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SNPs linked to sleep quality

Sleep graphic

SNPs to include in sleep studies: rs10462021, rs1154155, rs1799990, rs1801260, rs228697, rs2304669, rs2304672, rs2305795, rs2472297, rs4410790, rs4680, rs4804122, rs4964059, rs5751876, rs6265, rs6311, rs687577, rs73598374, rs738499, rs762551

Caffeine-related SNPs: CYP1A2 (rs762551) related to caffeine metabolism (23andMe,[1] Pathway Genomics[2],[3]), habitual caffeine consumption reviewed by 23andMe CYP1A1-CYP1A2 (rs2472297)[4] and AHR (rs4410790),[5] and ADA G22A (rs73598374).[6]

Quantified self-type SNPs: linked to healthy sleeping profiles with PER3 (rs57875989), ADA (rs73598374), ADORA2A (rs5751876), BDNF (rs6265), COMT VAL158MET (rs4680), PRNP (rs1799990),[7] genetic determination of sleep EEG profiles in healthy humans with ARNTL (rs95215856), ARNTL2 (rs5797225, rs7137588, rs4964059), CLOCK (rs1801260, rs95215860), PER2 (rs2304669), PER3 (rs228697, AB047536 5-repeat, rs10462021), AANAT (rs4238989) [available in 23andMe data: rs10462021, rs1801260, rs228697, rs2304669, rs4964059],[8] and in women, a link between depression and sleep quantity: GRIA3 (rs687577).[9] Repeating sequences in the circadian gene PERIOD3 (PER3) have been associated with sleep quality, but repeat data is not available from 23andMe.[10],[11]

Sleep malady SNPs: TCRA (rs1154155) related to essential hypersomnia,[12] P2RY11 (rs2305795, rs4804122) linked to narcolepsy,[13] TEF (rs738499) related to sleep disturbance in Parkinson’s disease,[14] Serotonin gene 5-HT2A -1438G/A polymorphism (rs6311) related to apnea and impulsive behavior,[15],[16] and TNFA (rs1800629) associated with obstructive sleep apnea but is not in 23andMe data.[17]


[1] Cornelis MC, El-Sohemy A, Kabagambe EK, Campos H. Coffee, CYP1A2 genotype, and risk of myocardial infarction. JAMA. 2006 Mar 8;295(10):1135-41.

[2] Sachse C, Brockmöller J, Bauer S, Roots I. Functional significance of a C–>A polymorphism in intron 1 of the cytochrome P450 CYP1A2 gene tested with caffeine. Br J Clin Pharmacol. 1999 Apr;47(4):445-9.

[3] Cornelis MC, El-Sohemy A. Coffee, caffeine, and coronary heart disease. Curr Opin Clin Nutr Metab Care. 2007 Nov;10(6):745-51.

[4] Sulem P, Gudbjartsson DF, Geller F, Prokopenko I, Feenstra B, Aben KK, Franke B, den Heijer M, Kovacs P, Stumvoll M, Mägi R, Yanek LR, Becker LC, Boyd HA, Stacey SN, Walters GB, Jonasdottir A, Thorleifsson G, Holm H, Gudjonsson SA, Rafnar T, Björnsdottir G, Becker DM, Melbye M, Kong A, Tönjes A, Thorgeirsson T, Thorsteinsdottir U, Kiemeney LA, Stefansson K. Sequence variants at CYP1A1-CYP1A2 and AHR associate with coffee consumption. Hum Mol Genet. 2011 May 15;20(10):2071-7.

[5] Cornelis MC, Monda KL, Yu K, Paynter N, Azzato EM, Bennett SN, Berndt SI, Boerwinkle E, Chanock S, Chatterjee N, Couper D, Curhan G, Heiss G, Hu FB, Hunter DJ, Jacobs K, Jensen MK, Kraft P, Landi MT, Nettleton JA, Purdue MP, Rajaraman P, Rimm EB, Rose LM, Rothman N, Silverman D, Stolzenberg-Solomon R, Subar A, Yeager M, Chasman DI, van Dam RM, Caporaso NE. Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. PLoS Genet. 2011 Apr;7(4):e1002033.

[6] Mazzotti DR, Guindalini C, Pellegrino R, Barrueco KF, Santos-Silva R, Bittencourt LR, Tufik S. Effects of the adenosine deaminase polymorphism and caffeine intake on sleep parameters in a large population sample. Sleep. 2011 Mar 1;34(3):399-402.

[7] Landolt HP. Genetic determination of sleep EEG profiles in healthy humans. Prog Brain Res. 2011;193:51-61.

[8] Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH. Genetic differences in human circadian clock genes among worldwide populations. J Biol Rhythms. 2008 Aug;23(4):330-40.

[9] Utge S, Kronholm E, Partonen T, Soronen P, Ollila HM, Loukola A, Perola M, Salomaa V, Porkka-Heiskanen T, Paunio T. Shared genetic background for regulation of mood and sleep: association of GRIA3 with sleep duration in healthy Finnish women. Sleep. 2011 Oct 1;34(10):1309-16.

[10] Goel N, Banks S, Mignot E, Dinges DF. PER3 polymorphism predicts cumulative sleep homeostatic but not neurobehavioral changes to chronic partial sleep deprivation. PLoS One. 2009 Jun 11;4(6):e5874.

[11] Viola AU, Archer SN, James LM, Groeger JA, Lo JC, Skene DJ, von Schantz M, Dijk DJ. PER3 polymorphism predicts sleep structure and waking performance. Curr Biol. 2007 Apr 3;17(7):613-8.

[12] Miyagawa T, Honda M, Kawashima M, Shimada M, Tanaka S, Honda Y, Tokunaga K. Polymorphism located in TCRA locus confers susceptibility to essential hypersomnia with HLA-DRB1*1501-DQB1*0602 haplotype. J Hum Genet. 2010 Jan;55(1):63-5.

[13] Kornum BR, Kawashima M, Faraco J, Lin L, Rico TJ, Hesselson S, Axtell RC, Kuipers H, Weiner K, Hamacher A, Kassack MU, Han F, Knudsen S, Li J, Dong X, Winkelmann J, Plazzi G, Nevsimalova S, Hong SC, Honda Y, Honda M, Högl B, Ton TG, Montplaisir J, Bourgin P, Kemlink D, Huang YS, Warby S, Einen M, Eshragh JL, Miyagawa T, Desautels A, Ruppert E, Hesla PE, Poli F, Pizza F, Frauscher B, Jeong JH, Lee SP, Strohl KP, Longstreth WT Jr, Kvale M, Dobrovolna M, Ohayon MM, Nepom GT, Wichmann HE, Rouleau GA, Gieger C, Levinson DF, Gejman PV, Meitinger T, Peppard P, Young T, Jennum P, Steinman L, Tokunaga K, Kwok PY, Risch N, Hallmayer J, Mignot E. Common variants in P2RY11 are associated with narcolepsy. Nat Genet. 2011 Jan;43(1):66-71.

[14] Viola AU, Archer SN, James LM, Groeger JA, Lo JC, Skene DJ, von Schantz M, Dijk DJ. PER3 polymorphism predicts sleep structure and waking performance. Curr Biol. 2007 Apr 3;17(7):613-8.

[15] Yin G, Ye J, Han D, Zhang Y, Zeng W, Liang C. Association of the 5-HT2A receptor gene polymorphisms with obstructive sleep apnea hypopnea syndrome in Chinese Han population. Acta Otolaryngol. 2012 Feb;132(2):203-9.

[16] Nomura M, Kusumi I, Kaneko M, Masui T, Daiguji M, Ueno T, Koyama T, Nomura Y. Involvement of a polymorphism in the 5-HT2A receptor gene in impulsive behavior. Psychopharmacology (Berl). 2006 Jul;187(1):30-5.

[17] Varvarigou V, Dahabreh IJ, Malhotra A, Kales SN. A review of genetic association studies of obstructive sleep apnea: field synopsis and meta-analysis. Sleep. 2011 Nov 1;34(11):1461-8.

BioCurious, a local DIYbio lab, now open for DIYgenomics experiments


BioCurious meets world: The next big thing to come out of a Silicon Valley garage: BioCurious, a hackerspace for biotech, is now open to the public! For $150 a month, amateurs, entrepreneurs, and professional scientists get access to tools, classes, and community at our 2,400 square foot lab in Sunnyvale. Make genetically-engineered bacteria, sequence DNA, find the tools to get your bio-project growing, or make friends with amateurs and experts in the community.

BioCurious features a full wet lab, office space, and co-working area. Membership at BioCurious includes access to gel electrophoresis, real time PCR, incubators, fridges, freezers, and we are adding new equipment all the time. Last year, 239 amazing people donated $35,319 on Kickstarter to catapult BioCurious out of the garage and into a full lab space. Over the past year, the BioCurious volunteers established a non-profit business entity, held meet-ups, acquired donated equipment, evaluated lab spaces, and established safety and waste disposal procedures. Why? We believe that innovations in biology should be accessible, affordable, and open to everyone. We’ve built a community biology lab for amateurs, inventors, entrepreneurs, and anyone who wants to experiment with friends.

Education: Beginners can become experts in their spare time. In one of our first classes, we made bacteria glow using DNA from jellyfish, the “hello world” experiment for synthetic biology. Hands-on classes in DNA sequencing, bioinformatics, hardware hacking, and more, are on the schedule. Our “Business of Biotech” lecture series is perfect for people trying to break into this growing field. And classes for everyone from executives to pre-K young scientists are in the works. Membership is not required, and most classes are open to all ages. Visit to sign up – spaces go quickly!

Community: Find co-discoverers, co-founders, and friends at BioCurious, whether you’re looking for the creative spark of a novice or the technical expertise of a professional scientist. BioCurious is the first lab of its kind in the Bay Area, allowing anyone to participate in science. Our members come from backgrounds spanning economics, philosophy, and art, as well as science and engineering. Members can host meet-ups. Planned activities include science projects, art shows and movie nights. We are collaborating to build something amazing. That’s the spirit of BioCurious.

Innovation: Have a great idea, but don’t want to pursue it at work or school? We think experiments need a place to flourish. Builders and makers need a place to prototype. And good ideas need to become reality. BioCurious is a not-for-profit organization and does not make any claim to member intellectual property. We encourage start-ups and entrepreneurs to use our facilities and meeting rooms, and have special deals for dedicated bench space, equipment housing, and cold storage.

Change the World: We’ve come a long way over the last year. Our community now includes over 500 members in the Bay Area. At the Maker Faire we wowed thousands of visitors, and won an Education Award. We presented at an International Synthetic Biology Conference. We piloted hands-on biotech classes for Singularity University. And now we’re pleased to open the doors of our new lab in Sunnyvale. We’re starting a new biotech revolution in the Valley; come join us. Become a member today! Visit Check out upcoming classes ( Come see the lab, get a day pass or take a tour, and see the next big thing to come out of a Silicon Valley garage. Stay Curious, Eri Gentry, Executive Director Founding Directors: Kristina Hathaway, Joseph Jackson, Tito Jankowski, Raymond McCauley, Josh Perfetto BioCurious: 845 Stewart Drive, Suite C, Sunnyvale, California Current hours: 12 noon – 10 PM weekdays, 10 AM – 10 PM weekends

Self-tracking conference paper opportunity




A special AAAI Spring Symposium will be investigating Self-tracking and Collective Intelligence for Personal Wellness at Stanford March 26-28, 2012.

A call for papers has been extended to October 17, 2011 (2 pages are due on October 17, the full 6 page submission is due on January 1, 2012). Paper topics should be in the areas of personal wellness programs, self-tracking experimentation, collective intelligence, citizen science, and DIY community tools and projects.

The specific focus of the conference is self-tracking technologies for monitoring personal health conditions such as sleep, diet, excise, vital data, and for analyzing personal medical and genome data, and collective intelligence as a potential resource to find useful knowledge for personal wellness from knowledge from others.

More information is available at the conference website. DIYgenomics will be running a session at the symposium.

Genetic Testing to Treat Disease: Should We Do It?

If you could take a genetic test as an infant and prevent diseases from occurring later in life, would you?  If the costs of testing and follow-up treatment were low enough I think almost everyone I know would answer yes to this question.  Indeed, if the tests and treatments were offered free of charge by government or a health care provider, you could argue that denying the test could be an unethical act of “willful blindness.”  As genetic testing gets more and more accurate, these ethical questions become much more than classroom debate topics, they become real issues.

For me, the question of genetic testing has special significance because I live with chronic back pain caused from a disease that many experts in the field believe has a genetic component.  While researchers have not isolated the gene that caused the development of my Scheuermann’s disease, multiple case studies of monozygotic twins with the disease suggest a genetic linkage.

If a Scheuermann disease-causing gene were to be isolated, then early genetic testing may offer huge rewards to those who find out they have the gene early in life.  Special spinal braces are often indicated for Scheuermann’s sufferers because the disease causes a curving of the spine.  One must use these braces early in life, usually as a teenager; because once the spine is fully developed they lose effectiveness.  Early diagnosis is important for Scheuermann’s disease just like many other chronic diseases including heart disease, and type 1 diabetes to name a few.  There are treatments for all of these diseases I just mentioned; the key is knowing early enough to implement them.

The knowledge that you are genetically predisposed to a chronic disease can be a lot to handle.  It can have a number of far-reaching implications.  Genetic testing offers the possibility of knowing whether or not you could pass your disease on to your children.  This kind of knowledge can be hard to process but that does not, in my opinion, mean that we should ignore it.  Knowledge of our diseases gives us power over them, keeping us from falling into the role of “victim”.

For me, the knowledge that I have Scheuermann’s disease means a number of things.  It means I have to swim at least an hour a day to keep my pain in check.  It means I have to do a series of stretches everyday to keep my core strong and to keep my tight hamstrings, an unusual symptom of the disease, loose.  Swimming, stretching, and a top-quality mattress enable me to control my disease and live a happy, fulfilling, and hopefully long life.

Blog post by Jon deKay

Longevity genomics paper retracted

(cross-posted at Broader Perspective)

DNA image




On July 22, 2011, a high-profile longevity genomics paper published in Science in July 2010 was retracted. The paper, ‘Genetic Signatures of Exceptional Longevity in Humans,’ was the work of Thomas Perls and Paola Sebastiani (Boston University). The initial study had been revised per editorial concerns that arose last year, but has now been retracted possibly due to issues related to the replicatability the findings.

The revised study results were presented by the team at the American Aging Association meeting in June 2011. These data featured nine single SNP associations (versus two previously), and linked 281 SNPs to signatures for exceptional longevity (versus 180 SNPs previously). The overall conclusion remained unchanged – that

centenarians, while having the same disease mutational profiles as non-centenarians, have other specific aspects to their genetic profiles which indicate a signature for exceptional longevity

Sage Commons Congress drives participatory medicine

(cross-posted at Broader Perspective)

The second Sage Commons Congress was held in San Francisco CA April 15-16, 2011. Conceptually an ‘open science,’ ‘data 2.0,’ ‘health 2.0,’ and ‘medicine 2.0’ event, the main purpose was for a variety of working groups to collaborate and outline goals for future work. The open science focal points for the group were data (aggregation, packaging, access, and usability) and public engagement. Of particular note was the launch of a new journal,Open Network Biology, which aims to facilitate experiment reproducibility through improved access to underlying data. The event is summarized here, and conference videos and presentations are available here.

The congress was an example of the growing activity in alternatives to the traditional conduct of health research and medicine, and important as an ongoing collaborative effort between many open health science initiatives. Alternative efforts could become a key partner in traditional health care delivery, particularly in realizing preventive medicine through measurement and intervention while conditions are still pre-clinical. Boutique physicianshealth social networksquantified self health trackingpatient-controlled health records, and patient-organized clinical trials could be important features in the near-term health landscape.