Figure out some interesting example SQL queries

[simonw]

My knowledge of genetics has left me short here. I'd love to be able to provide some interesting example SELECT queries - maybe one that spots if you are likely to have red hair?

[simonw]

Thanks to help from Dr. Laura Cantino at Science Hack Day San Francisco I've been able to pull together this query:

select rsid, genotype, case genotype
  when 'AA' then 'brown eye color, 80% of the time'
  when 'AG' then 'brown eye color'
  when 'GG' then 'blue eye color, 99% of the time'
end as interpretation from genome where rsid = 'rs12913832'

See also https://www.snpedia.com/index.php/Rs12913832 - in particular this table:

[simonw]

[cobiadigital]

Risk of autoimmune disorders: https://www.snpedia.com/index.php/Genotype

select rsid, genotype, case genotype
  when 'AA' then '2x risk of rheumatoid arthritis and other autoimmune diseases'
  when 'GG' then 'Normal risk for autoimmune disorders'
end as interpretation from genome where rsid = 'rs2476601'

[cobiadigital]

The "Warrior Gene" https://www.snpedia.com/index.php/Rs4680

select rsid, genotype, case genotype
  when 'AA' then '(worrier) advantage in memory and attention tasks'
  when 'AG' then 'Intermediate dopamine levels, other effects'
  when 'GG' then '(warrior) multiple associations, see details'
end as interpretation from genome where rsid = 'rs4680'

[cobiadigital]

rs7903146 Influences risk of Type-2 diabetes
https://www.snpedia.com/index.php/Rs7903146

select rsid, genotype, case genotype
  when 'CC' then 'Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes.'
  when 'CT' then '1.4x increased risk for diabetes (and perhaps colon cancer).'
  when 'TT' then '2x increased risk for Type-2 diabetes'
end as interpretation from genome where rsid = 'rs7903146'

[cobiadigital]

Both rs10757274 and rs2383206 can both indicate higher risks of heart disease
https://www.snpedia.com/index.php/Rs2383206

select rsid, genotype, case genotype
  when 'AA' then 'Normal'
  when 'AG' then '~1.2x increased risk for heart disease'
  when 'GG' then '~1.3x increased risk for heart disease'
end as interpretation from genome where rsid = 'rs10757274'

select rsid, genotype, case genotype
  when 'AA' then 'Normal'
  when 'AG' then '1.4x increased risk for heart disease'
  when 'GG' then '1.7x increased risk for heart disease'
end as interpretation from genome where rsid = 'rs2383206'

[cobiadigital]

rs53576: the oxytocin receptor (OXTR) gene

select rsid, genotype, case genotype
  when 'AA' then 'Lack of empathy?'
  when 'AG' then 'Lack of empathy?'
  when 'GG' then 'Optimistic and empathetic; handle stress well'
end as interpretation from genome where rsid = 'rs53576'

[cobiadigital]

rs1333049 associated with coronary artery disease
https://www.snpedia.com/index.php/Rs1333049

select rsid, genotype, case genotype
  when 'CC' then '1.9x increased risk for coronary artery disease'
  when 'CG' then '1.5x increased risk for CAD'
  when 'GG' then 'normal'
end as interpretation from genome where rsid = 'rs1333049'

[cobiadigital]

RS1800955 is related to novelty seeking and ADHD
https://www.snpedia.com/index.php/Rs1800955

select rsid, genotype, case genotype when 'CC' then 'increased susceptibility to novelty seeking' when 'CT' then 'increased susceptibility to novelty seeking' when 'TT' then 'normal' end as interpretation from genome where rsid = 'rs1800955'