Showing posts with label minion. Show all posts
Showing posts with label minion. Show all posts

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 deCODEme.com 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, 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) http://www.engadget.com/2014/10/14/samsung-5g-network-tests-oh-god-the-speed/

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!

Datanami, Woe be me