When Wellcome Sanger Institute geneticist Eugene Gardner set out to look for a specific type of genetic mutation in a massive database of human DNA, he figured itd be a long shot. Transposonsalso known as jumping genes because they can move around the genomecreate a new mutation in one of every 15 to 40 human births, but thats across the entire 3 billion base pairs of nuclear DNA that each cell carries. The sequencing data that Gardner was working with covered less than two percent of that, with only the protein-coding regions, or exons, included. Doing a quick calculation, he determined that, in the best-case scenario, he could expect to find up to 10 transposon-generated variants linked to a developmental disease. And we really might get zero, he says. This whole thing might be for naught.
But Gardner had recently developed the perfect tool to find the sort of de novo mobile element insertions that come about as a result of transposon movements and are often overlooked in genetic screens and analyses. As a graduate student in Scott Devines lab at the University of Maryland, Baltimores Institute for Genome Sciences, he had spent many hours making the software for the mobile element locator tool he dubbed MELT. The program was easy to use, so when Gardner moved across the Atlantic for a postdoc in Matthew Hurless lab at Sanger near Cambridge and gained access to a database of exomes from 13,000 patients with developmental disorders, he figured running the tool was worth a try.
There is tremendous value for these families that get a diagnosis.
Dan Koboldt, Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Childrens Hospital
Of those 13,000, Gardner focused on 9,738 people in the Deciphering Developmental Disorders (DDD) study whose parents exomes had also been sequenced, making it easier to single out variants present in the child but not in mom and dad. And as it turned out, he did get some hits. MELT picked up 40 potentially transposon-generated variants, which Gardner sat down at his computer to review using the raw sequencing data. Nine appeared to be true de novo mobile element insertions. I remember being in my desk doing the visualization of all the putative de novo variants after I got the first results off the pipeline, he recalls. I remember being excited: I think I might have found a diagnostic de novo!
Discussing the literature on the genes affected by such insertions with clinicians and other colleagues, Gardner narrowed the list down to four insertions found in genes that may be causing or contributing to four different patients disorders. He sent these results off to the physicians who had referred each of the patients to the database, and all the doctors confirmed that the results made sense to them given what had been published on those genes and what they knew about other cases involving patients with mutations in the same sequences. In one case, the physician had already linked the patients disorder to the gene Gardner had identified; in the other three cases, the patients were still undiagnosed.
There is tremendous value for these families that get a diagnosis, says human geneticist Dan Koboldt, who has collaborated with Hurles in the past and has used MELT in his studies of rare disease at the Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Childrens Hospital in Columbus, Ohio, but who was not involved in Gardners recent study. A genetic answer not only can help physicians connect patients to appropriate medical and counseling resources; it puts an end to the diagnostic odyssey that families affected by rare disease often endure.
Whats more, the finding of four potentially causative hits out of the nearly 10,000 cases provides first estimate of how commonly such mobile element insertions underlie developmental disorders. Whats interesting about this study is that its taking a very broad approach, says Ian Adams, a developmental biologist at the University of Edinburghs MRC Human Genetics Unit who was not involved in the research. Rather than look for transposon activity in a specific disorder, its casting a much broader net in trying to find what type of diseases this class of mutations could be contributing to.
This approach is important, agrees Adamss MRC Human Genetics Unit colleague Jose Garcia-Perez, a transposable elements expert who was also not involved in the new research. In the last few years, two studies have used a tool developed around the same time as MELT to search for de novo mobile elements in people with autism spectrum disorder, but neither identified any that were likely to be responsible for the patients symptoms. [Gardners] study shows that, no matter whats [been found] recently, its something that should be explored in further detail in the future, says Garcia-Perez. [The study] actually shows a real connection between . . . transposition with that particular [type of] disorder. Koboldt adds: The reason this is an important study is that it establishes [that these] variants do occur and [that] they can be pathogenic.
Gardner says he hopes that his methods can be used to explore other diseases, from both a research and a clinical perspective. Adams says MELT does appear to be widely applicable to other datasets. Such a tool could be a boon to research on transposons, given that their movements are often missed by normal screening tools, Adams adds. I think [MELT is] something that could be readily built into existing pipelines.
Jef Akst is managing editor ofThe Scientist. Email her atjakst@the-scientist.com.
Original post:
Transposons Identified as Likely Cause of Undiagnosed Diseases - The Scientist
- June 11th At Westport, CT: Federal Red Flags, HIPAA Security Rules and Fraud Prevention - November 7th, 2009 [November 7th, 2009]
- Do not learn Dvorak! - November 7th, 2009 [November 7th, 2009]
- You Can’t Solve Problems By Making It Illegal To Have The Problem - November 7th, 2009 [November 7th, 2009]
- A Force Fix for Healthcare - November 7th, 2009 [November 7th, 2009]
- Yahble, HIT, Bubblecon, BIZDEV!, Solid State - November 7th, 2009 [November 7th, 2009]
- 15 things that suck about the Palm Pre - November 7th, 2009 [November 7th, 2009]
- What an Indie Genomics Lab Looks Like - November 7th, 2009 [November 7th, 2009]
- Practice Fusion: Class D Felony? - February 26th, 2010 [February 26th, 2010]
- Practice Fusion Responds - March 7th, 2010 [March 7th, 2010]
- Practice Fusion: Do the math: $44,000 is a LIE - March 10th, 2010 [March 10th, 2010]
- How Much Until Doctors Approve of 23andMe? - March 10th, 2010 [March 10th, 2010]
- Biochemicals as Media, Not Methods - March 10th, 2010 [March 10th, 2010]
- More Practice Fusion Reality Distortion - March 10th, 2010 [March 10th, 2010]
- Same Test Results: 23andMe is Myriad is BRCA is Medicine - March 12th, 2010 [March 12th, 2010]
- BRCA is 23andMe is Myriad is Medicine - March 13th, 2010 [March 13th, 2010]
- Getting Serious About Genomics as Common Medical Practice - March 15th, 2010 [March 15th, 2010]
- The New John Mackey of Genetics: Linda Avey? - March 15th, 2010 [March 15th, 2010]
- Keep the Medical, Well, Medical - March 16th, 2010 [March 16th, 2010]
- If 23andMe shuts down, it won’t be for some mundane reason like the bills weren’t paid - March 16th, 2010 [March 16th, 2010]
- If I Run A Medical Practice, How Do I Use A 23andMe? - March 17th, 2010 [March 17th, 2010]
- 23andMe Contract in Bad Faith - March 19th, 2010 [March 19th, 2010]
- Doctors CANNOT Use 23andMe Due To 23andMe’s Bad Faith Contract - March 20th, 2010 [March 20th, 2010]
- Pathway Compared to 23andMe and Navigenics - March 22nd, 2010 [March 22nd, 2010]
- There’s a Word for “Views Differ” When One View Is The State - March 24th, 2010 [March 24th, 2010]
- Association for Molecular Pathology, et al. v. USPTO, et al. – Opinion - March 29th, 2010 [March 29th, 2010]
- Birth of a Super Villain - April 3rd, 2010 [April 3rd, 2010]
- “Medical Products” like 23andMe must not become the new “Financial Products” - April 4th, 2010 [April 4th, 2010]
- How I Would Apply Genomic Technology In Clinical Use Today - April 5th, 2010 [April 5th, 2010]
- Gmail Enterprise: World’s Best EMR - April 6th, 2010 [April 6th, 2010]
- Brief Primer on Health Law Compliance - April 9th, 2010 [April 9th, 2010]
- Spoiler: You ARE the “Valids” - April 9th, 2010 [April 9th, 2010]
- Rachel Lehmann-Haupt Line by Line Take Down - April 9th, 2010 [April 9th, 2010]
- Is Medicare Bankrupt? What the Hell Is Going On? - April 17th, 2010 [April 17th, 2010]
- The Big Shuffle: Medicare Cuts Rates by 21.3% (but not “technically”) - April 17th, 2010 [April 17th, 2010]
- “Tech Hiring Binge” == “Fear for Your Job, Nerds” - April 18th, 2010 [April 18th, 2010]
- How Bad is Bad? $.20 on the Private Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- Update: How Bad is Bad? It Used to Be $.45 on the Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- World’s Best “EMR” for $1000: Google Spreadsheets + iPad - April 21st, 2010 [April 21st, 2010]
- Don’t Insult Me with your “AOL Keyword” Strategy, Google Health - April 21st, 2010 [April 21st, 2010]
- How to Play LAWGAMES - April 23rd, 2010 [April 23rd, 2010]
- Top 4 Predatory Schemes Encroaching on American Medicine: Part 1 - April 25th, 2010 [April 25th, 2010]
- What’s the Big Deal About iPads? - April 27th, 2010 [April 27th, 2010]
- Got Google Android for Google I/O - April 27th, 2010 [April 27th, 2010]
- Google Enterprise meets HIPAA and HITECH Compliant Laws - April 29th, 2010 [April 29th, 2010]
- Pixels of Accuracy CHALENGE: Diagnostic Medical Imaging - April 29th, 2010 [April 29th, 2010]
- 23andMe Launder AlioGenetics Doesn’t Even Bother to Remove 23andMe Logo - April 30th, 2010 [April 30th, 2010]
- Anthem of CT Denies $600 Until “Subscriber Responds to our Coordination of Benefits Questionnaire” - May 1st, 2010 [May 1st, 2010]
- Apple And Google Team Up To Launch Revolutionary Mobile Health System - May 1st, 2010 [May 1st, 2010]
- Funny Pictures from This Year Building the Medical Practice - May 6th, 2010 [May 6th, 2010]
- Remote Medical Video Monitoring on iPad and iPhone - May 7th, 2010 [May 7th, 2010]
- Google Calendar Overhead Waiting Room Display - May 7th, 2010 [May 7th, 2010]
- Various Whiteboards on Solid State Medical Operations - May 7th, 2010 [May 7th, 2010]
- The Raw Facts about Counsyl - May 7th, 2010 [May 7th, 2010]
- Brawndo: Still Mutilating Thirst, Still Not Yet Sold at the Stop-n-Shop Pharmacy - May 9th, 2010 [May 9th, 2010]
- Video: Google Enterprise to Outsource Medical Administration - May 9th, 2010 [May 9th, 2010]
- Gattaca: “The Matrix” of Genomics - May 11th, 2010 [May 11th, 2010]
- 23andMe Now Diagnoses Fatal Tay-Sachs Disease - May 12th, 2010 [May 12th, 2010]
- Why Was Pathway Targeted for FDA Enforcement and Not 23andMe? - May 15th, 2010 [May 15th, 2010]
- John Dolan on Aging and the Horrifying Conclusion of GWAS - May 16th, 2010 [May 16th, 2010]
- Sam R. Riley Wants To Tell You About Practice Fusion - May 17th, 2010 [May 17th, 2010]
- Response to “Genomic Medicine: Lost” - May 19th, 2010 [May 19th, 2010]
- Death And Taxes: CMS to IRS - May 19th, 2010 [May 19th, 2010]
- Please Stop Antagonizing the AMA - May 26th, 2010 [May 26th, 2010]
- Dan Vorhaus, Attorney At Law, Legally Advises Medical Doctors Can Use 23andMe To Provide Medical Advice - May 28th, 2010 [May 28th, 2010]
- Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation - June 7th, 2010 [June 7th, 2010]
- OpenPCR: DNA amplification for anyone - June 10th, 2010 [June 10th, 2010]
- FDA sends letters to 5 genetic testing companies - June 11th, 2010 [June 11th, 2010]
- Amazon And The NIH Team Up To Put Human Genome In The Cloud - March 31st, 2012 [March 31st, 2012]
- ReproSource Comments on New Study Linking Infertility to Genetics - April 25th, 2012 [April 25th, 2012]
- Genetics 101 Part 1: What are genes? - Video - April 30th, 2012 [April 30th, 2012]
- Red Ice Radio - David Icke - Hour 1 - The Manipulation of Humanity - Video - April 30th, 2012 [April 30th, 2012]
- Genetics Part 5: Human Genetic Disorders - Video - April 30th, 2012 [April 30th, 2012]
- C2CAM - The Nephilim, Genetic Manipulation - April 30th, 2012 [April 30th, 2012]
- Human Nature talk with Robert Sapolsky, Gabor Mate, James Gilligan, Richard Wilkinson - Video - April 30th, 2012 [April 30th, 2012]
- Human Genetic Diseases - Video - April 30th, 2012 [April 30th, 2012]
- Alien Scientist on Genetics, Implants - April 30th, 2012 [April 30th, 2012]
- Research and Markets: Genetics, 6th Edition International Student Version Continues To Educate Today's Students for ... - May 4th, 2012 [May 4th, 2012]
- Myriad Genetics to Present at the Bank of America Merrill Lynch 2012 Health Care Conference - May 4th, 2012 [May 4th, 2012]
- Genetics may explain some people's dislike of meat - May 4th, 2012 [May 4th, 2012]
- 'Blond Genes' May Vary Around the World - May 4th, 2012 [May 4th, 2012]