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Author: Brian Krueger, PhD | Views: 15948 | Comments: 0

Image courtesy of Shutterstock
If you’re an avid follower of popular science in today’s news media, you might have noticed a recurring theme. Genomics is everywhere. On an almost weekly basis, the New York Times, the New Yorker, Forbes and a myriad of other outlets are publishing stories with overly optimistic ledes about doctors and gene sequencers being replaced by apps and iPhone accessories. You would be forgiven if you thought genomics was “solved” and we’re 5 years out from creating a Star Trek inspired “tricorder” that near instantly sequences your genome and tells you, without equivocation, what malady is afflicting you and how exactly to overcome said disorder. The fact of the matter is that we’re not there yet, not by a long shot.

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Author: Brian Krueger, PhD | Views: 6254 | Comments: 0
The Advances in Genome Biotechnology conference starts tomorrow in Marco Island, FL. Twitter and the blogs have been a flurry of speculation about what the major vendors will present at this years’ meeting. In previous years we’ve seen the introduction of new, “disruptive” technologies such as the ion torrent platform, the Oxford Nanopore Minion and the PacBio RS. Like many, I have mixed emotions about this conference. It’s more CES than science. Given the history of the major announcements and where those products are now 3 and 5 years out it’s hard to get excited about a show stopper. While technically impressive, the MinIon is still mired in problems that were glossed over in the fanfare of the original announcement and PacBio is FINALLY starting to deliver on the promises it made eons ago. I should also mention my disappointment with Ion Torrent here. This is yet another company that made a major announcement at AGBT and failed spectacularly. Keith Robison thinks they still have a sho . . . More
Author: Brian Krueger, PhD | Views: 6665 | Comments: 0
Yesterday marked the kickoff of the JP Morgan Healthcare Conference in San Francisco. Following last years’ lead, Illumina once again used this platform as an opportunity to announce the release of a number of new products including 4 “New” sequencing systems ahead of the more scientifically focused Advances in Genome Biotechnology conference in February. At this same time in 2014, Illumina presented the HiSeq X ten sequencing system which is a system for population scale genomics composed of ten HiSeq X sequencers. Illumina touted this system’s reduced reagent price, increased speed, and expanded capacity. It has now taken much of the technology from this HiSeq X system and put it into two new lower tier models: the HiSeq 3000 and HiSeq 4000.

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Author: Brian Krueger, PhD | Views: 6067 | Comments: 0
Illumina, the world leader in short read DNA sequencing, made a series of very big announcements yesterday at the JPMorgan Healthcare Conference. These developments have many sequencing labs around the world excited and worried all at the same time. The excitement comes from the fact that it appears on the surface that Illumina has broken the $1000 genome* barrier – the worry comes from the realization that only a few of us can afford it.

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Author: Brian Krueger, PhD | Views: 6726 | Comments: 0
It's been a long run and we have a strong readership of the press releases but sadly I no longer have the time or the interest to continue posting press releases on the site.  My additional work commitments here at Duke have really limited the amount of time I can devote to this and grabbing the press releases every night/morning for an hour or two just became tedious.  I'd like to spend my free time doing more creative things so hopefully I'll give my neglected blog some attention over the next few months.

To those who have been loyal followers of the press releases: Thanks for your devotion and continued support.  It does pain me to stop posting the press releases knowing they are served to nearly a million visitors a month, but I just do not have the time or desire to continue these activities.  I will, however, continue to post/link to mainstream news stories and blog posts I find interesting, so keep an eye on twitter and the right hand column here on the blogs.  I'll be adding a "from the web section" shortly.

The blogs will still be here for anyone that would like to use them as an outlet.  Just send me an email or contact me on twitter!

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Author: Brian Krueger, PhD | Views: 16815 | Comments: 9
Last by Michael Schatz on Feb 26, 2013, 12:13am
Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted. There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives. This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite the ridiculous parties and “showgirl” casino nights. The atmosphere here is unlike any other science conference I’ve attended. It’s like the bastard child of a Gordon Conference and a Las Vegas Porn Convention. I really hope that the deep pockets of Sequencing Centers are more influenced by the science than the free dinner parties and alcohol, but I have pretty low confidence in humanity. Regardless, I think everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology.

The PacBio talk came on the heels of what felt like a warm-up opening act from Jeremy Schmutz of the Hudson Alpha Institute. Schmutz has been working with a start-up that was recently acquired by illumina called . . . More
Author: Brian Krueger, PhD | Views: 7291 | Comments: 0
As the second day of AGBT kicked off, it became quite clear that this meeting would be dominated by medical genomics. There were a few talks sprinkled in about gut or sewer microbiomes but the vast majority of the talks the last two days have been on clinical genomic sequencing. This is fine by me since it’s exactly what we do in the Genomic Analysis Facility in Duke’s Center for Human Genome Variation. It’s really nice to see how other centers are approaching these problems. Unfortunately, this is one of the few opportunities we have to peek into each other’s operations.

Yesterday’s first talk was by Russ Altman of Stanford University. Russ has been a leader in the field of pharmacogenomics and he presented his work on developing the Pharmacogenomics Knowledgebase (PharmGKB, pharmGKB.org). He led by saying, “Don’t ever give a talk about a website,” and in his case it was true because WiFi in the conference room was down for the majority of his talk. He urged the crowd to follow along on the website, but only those of us with a cell connection could join him. Russ pointed out the major drawbacks of using GWAS and SNP chips for obtaining information about pharmacoenomic associations and joined pretty much everyone else in saying that the standard t . . . More
Author: Brian Krueger, PhD | Views: 7196 | Comments: 2
Last by Brian Krueger, PhD on Feb 21, 2013, 11:42pm
Today I dusted off my luggage and headed down to the annual Advances in Genome Biology and Technology meeting in Marco Island, FL.  Historically, this meeting has been the Detroit Auto Show of Genomics where companies and labs release their beautiful shiny new products and methodologies.  In past years, attendees were showered with fireworks displays and epic swag bags.  The tone this year is palpably more mutated.  One only has to point to the display banners located on the AGBT presenter stage for evidence of this: banners for Bronze and Silver Sponsors appear to hang waiting for accompaniment by Gold and Platinum brethren…there’s even space allocated for them.  

Despite the tightened biotech purse strings, the event appears from the outset to be extremely well organized.  There could be a few more power outlets for those of us carrying a small fortune in lithium powered devices, but I guess I’ll manage.  And of course there’s no live streaming or any form of web enabled anything…but I can gripe about that in a long winded and whiny post next week.

The evening opened with a brief introduction with a description of some new meeting changes.  This is the biggest AGBT yet with over 800 attendees.  A new abstract selection committee was created . . . More
Author: Brian Krueger, PhD | Views: 4211 | Comments: 3
Last by Brian Krueger, PhD on Sep 28, 2012, 5:02pm
One of the big stories that blew up on the internet the other day was the publication of some results that reportedly show that females who have birthed males have male DNA in their brain. That’s pretty cool stuff! This isn’t uncommon, it’s called microchimerism, or the deposition of cells or DNA from the fetus to the mother or vice versa. It has been shown in both mice and humans that the blood of the mother contains snippets of fetal DNA and even whole cells. These have even been used to completely sequence a fetal genome using only the blood of the mother. The finding that these DNA fragments or cells can deposit themselves in the human brain is novel, and potentially cool from a brain regulation standpoint. Maybe baby boy brain cells change the mother’s brain?

However, a quick read of the abstract of the paper yesterday immediately raised a few red flags in my own brain (absolutely full of male cells, by the way). The “discovery” was made using quantitative real-time PCR and only quantitative real-time PCR on a highly repetitive male gene on the Y chromosome. Most people who aren’t scientists don’t . . . More
Author: Brian Krueger, PhD | Views: 4901 | Comments: 2
Last by Brian Krueger, PhD on Sep 08, 2012, 12:05pm
In 1990, the scientific community embarked on a landmark experiment to completely sequence the human genome. At the time, it was assumed that knowing the exact sequence of the human genome would provide scientists all of the information they ever wanted to know about genomics and how DNA contributes to human disease. At least this is how the project was presented to the public, however, every genome scientist knew that obtaining the sequence of the human genome was a lot like getting a cake recipe that listed all of the ingredients but didn't explain at all how much of each ingredient to use, how to mix the ingredients together or how long to bake that mixture to create a delicious cake. Compound that with the fact that the list contains over 35,000 ingredients and you can quickly understand why the sequence alone wasn’t very informative. We spent over 3 billion dollars to obtain this sequence and since the final publication of the sequence in 2003, the media has questioned its usefulness. Apparently, because cancer wasn’t cured in 10 years, the human genome project is largely seen by the media as a colossal waste of money; however, obtaining this sequence has been invaluable in speeding up research and has significantly contributed to our understanding of how som . . . More
Author: Brian Krueger, PhD | Views: 22623 | Comments: 6
Last by Mike Gruidl on Feb 22, 2013, 1:22pm
It's bound to happen in every lab. Someone is going to get distracted and for whatever reason a box full of tubes or tubes themselves are going to accidentally get dropped in the lab's liquid nitrogen container. A lot of people might say, "Screw it," and leave those samples on the bottom of the tank. This might be a good solution for some samples, but what happens when you drop half a rack of boxes to the bottom of your tank? And what happens when those boxes are full of very important cell lines that keep your lab running?

I don't want to admit it, but this is exactly what happened to me today. I was preparing an order for a collaborator and getting 5 of my cell lines out of liquid nitrogen storage. I was explaining to my summer students how to safely handle liquid nitrogen, always wear cryoprotective gloves, lift the rack slowly and be sure to drain all of the liquid nitrogen before handling the boxes, etc. I got the box I needed, and put the rack back in the tank while I was hunting for my cells. Unfortunately, I forgot to put the wire back in the rack that holds the boxes in place. When I went to put the box back that I was handling, I pulled the rack up and half the boxes were gone. "Oh, shit."

So now the rack doesn't fit in . . . More
Author: Brian Krueger, PhD | Views: 2367 | Comments: 0

GFAJ-1 Credit: Wolfe-Simon et al
Almost a year and a half ago, NASA ignited a media firestorm after it announced the discovery of a new organism with alien implications. The whole fiasco began when a scientist found a new bacteria in Mono Lake that could grow in the presence of high concentrations of toxic compounds. These types of bacteria are not uncommon on earth. Life seems to find a way to thrive at all extremes and a salty lake in California is no exception to this rule. Researchers have discovered a diversity of life in hot springs, at undersea volcanic vents, and on the cold arctic sea floor. The discovery of this new bacteria; however, was remarkable because the researchers believed that it could use arsenic in the place of phosphate. To the general public, this may sound trivial, but many of the biochemical reactions that provide life require phosphates. The reason why arsenic is so toxic to humans is that it injects itself into all of the processes that use phosphate and prevents those processes from working properly. For example, the molecular backbone that keeps our DNA together is composed of phosphate; the energetic molecules that are produced by the power factories in our cells are composed of phosphate; the specific addition of phosphate to some proteins turns them on or off. Phosphate and its derivatives are essential for life, so to find a bacteria that could function without phosphate and use arsenic in its place was an amazing discovery.

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Author: Brian Krueger, PhD | Views: 3902 | Comments: 7
Last by Martin J Sallberg on Feb 15, 2013, 6:18am
Open science is a wonderful concept, but what happens when reporters start writing stories on data that has not been properly reviewed and vetted by the scientific establishment? Before this week, I had never really considered this question. Open science at its core is a wonderful utopian idea where scientists do their work in the open and publish their notebooks in real time on the web for everyone to see. The idea is that with this kind of transparency, better science will be done and scientists can collaborate more easily. Because all of the data will be on the internet and searchable, more scientists will be able to benefit from the open resource. Of course, there are numerous criticisms of open science. One being that it will be extremely easy for researchers in highly competitive fields to be scooped by competitors who have bigger labs or more resources at their disposal. However, it didn't occur to me until I saw stories popping up that open science could be abused by the media.

Almost a year ago, NASA held a press conference touting that it had found "alien" life. A group of researchers reported that they had found a bacteria (GFAJ-1) in Mono Lake that incorporated arsenic in place of phosphate in its DNA backbone. This press conference and the sub . . . More
Author: Brian Krueger, PhD | Views: 14154 | Comments: 0
So I came across a movie about Stanislaw Burzynski and his controversial antineoplastons treatment. So I'm pretty sure you are scratching your head wondering what an antineoplaston is? Apparently Burzynski created this convoluted phrase to use instead of simply saying, its a peptide. But take it from top here gang. In 1968, Burzynski graduated from medical school at age 24 in Poland, at age ~25 he also received a doctorate in biochemistry, making him one of the country's youngest M.D., Ph.D. Are you kidding me, when did he start his MSTP training program at age 17? The claim to the Ph.D. is slightly dubious as the medical school at that time was not known to grant Ph.D.'s and faculty at the Medical Academy of Lubin report that Burzyinski only did one year of a lab research project while in medical school to receive this mystery doctorate. Also the guy never received any specialized training in cancer or cancer therapeutics. So flash forward to 1973, Burzynski has spent the past three years at Baylor COM working in a lab isolating peptides from rat brains. He receives his license and is able to practice medicine in the US and also gets a three year grant to study urinary pepti . . . More
Author: Brian Krueger, PhD | Views: 2506 | Comments: 4
Last by Brian Krueger, PhD on Oct 24, 2011, 8:40am
Here are the slides from the presentation I gave on Monday. We recorded a video, but I'm not sure how it turned out. I have a feeling the audio is going to be bad so I might just sit down and do it over again this weekend on my laptop.

Two of the slides are movies. The first is a clip from "Flock of DoDos" where some lady says scientists are horrible communicators and the other is the AARP shrimp on treadmills commercial.

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Author: Brian Krueger, PhD | Views: 2459 | Comments: 2
Last by Brian Krueger, PhD on Oct 17, 2011, 11:55am
AARP put out a commercial a few months ago deriding wasteful spending in Washington. Unfortunately, the soundbytes don't accurately represent the full story behind the spending. Have a watch before continuing.

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Author: Brian Krueger, PhD | Views: 3130 | Comments: 0
In the current political climate it has become clear that science is a major target of Republican directed budget cuts. However, the soundbytes of politics do not represent the importance of science in our lives. Because of this, I think it's extremely important that we explain why some of our model systems are so important for understanding how viruses and ultimately human disease work.

In the lab that I run, we currently work on mutating two different herpesviruses. One of these is Kaposi's Sarcoma Herpesvirus (KSHV) and the other is Murid Herpesvirus 68 (MHV68). Both of these viruses are gammaherpesviruses. In humans, KSHV only really ever becomes a problem in individuals who have a compromised immune system such as those infected with human immunodeficiency virus (HIV). KSHV is an interesting virus because its default program is latency, meaning that once it gets into your cells, it turns itself off and waits for conditions which allow it to grow and take over. This is akin to a bear hibernating in the winter. We do not understand how or w . . . More
Author: Brian Krueger, PhD | Views: 603 | Comments: 0
Wow! Mrs. Irish has posted pictures of her students using the microscope, slides and workbooks that we helped purchase for her classroom. This is exactly why we work so hard to try to bring in donations through the DonorsChoose program.

There are still 60 or so unfunded projects on our giving page, sp please stop by and help in any way you can.

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Author: Brian Krueger, PhD | Views: 888 | Comments: 0

Mr. Bradham in class
Today's featured DonorsChoose project is: Launch a Rocket of Success. Mr. Bradham is looking to buy rocket kits for his science class to teach his students about physics and space exploration. He says that his students are, "eager for knowledge. Unfortunately, they lack the adequate financial means to provide for supplies that could further their understanding of science concepts." Mr. Brandham is looking for a "hook" to get students interested in and excited about science and from past experience with rocketry programs he has found that students are captivated by rocket launches and this provides a stepping stone for him to teach other science concepts in the classroom.

I can't argue with Mr. Bradham's logic. I remember when I was a kid and I got a hold of my first rocketry set. It was a basic ESTES model that I had to glue and assemble myself. I really enjoyed learning about the physics and chemistry of the launches. Launching the rockets in my local park was always a blast, but the hobby was expensive! The engines for my rockets were like $5 and for a grade schooler with a tiny allowance of a couple dollars a month it was hard to fuel my obsession. I think it's very sad that Mr. Bradham can't get the funding from his school for this project because he teaches in a high poverty district. I see enormous value in this type of activity as a teaching tool. The excitement of a rocket launch can quickly translate into student fervor in the class room to try to understand how to make the rockets fly higher and faster.

Mr. Bradham has a long way to go to fund his project though, so we need your help! Every little bit counts, so please donate whatever you can to make this happen.

You can view more projects by visiting our giving page.

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