Pharmacogenomics (PGx) is the study of how an individual's genetic makeup affects their response to drugs. Genetic variants in drug-metabolizing enzymes, drug transporters, and drug targets explain a significant proportion of variability in drug efficacy and adverse drug reactions.
CYP450 Enzyme Polymorphisms
Cytochrome P450 (CYP) enzymes metabolize approximately 75% of marketed drugs. Genetic variants create four metabolizer phenotypes: poor (PM), intermediate (IM), normal/extensive (NM/EM), and ultrarapid (UM).
CYP2D6 — codeine/morphine: Poor metabolizers cannot convert codeine to morphine (no analgesia, codeine is a prodrug). Ultrarapid metabolizers produce toxic morphine concentrations — FDA black box warning against codeine in breastfeeding mothers who are UM (neonatal morphine toxicity and death reported).
CYP2C19 — clopidogrel: Clopidogrel is a prodrug requiring CYP2C19 activation to its active thiol metabolite. Poor metabolizers (common in East Asian populations) cannot activate clopidogrel — diminished antiplatelet effect → stent thrombosis risk. FDA added a black box warning. Prasugrel or ticagrelor are alternatives.
HLA Typing and Drug Hypersensitivity
HLA (Human Leukocyte Antigen) genes encode proteins that present peptide antigens to immune cells. Certain HLA variants cause immune-mediated severe adverse drug reactions.
HLA-B*5701 and abacavir: HIV antiretroviral. Carriers of this allele develop a severe hypersensitivity reaction (fever, rash, multi-organ involvement) upon abacavir exposure. Prospective HLA-B*5701 screening before prescribing has virtually eliminated this reaction. FDA-mandated testing.
HLA-B*1502 and carbamazepine: Antiepileptic. Carriers (predominantly Southeast Asian populations) are at dramatically elevated risk for Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) — life-threatening skin reactions. FDA recommends testing in at-risk populations before initiation.
Cancer Susceptibility Genes
BRCA1 / BRCA2: Tumor suppressor genes encoding DNA repair proteins. Pathogenic germline variants confer ~70–80% lifetime risk of breast cancer and 40–60% ovarian cancer risk (BRCA1). Risk management options: intensive surveillance, chemoprevention (tamoxifen), risk-reducing salpingo-oophorectomy, prophylactic mastectomy. Cascade testing of relatives is recommended.
APOE ε4: The APOE ε4 allele is the strongest genetic risk factor for late-onset Alzheimer's disease. Carrying one ε4 allele increases risk ~3-fold; two copies ~12-fold. It is not deterministic — many ε4/ε4 individuals do not develop Alzheimer's. Its role in cholesterol metabolism and neuroinflammation is under active investigation.
Genetic Testing Modalities
Karyotype: visualizes all chromosomes; detects aneuploidies and large structural rearrangements.
FISH: fluorescently labeled probes hybridize to specific chromosomal loci; detects known deletions/duplications/translocations rapidly.
PCR: amplifies specific DNA sequences; used for single-gene disorder testing, pathogen detection, and mutation confirmation.
Microarray (chromosomal SNP array): detects copy number variants (CNVs) across the genome at higher resolution than karyotype.
Whole exome sequencing (WES): sequences all protein-coding regions (~1–2% of genome but ~85% of known disease-causing variants).
Whole genome sequencing (WGS): sequences entire genome including non-coding regions; highest sensitivity, most complex interpretation.
Prenatal and Newborn Genetic Screening
Cell-free DNA (NIPT): analyzes fetal DNA circulating in maternal blood; screens for trisomy 21, 18, 13, and sex chromosome aneuploidies from 10 weeks gestation; high sensitivity/specificity, non-invasive but a screening test — positive results require diagnostic confirmation.
Amniocentesis: 15–20 weeks; samples amniotic fluid containing fetal cells; diagnostic (karyotype, FISH, microarray); ~0.1–0.3% procedure-related loss risk.
Chorionic villus sampling (CVS): 10–13 weeks; samples placental tissue; earlier diagnosis; similar loss risk to amniocentesis.
Newborn screening: Guthrie card heel-stick blood spot tests all newborns for dozens of metabolic, endocrine, and hematologic disorders (PKU, congenital hypothyroidism, galactosemia, sickle cell, CAH, SCID). Early treatment for PKU (low-phenylalanine diet) and congenital hypothyroidism (levothyroxine) prevents irreversible intellectual disability.