US clinics quietly embrace whole-genome sequencing @ Nature News

read the full article
As hospitals and insurers battle over coverage for single-gene diagnostic tests, and the US Food and Drug Administration cracks down on the products of personal genomics companies, a growing number of doctors are relying on the sequencing of either the whole genome or of the coding region, known as the exome.
"If one hospital is doing it, you can be sure others will start, because patients will vote with their feet," Elizabeth Worthey, a genomics specialist at the Human and Molecular Genetics Center (HMGC) of the Medical College of Wisconsin in Milwaukee, said at the Personal Genome meeting at Cold Spring Harbor Laboratory in New York last weekend.
In May 2009, the genetic-technology provider Illumina, based in San Diego, California, launched its Clinical Services programme with two of its high-throughput genome analysers. The company now has 15 such devices dedicated to this programme.
Illumina provides the raw sequence data attained from a patient's DNA sample to a physician, who passes it on to a bioinformatics team, which works to crack the patient's condition. However, Illumina is working to develop tools to help physicians navigate genomes and identify genes already associated with diseases, as well as novel ones.
So far, the company has sequenced more than 24 genomes from patients with rare diseases or atypical cancers at the request of physicians at academic medical centres. The standard US$19,500 price tag is typically covered by the patient, by means of a research grant, or with the help of private foundations, although one patient is currently applying for insurance reimbursement. 

I would be really surprised if insurance is able to cover for exome sequencing in any conditions. Also see my Commentary on Personal Genomics testing

Genomes: $1K to seq $1 Mil to analyse

Genomes: $1K to seq $1 Mil to analyse

By Kevin Davies

October 1, 2010 | It is doubtful that the scientists and physicians who first started talking about the $1,000 genome in 2001 could have imagined that we would be on the verge of that achievement within the decade. As the cost of sequencing continues to freefall, the challenge of solving the data analysis and storage problems becomes more pressing. But those issues are nothing compared to the challenge facing the clinical community who are seeking to mine the genome for clinically actionable information—what one respected clinical geneticist calls “the $1 million interpretation.” From the first handful of published human genome sequences, the size of that task is immense.

LOL I would like to see where the $1 million dollars is trickling to.. it may not cost as much as $1 million to analyze most data but the infrastructure costs are possibly ~ $1 million. I do hope to get a pay increment if the $1 million does trickle down to me though!

 edit: added link to article and guess what? Kevin Davies wrote a book! 
very curious now.
 

The Solexa Story

Ya I love universal truths like things are invented over beer

BGI Hong Kong has big plans and hopes to sequence all the genetics in the world.

http://www.bio-itworld.com/2010/09/29/bgi-hk.html
BGI Hong Kong has big plans and hopes to sequence all the genetics in the world.

Interesting read! But I do wonder if it's good thing if all the genetics are sequenced by one monolithic company

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!