Introduction to Genomics – Key Vocabulary

A comprehensive set of vocabulary flashcards covering fundamental concepts, technologies and terminology from the lecture on genomics, Sanger and next-generation sequencing, bioinformatics and omics applications.

Genome

The complete set of DNA belonging to an organism.

Genomics

The study of structure, function and mapping of genomes.

Human Genome Project (HGP)

International effort that produced the first draft human genome sequence in 2001 (~US$2.7 billion).

Sanger Sequencing

First‐generation DNA sequencing method that uses chain‐terminating dideoxynucleotides and gel or capillary electrophoresis to read ~1000 bp per run.

Chain-Terminating Dideoxynucleotide (ddNTP)

A nucleotide lacking a 3′-OH group; incorporation stops DNA polymerase extension, enabling sequence determination.

Radio-Labelled ddNTP

Dideoxynucleotide tagged with a radioactive isotope to visualise terminated fragments on a gel (classic Sanger method).

Gel Electrophoresis

Technique that separates DNA fragments by size through an agarose or polyacrylamide matrix using an electric field.

Capillary Sequencing

Automated version of Sanger sequencing that separates DNA fragments in thin capillaries; used in the HGP.

Shotgun Sequencing

Strategy that randomly shears a genome into overlapping fragments, sequences them, and assembles the reads computationally.

Restriction Enzyme

Endonuclease that recognises specific DNA sequences and cuts both strands (e.g., EcoRI, BamHI).

EcoRI

Restriction enzyme that recognises GAATTC and produces sticky ends.

BamHI

Restriction enzyme that recognises GGATCC and produces sticky ends.

Fragmentation

Physical or enzymatic breaking of DNA into smaller pieces for sequencing.

Sonication

Use of ultrasonic energy to shear DNA into random fragments.

Contig

A set of overlapping DNA sequences that together represent a contiguous stretch of genome.

Shotgun Assembly

Bioinformatic process aligning overlapping reads to reconstruct the original genome sequence and form contigs.

Bioinformatics

Application of computational methods to store, analyse and interpret biological data such as DNA sequences.

Reference Genome

High-quality representative genome sequence used as a standard for alignment and comparison.

UCSC Genome Browser

Web-based tool for visualising and analysing reference genomes (http://genome.ucsc.edu/).

NCBI

National Center for Biotechnology Information; provides sequence databases and analysis tools.

Ensembl

Joint EMBL-EBI/Wellcome Sanger project offering annotated vertebrate genome data.

Next-Generation Sequencing (NGS)

High-throughput sequencing technologies capable of producing millions to billions of reads in parallel.

High-Throughput Sequencing

Alternative term for NGS highlighting the large volume of data generated per run.

Sequencing by Synthesis (SBS)

Illumina NGS chemistry that detects fluorescently labeled nucleotides added one base at a time.

Illumina Sequencing

Widely used SBS platform providing short reads (≈100-300 bp) in a massively parallel fashion.

Reversible Terminator

Fluorescent nucleotide with a removable blocking group allowing cyclic single-base extension in SBS.

Flow Cell

Glass slide or chip containing thousands of nanowells where clonal DNA clusters are sequenced in parallel.

Library Preparation

Laboratory workflow that fragments DNA/RNA and ligates adapters to create molecules compatible with a sequencer.

Adapter Ligation

Attachment of synthetic oligonucleotide sequences (adapters) to DNA fragments to enable amplification and sequencing.

Index (Barcode)

Short, unique nucleotide tag incorporated into adapters to identify individual samples pooled in one run.

Demultiplexing

Bioinformatic step that separates pooled reads back to their original samples using index sequences.

Read Alignment

Computational mapping of sequencing reads to a reference genome or assembly.

Nanopore Sequencing

Technology that measures changes in ionic current as single DNA or RNA molecules pass through protein nanopores to infer sequence.

Motor Protein (Nanopore)

Enzyme that unwinds DNA and controls its speed through the nanopore during sequencing.

RNA-Seq

NGS method that sequences all RNA transcripts in a sample to profile gene expression (the transcriptome).

Transcriptome

The full set and quantity of RNA molecules present in a cell or tissue under specific conditions.

ChIP-Seq

NGS technique combining chromatin immunoprecipitation with sequencing to map protein–DNA interactions genome-wide.

Omics

Collective term for large-scale biological data sets (genomics, transcriptomics, proteomics, metabolomics, etc.).

Epigenomics

Study of heritable chemical modifications to DNA and histones that affect gene activity without altering sequence.

Proteomics

Global analysis of all proteins expressed in a cell, tissue or organism.

Metabolomics

Comprehensive analysis of small-molecule metabolites in a biological sample.

Microbiome

Community of microorganisms (and their genomes) inhabiting a particular environment, such as the human gut.

PCR (Polymerase Chain Reaction)

Technique that amplifies a specific DNA region exponentially using DNA polymerase and thermal cycling.

qPCR (Quantitative PCR)

Real-time PCR method that monitors DNA amplification each cycle to quantify starting material.

Reporter Assay

Experiment that links regulatory DNA to an easily measured gene (e.g., luciferase) to study promoter/enhancer activity.

Massively Parallel Sequencing

Characteristic of NGS platforms that perform thousands to millions of sequencing reactions simultaneously.

Consensus Sequence

Agreed-upon nucleotide sequence derived from aligning multiple reads; represents the most common base at each position.

Dideoxy Sequencing Chemistry

Use of ddNTPs in Sanger sequencing to terminate elongation and generate length-determined fragments.

Applications of NGS

Include genome assembly, variant discovery, RNA-seq, ChIP-seq, epigenomics, metagenomics, and clinical diagnostics.