Friday, 9 October 2015

What is personal genomics?

Wikipedia calls it as

"Personal genomics is the branch of genomics concerned with the sequencing and analysis of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips (typically 0.02% of the genome), or partial or full genome sequencing. Once the genotypes are known, the individual's genotype can be compared with the published literature to determine likelihood of trait expression and disease risk."

the irony of the matter is that no one man is an island. 

The allure of personal genomics is invariably the ability to use something like a tricorder or minION to collect data about your personal genome and suggest an action for you, specific to your genome, so that you may act on the full potential of your GATTACA

you might have been told how special you are. One in a billion. To make sense of what your genes are saying, you actually need to find rare individuals in sufficient quantities to make a statistical inference that the bunch of you who share this variant in your DNA that predisposes you to a XX% risk of being an XX person. 

the (100% - XX% ) chance of you being otherwise is often not explained well enough. Where would you find this missing variability? 

There's epigenetics which i would argue is more PERSONAL genomics than the PG offerings out there. These variations account for the environmental impact that is quantifiable by genetic testing. Most tests are research use only I presume. 
There's structural variations which potentially affects the genome more than SNPs, and trying to predict the phenotypic effects of SVs will probably plague the next generation of bioinformaticians and geneticists.
There's also the rare variants which may explain the missing heritability 
Then there's the very intimate microbiome which consists of microbes that may hold an entirely different genome from you but affects your health in such a strong way that I think personal genomics should include this category.

 So while cheaper sequencing technologies has enabled projects like The Personal Genome Project (PGP) or there's still a lot more to YOU than what your genes say about you through SNPs. 

That said, I am happy to genotype my SNPs with 23andMe kits or a kit from Xcode Life Sciences  to make an informed decision on maximising my exercise potential (and minimising the harm), but I need to be mindful to not ignore there's stuff that I may not carry personally but can make me into a roadkill statistic (1 in the 6426 ) or suffer an heart attack as a result of a stupid co-worker ... 

Live long and prosper , don't sweat the small stuff. (unless they are rare and have a combinatorial effect greater than its sum)

Saturday, 12 September 2015

Mining Massive Datasets by Stanford University on Coursera.

Mining Massive Datasets by Stanford University on Coursera.

Let the fun begin ... 

 In the next seven weeks, we will present to you many of the important tools for extracting information from very large datasets.  Each week there will be a number of videos to watch, and one or more homeworks to do.  The materials are backed up by a free on-line textbook, also published by Cambridge University Press, also called "Mining of Massive Datasets."  You can download the book at

The first week is devoted to two topics:

  1. MapReduce: A programming system for easily implementing parallel algorithms on commodity clusters.  This material is in the first four videos available for the week.
  2. Link Analysis: The remaining seven videos discuss the PageRank algorithm that made Google more effective than previous search engines.
There is also a single homework covering both topics.  This homework is classified as "Basic."  See below for an explanation of basic vs. advanced work, and the significance.

Thursday, 3 September 2015

The Workflow | Ion S5 Next Generation Sequencing System

Thermo Fisher Scientific recently announced their new sequencer, the Ion S5™ Sequencer. The system was designed to free up researchers time with a simple load and go reagents and fast sequencing times. In the video below, you will see how simple the Ion S5 System is to setup. First, the video walks through initialization, a quick 30 minute process that gets the system ready for sequencing. Then, you just simply need to swap out the old chip used for initialization with the chip with your sample, loaded during an Ion Chef™ System run. And as far as speed on the Ion S5 System is concerned, sequencing is fast – allowing you to complete a run in as little as two hour thanks to the semiconductor sequencing technology.

Kevin: Hmmm why choose S5 for a model name .. don't you know about ?

Monday, 8 June 2015

Careers with Lee Kong Chian School of Medicine

Helping a friend
Look for a Postdoctoral Research Fellow in the Laboratory of Assistant Professor Xueli Guan

Research Assistant

Saturday, 4 April 2015

four mistakes to avoid if you are analyzing data: useful reminder!

I have been following plotly for a while ... haven't had public data that I can play with on this though ... anyway they have a blog post that is a compilation of the 4 deadly sins of data analysis. Do check it out!

Saturday, 15 November 2014

What 5G mobile networks portends for the future of personal genomics

ok I saw this a while back (a month ago, yes I have been busy)

I am already very impressed with 4G (LTE) speeds but with 5G you can possibly achieve 150 mb/s to 940 mb/s which is mind blowing ...

Considering that you could then possibly upload via your mobile devices, your own 100 Gb bam file in about 10 seconds (sorry I wasn't thinking how much faster a youtube video would stream). Now Google is saying that they can store your genome (actually they meant your 30x WGS bam file) for $25 a year. But with 5G speeds, why would I even bother with that?

Heck, maybe in the future with an USB OTG cable connected to Oxford Nanopore's MinION your android phone will be able to sequence and upload in realtime your DNA obtained from a buccal swab. The cloud will have the fastq reads aligned and call variants instantaneously and download the 100 Gb bam to your microsd card.

Possible applications:

  1. Maybe in the future other than asking if you have a drug allergy, pharmacists will request to 'scan' your DNA for the most efficient drug. 
  2. another possible application might be having your DNA be your own personal identity card, 
  3. more routine sequencing of the human microbiome to monitor your health in relation to the gut microflora or other sites.

I am keen to find out what you think you can do if you could carry your whole genome sequencing with you and upload via mobile networks. Drop in your comments please!

Saturday, 13 September 2014

Datanami, Woe be me