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Welcome to DIYgenomics!

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DIYgenomics

Promoting health awareness

 

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

  1. MTHFR Study: MTHFR mutation purportedly leading to Vitamin B deficiency and higher homocysteine levels (in process, began 6/11/10)
  2. Aging Study: apply existing GWAS to peer cohort data for top ten areas of aging, 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)
  3. 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)
  4. Type 2 Diabetes/Obesity: apply novel loci/variants from Cristen Willer's recent work (Nature Genetics paper)
  5. Apply 160 variants implicated in cardiovascular disease to the peer cohort (Arking, Trends Genet 2009, paper)
  6. 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
  7. APOE4 genotyping together with mid-life cholesterol management programs; (imaging recommendation); NIH conference proceedings re: AD & Preventing Cognitive Decline (April 2010)
  8. 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)
  9. Prostate: apply genotyping data to personalized medicine prostate management (e.g., Soar Biodynamics)
  10. Preventive medicine blood tests: apply Leroy Hood's preventive screening blood assays to peer cohort (Jim Heath from Caltech testing at UCLA
  11. 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.
  12. 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
  13. 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.
  14. Investigate propensity for gastrointestinal and liver disease, IBD (inflammatory bowel disease), Crohn's disease, etc. (Melum, World Gastroenterol 2009, paper) 
  15. 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

  1. Pharmacogenomics: apply genotype/pharmacogenomic associations from the PharmGKB database to peer cohorts
  2. 'Environmentome' - tie genotyping data to environmental data: toxins, stress, etc. (environmental pollutants test)
  3. Dislike of low-sodium foods
  4. Linking food intake/digestion/etc. with microbiota. (Ruth Ley, Cornell); NYT microbiome article

 

Behavioral Studies

  1. Apply Correlated Genotypes in Friendship Networks study to peer cohort (James Fowler, UCSD)
  2. Are you a bad driver? Examine BDNF (neuroplasticity) genotypes and driving records; same gene predicts stroke recovery
  3. Investigate DRD4 novelty-seeking / risk-taking / externalizing / acting out genotype together with behavioral data
  4. Investigate DRD4, HTR1B (serotonin receptor gene) and other genes implicated in the development of ADHD (article)
  5. Examine serotonin transporter gene (HTTLPR/SLC6A4) & depression (mutation inhibits the neural circuit which processes negative emotion), paper, article
  6. 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)
  7. Scientists find first genes linked to stuttering Examine genotype and phenotype data for stuttering
  8. Athletic performance enhancement: sprinter/endurance genes
  9. Productivity: identify and investigate genes related to productivity, also possibly concentration, creativity, and deferred gratification (the Stanford Marshmallow Experiment) (from QS NYC)
  10. Personality disposition: apply the Atlantic article re: genetic tendency of people to be like 'Orchids' or 'Dandelions' (from QS NYC)
  11. 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.
  12. Investigate dopamine transmitter COMT's purported linkage to the ability to resolve conflict (Posner, Phys Life Rev 2009, paper)

 

Microbiome studies

  1. Apply HITChip analysis of gut microbiota from University of Bologna centenarian study to peer cohort

 

Other Genomic-related Studies

  1. 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
  2. Apply traditional economic/financial risk & actuarial models to multigenic disease risk prediction
    • Need databases of longitudinal genotype/phenotype longitudinal data to test
  3. Develop a list of core SNPs/loci that should be reviewed for conditions (GAPPNET)
  4. 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.
  5. Innovate low-cost, non-prescription based finger-stick blood tests, saliva and urine panels for self-testing with synthetic biology or other methods
  6. 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

 

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