WGS, SNP test and WES

For broad downstream sequence analysis, WGS generally provides more information than a SNP array or WES. That does not make WGS the best or most economical choice for every question: an array may be enough for known markers, while WES can target coding genes. Before sequencing, clarify the purpose, quality requirements, cost, privacy and access to the resulting data.

A SNP array assays a predefined set of positions. It can be useful for particular ancestry models or for checking measured markers. Positions not included were not directly assayed; some providers add imputed estimates, which should be identified as such. Whether an existing export is sufficient depends on whether it contains the required markers at adequate quality.

WES targets exons, the regions that are usually translated into proteins after RNA splicing. Actual coverage varies with the capture design and laboratory. Non-coding regions and some structural or repeat variants are less comprehensively assessed. WES can suit a well-defined question, but it is not equivalent to whole-genome sequencing.

WGS captures sequence information beyond exons and can support a wider range of downstream analyses. Results still depend on sequencing depth, sample quality, reference and analysis method. Difficult regions, repeats and structural changes can remain incomplete or ambiguous even in WGS data. Whether a new question can be answered without another laboratory analysis depends on the available files and the method required.

FASTQ contains sequenced reads and their quality values. BAM or CRAM contains aligned reads; VCF contains variants called from the data. These files are not interchangeable, and their suitability depends on the workflow. Ask the provider which original and companion files are available, which reference was used and how the files can be stored securely.

WGS can provide a suitable basis for broad sequence analysis, but it does not automatically produce a clinically actionable result. Quality control, coverage, laboratory method, privacy, cost, file access and the specific question still matter. A WGS dataset replaces neither medical diagnosis nor clinical confirmation when a result could have medical consequences.