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Welcome to DIYgenomics!
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DIYgenomics
Promoting health awareness and vitality
Studies:
Other Projects:
OPEN-SOURCE SOFTWARE COMMUNITY - FUNDRAISING - HELP NEEDED - GENOMIC RESEARCH RESOURCES - PUBLISHING
DIYgenomics citizen science experiments: Replicate, extend, and develop new studies linking genotype with phenotype/behavior/environment in peer cohorts. Studies may involve a combination of genomic data + phenotypic biomarker data + self-reported observational data + environmental data. The format is typically in the form of genomics + phenotypic information + intervention.
Disease Studies
- MTHFR Study: MTHFR mutation purportedly leading to Vitamin B deficiency and higher homocysteine levels (in process, began 6/11/10)
- Aging Study: apply existing GWAS to peer cohort data for top ten areas of aging pathologies, measure corresponding phenotypic markers of aging, and attempt to ameliorate with interventions
- Top ~ten biological mechanisms of aging in GWAS: neurodegenerative disease, osteoporosis, IGF-1/Insulin signaling, lipoprotein metabolism, inflammation, immune system function, DNA damage repair, telomere length, transcription (ex: RNA editing), catabolism, mitochondrial health, cell cycle/stem cell health, protein function, blood operations
- Top ~ten phenotypic biomarkers of aging: blood pressure and hypertension, cholesterol (HDL/LDL/triglycerides; LDL particle size), BMI, Framingham Risk Score, VO2 max, erythrocyte glycoslyation, telomere length, lymphocyte growth capability, granulocyte strength.
- Example: effect of CoQ10 deficiency (paper)
- Cholesterol management - link genes with physical biomarkers, test the efficacy of supplements (niacin, etc.) and other remedies. References: Ron Krauss (DIYbio lab test: Cholestech LDX)
- Type 2 Diabetes/Obesity: apply novel loci/variants from Cristen Willer's recent work (Nature Genetics paper)
- Apply 160 variants implicated in cardiovascular disease to the peer cohort (Arking, Trends Genet 2009, paper)
- Macular degeneration study - examine variants, protective variants, and efficacy of supplementation products, participate in MacuCLEAR small molecule remedy clinical trials and explore other new drugs
- APOE4 genotyping together with mid-life cholesterol management programs; (imaging recommendation); NIH conference proceedings re: AD & Preventing Cognitive Decline (April 2010)
- Cancer - risk review and drug response for multiple cancers; check for B-RAF mutations
- Review boutique medicine personalized oncology offerings provided by CollabRx (Palo Alto CA) and FoundationMedicine (Cambridge, MA)
- Prostate: apply genotyping data to personalized medicine prostate management (e.g., Soar Biodynamics)
- Preventive medicine blood tests: apply Leroy Hood's preventive screening blood assays to peer cohort (Jim Heath from Caltech testing at UCLA)
- Brain cancer, genomics and drug response; determine risk susceptibility to glioblastoma from genomic profiles, estimate drug response to TEMODAR/Temozolomide, apply citizen science research from Ben Williams (Surviving "Terminal" Cancer - Clinical trials, drug cocktails & other treatments your oncologist won't tell you about), 14 year glioblastoma survivor. Resource: Clinical Trials and Treatment Options for Brain Tumors.
- Occular study: Review disease-causing mutations that are associated with ocular diseases such as glaucoma, cataracts, strabismus, corneal dystrophies and a number of forms of retinal degenerations in the peer cohort; link with phenotypic biomarkers and interventions. Resource: eyeGENE® - National Ophthalmic Disease Genotyping Network
- Asthma study - apply 43 genes found in asthma to peer cohort together with phenotypic biomarkers and interventions. Paper: Weiss, Curr Opin Genet Dev. 2009 Jun;19.
- Investigate propensity for gastrointestinal and liver disease, IBD (inflammatory bowel disease), Crohn's disease, etc. (Melum, World Gastroenterol 2009, paper)
- Investigate genomic markers for kidney health and phenotypic interventions for lowering creatinine and raising eGFR (DIYbio lab test: StatSensor Creatinine and eGFR testing)
Drug and Environmental Response Studies
- Pharmacogenomics: apply genotype/pharmacogenomic associations from the PharmGKB database to peer cohorts
- 'Environmentome' - tie genotyping data to environmental data: toxins, stress, etc. (environmental pollutants test)
- Dislike of low-sodium foods
- Linking food intake/digestion/etc. with microbiota. (Ruth Ley, Cornell); NYT microbiome article
Behavioral Studies
- Apply Correlated Genotypes in Friendship Networks study to peer cohort (James Fowler, UCSD)
- Are you a bad driver? Examine BDNF (neuroplasticity) genotypes and driving records; same gene predicts stroke recovery
- Investigate DRD4 novelty-seeking / risk-taking / externalizing / acting out genotype together with behavioral data
- Investigate DRD4, HTR1B (serotonin receptor gene) and other genes implicated in the development of ADHD (article)
- Examine serotonin transporter gene (HTTLPR/SLC6A4) & depression (mutation inhibits the neural circuit which processes negative emotion), paper, article
- Evaluate the MAOA "warrior gene" and higher levels of aggression with provocation (Rose McDermott, Princeton, paper, article; PLoS One paper); NPR story; interpret allele repeats (lower # is more aggressive)
- Scientists find first genes linked to stuttering Examine genotype and phenotype data for stuttering
- Athletic performance enhancement: sprinter/endurance genes
- Productivity: identify and investigate genes related to productivity, also possibly concentration, creativity, and deferred gratification (the Stanford Marshmallow Experiment) (from QS NYC)
- Personality disposition: apply the Atlantic article re: genetic tendency of people to be like 'Orchids' or 'Dandelions' (from QS NYC)
- Evaluate bully/victim predisposition in the peer cohort: genes may be a ~60% factor in bullying (antisocial behavior, impulsive tendencies, thrill seeking), and a 75% factor for victims of bullying (introversion, more emotional, tendency to cry more easily). There could be a genetic classification system for bullies/victims. Harriet, A., et al. (2008). "Genetic and environmental influences on victims, bullies and bully-victims in childhood." J Child Psychol Psychiatry 49(1):104-112.
- Investigate dopamine transmitter COMT's purported linkage to the ability to resolve conflict (Posner, Phys Life Rev 2009, paper)
Microbiome studies
- Apply HITChip analysis of gut microbiota from University of Bologna centenarian study to peer cohort
Other Genomic-related Studies
- Investigate structural variation by applying CNV analysis to genotyping data. Resources: Sanger CNV project, CNV-SEQ for NGS data, PennCNV (hidden Markov model to infer CNV from HapMap data); investigate Steve McCarroll at the Broad Institute's indirect method of looking for CNV
- Investigate CNV in the context of disease as a continuum, e.g.; few CNV is anxiety, many is paranoid schizophrenia
- Apply traditional economic/financial risk & actuarial models to multigenic disease risk prediction
- Need databases of longitudinal genotype/phenotype longitudinal data to test
- Develop a list of core SNPs/loci that should be reviewed for conditions (GAPPNET)
- Self-genotyping: Even better than having low-cost DNA sequencing data would be being able to self-genotype in DIYbio labs. Example: Katherine Aull genotyped herself for hemochromatosis.
- Innovate low-cost, non-prescription based finger-stick blood tests, saliva and urine panels for self-testing with synthetic biology or other methods
- Open-source resources needed
- Large-scale phenotypic databases - aggregate existing datasets in standard ontologies
- List of risk alleles; genotypes are typically noted as A/C for example which denotes Major allele/Minor allele or Ancestral/Derived, but either could be the variation. Automate collection of risk allele, odds ratios, population prevalence and other related data from papers.
- List of gene function at standardized levels of onotology
DIYgenomics citizen science ethics and standards
- Citizen science analog of an IRB (institutional review board)/ethics committee for human biomedical research
- Standards development for citizen science
- Defined tiers of participation (e.g.; question posing forums)
- Look up your SNPs and add them to the citizen science database
- Add your genotyping or sequencing file to the citizen science database
- Indicate degree of interest/willingness to participate in the phenotypic aspect of citizen science studies
- Contribute questions, research, analysis, background literature review, results write-up, etc.
- Particpant acknowledgement: Anonymous, Nonanonymous
- Nomenclature
- Coordinating Investigator
- Citizen Science Ethics Officer
Personal Genome Analysis Startups
WikiGenetics
Welcome to DIYgenomics!
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