SeqCentral not just another company using Cloud computing for genomics

It is not everyday you see a bioinformatics company get featured on Techcrunch. Not by my count anyway. SeqCentral's website hasn't officially launched yet but they did launch on Techcrunch disrupt (check their twitter).
SeqCentral, LLC, aims to provide and harness the high-performance computational power of the cloud as a usable, collaborative, online service to all members of the computational genomics community.


Using the cloud to do computational genomics isn't terribly new. But the collaborative aspect is. 


SeqCentral will allow scientists to compare their data to others to see if their sequencing is new or if it is “known.” The startup will bring in public data from universities, research organizations, and companies and allow you compare your sequencing to this existing data.

And SeqCentral, which costs $99 per year for scientists, wants to help you do more than just be able to find additional data, but also aims to connect members of the genomics community, encouraging collaboration around sequencing.

Other than the cheap price, which is 'democratizing', I find the idea of asking scientists to share their new sequencing data using their platform daring!

Granted that it only speeds up the sharing process if the data is due to be in public domain (due to public research funding). I had the crazy idea that if the clients would allow sequencing providers can share info that they have clients sequencing same samples (cancer cell lines for example) this way both Client A and Client B can save $ on sequencing coverage. Ultimately, I felt that it wouldn't work out as MTAs are such a hassle. Good Luck to SeqCentral though! I am rooting for ya..

Commentary on Personal Genomics testing

I was reading the usual "say no to personal genetics tests" blog post

 The Empty (and Misleading) Promises of Do-It-Yourself Genetic Tests

I shall go out on a limb here and declare up front, I am ambivalent about personal genetic tests. In addition, I am wholly against unscrupulous consumerism that overpromises (which might be genetic tests for factors that can't possibly be done now with our current scientific knowledge e.g. intelligence testing, for a list of good examples you may refer to "Some of the 40 behavioral genes that are tested  here." There are a few of the behavioural genes which I believe are bona fide but 'self detoxification' has to be a joke, I hope)

That being said, I would like to offer the flipside of the story. 

The term 'increased risk' is contentious. If you recall the "Toyota Recall" fiasco, did you manage to get any numbers on the increased risk of driving one of the affected cars? The difference is 0.00028 percent according to this page. 

Would that stop you from not sending your car in?

Of course not, and I am not urging you to stop as well. 

But the point is not wholly about the increased risk, but rather your right to know the risks that you are taking. Knowledge is a double edged sword, I recall a friend being tormented by her positive results for early Down's Syndrome screening for her unborn child. Only the negative results from her amniotic fluid test set her mind at rest. Yet I believe no one would ask that the results of the first test be kept private from a patient to prevent undue worry. And I am sure the doctor explained the test fully. But it is only natural for my friend to be worried. 

I do agree with Taralyn, without a healthcare professional explaining the results of the test, the potential for abuse and fear mongering is there. However, she should expect the average consumer who chooses a genetic test, is not an average consumer. He or she is likely an educated consumer, who has an idea of what the test portends or has a known family history of cancer / genetic disease and wishes to have the knowledge to better manage his/her lifestyle.

And to Taralyn, I would like to answer with a "YES" to your question of "Will I ever be able to air-mail a swab of my saliva for my genetic read-out?" Not because you should but you can if you so choose to. This is because the technology is here.

The Broad’s Approach to Genome Sequencing (part II)

Bio-IT World | Since 2001, computer scientist Toby Bloom has been the head of informatics for the production sequencing group at the Broad Institute. Her team is the one that has to cope with the “data deluge” brought about by next-generation sequencing. Kevin Davies spoke with Bloom about her team’s operation, successes and ongoing challenges.

They have to deal with 0.5-1 terabases a day! That's a lot to handle!

Whole transcriptome of a single cell using NGS

I think the holy grail of gene profiling has to be single molecule sequencing from a single cell. Imagine the amount of de novo transcriptomics projects that will spring up when that becomes an eventuality!

Posted by Alison Leon on Aug 12, 2010 2:00:42 PM

Are you struggling with conducting gene expression analysis from limited sample amounts? Or perhaps you're trying to keep up with new developments in stem cell research. If so, you might be interested in a recent Cell Stem Cell publication discussing single-cell RNA-Seq analysis (Tang et al., Cell Stem Cell, 2010). In their research, Tang and colleagues trace the conversion of mouse embryonic stem cells from the inner cell mass (ICM) to pluripotent embryonic stem cells (ESCs), revealing molecular changes in the process. This is a follow-on to two previous papers, in which the proof of concept (Tang et al., Nature Methods, 2009) and protocols (Tang et al., Nature Protocols, 2010) for these experiments were detailed.

Using the SOLiD™ System (16-plex, 50-base reads) and whole transcriptome software tools, researchers performed whole transcriptome analysis at the single-cell level (an unprecedented resolution!) to determine gene expression levels and identify novel splice junctions. 385 genes in 74 individual cells were monitored during their transition from ICM to ESC. Validation with TaqMan® assays corroborated this method’s high sensitivity and reproducibility.

According to Tang et al., this research could form the basis for future studies involving regulation and differentiation of stem cells in adults. In addition, further knowledge about developing stem cells could lead to information about how disease tissues, including cancers, develop.

Simple Copy Number Determination with Reference Query Pyrosequencing (RQPS)

Simple Copy Number Determination with Reference Query Pyrosequencing (RQPS)

Zhenyi Liu^1,3, Daniel L. Schneider¹, Kerry Kornfeld¹, and Raphael Kopan^{1,2,3 1} Department of Developmental Biology, School of Medicine, Washington University, St. Louis, Missouri 63110, USA
² Division of Dermatology, Department of Medicine, School of Medicine, Washington University, St. Louis, Missouri 63110, USA

The accurate measurement of the copy number (CN) for an allele is often desired. We have developed a simple pyrosequencing-based method, reference query pyrosequencing (RQPS), to determine the CN of any allele in any genome by taking advantage of the fact that pyrosequencing can accurately measure the molar ratio of DNA fragments in a mixture that differ by a single nucleotide. The method involves the preparation of an RQPS probe, which contains two linked DNA fragments that match a reference allele with a known CN and a query allele with an unknown CN. 

Pysam - python module for read and manipulating sam files

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. 

Looks promising! but failed at compile as I as missing a module on CentOS 5.4

python setup.py build
Traceback (most recent call last):
  File "setup.py", line 9, in ?
    import os, sys, glob, shutil, hashlib
ImportError: No module named hashlib

To be continued....

The Broad’s Approach to Genome Sequencing (part I)

In Part I of a two-part exclusive interview, Nicol and Nusbaum share some of the keys to the Broad’s sequencing success with Bio-IT World chief editor Kevin Davies. 

excerpted
NUSBAUM: The cost of storage is coming down very slowly [compared to sequencing costs]. It’s not very hard to foresee a time when storage is half the [total] cost [of sequencing].
NICOL: Or we store it as DNA – and resequence it!
NUSBAUM: It’s been a couple of years since we saved the primary [raw image] data. It is cheaper to redo the sequence and pull it out of the freezer. There are 5,000 tubes in a freezer. Storing a tube isn’t very expensive. Storing 1 Terabyte of data that comes out of that tube costs half as much as the freezer! People [like Ewan Birney at EBI] are working on very elaborate algorithms for storing data, because you can’t compress bases any more than nature already has. The new paradigm is, the bases are here, only indicate the places where the bases are different . . . In 2-3 years, you’ll wonder about even storing the bases. And forget about quality scores.
The cost of DNA sequencing might not matter in a few years. People are saying they’ll be able to sequence the human genome for $100 or less. That’s lovely, but it still could cost you $2,500 to store the data, so the cost of storage ultimately becomes the limiting factor, not the cost of sequencing. We can quibble about the dollars and cents, but you can’t argue about the trends at all.



My comments:
It seems terribly weird that DNA is more 'efficient' than HDD (or archival tapes) for storing data. Granted cost wise, it might be cheaper to store DNA but they neglected to factor in the time required to find that tube, process it. And the cost to implement a LIMS so that you CAN find that tube, and the man hours used to seq the DNA.
Looking forward to Part II of the interview!
what are your thoughts?