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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...
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Humble beginnings!

It all starts when you start running towards Biology in your high school, not because you love and live biology but mostly because you loathe mathematics. At least that would be the case with the majority of us. I find no need to confess here as I went on to become a Veterinarian. 

 I know my blog's name is Ramblings of a Bioinformatician and without the mathematical aptitude, it is futile to wish for specialization in this field (I would equate that to an Aston Martin Vantage with a Citroen C1 engine)! I do not loathe mathematics but somehow fell for this pernicious trend of calling oneself a 'math-person' and 'not-a-math-person'! This psychology and related humbuzz are explained in detail in this article -  "There’s one key difference between kids who excel at math and those who don’t".

But then again, there was this unsettled feeling. Having spent those numerous one-hour slots in private internet browsing centres, having dismantled the assembled home PC's hardware parts and unable to put it back together, I evolved to be that guy who treasures his 126MB RAM, 2GB hard drive, single core, Pentium-3, assembled computer - pretty good one by Indian standards of the 2000s I should say. I would often wonder when I could draw something on Microsoft Paint and listen borrowed music on my Winamp player. I was into my third year of Veterinary science degree when I got the first upgrade to a new PC with better memory and hard drive with AMD-Athlon in it and along came a dial-up modem with 256kbps internet. Unleashing the power of internet I thought! Often used to spend many minutes together waiting just for a Netscape or Yahoo page to load.

And later came Windows XP, the window to merriment of better graphics and interface. Still stuck in that sleepy town in a corner of India that will forever stay French, I was unaware of the beautiful shiny interface that Apple Computers had to offer. Years rolled past swiftly and I was stuck in the technology hiatus, I graduated with a first class in Veterinary degree and joined a MSc degree in Biosystems & Informatics at a University in England. Well that was the big entrance! I was thrown into the deep-end, studying how to develop applets in Java and how to write CGI scripts in the first week of my masters. I was like a chicken let loose in a Tesco Extra store - not knowing what to find in which aisle. I ran around in a never-ending recursive learning loop until I met this guy Russell Martin, my web-programming module tutor. I should say it takes a good teacher to make a good student, but it takes a great teacher to create the student. He taught HTML and Perl modules through which I understood the concept of objects and functions. I also learnt how to connect them to biology. What was otherwise a pretty dull and boring discourse of online and paper text became interesting. I still owe it to Russ for instilling the spark in my otherwise Biological brain. 

 Somehow I survived the onslaught of Java programming for one more semester and to this day Java is something I stay away from. I have developed some kind of unknown aversion towards that particular language. A few weeks later in my second semester I was introduced to BioLinux and the usage of terminal for shell commands, I did really feel - 'WOW!'. I liked what it did to the input! And I learnt all that they show on the movie The Matrix were real unix commands and running on real a terminal, 'WOW' again! Those fluorescent characters on a black background did get me hooked for good! From there began my journey into the multiverse of Bioinformatics. I haven't looked back ever since and here I am handling several nodes of high performance computers, deploying codes onto the cloud, running thousands of operations every second and analysing several terabytes of genomics data every day. From a humble beginning to a busy life this, it definitely is a big journey. This is when I feel it's apt to quote Robert Frost "And miles to go before I sleep,. And miles to go before I sleep!".

 Watch out for more such babbles from me as I have decided to write my mind out a bit more often these days!

 Signing off for now.

 Venkatesh Chellappa, BVSc. & AH, MSc (Biosystems & Informatics)

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