Off Topic: DNA data finally being used to identify diseases caused by genes- June 2023

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New AI tool searches genetic haystacks to find disease-causing variants

Washington Post $$

• "The scientists built the algorithm, called PrimateAI-3D, using the genetic blueprints of 233 different primate species. This base brings into sharp relief the variants that can be tolerated by primates, including humans, and those that prove deadly. Scientists look for places where the sequence is the same from one primate to another, a clear sign that any change is disastrous."
• "Illumina said it will make the new tool broadly available in future releases of its software products."
• "By testing the new algorithm on hundreds of thousands of patient genomes in UK Biobank, “we found that 97 percent of the general population carries a rare variant” that has some kind of significant affect on health, Farh said. Although the algorithm cannot account for the influence of diet and environmental factors, he explained,..."
• "The National Institutes of Health estimates that genome sequencing is now generating up to 40 billion gigabytes of data each year, the equivalent of roughly 10 million full genomes."

• This is a review of: A global catalog of whole-genome diversity from 233 primate species - Science   PrePrint

Reminder: Genetics, of course, is unaware of health changes due to:

• supplements,
• what you eat,
• toxins,
• exercise,
• sleep duration
• stress level,
• pollution,
• DNA of your bionome
• Health of your parents in the year before your birth
• Your season of birth
• How often you get outdoors
• Infection by viruses, such as COVID. that deactivate scores of genes - such as the Vitamin D receptor

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VitaminDWiki – Genetics category contains

326 articles in the Genetics category

see also

• Vitamin D Receptor has 493 items
• Vitamin D Binding Protein = GC has 174 items
• CYP27B1 has 58 items
• CYP24A1 in title of 34+ items
• CYP24R1 25+ items
• Calcidiol has 45 items
• Calcitriol has 56 items
• Topical Vitamin D
• Nanoemulsion Vitamin D may be a substantially better form
• 1289 genes changed with higher doses of Vitamin D - RCT Dec 2019
• CYP3A4 (7 as of Dec 2022)
• Getting Vitamin D into your body

Vitamin D blood test misses a lot

• Vitamin D from coming from tissues (vs blood) was speculated to be 50% in 2014, and by 2017 was speculated to be 90%
• Note: Good blood test results (> 40 ng) does not mean that a good amount of Vitamin D actually gets to cells
• A Vitamin D test in cells rather than blood was feasible (2017 personal communication)
•    Commercially available 2019
  • However, test results would vary in each tissue due to multiple genes
• Good clues that Vitamin D is being restricted from getting to the cells
  1) A vitamin D-related health problem runs in the family
  • especially if it is one of 51+ diseases related to Vitamin D Receptor
  
  2) Slightly increasing Vitamin D shows benefits (even if conventional Vitamin D test shows an increase)
  3) Vitamin D Receptor test (<$30) scores are difficult to understand in 2016
  • easier to understand the VDR 23andMe test results analyzed by FoundMyFitness in 2018
  
  4) Back Pain
  • probably want at least 2 clues before taking adding vitamin D, Omega-3, Magnesium, Resveratrol, etc
    • The founder of VitaminDWiki took action with clues #3&4