Skip to main content

Exome or Whole Genome Sequencing?

This is one of the most discussed topics especially in Clinical Genomics! Affordability, accuracy, feasibility and of course time consumption - based on these factor mostly, which sequencing technology is more suitable for clinics? Whole Exome Sequencing or Whole Genome Sequencing? (WGS or WES, WGS vs WES) So here's my 2 cents on this discussion! When it comes to DNA sequencing there has always been a raging debate over the choice of Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WXS) for routine use. Whole genome sequencing (WGS), as the name suggests is the process of obtaining the entire genome. In most cases however, this is far from practical and only 95-97% of the genome is covered because it is technically difficult to sequence certain regions of the genome (high GC content, large repeat regions, centromeres, telomeres, etc.) with existing technology. “It’s very fair to say the human genome was never fully sequenced,”  - Craig Venter “The human genome ha

Malaysia Airlines Flight MH370 - the most logical explanation to what happened!

MH370 A different point of view

Here are the excerpts from an article by a pilot called Chris Goodfellow which make sense in my head and I thought it would make sense to many of my friends with a similar wavelength!

Here we go!

A lot of speculation about MH370. Terrorism, hijack, meteors. I cannot believe the analysis on CNN - almost disturbing. There could be a more simple explanation of this event.


Loaded 777 departs midnight from Kuala to Beijing. Hot night. Heavy aircraft. About an hour out across the gulf towards Vietnam the plane goes dark meaning the transponder goes off and secondary radar tracking goes off. 

Two days later we hear of reports that Malaysian military radar (which is a primary radar meaning the plane is being tracked by reflection rather than by transponder interrogation response) has tracked the plane on a southwesterly course back across the Malay Peninsula into the straits of Malacca.

When I heard this I immediately brought up Google Earth and I searched for airports in proximity to the track towards southwest.

The left turn is the key here. This was a very experienced senior Captain with 18,000 hours. Maybe some of the younger pilots interviewed on CNN didn't pick up on this left turn. We old pilots were always drilled to always know the closest airport of safe harbor while in cruise. Airports behind us, airports abeam us and airports ahead of us. Always in our head. Always. Because if something happens you don't want to be thinking what are you going to do - you already know what you are going to do. Instinctively when I saw that left turn with a direct heading I knew he was heading for an airport. Actually he was taking a direct route to Palau Langkawi a 13,000 foot strip with an approach over water at night with no obstacles. He did not turn back to Kuala Lampur because he knew he had 8,000 foot ridges to cross. He knew the terrain was friendlier towards Langkawi and also a shorter distance.

Take a look on Google Earth at this airport. This pilot did all the right things. He was confronted by some major event onboard that made him make that immediate turn back to the closest safe airport.
For me the loss of transponders and communications makes perfect sense if a fire. There was most likely a fire or electrical fire. In the case of fire the first response if to pull all the main busses and restore circuits one by one until you have isolated the bad one.

If they pulled the busses the plane indeed would go silent. It was probably a serious event and they simply were occupied with controlling the plane and trying to fight the fire. Aviate, Navigate and lastly communicate. There are two types of fires. Electrical might not be as fast and furious and there might or might not be incapacitating smoke. However there is the possibility given the timeline that perhaps there was an overheat on one of the front landing gear tires and it blew on takeoff and started slowly burning. Yes this happens with underinflated tires. Remember heavy plane, hot night, sea level, long run takeoff. There was a well known accident in Nigeria of a DC8 that had a landing gear fire on takeoff. A tire fire once going would produce horrific incapacitating smoke. Yes, pilots have access to oxygen masks but this is a no no with fire. Most have access to a smoke hood with a filter but this will only last for a few minutes depending on the smoke level. (I used to carry one of my own in a flight bag and I still carry one in my briefcase today when I fly).

What I think happened is that they were overcome by smoke and the plane just continued on the heading probably on George (autopilot) until either fuel exhaustion or fire destroyed the control surfaces and it crashed. I said four days ago you will find it along that route - looking elsewhere was pointless. 

This pilot, as I say, was a hero struggling with an impossible situation trying to get that plane to Langkawi. No doubt in my mind. That's the reason for the turn and direct route. A hijack would not have made that deliberate left turn with a direct heading for Langkawi. It would probably have weaved around a bit until the hijackers decided on where they were taking it...



Click to read the original article by Chris Goodfellow 



Here are some difficulties of Chris Goodfellow's theory

According to Chris there maybe a blown out nose gear produced smoke and filled the cockpit. Take off time of MH370 was 12.41 am and reached the cruising altitude of 35000ft at about 1:07 ie. approximately 26 mins after take off. ACARS was shutdown at about the same time. Last communication (hand off acknowledgment) was made 12 mins after ACARS is off. Change of heading was made after about 1hr from this. So my question is , does it take about 1.45 hrs to take such huge amount of smoke to enter the cockpit . even if the cockpit is more secure there maybe ventilation from the cargo hold for the smoke to reach the passenger cabin that may get noticed by any of the flight attendants and could have informed the pilots. Another question is , If it is caused by an electrical fire the pilots might get an electrical system failure alarm at the moment the ACARS went down or an alarm for the ACARS failure may went off. Then why the pilots not notices that and made a distress call instead of "all right, good night" at the time of last communication which is made 12 mins after the ACARS shutdown. Transponder went off 2 mins after last communication and why the first officer didn't tuned to the next controller frequency within that 2 mins. By this I'm not saying that the pilots did this but there maybe an expert hand if the systems are deliberately turned off. Previous records of the first officer shown that he permitted passengers to travel in the cockpit, so there might be a passenger who requested for a jump seat travel did this. 


Venkatesh Chellappa


Comments

Popular posts from this blog

How to upgrade R version on Ubuntu?

So we all have spent some quality time googling for an easy way to upgrade our R installation to the latest version on Ubuntu! Else why would you be here?! right?! Here are some quick steps to upgrade your R to latest version!  R-installations are tied up to their Ubuntu versions and hence are connected to the Ubuntu Distribution name like Trusty Tahr or Precise Pangolin. The trick here is to send a message to the repository with your latest Ubuntu distribution name, so it will pick up the latest version and update whatever is the new one out!  Just follow these steps, (simply copy-paste these commands in sequence, it will work, fingers crossed!)   1. Get the Ubuntu distribution name matching your current Version of ubuntu  distname=$(lsb_release -c -s)   2. Select the nearest CRAN mirror to you  echo "deb http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu $distname/" | sudo tee -a /etc/apt/sources.list > /dev/null  3. Authenticate download from the CRAN mir

How do I get into Veterinary School?

What advice would you give to any aspiring candidate who is seeking to become a veterinarian? As we have seen in the recent past, Boromir tends to be pessimistic about most of the things we could do and say. But do not let Boromir discourage you. Here are some tips for you to prepare yourself to start a career as a Vet. Future Vet Website is an excellent place to start if you are looking for organised information. They advise you briefly about the necessary steps while you are in High School and as a College undergraduate. They also have lots of other interesting materials to read. Otherwise here are my simple tips -  Firstly ask yourself whether you are an animal lover - there's no point in being scared of animals, hate animals or indifferent about animals if you want to be their guardian angel for the rest of your life! Secondly be sure you want to be a vet for the right reason - to care, nurture, protect and save! and not for that Maserati you always wanted to

Clinical Genomics - what is it?

What is Clinical Genomics? What's the difference between precision medicine and personalised medicine? Genomics is the study of an organism's entire genome (all the DNA for the discussion lets say)! Clinical Genomics is the study of: – the correlation between diseases and human genome – the interaction of medication and human genome – developing disease diagnostic methods from human genome - Finally - coming up with ways to treat that disease based on all this knowledge built with the help of genomics. When we think about genomics in treating a disease like cancer, we consider two aspects. First is the patient’s own genome, which is in every cell in their body. In their genome, they may have mutations that make them more susceptible to a particular type of cancer than someone who doesn’t have that particular type of mutation. For example, we know that individuals with specific inherited mutations in BRCA1 and BRCA2 genes are at a greater risk for bre