ABMGG Molecular Genetic Pathology flashcards

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

Chargaff base-pairing rule

In duplex DNA, adenine pairs with thymine and guanine pairs with cytosine, so %A=%T and %G=%C; GC content determines thermal stability of the duplex.

Melting temperature (Tm)

The temperature at which half of a DNA duplex is denatured into single strands. Higher GC content, longer length, and higher salt concentration increase Tm.

Proofreading exonuclease activity

The 3'→5' exonuclease function of certain DNA polymerases that removes misincorporated nucleotides, reducing replication error rates by roughly 10-100 fold.

A260/A280 ratio

Ratio of UV absorbance at 260 nm to 280 nm used to assess nucleic acid purity; about 1.8 for DNA and 2.0 for RNA, with lower values suggesting protein contamination.

Hybridization stringency

Conditions controlling duplex formation; higher temperature, lower salt, and added formamide increase stringency, improving discrimination of mismatched sequences.

Polymerase chain reaction (PCR)

Cyclic amplification using thermal denaturation, primer annealing, and polymerase extension to exponentially copy a target sequence defined by primer binding sites.

Ct value

Threshold cycle at which fluorescence exceeds background in real-time PCR; it is inversely proportional to starting template, with one cycle equal to a two-fold difference.

qPCR efficiency

Calculated as E = 10^(−1/slope) − 1 from a standard curve; efficiencies of 90-110% (slope −3.1 to −3.6) indicate acceptable amplification.

Sanger sequencing

Dideoxy chain-termination method using fluorescent ddNTP terminators separated by capillary electrophoresis; detects point mutations and small insertions/deletions.

Allele-specific PCR (ARMS)

Assay in which a primer's 3' end matches a specific variant, allowing selective amplification; requires controls because polymorphisms under primers can cause false negatives.

Analytical sensitivity (LoD)

The lowest analyte concentration reliably detected by an assay, typically determined with replicate testing across multiple runs and reported as the limit of detection.

CLIA test validation

Regulatory requirement to establish and document accuracy, precision, analytical sensitivity, analytical specificity, reportable range, and reference intervals before clinical use.

Proficiency testing

External evaluation of laboratory performance using blinded specimens for each regulated analyte; failures require corrective action and alternative assessment.

Unidirectional workflow

Physical and procedural separation of pre-amplification, amplification, and post-amplification activities to prevent amplicon contamination and false-positive results.

ACMG/AMP variant classification

Five-tier framework (pathogenic, likely pathogenic, uncertain significance, likely benign, benign) using criteria codes such as PVS1, PS, PM, PP, BA1, BS, and BP.

PVS1 criterion

Very strong evidence of pathogenicity for a predicted null variant (nonsense, frameshift, canonical splice site) in a gene where loss of function causes disease.

BA1 criterion

Stand-alone benign evidence when a variant's allele frequency in population databases exceeds the maximum expected frequency for the associated disease.

HGVS nomenclature

Standardized variant naming using prefixes c. for coding DNA, g. for genomic, and p. for protein, always referenced to a specified transcript or genome build.

Driver mutation

A somatic alteration that confers a selective growth advantage to a clone and is recurrently observed in a specific tumor type; it is a potential therapeutic target.

Tumor mutational burden

Number of somatic mutations per megabase of tumor DNA; high TMB (often ≥10 mut/Mb) may predict response to immune checkpoint inhibitors.

Variant allele frequency

Fraction of sequencing reads carrying a variant; in tumors it reflects tumor purity and clonality, and low values may suggest subclonal or germline origin.

Liquid biopsy (ctDNA)

Detection of circulating tumor DNA in plasma for noninvasive genotyping and monitoring; sensitivity is limited at low tumor burden, so false negatives occur.

JAK2 V617F

A somatic gain-of-function mutation in JAK2 present in most polycythemia vera and about half of essential thrombocythemia and primary myelofibrosis cases.

BCR-ABL1 fusion

t(9;22) translocation product defining chronic myeloid leukemia and some acute lymphoblastic leukemias; quantitative RT-PCR monitors major molecular response.

PML-RARA fusion

t(15;17) translocation defining acute promyelocytic leukemia; it predicts response to ATRA and arsenic trioxide and requires rapid molecular confirmation.

Minimal residual disease

Detection of residual leukemic cells below morphologic sensitivity (10^-4 to 10^-6) by NGS, PCR, or flow cytometry; it predicts relapse risk in AML and ALL.

HIV-1 viral load

Quantitative plasma HIV RNA in copies/mL or IU/mL used to monitor antiretroviral therapy; target not detected indicates suppression below assay limit.

16S rRNA sequencing

Broad-range bacterial identification and phylogenetic classification using conserved ribosomal gene sequences; useful in culture-negative infections but limited species resolution in some genera.

CYP2C19 poor metabolizer

Genotype with reduced CYP2C19 activity, impairing activation of clopidogrel and altering response to proton pump inhibitors and some antidepressants.

TPMT/NUDT15 deficiency

Reduced thiopurine methyltransferase or NUDT15 activity that increases risk of severe myelosuppression with azathioprine or mercaptopurine; genotyping guides dose reduction.

HLA-B*57:01

HLA allele strongly associated with abacavir hypersensitivity syndrome; screening before initiating abacavir reduces severe reactions.

STR identity testing

Short tandem repeat genotyping across core CODIS loci used for human identification, relationship testing, and chimerism monitoring after stem cell transplant.

Chromosomal microarray (CMA)

Genome-wide copy number analysis detecting deletions and duplications at kilobase resolution; it cannot detect balanced rearrangements or point mutations.

ISCN nomenclature

International System for Human Cytogenomic Nomenclature standardizing karyotype descriptions, such as 46,XX,t(9;22)(q34;q11.2), for consistent reporting.

Variant calling pipeline

Bioinformatic workflow aligning reads (e.g., BWA), calling variants (e.g., GATK), and annotating and filtering by quality, depth, and population frequency.