Current DNA Sequencing Technologies, Epigenetics, and Translational Genomics

Comprehensive vocabulary flashcards covering next-generation and long-read sequencing technologies, DNA methylation and epigenetics, genomic imprinting, uniparental disomy, inborn errors of immunity, translational genomics, gene therapies, and clinical variant classification based on BIOL 3240 lecture material.

Sequencing by Synthesis (SBS)

A short-read next-generation sequencing methodology utilized by Illumina platforms that determines nucleotide sequences by detecting fluorescently labeled nucleotides during DNA synthesis, generating reads up to $2 \times 300\,\text{bp}$.

Sequencing by Binding (SBB)

A short-read sequencing technology developed by Element Biosciences that utilizes multivalent dye-labeled polymers ("avidites") to detect high-affinity nucleotide binding without immediate enzymatic incorporation, significantly reducing error rates after homopolymer sequences.

Avidite

A dye-labeled polymer molecule conjugated with multiple identical nucleotides, used in avidity sequencing to achieve multivalent, high-affinity binding to target DNA clusters with low background noise.

Circular Consensus Sequencing (CCS)

A PacBio long-read sequencing mode where a circularized DNA fragment of approximately $10\text{--}30\,\text{kb}$ is sequenced iteratively across multiple passes to correct random single-pass errors and generate high-accuracy ($>99.9\%$) HiFi reads.

Continuous Long Read (CLR)

An early PacBio sequencing mode that performs a single pass over a long DNA insert ($>30\,\text{kb}$), maximizing read length at the cost of lower per-base accuracy compared to circular consensus sequencing.

Telomere-to-Telomere (T2T) Genome

A complete, gapless human reference genome assembly achieved through long-read sequencing technologies (PacBio HiFi and Oxford Nanopore) that resolved previously inaccessible regions, such as centromeric satellite arrays and ribosomal DNA repeats.

Adaptive Sampling

A real-time software-directed feature of Oxford Nanopore sequencing that selectively ejects unwanted DNA molecules from pores by reversing the voltage, enabling targeted enrichment or depletion without PCR amplification.

Haplotype Phasing

The computational or molecular determination of which specific homolog (maternal or paternal) carries each genetic variant across a chromosome, critical for resolving compound heterozygosity in recessive disorders.

Somatic Cell Nuclear Transfer (SCNT)

The laboratory procedure of transplanting a nucleus from a differentiated somatic cell into an enucleated oocyte, proving that differentiated cells retain the full genomic information required to develop into an entire organism.

Epigenetics

The study of stable, heritable changes in gene expression and cellular phenotype that occur through modifications like DNA methylation and histone changes without alterations to the underlying primary DNA sequence.

DNMT1

A maintenance DNA methyltransferase enzyme that specifically recognizes hemimethylated CpG sites generated during semiconservative DNA replication and methylates the newly synthesized opposite strand.

TET Enzymes (Ten-Eleven Translocation)

A family of dioxygenases ($\text{TET1}$, $\text{TET2}$, $\text{TET3}$) that catalyze the active oxidative demethylation of 5-methylcytosine to 5-hydroxymethylcytosine ($\text{5-hmC}$), which is critical for dynamic gene regulation in post-mitotic neurons.

CpG Island

A genomic region containing a high density of cytosine-phosphate-guanine dinucleotides (typically unmethylated when located near active gene promoters), which destabilizes nucleosomes to maintain an open, transcriptionally accessible chromatin state.

MECP2 (Methyl-CpG Binding Protein 2)

A nuclear transcriptional repressor that selectively binds methylated CpG dinucleotides to recruit chromatin-remodeling complexes; pathogenic variants causing loss of MECP2 function lead to the X-linked disorder Rett syndrome.

Genomic Imprinting

An epigenetic mechanism that restricts gene expression to a single parent-of-origin allele (maternal or paternal) via differential DNA methylation and heterochromatin establishment during gametogenesis.

Trisomy Rescue

A mitotic correction event during early embryogenesis in which a trisomic zygote ($47\,\text{chromosomes}$) sheds the supernumerary chromosome through anaphase lag, which can result in uniparental disomy if both remaining homologs originate from the same parent.

Isodisomy

A form of uniparental disomy in which an individual inherits two identical copies of a chromosome from a single parent, resulting in whole-chromosome loss of heterozygosity and risk of unmasking recessive alleles.

Heterodisomy

A form of uniparental disomy in which an individual inherits both non-identical homologous chromosomes from a single parent due to nondisjunction in meiosis I, requiring parental DNA testing for detection.

Schaaf-Yang Syndrome

An autosomal dominant disorder characterized by developmental delay, obesity, and autism-like features caused by truncating mutations in the paternally expressed, maternally imprinted MAGEL2 gene on chromosome $15\text{q}11\text{-q}13$.

Prader-Willi Syndrome (PWS)

An imprinting disorder caused by the loss of expression of paternal genes on chromosome $15\text{q}11\text{-q}13$ due to paternal microdeletion ($70\%$), maternal uniparental disomy ($25\%$), or imprinting defects ($\le 5\%$).

Angelman Syndrome (AS)

A neurodevelopmental disorder caused by the loss of expression of the maternally derived UBE3A gene on chromosome $15\text{q}11\text{-q}13$ via maternal deletion ($70\%$), UBE3A gene mutation ($20\%$), paternal uniparental disomy ($2\%$), or imprinting defects ($\le 5\%$).

Inborn Errors of Immunity (IEI)

A genetically heterogeneous group of monogenic disorders (primary immunodeficiencies) that impair immune cell development or effector function, predisposing individuals to recurrent infections, autoimmunity, autoinflammation, and malignancy.

X-linked Agammaglobulinemia (XLA)

A primary humoral immunodeficiency caused by loss-of-function mutations in BTK (Bruton tyrosine kinase), leading to a failure of B-cell maturation, absence of peripheral B cells, and complete lack of circulating immunoglobulins.

T-cell Receptor Excision Circles (TRECs)

Circular DNA byproducts generated during somatic V(D)J recombination of T-cell receptor genes in the thymus, quantified in newborn dried blood spots to screen for severe combined immunodeficiency (SCID) and T-cell lymphopenia.

Chronic Granulomatous Disease (CGD)

An inborn error of immunity caused by mutations in NADPH oxidase subunits (predominantly X-linked CYBB/gp91phox) that abolish the neutrophil respiratory burst, impairing clearance of catalase-positive pathogens.

Cryopyrin-Associated Periodic Syndromes (CAPS)

A spectrum of autosomal dominant autoinflammatory disorders (FCAS, Muckle-Wells syndrome, and NOMID) caused by gain-of-function variants in NLRP3, driving constitutive inflammasome activation and systemic interleukin-1 overproduction.

Sphingosine-1-Phosphate Lyase Deficiency

A monogenic syndrome caused by biallelic mutations in SGPL1 that disrupt the tissue S1P chemotactic gradient, impairing lymphocyte egress and presenting with profound lymphopenia, steroid-resistant nephrotic syndrome, and primary adrenal insufficiency.

Droplet Digital PCR (ddPCR)

An absolute quantification method where a DNA sample is partitioned into thousands of nanoliter water-in-oil droplets for individual endpoint PCR reactions, enabling sensitive detection and quantification of low-frequency somatic mosaicism.

Translational Genomics Research

An interdisciplinary field that translates basic scientific discoveries concerning the human genome into practical, evidence-based diagnostic tests, predictive models, and targeted therapeutics in clinical medicine.

Primary Finding (PF)

A pathogenic or likely pathogenic genetic variant identified via clinical exome or genome sequencing that directly explains the specific disease phenotype or clinical indication for which testing was ordered.

Secondary Finding (SF)

A pathogenic or likely pathogenic variant in a medically actionable gene (such as those specified on the ACMG curated list) that is identified through a deliberate search unrelated to the patient's presenting clinical indication.

Incidental Finding (IF)

A medically significant genetic variant identified without a deliberate targeted search, in a gene not included on the standard ACMG secondary findings list, that is unrelated to the original testing indication.

Ex Vivo Gene Therapy

A therapeutic strategy where patient cells (such as hematopoietic stem cells) are harvested, cultured, genetically corrected in a laboratory setting using viral or non-viral vectors, and then re-infused into the patient.

In Vivo Gene Therapy

A therapeutic strategy where a genetic construct packaged within a delivery vector (such as an adeno-associated virus) is injected directly into patient tissue or systemic circulation to transduce target cells in situ.

Insertional Mutagenesis

The inadvertent integration of recombinant viral vector DNA into host genomic loci, which carries the safety risk of activating cellular proto-oncogenes or disrupting tumor suppressor genes.

Exon Skipping

An RNA therapeutic mechanism in which synthetic antisense oligonucleotides bind pre-mRNA splice sites to exclude a mutation-bearing exon during processing, restoring the open reading frame to produce a partially truncated but functional protein.

RNA Interference (RNAi)

A biological process in which synthetic short interfering RNA (siRNA) duplexes load into the RNA-induced silencing complex (RISC) to guide sequence-specific degradation of complementary target mRNA transcripts.

Graft-Versus-Host Disease (GVHD)

A systemic immune complication of allogeneic hematopoietic cell transplantation in which immunocompetent donor T cells recognize the recipient host tissues as foreign and mount an inflammatory cytotoxic attack against them.

Polygenic Risk Score (PRS)

A single metric that aggregates the cumulative estimated effects of multiple single-nucleotide polymorphisms across the entire genome to quantify an individual's relative genetic susceptibility to a common polygenic disease.

Phenylketonuria (PKU)

An autosomal recessive inborn error of metabolism caused by deficient phenylalanine hydroxylase (PAH) activity, leading to hyperphenylalaninemia, neurotoxicity, white matter changes, and severe intellectual disability if not managed with a phenylalanine-restricted diet.

Sapropterin (Kuvan)

A synthetic oral dihydrochloride formulation of tetrahydrobiopterin ($\text{BH}_4$), the natural cofactor for phenylalanine hydroxylase, prescribed to enhance residual PAH enzyme activity in responsive patients with phenylketonuria.

Ornithine Transcarbamylase (OTC) Deficiency

An X-linked recessive urea cycle disorder caused by mutations in OTC that prevents ammonia detoxification, leading to acute neonatal hyperammonemic coma, respiratory alkalosis, and elevated urinary orotic acid excretion.

PIK3CA-Related Overgrowth Spectrum (PROS)

A group of asymmetric segmental overgrowth and vascular malformation syndromes resulting from postzygotic somatic gain-of-function mutations in PIK3CA, driving overactivation of the PI3K/AKT/mTOR signaling cascade.

Variant of Uncertain Significance (VUS)

A genetic sequence alteration evaluated under clinical ACMG/AMP interpretation criteria that cannot be definitively classified as pathogenic or benign due to insufficient, conflicting, or unconfirmed experimental and population evidence.