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Genome+Environment = Traits, [diseases], (treatments)

Hair: Baldness [alopecia](minoxidil) Eyes: [Near/Far-sightedness](glasses) Iris color [ARMD] (glasses) Face: [Developmental syndromes, Wrinkles] (Botox) Brain: ADHD(Ritalin); Depression(Prozac); Headache(analgesics) Sleep & Circadian (caffeine, amphetamine, modafinil)

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Genome+Environment = Traits, [diseases], (treatments)

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  1. Hair: Baldness [alopecia](minoxidil) Eyes: [Near/Far-sightedness](glasses) Iris color [ARMD] (glasses) Face: [Developmental syndromes, Wrinkles] (Botox) Brain: ADHD(Ritalin); Depression(Prozac); Headache(analgesics) Sleep & Circadian (caffeine, amphetamine, modafinil) Motion sickness (Dramamine, and Scopolamine) Ears: Sensitivity (hearing aids) Nose: Shape [breathing disorders] (CPAP) Lip: [Cleft palate] (surgery); [Hirsutism] (calcium thioglycolate) Mouth: Halitosis, throat exams; aerosols [airborne pathogens] Digestion [reflux, gas,ulcer] (antibiotics, antacids, PPIs) Back: Strain sensitivity [IDD] (analgesics) Skin: Perspiration, Body odor, Pheromones (deodorants) Surface texture [psoriasis] (topicals, photo-treatments) Immune components [acne] (topical antibiotics) Skin color [vitamin D & sunburn] (supplements, SPF cream) Hands: Dermatoglyphics [syndromes], [Arthritis](corticosteroids) Internal sensors: Proprioceptor, Repetitive stress (NSAIAs) Body: Height [Marfan] [short stature] (hGH) Weight [anorexia] [obesity] (Orlistat, Phentermine, Sibutramine) Allergies (antihistamines, cortisone, epinephrine, theophylline) Metabolic polymorphisms (vitamins, minerals, insulin) Feet: Plantar fasciitis (orthotic shoes) Athlete’s foot (miconazole, itraconazole, terbinafine, salicylate) Genome+Environment = Traits, [diseases], (treatments) 1933

  2. SNP chip vs Sequence : Breast Cancer 2x (1Mbp vs 3000Mbp) deCODEme: “does not include the high-risk but rare BRCA1 and BRCA2 breast cancer risk variants”. Navigenics: “Mutations in BRCA1 or BRCA2 are less common in the population and are only present in approximately 5 – 10% of families with breast and ovarian cancer.” 23andme: “Hundreds of cancer-associated BRCA1 and BRCA2 mutations have been documented, but three specific BRCA mutations are worthy of note because they are responsible for a substantial fraction of hereditary breast cancers and ovarian cancers among women with Ashkenazi Jewish ancestry”. Knome: Nearly complete genome sequence

  3. Valuable Personal Genome Sequences 1526 genes are highly predictive & medically actionable (inherited & cancer) at ~$2K per gene. PKU, Tay Sachs, Cystic Fibrosis, BRCA1/2, etc. (See Genetests.org) Pharmacogenomic drug/allele combinations: Herceptin, Iressa, .. Also: Ancestry, Forensics, Social Networking, Education, Research

  4. Prioritizing by odds ratio, actionability, FP consequences

  5. Common Disease – Common Variant Theory. How common? ApoE allele e4 : Alzheimer’s dementia, & hypercholesterolemia 15% in humans, >97% in chimps HbS 17% & G6PD 40% in a Saudi sample CCR5D32 : resistance to HIV 9% in caucasians

  6. One form of HIV-1 Resistance

  7. Association test for CCR-5 & HIV resistance Samson et al. Nature 1996 382:722-5

  8. But what if we test more than one locus? The future of genetic studies of complex human diseases. Ref(Note above graphs are active spreadsheets -- just click) GRR = Genotypic relative risk

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