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1.  Mutation of KCNJ8 in a patient with Cantú syndrome with unique vascular abnormalities - support for the role of K(ATP) channels in this condition 
KCNJ8 (NM_004982) encodes the pore forming subunit of one of the ATP-sensitive inwardly rectifying potassium (KATP) channels. KCNJ8 sequence variations are traditionally associated with J-wave syndromes, involving ventricular fibrillation and sudden cardiac death. Recently, the KATP gene ABCC9 (SUR2, NM_020297) has been associated with the multi-organ disorder Cantú syndrome or hypertrichotic osteochondrodysplasia (MIM 239850) (hypertrichosis, macrosomia, osteochondrodysplasia, and cardiomegaly). Here, we report on a patient with a de novo nonsynonymous KCNJ8 SNV (p.V65M) and Cantú syndrome, who tested negative for mutations in ABCC9. The genotype and multi-organ abnormalities of this patient are reviewed. A careful screening of the KATP genes should be performed in all individuals diagnosed with Cantú syndrome and no mutation in ABCC9.
doi:10.1016/j.ejmg.2013.09.009
PMCID: PMC3902017  PMID: 24176758
2.  An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge 
Brownstein, Catherine A | Beggs, Alan H | Homer, Nils | Merriman, Barry | Yu, Timothy W | Flannery, Katherine C | DeChene, Elizabeth T | Towne, Meghan C | Savage, Sarah K | Price, Emily N | Holm, Ingrid A | Luquette, Lovelace J | Lyon, Elaine | Majzoub, Joseph | Neupert, Peter | McCallie Jr, David | Szolovits, Peter | Willard, Huntington F | Mendelsohn, Nancy J | Temme, Renee | Finkel, Richard S | Yum, Sabrina W | Medne, Livija | Sunyaev, Shamil R | Adzhubey, Ivan | Cassa, Christopher A | de Bakker, Paul IW | Duzkale, Hatice | Dworzyński, Piotr | Fairbrother, William | Francioli, Laurent | Funke, Birgit H | Giovanni, Monica A | Handsaker, Robert E | Lage, Kasper | Lebo, Matthew S | Lek, Monkol | Leshchiner, Ignaty | MacArthur, Daniel G | McLaughlin, Heather M | Murray, Michael F | Pers, Tune H | Polak, Paz P | Raychaudhuri, Soumya | Rehm, Heidi L | Soemedi, Rachel | Stitziel, Nathan O | Vestecka, Sara | Supper, Jochen | Gugenmus, Claudia | Klocke, Bernward | Hahn, Alexander | Schubach, Max | Menzel, Mortiz | Biskup, Saskia | Freisinger, Peter | Deng, Mario | Braun, Martin | Perner, Sven | Smith, Richard JH | Andorf, Janeen L | Huang, Jian | Ryckman, Kelli | Sheffield, Val C | Stone, Edwin M | Bair, Thomas | Black-Ziegelbein, E Ann | Braun, Terry A | Darbro, Benjamin | DeLuca, Adam P | Kolbe, Diana L | Scheetz, Todd E | Shearer, Aiden E | Sompallae, Rama | Wang, Kai | Bassuk, Alexander G | Edens, Erik | Mathews, Katherine | Moore, Steven A | Shchelochkov, Oleg A | Trapane, Pamela | Bossler, Aaron | Campbell, Colleen A | Heusel, Jonathan W | Kwitek, Anne | Maga, Tara | Panzer, Karin | Wassink, Thomas | Van Daele, Douglas | Azaiez, Hela | Booth, Kevin | Meyer, Nic | Segal, Michael M | Williams, Marc S | Tromp, Gerard | White, Peter | Corsmeier, Donald | Fitzgerald-Butt, Sara | Herman, Gail | Lamb-Thrush, Devon | McBride, Kim L | Newsom, David | Pierson, Christopher R | Rakowsky, Alexander T | Maver, Aleš | Lovrečić, Luca | Palandačić, Anja | Peterlin, Borut | Torkamani, Ali | Wedell, Anna | Huss, Mikael | Alexeyenko, Andrey | Lindvall, Jessica M | Magnusson, Måns | Nilsson, Daniel | Stranneheim, Henrik | Taylan, Fulya | Gilissen, Christian | Hoischen, Alexander | van Bon, Bregje | Yntema, Helger | Nelen, Marcel | Zhang, Weidong | Sager, Jason | Zhang, Lu | Blair, Kathryn | Kural, Deniz | Cariaso, Michael | Lennon, Greg G | Javed, Asif | Agrawal, Saloni | Ng, Pauline C | Sandhu, Komal S | Krishna, Shuba | Veeramachaneni, Vamsi | Isakov, Ofer | Halperin, Eran | Friedman, Eitan | Shomron, Noam | Glusman, Gustavo | Roach, Jared C | Caballero, Juan | Cox, Hannah C | Mauldin, Denise | Ament, Seth A | Rowen, Lee | Richards, Daniel R | Lucas, F Anthony San | Gonzalez-Garay, Manuel L | Caskey, C Thomas | Bai, Yu | Huang, Ying | Fang, Fang | Zhang, Yan | Wang, Zhengyuan | Barrera, Jorge | Garcia-Lobo, Juan M | González-Lamuño, Domingo | Llorca, Javier | Rodriguez, Maria C | Varela, Ignacio | Reese, Martin G | De La Vega, Francisco M | Kiruluta, Edward | Cargill, Michele | Hart, Reece K | Sorenson, Jon M | Lyon, Gholson J | Stevenson, David A | Bray, Bruce E | Moore, Barry M | Eilbeck, Karen | Yandell, Mark | Zhao, Hongyu | Hou, Lin | Chen, Xiaowei | Yan, Xiting | Chen, Mengjie | Li, Cong | Yang, Can | Gunel, Murat | Li, Peining | Kong, Yong | Alexander, Austin C | Albertyn, Zayed I | Boycott, Kym M | Bulman, Dennis E | Gordon, Paul MK | Innes, A Micheil | Knoppers, Bartha M | Majewski, Jacek | Marshall, Christian R | Parboosingh, Jillian S | Sawyer, Sarah L | Samuels, Mark E | Schwartzentruber, Jeremy | Kohane, Isaac S | Margulies, David M
Genome Biology  2014;15(3):R53.
Background
There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.
Results
A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.
Conclusions
The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
doi:10.1186/gb-2014-15-3-r53
PMCID: PMC4073084  PMID: 24667040
3.  Development of a Scalable Pharmacogenomic Clinical Decision Support Service 
Advances in sequencing technology are making genomic data more accessible within the healthcare environment. Published pharmacogenetic guidelines attempt to provide a clinical context for specific genomic variants; however, the actual implementation to convert genomic data into a clinical report integrated within an electronic medical record system is a major challenge for any hospital. We created a two-part solution that integrates with the medical record system and converts genetic variant results into an interpreted clinical report based on published guidelines. We successfully developed a scalable infrastructure to support TPMT genetic testing and are currently testing approximately two individuals per week in our production version. We plan to release an online variant to clinical interpretation reporting system in order to facilitate translation of pharmacogenetic information into clinical practice.
PMCID: PMC3814487  PMID: 24303299
5.  The Potential Research Impact of Patient Reported Outcomes on Osteogenesis Imperfecta 
Background
Osteogenesis imperfecta (OI) is an inherited connective tissue disorder with many phenotypic presentations ranging from mild to severe. It is often called “brittle bone disease.” Treatment consists of physical therapy, surgical interventions, medications and, in some cases, experimental therapies. Because treatment is not standardized and is often experimental, information on the success of different methods is usually not available or well documented.
Questions/purposes
We therefore asked if social networking can make OI patients’ lives better. How would a bone disorder community work? Is it possible for patients to know how well they are doing in comparison to others like them, and if they are getting the most successful treatment for their disease?
Methods
An evaluation of how PatientsLikeMe®, a personal research and social networking website and database for patients with life changing illnesses, can aid in improving patient outcomes through the anonymous sharing of medical information.
Results
PatientsLikeMe® could help patients answer the question, “Given my condition, what is the best outcome I could hope to achieve, and how do I get there?” Participants could record their real-time day-to-day progress in achieving their treatment goals, such as preventing fractures, and share that with the community to help patients, caregivers, researchers and industry learn more about OI.
Conclusions
Social networking can change the lives of Osteogenesis Imperfecta patients for the better, and make them a part of the treatment discovery process. Here we present a possible OI online community and demonstrate its potential utility for patients and medical professionals alike.
doi:10.1007/s11999-010-1373-x
PMCID: PMC3049620  PMID: 20458644
6.  Sharing Health Data for Better Outcomes on PatientsLikeMe 
Background
PatientsLikeMe is an online quantitative personal research platform for patients with life-changing illnesses to share their experience using patient-reported outcomes, find other patients like them matched on demographic and clinical characteristics, and learn from the aggregated data reports of others to improve their outcomes. The goal of the website is to help patients answer the question: “Given my status, what is the best outcome I can hope to achieve, and how do I get there?”
Objective
Using a cross-sectional online survey, we sought to describe the potential benefits of PatientsLikeMe in terms of treatment decisions, symptom management, clinical management, and outcomes.
Methods
Almost 7,000 members from six PatientsLikeMe communities (amyotrophic lateral sclerosis [ALS], Multiple Sclerosis [MS], Parkinson’s Disease, human immunodeficiency virus [HIV], fibromyalgia, and mood disorders) were sent a survey invitation using an internal survey tool (PatientsLikeMe Lens).
Results
Complete responses were received from 1323 participants (19% of invited members). Between-group demographics varied according to disease community. Users perceived the greatest benefit in learning about a symptom they had experienced; 72% (952 of 1323) rated the site “moderately” or “very helpful.” Patients also found the site helpful for understanding the side effects of their treatments (n = 757, 57%). Nearly half of patients (n = 559, 42%) agreed that the site had helped them find another patient who had helped them understand what it was like to take a specific treatment for their condition. More patients found the site helpful with decisions to start a medication (n = 496, 37%) than to change a medication (n = 359, 27%), change a dosage (n = 336, 25%), or stop a medication (n = 290, 22%). Almost all participants (n = 1,249, 94%) were diagnosed when they joined the site. Most (n = 824, 62%) experienced no change in their confidence in that diagnosis or had an increased level of confidence (n = 456, 34%). Use of the site was associated with increasing levels of comfort in sharing personal health information among those who had initially been uncomfortable. Overall, 12% of patients (n = 151 of 1320) changed their physician as a result of using the site; this figure was doubled in patients with fibromyalgia (21%, n = 33 of 150). Patients reported community-specific benefits: 41% of HIV patients (n = 72 of 177) agreed they had reduced risky behaviors and 22% of mood disorders patients (n = 31 of 141) agreed they needed less inpatient care as a result of using the site. Analysis of the Web access logs showed that participants who used more features of the site (eg, posted in the online forum) perceived greater benefit.
Conclusions
We have established that members of the community reported a range of benefits, and that these may be related to the extent of site use. Third party validation and longitudinal evaluation is an important next step in continuing to evaluate the potential of online data-sharing platforms.
doi:10.2196/jmir.1549
PMCID: PMC2956230  PMID: 20542858
Personal health records; data visualization; personal monitoring; technology; health care; self-help devices; personal tracking; social support; online support group; online health community

Results 1-6 (6)