Tag Archives: genetics

From the Arxiv (What Caught My Eye Last Week)

Quantifying the impact of weak, strong, and super ties in scientific careers
Alexander Michael Petersen
PDF: http://arxiv.org/pdf/1509.01804v1.pdf
Soundbite: “We find that super ties contribute to above-average productivity and a 17% citation increase per publication, thus identifying these partnerships – the analog of life partners – as a major factor in science career development.”

Do we need another coffee house? The amenity space and the evolution of neighborhoods
César A. Hidalgo, Elisa E. Castañer
PDF: http://arxiv.org/pdf/1509.02868v1.pdf
Soundbite: “Neighborhoods populated by amenities, such as restaurants, cafes, and libraries, are considered to be a key property of desirable cities. … Finally, we use the Amenity Space to build a recommender system that identifies the amenities that are missing in a neighborhood given its current pattern of specialization.”

Liberating language research from dogmas of the 20th century
Ramon Ferrer-i-Cancho, Carlos Gómez-Rodríguez
PDF: http://arxiv.org/pdf/1509.03295v1.pdf
Soundbite: ” Those tenets can be summarized as a belief in the existence of word order constraints that cannot be explained by evolutionary processes or requirements of performance or learning, and instead require either (a) heavy assumptions that compromise the parsimony of linguistic theory as a whole or (b) explanations based on internal constraints of obscure nature.”
Interesting: “We submitted our commentary to PNAS but it was rejected. We hope that the availability of our submission helps to liberate language research from dogmas of the 20th century”

Estimating Reproducibility in Genome-Wide Association Studies
Wei Jiang, Jing-Hao Xue, Weichuan Yu
PDF: http://arxiv.org/pdf/1508.06715v1.pdf
Soundbite: “This can be used to generate a list of potentially true associations in the irreproducible findings for further scrutiny.”

Nucleosome positioning: resources and tools online
Vladimir B. Teif
PDF: http://arxiv.org/pdf/1508.06916v4.pdf
About: Gene Regulation Info
Includes: Nucleosome positioning datasets sorted by cell type

Combining exome and gene expression datasets in one graphical model of disease to empower the discovery of disease mechanisms
Aziz M. Mezlini, Fabio Fuligni, Adam Shlien, Anna Goldenberg
PDF: http://arxiv.org/pdf/1508.07527v1.pdf
Soundbite: “It is not unusual to observe a significant gene expression change in thousands of genes, the majority being a downstream, rather than the driver, effect (e.g. inflammation, drug response, etc) Additionally, and more importantly, there is a large heterogeneity in gene expression in cancer: many patients within the same subtype will appear to have an abberant expression. These variations are of unknown cause.”

Using Genetic Distance to Infer the Accuracy of Genomic Prediction
Marco Scutari, Ian Mackay, David Balding
PDF: http://arxiv.org/pdf/1509.00415v2.pdf
Soundbite: ” In human genetics, decay curves could be used study to what extent predictions are accurate and thus to improve the performance of medical diagnostics for the general population. In plant and animal breeding, on the other hand, it is common to incorporate distantly related individuals in selection programs to maintain a sufficient level of genetic variability.”

Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A. Neher
PDF: http://arxiv.org/pdf/1509.02483v1.pdf
Soundbite: “In most patients, the virus populations was initially homogeneous and diversified over the years, as expected for an infection with a single or small number of similar founder viruses (Keele et al., 2008). In two patients, p3 and p10, the first sample displayed diversity consistent with the transmission of several variants from the same donor.”
Soundbite: “Our reasoning proceeds as follows. Figure 6B indicates that diversity accumulates over a time frame of 2-4 years, i.e., about 1,000 days. Recombination at a rate of 10−5/bp/day hits a genome on average every 100 bps in 1000 days. Mutations further apart than 100bps are hence often separated by recombination and retain little linkage consistent with the observed decay length in Figure 7.”

Inadequate experimental methods and erroneous epilepsy diagnostic criteria result in confounding acquired focal epilepsy with genetic absence epilepsy
Raimondo D’Ambrosio, Clifford L. Eastman, John W. Miller
PDF: http://arxiv.org/pdf/1509.01206v1.pdf
Soundbite: “Because the authors could not induce focal seizures by FPI, they ended up comparing absence epilepsy in their controls with absence epilepsy in FPI rats, and concluded that they look similar. They also used inappropriate epilepsy diagnostic criteria that cannot distinguish between focal non-convulsive seizures and genetic absence epilepsy. Moreover, the authors failed to consider all literature conflicting with their conclusion, and surmised similarities between the absence epilepsy in their rats with the focal seizures we induce by rpFPI.”

Reduction of Alzheimer’s disease beta-amyloid pathology in the absence of gut microbiota
T. Harach, N. Marungruang, N. Dutilleul, V. Cheatham, K. D. Mc Coy, J. J. Neher, M. Jucker, F. Fåk, T., Lasser, T. Bolmont
PDF: http://arxiv.org/pdf/1509.02273v1.pdf
Soundbite: “Our results indicate a microbial involvement in the development of Alzheimer’s disease pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.”

Fractal Fluctuations in Human Walking: Comparison of Auditory and Visually Guided Stepping
Philippe Terrier
PDF: http://arxiv.org/pdf/1509.01913v1.pdf
Soundbite: “[B]ecause it can be assumed that AC and VC mobilize the same motor pathways, they can probably be used alternatively in gait rehabilitation. The efficiency of VC to enhance walking abilities in patients with neurological gait disorders needs further studies. However, the high gait variability induced by VC might have detrimental effects, for instance, a lower dynamic balance. This should be taken into account in the development of VC rehabilitation methods.”

The Brain Uses Reliability of Stimulus Information when Making Perceptual Decisions
Sebastian Bitzer, Stefan J. Kiebel
PDF: http://arxiv.org/pdf/1509.01972v1.pdf
Soundbite: “Our analysis suggests that the brain estimates the reliability of the stimulus on a short time scale of at most a few hundred milliseconds.”

Brain Model of Information Based Exchange
James Kozloski
PDF: http://arxiv.org/pdf/1509.02580v1.pdf
Coolness: IBM Neural Tissue Simulator (about NTS | NTS slides | 1st article)

Interplay between the local information based behavioral responses and the epidemic spreading in complex networks
Can Liu, Jia-Rong Xie, Han-Shuang Chen, Hai-Feng Zhang, Ming Tang
PDF: http://arxiv.org/pdf/1509.01321v1.pdf
Soundbite: “The spreading of an infectious disease can trigger human behavior responses to the disease, which in turn plays a crucial role on the spreading of epidemic…. Our finding indicates that, with the increasing of the response rate, the epidemic threshold is enhanced and the prevalence of epidemic is reduced.”

Identification and modeling of discoverers in online social systems
Matus Medo, Manuel S. Mariani, An Zeng, Yi-Cheng Zhang
PDF: http://arxiv.org/pdf/1509.01477v1.pdf
Soundbite: “We develop an analytical time-aware framework which shows that when individuals make choices — which item to buy, for example — in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators.”

Time-aware Analysis and Ranking of Lurkers in Social Networks
Andrea Tagarelli, Roberto Interdonato
PDF: http://arxiv.org/pdf/1509.02030v1.pdf
Soundbite: “Our goal in this work is to push forward research in lurker mining in a twofold manner: (i) to provide an in-depth analysis of temporal aspects that aims to unveil the behavior of lurkers and their relations with other users, and (ii) to enhance existing methods for ranking lurkers by integrating different time-aware properties concerning information-production and information-consumption actions.”

A Tack Board of Tags (HOTW July 19, 2015)

There have been some fantastic conversations on Twitter this week, on a huge diversity of topics and organized around some intriguing hashtags. I was personally involved with the Summit for the Mayo Clinic Center for Social Media (#MCCSM) and the local systematic review training course (UMTHLSysRev). It was a series of happy coincidences that led me to the events Astrobiology Science Conference 2015 (#AbSciCon); Inspirefest 2015, the future of science, technology, engineering, and mathematics with new perspectives on innovation, leadership and success (#inspirefest2015); and International Association for Suicide Prevention (#IASP2015). I was surprised to find two very relevant Twitter chats that were new to me: hereditary cancer chat (#hcchat) and the Internet of Things chat (#IoTchat). Last but far from least, the nursing-inspired #WhyWeDoResearch tag is a very motiving and inspiring meme to explore. I’ll put just a few examples of each below, hoping to intrigue you enough to go look at these yourself.


Mayo Clinic Center for Social Media | #MCCSM (#mccsm archive)


Systematic Reviews Workshop: Opportunities for Librarians |
#umthlsysrev (#umthlsysrev archive)


Astrobiology Science Conference 2015 | #AbSciCon


Inspirefest | #inspirefest2015


28th World Congress of the International Association for Suicide Prevention, Montreal, 2015 | #IASP2015 (#IASP2015 archive)


Hereditary Cancer Chat #HCchat
(#HCchat archive)


#IoTChat: Internet of Things Twittersphere Chats Evolve | #IoTchat


Why We Do Research Campaign (Weebly sites blocked in UM hospitals) [Campaign video 1; campaign video 2] | #WhyWeDoResearch (#WhyWeDoResearch archive)

Good Lord, People, 23andMe is NOT Dead!

Reposting from my personal genomics blog because I think it is important also for the audience of this blog.


23andMe

Good Lord, people, 23andMe is NOT dead! Or closed, or no longer taking orders, or anything like that. I hear this a lot.

“You know, I always wanted to get my genome tested. I was going to try 23andMe, but then the FDA shut them down. Oh, well, missed my chance. [sigh]”

NO! You did NOT miss your chance. Firstly, 23andMe is not closed for business. They still will take your money and your sample. They still will analyze the sample and give you results. From what I’ve been seeing in the results from folk I’ve been helping to look at their data, 23andMe seems to be running the test exactly the same way they always did, for the same SNPs.

They simply are, at this time, not offering their health reports to new customers. It isn’t the data that has changed – it iw what analysis is shared with the customer. Old fogies like me who got their tests done before the FDA folderol” still have access to our old 23andMe health reports, and they continue to improve them.

I have heard nothing to indicate that 23andMe are not working with the FDA to try to make it possible to release health reports again in the future. Issues around that get complicated and I’m going to save them for a later post. Right now, what if you wanted a test for some genetic health information? Can you do it? How long will you have to wait to find out the answers to your health questions?

You can still do it. It isn’t as easy as it was before, but it can be done. I’ve been spending a lot of time talking people through how to do this, and it is time to write it down. If nothing else, it will save me time. This will be the short short version, and I can answer more detailed questions and describe specifics, maybe give an example or two or three.

FIRST, THE DISCLAIMER

Risk is Not Just Genes

Making sense of genetic information is complicated even for experts, which most of us are not. Of course, part of the irony of looking at genetics for health conditions is that most of the time what causes the condition is not just the genetics, but genes PLUS something else. If you don’t find the genes for something, that doesn’t mean you can’t get it; if you do find the genes for something, it doesn’t mean you will get it. It is hardly ever a case of this=that.

What Does Risk Mean, Anyway?

There is also the challenge of figuring out how important the risk is, and whether or not to do something about it. So, my personal risk of celiac disease is over 4 times normal. Wow! That sounds like a lot, doesn’t it? But 4 times normal for celiac risk is still only 1 in 20 people, because normal is about 1 in a hundred. I know someone with celiac risk 17 times normal, which is 1 in 4 people. That’s getting to be pretty serious! But, while celiac is dangerous, it isn’t one of those conditions that is immediately deadly or painful. And my friend still has a 3 in 4 chance of NOT getting celiac, and that is a lifetime risk.

On the other hand, my risk of venous thromboembolism (VTE) is 1.5 times normal. That doesn’t sound like much does it? It’s higher, but only a little bit. So we don’t really need to worry about it, do we? Well, yes. VTE can kill you on the spot, and it is incredibly painful. And normal is 1 in 10 people for lifetime risk. For me, the risk is closer to 1 in 7.

Given that, according to 23andMe, my genetic risk of celiac is roughly 1/20 and my risk of VTE is 1/7, and adding in the comparative dangers of the two diseases, my docs got all excited about the VTE, and not terribly about the celiac. I hope you understand why now, and also a bit more about why genetic risk is complicated.

On Asking for Help

Last part of the disclaimer.

For both of these, celiac and VTE, 23andMe looks at SOME of the genes and SNPs known to be associated with the condition, but not ALL of them. So whatever 23andMe tells me about risk is only part of the picture. It looks at the most important genes, but is still only part of the picture. That’s why you need experts to put all the pieces together, and get more information to fill in the gaps from the 23andMe test.

Everyone always says, “Ask your doctor,” when it comes to finding something puzzling, confusing, contradictory, or worrisome in your genetic tests. I did, and found that most of my doctors didn’t have the expertise to make more out of it than I did. Some poohpoohed the 23andMe results, others made clinical decisions based on them without verifying with other tests, some asked for more medical tests to expand upon what 23andMe had, and one said, “You know more about this than I do, but I’m going to learn.” Here is a quote from an NEJM article a few months ago about the risks and benefits of trusting direct-to-consumer personal genomic services such as 23andMe.

“Clinicians will be central to helping consumer–patients use genomic information to make health decisions. Any regulatory regime must recognize this reality by doing more than simply adding the tagline on most consumer ads for prescription drugs: “Ask your physician.” That is insufficient guidance unless your physician has ready access to a clinical geneticist or genetic counselor.” Annas GJ, Elias S. 23andMe and the FDA. N Engl J Med 2014; 370:985-988. http://www.nejm.org/doi/full/10.1056/NEJMp1316367

Some of the personal genomics service offer phone-in access to genetic counselors. I tried that, and didn’t get helpful answers there, either. Even worse, one of the answers I got was blatantly wrong. It may have been just the genetic counselor who I happened to be talking with, so don’t judge the whole profession by that one person, but do be prepared to keep looking for info if needed. Where I found the most helpful information was in the 23andMe forums, BUT a lot of the info there was unreliable, and I had to sort out what was helpful and what wasn’t.

So, my recommendation is, absolutely DO ask your doctor, ask a genetic counselor if you can, but that might not be enough. You might need to do more research on your own, or find someone you trust to help you with this.

What Good Is It?

So, what good is it then? It gives you clues. Like a detective, you take the clues and look for more information, or ask for more thorough testing, or raise questions that weren’t being asked or addressed before. Some of the clues will be red herrings. Some of them may lead you to a prized solution. For me, these clues ended up dramatically improving my quality of life, and may have even saved my life.


So, now, the short short version. And PLEASE, if someone more expert than me with genomic data reads this and spots any errors, please say so!

PART ONE

1. Get your 23andMe test done.

Pic of the Day - PGenPGEN, Take 2

2. Log in at the 23andMe web site when you are notified that your results are ready.

23andMe

3. Click: Browse raw data.
23andMe: Getting to your raw data

It should look like this:

23andMe: Browse Raw Data

4. Click: Download raw data.
23andMe: Download Raw Data

5. Complete security procedure (log in again, answer security questions, etc.). It should look like this.

23andMe: Downloading Raw Data

6. Answer the question about what type of data and format you want. NOTE: I always choose ALL DNA, unless you have something else specifically in mind.

23andMe: Downloading ALL Your Raw Data Or ...

7. Find the file (which will be named something like genome_Firstname_Lastname_Full_12345678901234.txt)

PART TWO (A): Easier Way

Genetic Genie

Now you have choices. You can dig into the information the easier way, or the less easy way. Let’s start with the easier way.

1. Select a tool to do what you want with your data. There are LOTS of tools people have built to do useful things with 23andMe data files. One of my favorites is Genetic Genie, because it tells you about the MTHFR gene which has become so important in my life. I also am spending a lot of time with Promethease because it is so complete compared to most other 23andMe analysis tools. Lets start with these.

2. Go to the tool of your choice, such as:

Genetic Genie: http://geneticgenie.org/

Promethease: http://www.snpedia.com/index.php/Promethease

3. Follow the directions at the tool, but this almost always requires you to upload your 23andMe data file. Here are more details about doing this with Genetic Genie.

4. Last come what is always the tricky part — making sense of the information you get. That’s worth several posts, but for starters the main point to remember is that the 23andMe test is a place to start, not a final answer. In Genetic Genie, the code, analysis, and text are written by engaged amateurs, not by doctors or genetic counselors. They worked hard, collaborated with a lot of other people, and did a lot of research, but it isn’t going to say the same things your doctor might.

More Tools

23andMe: Tools for Everyone http://www.23andyou.com/3rdparty
NOTE: When 23andMe took out the health reports, they also edited this page to remove links to tools that provide health data from 23andMe data. So, this is interesting and useful, but not sufficient. You’ll have to look somewhere else for most tools.

23++ Chrome Extension: Get more from your data:
http://23pp.david-web.co.uk/getting-more-from-your-data/

Confessions of a Cryokid: Top 10 things to do with your FTDNA raw data (2011) http://cryokidconfessions.blogspot.com/2011/06/top-10-things-to-do-with-your-ftdna-raw.html

Genetic Genealogist: What Else Can I Do With My DNA Results: http://www.thegeneticgenealogist.com/2013/09/22/what-else-can-i-do-with-my-dna-test-results/

International Society of Genetic Genealogy: Autosomal DNA Tools: http://www.isogg.org/wiki/Autosomal_DNA_tools

Resqua: Q: What should I do after generating my Gene variance report? http://resqua.com/100005927200207/what-should-i-do-after-generating-my-gene-variance-report

Think Exponential: Get SNPd! http://thinkexponential.com/2013/01/10/why-you-should-get-snped/

PART TWO (B): Less Easy Way

Linking Disease Associations with Regulatory Information in the Human Genome

Actually, there are a LOT of different “less easy ways.” You can open the raw data file in a text editor and search manually for specific pieces of information. Or, if you code, you can write a little program to do some of the hard work for you.

Basically, it comes down to doing a lot of research, the hard way, by hand. But, believe it or not, I am doing it. I’ve had a lot of help from people who offered tips or comments in the 23andMe or MTHFR.net forums, on Facebook, on Twitter, and comments on these blogs. I am NOT an expert, but like most readers of this blog, just someone who wants or needs to know more. This is what I’ve learned and figured out on my own, offered as an example, nothing more.

Critical Background

23andMe gives SNP-based data. SNP stands for single nucleotide polymorphism. Polymorphism means something that can be itself but in different ways, our eyes are eyes whether they are blue or brown or hazel or violet or any other natural eye color. I won’t give an introduction to genetics here, but there are several online resources that explain these ideas, with one of the best resources being Genetic Home Reference from the US government. Depending on how much you want to know, you may wish to take the Coursera courses Introduction to Genetics and Evolution (Duke U) or Experimental Genome Science (U Penn).

1. What SNPs do you want to know about? Check here:

RegulomeDB (Stanford): Linking Disease Associations with Regulatory Information in the Human Genome: http://regulomedb.org/GWAS/

I have also found SNPs of interest in research articles, PUBMED, and other places, but this is a good start. The SNP identifier (what you need) will look something like this:

rs2187668

2. Find out which polymorphism is the one considered “healthy” or “normal”, and which one is the one associated with risk of disease? These maybe called “risk alleles” or
simply polymorphisms.

For example, for SNP “rs2187668” (one of the celiac risk SNPs) the risk indicator is (T), while the normal is (C).

3. Open your 23andMe raw data file in a text editor, like WordPad (Windows) or TextEdit or TextWrangler (Macintosh).

4. Search for the SNP you want to know about. The data will be in four columns:
– RSID
– Chromosome
– Position
– Genotype
You need to know about the first and last columns, RSID and Genotype. It will look a little like this.

rsid…..chromosome…..position…..genotype
… [many other rows of data] …
rs2187668…..6………32605884…..CT

So, this person (me) has for that SNP one risk allele “T,” (which I happen to know is from my dad, by comparing it to his scan) and one normal allele “C,” (which must, by default, be from my mom, since for every gene pair we have gotten one from each parent).

5. Repeat for all the other SNPs associated with the condition you are researching.

6. Search for more information and articles about those SNPs, the condition, and more. You can’t make sense of this without more information. And ask lots of questions.

More Tools

ENCODE:
About: http://www.genome.gov/encode/
Data: http://genome.ucsc.edu/encode/

ENSEMBL Genome Browser: http://useast.ensembl.org/

OpenSNP: https://opensnp.org/ OR https://opensnp.org/snps/

SNPedia: http://www.snpedia.com/

UCSC Genome Browser: http://genome.ucsc.edu/

The Neel Lecture — Hashtags of the Week (HOTW): (Week of May 12, 2014)

In the HOTW posts (Hashtag of the Week) we usually collect a bunch of tweets to illustrate topics or concepts. There are a few posts that mention Twitter tools, but not a lot. Today I’d like to talk about Storify, and am using the opportunity of having this morning livetweeted the James Neel Lecture by Richard P. Lifton. Livetweeting means to tweet about something while it is going on in real time.

To prepare for livetweeting I open web pages for the event, the speaker, and some of their articles. I make sure there is a good hashtag that isn’t likely to be misunderstood as being for something else. I check to see if it is possible to create an automatic archive of the event tweets. I also usually ask permission, if there is a chance. If there is not a chance to ask, the assumption is that events open to the public are permissible to tweet. (NOTE: If you are organizing an event, remind speakers to tell folk if and when they do NOT want things they say to be tweeted!) In this case, Dr. Lifton granted permission, with the caveat of excluding the portion of the presentation on current unpublished research. When he got to that part, he said, “Please don’t tweet this slide.” It works.

After the event finished, I was able to push all the tweets into a tool called Storify to create a kind of ‘story’ for the event. The tweet at the beginning of this post gives a link to the Storify for this event. While a Storify can be embedded in a web page, just like Youtube videos and tweets, it isn’t something that fits well in this blog, so I encourage you to go look at it there.

As you look at the Storify, you’ll notice that, as is usual with the blogged tweets, the individual tweets will show photos or certain other kinds of content. You may notice other content in addition to the tweets! There are pictures and links included, and even readable scrollable copies of entire article PDFs! Being a really academic presentation, this one was studded with research articles. Some of them are articles referenced by Dr. Lifton in his presentation, but others are simply articles on topics he mentioned. Don’t blame him for any errors in transmission – that would be my doing, probably misunderstanding something he said, since I’m not a geneticist. I hope that the overview this provides of the lecture might be useful to those who were unable to attend in person.


First posted at THL Blog: http://thlibrary.wordpress.com/2014/05/12/the-neel-lecture-hashtags-of-the-week-hotw-week-of-may-12-2014/

The Future of Genomic Medicine #FOGM14 — Hashtags of the Week (HOTW): (Week of March 21, 2014)

Lantern Slides: Heritance of Clefting

The image above is from one of the earliest studies on the genetics of clefting done here at the University of Michigan School of Dentistry. Those were the days, weren’t they? You had to track signs and symptoms across generations, for decades, trying to deduce large scale patterns. Now we spit in a tube and mail it off.

Pic of the Day - PGen

The Future of Genomic Medicine was just happening. It was being actively tweeted by a number of leading figures in healthcare and science — Eric Topol, Carl Zimmer, Dr. Khoury from the CDC, Magdalene Skipper from Nature, and (uh) Al Gore, just for starters. It was so active that the original hashtag, #FOGM14, had to be dropped because of spammers, and they group switched to #FOGM2014. It was so active that even though it happened two weeks ago, the hashtags are still active on Twitter with people continuing the conversations around the conference. Here are just a highly selected few tweets with interesting thoughts, resources, and take-aways from this important conference.


First posted at THL Blog: http://thlibrary.wordpress.com/2014/03/24/the-future-of-genomic-medicine-fogm14-hashtags-of-the-week-hotw-week-of-march-21-2014/

Exploding & Exploring #PGSethics (via #23andMe vs the #FDA) — Hashtags of the Week (HOTW): (Week of December 2, 2013)


RiskBites: 23andMe, FDA and DNA health profiling: http://www.youtube.com/watch?v=VZXDtTNqDuQ

As you’ve probably already heard, on November 22nd the FDA sent a Warning Letter to the personal genomics company 23andMe. As someone who has participated in clinical studies about personal genomics and blogs (occasionally) about this area, my social media streams have been EXPLODING!

Just through Twitter (for which it is easier to grab numbers), in the past 3 days there have been over two thousand more posts mentioning 23andMe, and over 500 new mentions in my own Twitter interactions stream. I cannot keep up, I can’t read them all, much less reply. Friday night the conversation was burning the wires, and I finally had to stop to sleep. I promised I’d get back to folk in the morning. In the morning, I had 250 new interactions. While I tried to read those, I made it through about 50, and in that time another 163 had arrived. During the conversations, a number of us decided we had so many folk in the conversation we needed a new hashtag to corral the content. We decided to use #PGSethics for “Personal Genomics Services, Ethics.” Obviously, this is the topic of the moment, but this blog post is going to require being extremely selective to merely hint at the boundaries of the conversations occurring even as I write this. Also, because the very nature of the topic is enormous, with complex issues, much of the conversation is shifting back and forth between Twitter and blogs. Analyzing all this will make a fabulous doctoral dissertation for someone!

Here are the main hashtags I am using to track this, BUT with a huge caveat. Most of the conversation is not happening through hashtags right now, and I seem to be being cc’d on much of several conversations. And since many of the most pungent comments don’t even include the word “23andMe” the only way to really find what people are saying is by sheer brute force digging. Still, this is a start.

#23andMe: https://twitter.com/search?q=%2323andme&src=typd
#FDA: https://twitter.com/search?q=%23FDA&src=typd
#PGSethics: https://twitter.com/search?q=%23PGSethics&src=hash


First posted at: THL Blog http://wp.me/p1v84h-1yJ

Rare Disease Innovation Driven By and Driving Open Science

PICT0029.JPG

When you hear the word “rare”, don’t you instinctively think of something precious, something unique and valuable, treasured and guarded and preserved with great care and tenderness? I do. The image above is of a medical magical amulet from the famed collection by Dr. Campbell Bonner.

An amulet is, “any object which by its contact or close proximity to the person who owns it, or to any possession of his, exerts power for his good, either by keeping evil from him and his property or by endowing him with positive advantages.” (According to Dr. Bonner’s definition, Bonner, C. Studies in Magical Amulets. Ann Arbor: University of Michigan Press, 1950. p. 2.)

Magical Amulets: http://www.lib.umich.edu/magical-amulets

I was working on the next installment of the Bubble/Blur series, but today is Rare Disease Day. A pretty special day, and pretty near and dear to my heart. Any time I wasn’t in meetings today, I was probably watching the inaugural NIH Rare Disease Day webcast, which was held partly in honor of the 20th anniversary of the existence of the NIH Office of Rare Disease Research. The event went on all day, and continues tomorrow.

Rare Disease Day @ NIH: https://events-support.com/events/Rare_Disease_Day/page/242

I didn’t get to see as much as I wanted. Not to diminish the other wonderful presentations that excited me so much throughout the day, but the most powerful part was at the end of the day, with the screening of the documentary “Here. Us. Now.”

Leading up to the screening, it was obvious from the atmosphere (which conveyed to me a sense of approaching awe) that the event planners knew we were about to see something very, very special.


Here. Us. Now. http://globalgenes.org/here-us-now/ Trailer: https://www.youtube.com/watch?v=LPK6pGFHAa0

“The Hempels’ story reveals the grim truth that rare disease is all too commonplace. Despite unprecedented investment in medical research and development, there are thousands of known rare diseases and disorders without treatments and cures. It’s a broken system moving at a tedious pace, and it leaves heart-rending personal stories in its wake.”

Both parents were experts in business with little knowledge of healthcare before their daughters were diagnosed with a rare fatal genetic disease (Niemann Pick Type C). Guess what? They are now the experts. They used their expertise in business to create what they describe as essentially a new business, a start up. It sounds almost like a “House that Jack Built” kind of story. The business focuses explicitly on doing the needed research, to share the results, to foster the necessary innovation, to drive the discoveries, to save their daughters’ lives.

What I was hearing as I listened and watched the movie were arguments in favor of a wholesale revisioning of the methods and practice and institutions of science, healthcare, publishing, and the governmental oversight agencies responsible for all of these. I want very much to have a chance to see the entire movie. I want to watch it closely. I want the DVD. I want to show it to people. I want to have a viewing here at the University of Michigan. I haven’t seen the entire movie, and I already want it to be required viewing for a wide range of people.

So you can better understand why I feel this way, I want to share just a few snippets of the ideas that most captured my attention in the tweets I sent while watching it, listening to them tell the story of the many barriers they encountered, and the solutions they created with determination, focused intent, planning, love, effort, and lots and lots of money; and the ways they used what they learn to advance the research in this area around the world, strategies they’ve share with other parents and families who share in these explorations and trials.

This is the story of one family. But this is also a story that encompasses virtually every major trend currently emerging in science and healthcare — the need for open access and open science, the empowered patient movement, personalized medicine, the difficult dynamic between transparency and privacy in healthcare and research, the shifting dynamic of how scholarship is defined and how knowledge is shared and how communities are built. These two parents have been transformed by their experiences with rare disease, have seized on to anything and everything that will let them make the difference they are trying to make. As a result, they are not just changing life for their own family, but for countless others. As they tell their story, they continue to change attitudes toward what is best practice in science research and healthcare innovation.

Another friend of mine said it rather well. This is not just what this one family is doing, although the story of the Hempel Family really is a lodestone for the entire conversation, but it is bigger than them. That is because all around the globe, every day, there are other patients and families doing the same kinds of things. Maybe not at the same scale or with the same scope, but trying to change things for themselves and others with their disease. Doing their own research and sharing it. Educating their doctors, who are NOT the experts in these rare conditions. Educating other patients on how to educate their healthcare team. And on and on. And what happens?

For the Hempels, they found not a cure, but a treatment. Something that helps. They were able to find friends and allies who helped them push it through the system, and get FDA approval to use this to help improve the quality of life for their children, and for others with the same condition. It really IS like magic. For the rest of us?