Category Archives: personal

This blog in 2013

In something of an end-of-year tradition, WordPress provides users with an effort-free blog post in the form of an annual report. Here is mine.

My ambitious plan at the start of 2013 was to aim for 4 posts a month. I managed 28 and I’m happy with that; about one every two weeks.

Looking forward to a new year of blogging. All the best to you and yours for 2014.

Using the Ensembl Variant Effect Predictor with your 23andme data

I subscribe to the Ensembl blog and found, in my feed reader this morning, a post which linked to the Variant Effect Predictor (VEP). The original blog post, strangely, has disappeared.

Not to worry: so, the VEP takes genotyping data in one of several formats, compares it with the Ensembl variation + core databases and returns a summary of how the variants affect transcripts and regulatory regions. My first thought – can I apply this to my own 23andme data?

Read the rest…

23 and me – yes, me – part 2

Sample journey and arrival

fedex-delivered

Spitting across the Pacific

My tube of spit arrived at the lab on May 19. Six days door-to-door via Guangzhou, Anchorage and Memphis to LA.

23andmeraw

23andMe raw data menu

On arrival, a confirmatory email: “The spit sample you recently submitted to 23andMe for the person listed above has been received by the laboratory and is now pending analysis; the process usually takes 6-8 weeks. You will receive another email notification from us as soon as the data for this sample are ready to be accessed through your 23andMe account.”

In the meantime, there’s plenty to explore at the 23andMe website. Anyone can create a demo account, which allows you to explore anonymous sample data to get a feel for what you’ll see when your own sample is processed. Naturally, I’m most excited by the options to browse and download raw data. You can also participate in around 20 health and genetics surveys which are a good way to kill time, although not many of them provide instant personal gratification.

Next update – some time in July.

23 and me – yes, me – part 1

Until recently, I was not even aware that there is a DNA day. Nor can I tell you exactly when and where I noticed that 23andMe, the personal genomics company, launched a sale to celebrate the day – I imagine it flashed by on Twitter or FriendFeed. I can tell you that like many others I decided that finally, I could justify the expense, signed up (with around 15 minutes to spare – thanks to the 17 hour Sydney/California time difference) and I’m now waiting for sample arrival and processing.

I thought it might be interesting to blog the experience and provided that I don’t discover anything disturbing (finding out that I’m actually a woman, for example), I’ll share some of my data here. Related posts will be tagged with “23andme” and here is part 1 which covers sign-up, delivery, sample collection and return.
Read the rest…

Temporary blogging hiatus

I’m now immersed in the process of moving from Brisbane to Sydney (with no new accommodation as yet), in preparation for my new role at CSIRO starting March 2.

Consequently, it will be quiet here for at least a couple of weeks. I’ll be sending the occasional tweet and the odd item to FriendFeed, but nothing substantial until home internet is up and running again.

Anniversary #2

Managed to fly through my blog anniversary.

August 2 marks two years here at wordpress.com. Stats as of now: 677 posts, 10 pages, 49 categories, 255 tags, 1,128 approved comments and 67,184 spam comments (!).

Blogging has really dropped off in the past few months, but I have some ideas about that. Stay tuned, thanks for reading and commenting.