Diagnostic Genomics: Isolation and Assessment of Genomic DNA

Vocabulary flashcards related to Diagnostic Genomics Lecture 2 focusing on Isolation and Assessment of Genomic DNA.

Clinical Specimens

Samples such as whole blood, serum, buffy coat, urine, CSF, POC, amniocentesis, tumor biopsy, and buccal swab used in diagnostic genomics.

Germline Alteration

Genetic alteration originating in the gametes and present in every tissue of an individual (e.g., Trisomy, Familial conditions).

Somatic Alteration

Genetic alteration occurring post-birth and present only in a subset of tissues (e.g., B-raf mutation in tumor).

Maternal Contamination

Presence of maternal DNA in samples like Products of Conception (POC) or Amniocentesis samples.

Chaotropic Agent

A substance that disrupts the hydrogen bonding network in water, leading to denaturation of proteins and inactivation of nucleases (e.g., Guanidinium thiocyanate).

EDTA

Ethylenediaminetetraacetic acid, a chelating agent used to inhibit nucleases by binding divalent cations like Mg2+ and Ca2+.

DNAse

Enzyme that degrades DNA and can be inhibited by EDTA or chaotropic agents.

RNAse

Enzyme that degrades RNA; highly robust and difficult to inactivate, requiring special treatments like DEPC or baking glassware.

OD260/280 ratio

Spectrophotometric measurement used to assess the purity of DNA and RNA; a ratio of ~1.8 for pure DNA and ~2.0 for pure RNA.

DEPC

Diethylpyrocarbonate, a chemical used to inactivate RNAses by modifying amine groups in proteins; must be removed before reverse transcription.

Spectrophotometry

Method to quantify nucleic acids by measuring absorbance at 260 nm; can be affected by contaminants like RNA or protein.

Fluorimetry (Qubit)

Method to quantify double-stranded DNA using a fluorescent dye that binds specifically to dsDNA; more sensitive than spectrophotometry and less affected by contaminants.

Solid Phase Extraction

Method to isolate nucleic acids using silicates that bind DNA and RNA under high salt conditions, allowing for washing away contaminants and elution of pure nucleic acids.

Guanidinium Thiocyanate-Phenol Chloroform extraction

Method used for RNA isolation. GuSCN denatures proteins while Phenol and Chloroform help separate RNA from DNA and proteins during centrifugation based on pH.