigating and interrogating which reads in which regions are actually causative of a certain disorder, condition, or disease.
Hi throughput has helped improve the quality of life immensely through fast diagnosis, tracking, and...
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Drake AMUTUHEIRE made a comment
I attended the power of genomics to understand COVID-19. I can't wait to learn about how the metadata is produced and shared. That's where my interest lies.
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Drake AMUTUHEIRE made a comment
Many thanks for introducing us to this course, it has built a tunnel for my future in bioinformatics!
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Drake AMUTUHEIRE made a comment
Thanks so much for the course and for the many resources!
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Drake AMUTUHEIRE made a comment
QN1
They will produce the same outputQN2
> ggplot(data = iris, aes(x = Sepal.Length, y = Petal.Length, color = Species)) + geom_boxplot()QN3
+ facet_wrap(~Species, scale='free_y') + labs(x = "Sepal Length", title = "Petal vs Sepal Length") -
Drake AMUTUHEIRE made a comment
Thanks team!
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Drake AMUTUHEIRE made a comment
Thanks a bunch!
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Drake AMUTUHEIRE made a comment
This course had a lot interesting information I think everyone would need more so the health professionals. I can't thank the tutors more, you have given us the full best of the genomics of say infectious diseases. I would recommend any of my peers to take this class too!
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The way information is dispensed from the public policy makers to the general public is very crucial and critical. You don't want the public to resist adherence to the measures put aside by the health professions and government, to protect and save people. The reasons why some of the measures are put in certain ways should be clear enough and feasible to...
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I think there is more to talk about the ethical considerations in future studies for the pandemics. Also, the relationship between the clinicians, bioinformaticians, laboratory technologists should be harnessed so that we prevent any internal fights between these different health fields.
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Drake AMUTUHEIRE made a comment
This information will help us reduce on the severity of an outbreak on pandemic if some if not all of the public health measures to curb and diagnose the virus are put into our routine laboratory practices.
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Drake AMUTUHEIRE made a comment
The reluctance of people not wanting to test for COVID-19 was a similar here in Uganda because most of the population live on a daily income. This threatens the surveillance measures put aside by the ministry of health and its partners. Also a few or no diagnostic kits at some point was observed in most of the areas because we couldn't manage to compete with...
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Drake AMUTUHEIRE made a comment
The Delta variant was the most lethal variant that caused most of the deaths in Uganda. Omicron on the other hand didn't have any phenotypic characteristics for most of the people that got infected. Literally everyone around about say 85% contracted omicron that presented just mild effects.
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Drake AMUTUHEIRE made a comment
Each of the networks has an algorithm that is being used in collection and analysis of results of sequencing. Of course this is done by centrally located organizations that are leading in the process of surveillance like Africa CDC for the case Africa and COG-UK for the United Kingdom.
Development of algorithms by COG to sample out which patient samples...
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Drake AMUTUHEIRE made a comment
I think with no doubt vaccination is the best way to curb the virus. Under my work setting I have been surrounded by people face covering with a lot of hand hygiene using clean water, soap and sanitizer.
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Drake AMUTUHEIRE made a comment
My most interesting part was how Dr. Mariana and her team in Argentina managed to collect and analyze data from over 59 districts with the low resources at their plate. Another one is how the SARS-CoV-2 uses its ability to take-up the process of the human cell and evolve to move into another patient for infection.
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First thing that came to my mind as a common man on the streets was we are in a very strange situation that could take all of us in the Low and Middle income countries (LMICS).
My second thought was maybe the developed countries are too selfish to provide the vaccine doses to these countries that do not have enough. But another thought was some of these...
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Drake AMUTUHEIRE made a comment
In Uganda, there were a number of partners working together alongside the Ministry of health (MOH) in the surveillance of COVID-19. These include; Uganda Virus Research Institute (UVIRI), Infectious Diseases Institute (IDI), Makerere University, Uganda National Health Laboratories (UNHLS).
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Drake AMUTUHEIRE made a comment
setosa1 == setosa.sub1
str(setosa.sub2)
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x <- c(3, 10, 30)
m <- rep(x, times=2)
m
3 10 30 3 10 30
n <- c(x, 0, x)
n
3 10 30 0 3 10 30
n==m
TRUE TRUE TRUE FALSE FALSE FALSE FALSE
Warning message
In n == m : longer object length is not a multiple of shorter object length
length(n)
7
length(m)
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Drake AMUTUHEIRE made a comment
Q1. Yes I did
Q2. Yes it is helpful
Q3. Yes it is helpful
Q4. yes I did manage to go back to the last command that I was on
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Drake AMUTUHEIRE made a comment
The development of mutations in the first place gives medical practitioners like clinicians a hard time in treating the different strains that evolve. Other areas like high transmissibility, increased rate of infection, and maybe the cost of and time of making more research about the new virus yet this happens in an emergency situation.
Having to know the...
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Drake AMUTUHEIRE made a comment
The spike is generally to allow the SARS-CoV-2 to bind with the membrane of the host cell. The host cell has receptors angiotensin-converting enzyme 2 (ACE2) receptor and TMPRSS 2 that the spikes bond to before the virus can make an intracellular movement.
The spikes are an evolution for the adaptation of the virus. They increase the surface area for...
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Drake AMUTUHEIRE made a comment
Stuff is extremely hard on the first encounter, but after two to four reviews, I tend to grasp the concepts.
I appreciate!
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I chose easy for someone to understand, I think this has very many factors like short and precise, clean, includes enough comments, well-edited. I think this is what clean code encompasses.
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Drake AMUTUHEIRE made a comment
#!/usr/bin/env bash
# Define a function that takes the a filename as first argument
filename=$1
read -p "Enter a filename: " $1
function file_exits () {
echo [[ -e $1 ]]
if [[ ! -e $1 ]]
then
echo "File does not exist: " $1
fi
} -
Drake AMUTUHEIRE made a comment
#!/usr/bin/env bash
for (( i=1; i<5; i++ ))
do
if [[ $i -eq 2 ]]
then
echo "fizz"
else
echo "buzz"
fi
done -
Drake AMUTUHEIRE made a comment
I like his advice on how you don't have to rush through the tools, this is helping me so well. Thanks for this.
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Drake AMUTUHEIRE made a comment
#!/usr/bin/env bash
# Enter a variable called cut
cut="$2"# set the variable to quality
cut=qualityif [[ ${quality} == "Fair" ]] || [[ ${quality} == "Good" ]]
then
echo "Insufficient quality to proceed"
elif [[ ${quality} != "Premium" ]] || [[ ${quality} != "Ideal" ]] || [[ ${quaality} != "Very good" ]]
then
echo "Invalid... -
Drake AMUTUHEIRE made a comment
1. fruits=("pineapple" "peach" "raspberry" "plum" "apple" "kiwi")
2. echo "${#fruits[@]}"
63. echo "${fruits[5]}"
kiwi -
@KabeloMaloka thanks, this was helpful!
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Drake AMUTUHEIRE made a comment
Many thanks!
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Drake AMUTUHEIRE made a comment
The most interesting part for me was how the Pandemic was tracked from China in December as it spread throughout the world. Also, another point is how fast the diagnosis of the primers was developed and how it helped in the diagnosis of the virus, in just a month all this was ready for the world to track the disease.
The different methods of sequencing were...
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Drake AMUTUHEIRE made a comment
For every news bulletin that I watch, the headline is vital to me. The headlines from Italy were not paratable for anyone, e.g. "The virus kills another 200,000 people, " and also, "One million people infected with the virus." This to lay man would mean all these people are going to die as per the last bulletin they watched. It triggers a lot of anxiety...
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Drake AMUTUHEIRE made a comment
The first case in Uganda was recorded on the 21 March 2020
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Thanks for this once more sir!
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Thanks, Richard for this, but with all these mutations around, if you can't have a clear diagnosis for an ailment and find a vaccine, which is easily done by knowing the genetic code especially for the laboratory-engineered microorganism using NGS, then we are going to find a number of drugs on the market that are either resistant or don't work the disease at...
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Drake AMUTUHEIRE made a comment
The measures taken during that time by governments were quite feasible just like today, e.g. crossing schools, markets and restricting of movement of people through lockdowns just after the world war, must have been s struggle to implement most of them. Very interesting how some the populations around the world have failed to adhere to the communications, I...
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Drake AMUTUHEIRE made a comment
Without the intervention of genomic technologies, we would have classified COVID-19 as the normal flu maybe, which would be disastrous because the treatment given would be the wrong one for this virus, hence numerous amounts of deaths than the ones we had. On the other hand, it would take many more years to diagnose this virus just like it was for the cases of...
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Drake AMUTUHEIRE made a comment
The influenza, Ebola and Marburg viruses are some of the viruses that are spread through the same way as SARS-CoV-2. Ebola and Marburg transmitted more through the fomite method while influenza is mostly through the the air.
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Drake AMUTUHEIRE made a comment
The first case of COVID-19 was an imported case from UAE where the person had gone for a business trip
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Drake AMUTUHEIRE made a comment
Thanks for the glossary
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So proud to be here, thanks!
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Thanks so much Cameron, it worked perfectly!
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Drake AMUTUHEIRE made a comment
Ready for the journey!
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Drake AMUTUHEIRE made a comment
Hi, I'm Drake a biomedical engineer from Uganda. I'm currently working as a clinical engineer in one of the hospitals here in Uganda! I am a prospective master's student in Bioinformatics and I think this course will enrich me with the information that I will need for both my study and the field. So excited for the next three weeks.
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Drake AMUTUHEIRE made a comment
This course has been so informative, as someone who is trying to join the bioinformatics field, I can confirm that I am being strengthened spiritually. Huh!
Thanks to all the tutors!
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Drake AMUTUHEIRE made a comment
Hi tutor,
So, when I try saving the environment variable permanently using the first method, it outputs the command below.[ Error in writing /etc/environment\: \Permission denied ]
I don't know where I am going wrong
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Drake AMUTUHEIRE made a comment
This should be one of the easiest commands I have learned in addition to the others!
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Drake AMUTUHEIRE made a comment
sort fruit.txt | uniq -iD > repeated_fruit.txt
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Drake AMUTUHEIRE made a comment
Thanks for sharing!
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Drake AMUTUHEIRE made a comment
I haven't used it before but hoping this course will give me the basic guide for it.
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Drake AMUTUHEIRE made a comment
Sounds good, Thank you!
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Drake AMUTUHEIRE made a comment
Hi, I'm Drake AMUTUHEIRE. I'm a biomedical engineer from Uganda and a prospective masters student in Bioinformatics from Uganda. I want to be able to learn how analyze genomic sequence reads especially genomes of infectious diseases using Linux and able to deposit the sequences in R.
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Drake AMUTUHEIRE made a comment
Thanks for this course!
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Drake AMUTUHEIRE made a comment
The scenario where I was undecided was for the two deaf parents who want a deaf offspring that they can communicate to easily, how about if the child realizes that his/ her parents did this without his/ her consent. Putting in all the ethical considerations this was a hard one for me, I had to think twice,
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Drake AMUTUHEIRE made a comment
A: As far as if an individual who doesn't follow the preventive measures yet they actually know they know the consequences are not as good as they want. Regular sensitization and keeping in touch with these individuals if possible because these are complex situations especially to the clinician.
C: Taking scenario C for example, I think if someone has the... -
Drake AMUTUHEIRE made a comment
Absolutely, all these new findings related to and concerned with genomic data have to be shared between researchers but putting in mind the ethical considerations as far the the patient information is concerned. If patient X is comfortable with being put in a book or research paper, its rightly okay to do but should know that there is always cost to this such...
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Drake AMUTUHEIRE made a comment
For me where this becomes more interesting is at what percentage should an incidental finding be called an incidental finding with the different probabilities that an individual is likely to be symptomatic
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Drake AMUTUHEIRE made a comment
As a young person of her age, its not the right time for her to get this testing. The psycho-social implications of releasing these results to Carly are not easy pill to swallow. Maybe at a later age like 20 plus something. But this doesn't deter me from explaining to her what the disease entails, what the phenotypic effects incase one has been found...
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Drake AMUTUHEIRE made a comment
A big thanks to Mathew for taking time to share his story with us and upload him for taking the presymptomatic test. It is not an easy decision to make, like he said about 90% of folks in the population that are susceptible to HD don't take the tests.
I think the fact that his GP advised him to join the counselors which he did helped him tremendously to...
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Drake AMUTUHEIRE made a comment
The first challenge is the kind of feedback that you get especially after dispensing the genetic results to the patient.
Putting in mind the kind of family that one partner is in, e.g. if someone is in an interracial marriage, number of children in the family, which brings us to the financial implications of the results, the psycho-social aspect should as...
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Drake AMUTUHEIRE made a comment
It would be my pleasure to be part of this team at some point
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Drake AMUTUHEIRE made a comment
In my own view, gene editing of the embryos should be done after thorough research that the individuals we are going to have are going to suffer consequences that have effects of death or maybe research that is novel. Otherwise we shouldn't be allowing this to go on casually. We are going to reach a point where scientists are going to misuse this procedure and...
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Drake AMUTUHEIRE made a comment
It's the building block for gene therapy for the next research studies. With all these major challenges like the body identifying the vector and the gene therapy as a pathogen, we need more studies. Also, having the costs coming down will help in this treatment procedure just like we have seen in diagnosis using PCR
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Drake AMUTUHEIRE made a comment
Tailoring management of a patient to their own genome is what I would like to have access to. It reduces on the time taken through an easy and synchronized known therapy administration than using a reactive approach.
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Drake AMUTUHEIRE made a comment
Not yet, maybe because I haven't tested but all is moving smoothly in my family for now
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I think personalized medicine, Pharmacogenetics, and targeted therapy will be pivotal in improving the healthcare of different people. This is because if you can identify a genetic error specific to an individual and then get therapy and treatment for that condition.
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Drake AMUTUHEIRE made a comment
Generally, the whole of week three has been so informative but my waaw moment has been learning about the Variants of Uncertain Significance that are predeposited within disease genes associated with certain conditions.
In the same spirit analyzing the data of next-generation sequencing has been quite tasking for me, this is coupled with relating this data...
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Drake AMUTUHEIRE made a comment
Generally, the whole of week three has been so informative but my waaw moment has been learning about the Variants of Uncertain Significance that are predeposited within disease genes associated with certain conditions.
In the same spirit analyzing the data of next-generation sequencing has been quite tasking for me, this is coupled with relating this data...
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Drake AMUTUHEIRE made a comment
I think using the terms interchangeably is the best option because most of the patients today have access to the internet and will go further to search what the hell is happening in their bodies and this will make it easy for them to understand.
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SNPs can be either developed genetically or by external factors which contribute to the phenotypic traits that they use for evolution and to fight natural selection. Different people have lived under environmental conditions that cause the body to adapt to such environments.
Having to identify specific SNPs within a given population will help in diagnosing...
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Drake AMUTUHEIRE made a comment
For me, I would at first feel sad, undeserved, not loved, feel unlucky if at all I was diagnosed with some of the incidental findings.
But for the case of whether I need to get the information or the clinician has the right to provide me with the result is a matter of consent and of course, I am always curious to know what's going on in the background.