Blogging My Genome, episode 3: data wrangling

After learning about Illumina's Understand Your Genome (UYG) program at ASHG 2013, I decided to sign up to get my genome sequenced. This is the third in a series of blog posts I'm writing about my own adventure in very personal genomics.

Along with my clinical report, Illumina delivered a portable hard drive (pictured) containing the underlying next-generation sequencing data. Given my computational genomics background, this was the product I'd most been looking forward to receiving. In fact, after picking it up, I found myself hastily biking five miles through the rain to get it to a computer!

The drive is protected using TrueCrypt, with the encryption key e-mailed separately. I installed the TrueCrypt on my Linux workstation, mounted the drive, and started to look around:

Blogging My Genome, episode 2: scratching the surface

After learning about Illumina's Understand Your Genome (UYG) program at ASHG 2013, I decided to sign up to get my genome sequenced. This is the second in a series of blog posts I'll write about my own adventure in very personal genomics!

Three months after shipping my blood sample off to the lab for whole-genome sequencing (WGS), I got the long-awaited message to come in and go over my results. And so on a rainy Friday afternoon I biked over to Stanford for genetic counseling. I was very excited, and yet not without awareness of the ~1% chance I could see one of the known pathogenic findings on the American College of Medical Genetics list for genome sequencing reports, and perhaps up to ~5% chance of some other medically actionable finding.

Fortunately, nothing like that came up. In fact, my report is quite unremarkable, which is of course a good thing:

Blogging My Genome, episode 1: parting with my blood (and treasure)

After learning about Illumina's Understand Your Genome (UYG) program at ASHG 2013, I decided to go ahead and sign up to get my genome sequenced. This is the first in a series of blog posts I'll write about my own adventure in very personal genomics!

UYG gets you:

• "Deep" whole-genome squencing (WGS) from a blood sample
• Bioinformatics and clinical interpretation through Illumina's CLIA lab
• Report sent to your clinician
• Raw data on a portable hard drive
• Day-long workshop with other participants
• iPad with the MyGenome app

...for $5,000, which isn't too bad given what's included. The pricing probably reflects that the program is mainly an outreach effort aimed at subject matter experts.

Ribosome profiling confirms widespread stop codon readthrough in flies

A recent eLife paper from the Weissman lab at UCSF uses high-throughput ribosome profiling to show that many Drosophila melanogaster (fruitfly) genes undergo an unusual translation process called stop codon readthrough - confirming many of, and expanding on, our earlier predictions based on computational comparative genomics. Stop codon readthrough occurs when a translating ribosome reaches an in-frame stop codon in an mRNA but, instead of terminating as usual, continues on with translation - as if the stop codon were a sense codon. This gives rise to a protein isoform with an extended C-terminal region, potentially modifying its function or localization.

Stop codon readthrough is a long-known but fairly obscure "recoding" mechanism, which wasn't believed to play a widespread role in metazoan gene expression, save for selenoproteins and a few other intriguing but isolated examples. Now we know that it actually affects hundreds of fly genes - and moreover that, in many cases, the products confer biological functions conserved throughout many millions of years of evolution.

Building OCaml programs in Cloud9 IDE

Cloud9 IDE is one of several new cloud-based products providing the ability to edit, build, test, and deploy code through a collaborative web application. Cloud9 IDE has one especially powerful feature: each workspace (i.e. project or repo) has a Linux home directory persisted along with the code and other settings, and you get a full bash terminal in this directory with modest but usable resource limits. This means it's possible to install and use a full OCaml toolchain inside, much like my previous effort on Travis CI.

I prepared a script to automate the process of installing OCaml and OPAM inside a Cloud9 IDE workspace. Enter into the terminal in any workspace:

curl -L https://raw.github.com/mlin/c9-ocaml/master/c9-ocaml.sh | bash -ex
eval $(opam config env)

The OCaml toolchain and OPAM are then ready to go. Here's a screenshot of compiling and running 'Hello, world!':