Sanger sequencing names a laboratory method. Whole-genome sequencing describes how much DNA is examined. They answer different questions.
DNA sequencing determines the order of the four bases, A, C, G and T. To understand the terminology, separate how those bases are read from which parts of the DNA are selected for analysis.
How DNA is read
A sequence read is the base sequence reported for a stretch of DNA. Technologies differ in how they detect bases, how much DNA each read spans and how many fragments they analyse simultaneously. These differences shape the information researchers can obtain.
Before sequencing, samples are processed to obtain DNA suitable for analysis. These stages can involve different teams: Uk Biocentre, for example, handles sample processing and offers sequencing through on-site partners.
“Next-generation sequencing”, or NGS, covers a range of technologies. The NHS Genomics Education Programme includes both short-read and long-read approaches under that label. Describing the actual approach gives a clearer picture of a project than the term NGS alone.
Sanger sequencing uses chain termination. DNA copies stop growing at different positions, producing fragments of different lengths. Separating these fragments by size and identifying their labelled terminal bases allows the sequence to be determined.
Sanger remains useful for examining a specific DNA region or checking selected findings from another method. Its relatively limited throughput makes it less suited to large-scale projects than technologies that analyse many fragments in parallel.
High-throughput short-read sequencing analyses large numbers of relatively short DNA fragments simultaneously. Computer analysis then places the reads against a reference sequence or uses them to reconstruct longer sequences.
This supports large-scale investigation of sequence differences, including single-base changes. Where similar sequences occur in several locations, however, a short read can be difficult to place uniquely. Repetitive regions and some larger rearrangements are consequently harder to resolve.
Long-read sequencing produces longer continuous stretches of sequence. Technologies detect bases through different signals, including monitoring DNA synthesis or measuring electrical changes as DNA passes through a nanopore.
Longer reads can span repetitive regions and reveal connections that shorter fragments miss, helping researchers investigate structural changes such as large insertions or rearrangements. The benefit lies in the additional context within each read.
Which parts of DNA are analysed
Targeted, whole-exome and whole-genome sequencing describe the scope of investigation. They can be combined with different technologies: a whole-genome project, for instance, can use short-read or long-read approaches.
Targeted sequencing examines selected DNA regions, from a single region to a panel of genes relevant to the research question. Concentrating on defined targets reduces the amount of unrelated sequence data requiring interpretation. The selection also sets the investigation’s boundaries: variation outside those regions generally remains beyond its reach.
Whole-exome sequencing focuses on protein-coding exons, the sections of genes that encode proteins, rather than every part of every gene. It offers a broader search across coding regions and can support investigations where researchers suspect a protein-coding change but have no single clear gene to examine. Most non-coding DNA, including regulatory regions, falls outside that scope.
Whole-genome sequencing examines DNA across coding and non-coding regions, widening the search beyond an exome or defined panel. This creates more opportunities for discovery and more data to analyse.
The breadth of the search is separate from the reliability of individual findings. Technology and analysis affect which regions and variant types can be assessed confidently; “whole genome” is not a guarantee of complete detection everywhere.
Matching the approach to the research question
Suppose researchers want to examine variation in a defined group of genes. Targeted sequencing offers a focused route. A broader search for protein-coding changes could use whole-exome sequencing; investigating non-coding regions as well points towards whole-genome analysis. If the question concerns a large rearrangement, read length becomes particularly relevant alongside scope.
The available biological material and planned analysis also influence which approach is practical. Coverage matters too: depth describes how many reads support a position, while breadth describes how much of the intended region has been read. A broad search still needs sufficient evidence in the regions that matter.
Finding a sequence difference is only the start of interpretation. Establishing its biological or clinical significance requires additional evidence. A useful sequencing plan brings method, scope, coverage and interpretation together around a defined question, rather than treating the largest dataset as the best answer.
