AGMT flashcards

32 cards. Read the term and the definition here. The deck at the top of this page is optional.

Sanger sequencing

Dideoxy chain termination method using fluorescently labeled ddNTPs; capillary electrophoresis separates fragments; gold standard for single-nucleotide variants and small indels; read length ~500–1000 bp.

Next-generation sequencing

Massively parallel sequencing of millions of DNA fragments; short-read platforms (Illumina) produce 75–300 bp reads; used for panels, exomes, genomes, and RNA-seq; high throughput but shorter reads.

Digital PCR

Partitions sample into thousands of droplets; performs PCR in each partition; enables absolute quantification and detection of variant allele fractions as low as 0.01–0.1%; useful for rare variant detection.

MLPA

Multiplex ligation-dependent probe amplification; detects copy number changes of exons; peak height ratios <0.7 or >1.3 suggest loss or gain; cannot detect balanced rearrangements or point mutations.

Chromosomal microarray

Comparative genomic hybridization (aCGH) or SNP array; detects copy number variants and regions of homozygosity; resolution 10–100 kb; does not detect balanced translocations or low-level mosaicism.

Karyotyping

G-banded chromosome analysis at 400–550 band resolution; detects aneuploidy, large structural rearrangements (>5–10 Mb), and balanced translocations; requires dividing cells.

FISH

Fluorescence in situ hybridization; locus-specific probes detect deletions, duplications, and translocations (e.g., BCR-ABL1); resolution ~100 kb–1 Mb; can be performed on interphase nuclei.

Methylation-specific PCR

Assesses DNA methylation at CpG islands; used for imprinting disorders (Prader-Willi/Angelman, Beckwith-Wiedemann) and MLH1 promoter hypermethylation; bisulfite treatment converts unmethylated cytosine to uracil.

Central dogma

DNA is transcribed to RNA, which is translated to protein; transcription occurs in the nucleus, translation on ribosomes; post-translational modifications affect protein function.

Nonsense mutation

A single nucleotide change creates a premature stop codon, leading to truncated protein; often results in loss of function; example: c.76A>T (p.Lys26*) in CFTR.

Frameshift mutation

Insertion or deletion of nucleotides not a multiple of three, altering the reading frame; typically leads to premature stop codon and truncated, nonfunctional protein.

Penetrance

Proportion of individuals with a pathogenic variant who exhibit the phenotype; age-dependent penetrance is common in adult-onset disorders such as BRCA1/2 and Lynch syndrome.

Variable expressivity

Same genotype produces different phenotypes among individuals; influenced by modifier genes, environment, and stochastic factors; distinct from penetrance.

Genomic imprinting

Parent-of-origin-specific gene expression; examples: 15q11-q13 (Prader-Willi/Angelman) and 11p15.5 (Beckwith-Wiedemann/Silver-Russell); disruptions cause imprinting disorders.

Mitochondrial inheritance

Maternal transmission of mtDNA; heteroplasmy (mixture of mutant and wild-type mtDNA) and threshold effect cause variable phenotype; examples: MELAS, MERRF, LHON.

Trinucleotide repeat disorders

Dynamic mutations caused by expansion of triplet repeats; examples: Huntington disease (CAG in HTT), fragile X syndrome (CGG in FMR1), myotonic dystrophy (CTG in DMPK); anticipation occurs.

ISCN nomenclature

International System for Human Cytogenomic Nomenclature; standardizes karyotype description; examples: 46,XX normal female; 47,+21 trisomy 21; 46,XY,t(9;22)(q34;q11.2) Philadelphia chromosome.

Robertsonian translocation

Fusion of two acrocentric chromosomes (13,14,15,21,22); carrier has 45 chromosomes; risk for unbalanced offspring, e.g., translocation Down syndrome.

Mosaicism

Presence of two or more cell lines in an individual; detected by karyotype (≥10–20 cells analyzed) or CMA (less sensitive for low-level); example: mosaic trisomy 21 (46,XX/47,XX,+21).

Microdeletion syndrome

Small chromosomal deletion detected by CMA or FISH; examples: 22q11.2 deletion (DiGeorge), 15q11-q13 deletion (Prader-Willi/Angelman), 7q11.23 deletion (Williams), 5p deletion (cri-du-chat).

Autosomal dominant inheritance

Affected individual has an affected parent (unless de novo); 50% recurrence risk for each offspring; examples: Huntington disease, Marfan syndrome, familial hypercholesterolemia.

Autosomal recessive inheritance

Both parents are carriers (usually unaffected); 25% recurrence risk; consanguinity increases risk; examples: cystic fibrosis, sickle cell disease, Tay-Sachs disease.

X-linked recessive inheritance

Males affected; females carriers (usually unaffected); no male-to-male transmission; 50% of sons of carrier female affected; examples: Duchenne muscular dystrophy, hemophilia A/B.

Bayesian analysis

Combines prior and conditional probabilities to calculate carrier risk; example: prior 1/4, conditional (unaffected child) 1/2 → posterior (1/4×1/2)/[(1/4×1/2)+(3/4×1)] = 1/7.

Hardy-Weinberg equilibrium

p² + 2pq + q² = 1; carrier frequency = 2pq; if q is small, 2pq ≈ 2q; example: q = 1/50 → carrier frequency ≈ 1/25.

Noninvasive prenatal testing

Screens for fetal trisomies 21, 18, 13 using cell-free fetal DNA (cffDNA) from maternal blood; high sensitivity and specificity; positive results require diagnostic confirmation by CVS or amniocentesis.

Newborn screening

Mandated in all US states; typically includes congenital hypothyroidism, PKU, CF, sickle cell disease, hearing loss; uses dried blood spots; tandem mass spectrometry.

Pharmacogenomics

Genetic variants affecting drug metabolism; examples: CYP2C19 and clopidogrel, CYP2D6 and codeine, TPMT and thiopurines, HLA-B*57:01 and abacavir.

Preimplantation genetic testing

PGT-A (aneuploidy), PGT-M (monogenic), PGT-SR (structural rearrangements); requires in vitro fertilization; biopsy at blastocyst stage; used to select unaffected embryos.

CLIA

Clinical Laboratory Improvement Amendments; federal regulation of clinical laboratories; requires certification, proficiency testing, quality control, and personnel qualifications; enforced by CMS.

Proficiency testing

External evaluation of laboratory performance; required for CLIA-certified tests; failures require corrective action; ensures accuracy and reliability of test results.

ACMG variant classification

Pathogenic, likely pathogenic, uncertain significance (VUS), likely benign, benign; based on evidence categories: population, computational, functional, segregation, de novo, allelic.