def pain_sensitivity(genome):
"""Pain sensitivity."""
return unphased_match(genome["rs6269"], {
"AA": "Increased sensitivity to pain",
"AG": "Typical sensitivity to pain",
"GG": "Less sensitive to pain",
None: "Unable to determine"})
def blond_vs_brown_hair(genome):
"""Hair color; blond versus brown."""
return unphased_match(genome["rs1667394"], {
"CC": "Greatly decreased odds of having blond hair vs. brown",
"CT": "Decreased odds of having blond hair vs. brown",
"TT": "Typical odds of having blond hair vs. brown hair",
None: "Unable to determine"})
def bitter_taste(genome):
"Bitter taste perception."
return unphased_match(genome["rs713598"], {
"CC": "Probably can't taste certain bitter flavours",
"CG": "Can taste bitter flavours that others can't",
"GG": "Can taste bitter flavours that others can't",
None: "Unable to determine"})
def red_hair(genome):
"""Hair color; odds for red hair."""
return unphased_match(genome["rs1805007"], {
"CC": "Typical odds for red hair",
"CT": "Substantially increased odds for red hair",
"TT": "Greatly increased odds for red hair",
None: "Unable to determine"})
def norovirus_resistance(genome):
"""Norovirus resistance (most common strain)."""
return unphased_match(genome["rs601338"], {
"AA": "Resistant to most common strain",
"AG": "Likely not resistant to most common strain",
"GG": "Likely not resistant to most common strain",
None: "Unable to determine"})
def muscle_performance(genome):
"""Muscle performance."""
return unphased_match(genome["rs1815739"], {
"CC": "Likely sprinter, perhaps endurance athlete (two copies)",
"CT": "Likely sprinter, perhaps endurance athlete (one copy)",
"TT": "Unlikely sprinter, but likely endurance athlete (no copies)",
None: "Unable to determine"})
def malaria_resistance(genome):
"Malaria resistance (Duffy antigen)."
return unphased_match(genome["rs2814778"], {
"CC": "Likely resistant to P. vivax",
"CT": "Likely to have some resistance to P. vivax",
"TT": "Likely not resistant to P. vivax",
None: "Unable to determine"})
def alcohol_flush_reaction(genome):
"Alcohol flush reaction."
return unphased_match(genome["rs671"], {
"AA": "Extreme reaction (no copies of the ALDH2 gene)",
"AG": "Moderate reaction (one copy of the ALDH2 gene)",
"GG": "Little to no reaction (two copies of the ALDH2 gene)",
None: "Unable to determine"})
def lactose_intolerance(genome):
"Lactose intolerance."
return unphased_match(genome["rs4988235"], {
"AA": "Likely lactose tolerant",
"AG": "Likely lactose tolerant",
"GG": "Likely lactose intolerant",
None: "Unable to determine"})
def earwax_type(genome):
"Earwax type."
return unphased_match(genome["rs17822931"], {
"CC": "Wet earwax (sticky, honey-colored)",
"CT": "Wet earwax (sticky, honey-colored)",
"TT": "Dry earwax (flaky, pale)",
None: "Unable to determine"})
def biological_age(genome):
"""Biological aging (telomere lengths)."""
assert_european(genome)
ages = {
"rs10936599": {"TT": 7.82, "CT": 3.91, "CC": 0, None: 0},
"rs2736100": {"AA": 3.14, "AC": 0, "CC": -3.14, None: 0},
"rs9420907": {"AA": 0, "AC": -2.76, "CC": -5.52, None: 0},
"rs755017": {"AA": 0, "AG": -2.47, "GG": -4.94, None: 0},
"rs11100479": {"CC": 5.98, "CT": -2.99, "TT": 0, None: 0},
"rs10165485": {"TT": 0, "CT": -2.23, "CC": -4.46, None: 0},
}
age = [unphased_match(genome[rsid], t) for (rsid, t) in ages.items()]
def qual(age):
if age <= 0:
return "younger"
elif age > 0:
return "older"
msg = "From %.1f years %s to %.1f years %s than actual age\n" % (
abs(min(age)), qual(min(age)), abs(max(age)), qual(max(age)))
msg += "The sum is %.1f years %s, compared to actual age" % (
abs(sum(age)), qual(sum(age)))
return msg
def aspargus_detection(genome):
"""Aspargus metabolite detection."""
assert_european(genome)
return unphased_match(genome["rs4481887"], {
"AA": "Higher odds of smelling aspargus in urine",
"AG": "Medium odds of smelling aspargus in urine",
"GG": "Typical odds of smelling aspargus in urine",
None: "Unable to determine"})
def eye_color(genome):
"Eye color."
assert_european(genome)
return unphased_match(genome["rs12913832"], {
"AA": "Brown eyes, although 14% have green and 1% have blue",
"AG": "Most likely brown or green, but 7% have blue",
"GG": "Most likely blue, but 30% have green and 1% brown",
None: "Unable to determine"})
def blood_glucose(genome):
"""Blood glucose."""
assert_european(genome)
return unphased_match(genome["rs560887"], {
"CC": "Average fasting plasma glucose levels of 5.18mmol/L",
"CT": "Average fasting plasma glucose levels of 5.12mmol/L",
"TT": "Average fasting plasma glucose levels of 5.06mmol/L",
None: "Unable to determine"})
def smoking_behaviour(genome):
"""Smoking behaviour."""
assert_european(genome)
return unphased_match(genome["rs1051730"], {
"AA": "Likely to smoke more than average",
"AG": "Likely to smoke a little bit more than average",
"GG": "Likely to smoke typical amount of cigarettes per day",
None: "Unable to determine"})
def heroin_addiction(genome):
"""Heroin addiction."""
assert_european(genome)
return unphased_match(genome["rs1799971"], {
"AA": "Typical odds of addiction",
"AG": "Higher odds of addiction",
"GG": "Higher odds of addiction",
None: "Unable to determine"})
def caffeine_metabolism(genome):
"""Caffeine metabolism."""
assert_european(genome)
return unphased_match(genome["rs762551"], {
"AA": "Fast metabolizer",
"AC": "Slow metabolizer",
"CC": "Slow metabolizer",
None: "Unable to determine"})
def birth_weight(genome):
"""Birth weight."""
assert_european(genome)
weights = {
"rs7903146": {"TT": 0, "CT": -30, "CC": -60, None: 0},
"rs1799884": {"TT": +54, "CT": +27, "CC": 0, None: 0},
}
weight = [unphased_match(genome[rsid], w) for (rsid, w) in weights.items()]
return "From %.1fg to %.1fg (sum: %.1fg) compared to typical weight" % (
min(weight), max(weight), sum(weight))
def adiponectin_levels(genome):
"""Adiponectin levels."""
if genome.ethnicity == "asian":
r = unphased_match(genome["rs1851665"], {
"AA": "Slightly lower, which may be bad (rs1851665)\n",
"AG": "Typical (rs1851665)\n",
"GG": "Slightly higher, which is good (rs1851665)\n",
None: "Unable to determine for rs1851665\n"})
r += unphased_match(genome["rs7193788"], {
"AA": "Slightly higher, which is good (rs7193788)",
"AG": "Typical (rs7193788)",
"GG": "Slightly lower, which may be bad (rs7193788)",
None: "Unable to determine for rs7193788"})
return r
elif genome.ethnicity in [None, "european"]:
return unphased_match(genome["rs6444175"], {
"AA": "Lower, which may be bad",
"AG": "Slightly lower, which may be bad",
"GG": "Typical levels",
None: "Unable to determine"})
def hiv_aids_resistance(genome):
"""Resistance to HIV/AIDS."""
return unphased_match(genome["i3003626"], {
"DD": "Some resistance to most common strain of HIV",
"DI": "Not resistant, but may have slower disease progression",
"II": "Not resistant"})
def hair_curl(genome):
assert_european(genome)
return unphased_match(genome["rs17646946"], {
"AA": "Straighter hair on average",
"AG": "Straighter hair on average",
"GG": "Slightly curlier hair on average"})