DNA research

October 13, 2017

This is just a quick update on DNA research that I’ve been meaning to write. Because right now I am running another long-form article about DNA research (in English, for an eventual write-up in Bahasa), this will serve as a short precursor for that, I hope.

Exactly 40 years ago, two DNA sequencing technology was born. The first method that came up first was the Maxam-Gilbert sequencing (Feb 1977), followed by the Sanger sequencing (Dec 1977). Sanger’s method took off due to its versatility (it is easier), paving the way for the future that included the ambitious Human Genome Project (HGP, 1990). Nature has an editorial article about the future of DNA sequencing, making an argument that DNA sequencing would take off by killer application of the tech, i.e. how we apply it in the related fields. The cost for sequencing DNA gets pretty cheap nowadays, hovering around $1,500 in 2015. I have a question with this $1,500 figure. On which platform this figure is possible, how many coverages that would cover because the standard for clinical diagnostic is 30x coverage.

Say that we have this killer technology and killer application of this technology, there is another problem that we have to worry about. I heard from one of my professors that the raw data from a clinical diagnostic could be around 10-20 GB per human sample. That’s a lot of data. I am not sure if this is still true, so I need to double-check this one.

Okay, let’s change some gear. Here is an article published in PLOS Biology: 60 years ago, Francis Crick changed the logic of biology. In September 1957, he outlined the central dogma of molecular biology. The premise is simple: once the information (from DNA) is transformed into peptide/protein sequence, you can’t reverse it back into DNA sequence. He did predict that RNA could go back to DNA (I thought he didn’t), but he predicted so without a solid ground to make a good case on it. Then in 1970, David Baltimore (yes, that Baltimore classification guy) discovered reverse transcriptase enzyme (from retroviral?) that makes it possible for RNA to go back into its DNA form.

Now I’ve briefly talked about Crick, let’s talk briefly about Crick. Remember the HGP that I briefly mentioned up there? One important thing to know (among other important things) is that the DNA samples came from a number of different individuals. So the resultant DNA sequence generated was mosaic. But then, in 2007, J. Craig Venter’s DNA was sequenced completely (September 2007) by using the Sanger’s method. Then in 2008, James Watson’s (April 2008) DNA was completely sequenced with a new and rising sequencing technology: NGS Roche 454.

Okay, that’s all for today’s quick update.