THE FUTURE OF GENOMICS & INFORMATICS IN THE NEXT 5 YEARS

Tina Graves-Lindsay, Leader of the Reference Genomes Group at the McDonnell Genome Institute (MGI) at Washington University St. Louis, kicked off the session talking about the research involved in achieving the best human whole genome assembly. As a member of the Genome Reference Consortium, Tina’s team has been working to improve the current reference, GRCh38, and fixing a few genes that are not optimally represented for all individuals or ancestries.

The sequence plan starts with generating 60x coverage of PacBio long read data for a de novo assembly. From there, MGI incorporates BioNano or Dovetail data to create scaffolds that in some cases nearly cover entire chromosome arms. Since MGI is targeting difficult to assemble regions of the genome, they sequence bacterial artificial chromosomes (BACs) to fill the targeted regions and then incorporate all this data together to generate a very high quality whole genome assembly labeled the “Gold Genome”.

http://blog.dnanexus.com/2015-10-15-post-ashg-the-future-of-genomics-informatics-in-the-next-5-years/

Slides for the 1000 Genomes Project tutorial at ASHG 2015

The 1000 Genomes project is holding a tutorial at ASHG 2015.

This tutorial will cover and overview of the 1000 Genomes Data, how to access it and how it can be used.

1. 7:15 – 7:30 pm Overview of the data set Hyun Min Kang - University of Michigan
2. 7:30 – 7:45 pm How to access the data Holly Zheng Bradley - European Bioinformatics Institute
3. 7:45 – 8:00 pm Structural variants Eugene Gardener - University of Maryland
4. 8:00 – 8:15 pm Functional variation Stephen Montgomery - Stanford University
5. 8:15 – 8:30 pm Admixture Alicia Martin - Broad Institute
6. 8:30 – 8:45 pm Using LDLink Mitch Machiela - National Cancer Institute7. 8:45 – 9:00 pm Q&A

No registration is needed for this meeting. Slides will be posted after the meeting is finished.

Source link: http://www.1000genomes.org/ashg-2015-1000-genomes-tutorial-thursday-october-8th-7-9pm-baltimore-convention-center-room-327-leve

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)

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 athttp://www.mmds.org

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.

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 http://www.samsung.com/sg/galaxys5/ ?

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 http://jobs.jobstreet.com/sg/jobs/4568249?fr=30

Research Assistant
http://jobs.jobstreet.com/sg/jobs/4566463?fr=30

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!

http://blog.plot.ly/post/113557928802/four-mistakes-to-avoid-if-youre-analyzing-data