In whole genome diagnostics, the entire genome is sequenced. This approach enables the detection of structural and complex variants that cannot be fully resolved with exome-based methods. These variants are causative for a small number of cases that remain unsolved even after high-quality exome diagnostics such as our ExomeXtra®.
Our ExomeXtra® is the most effective first step in clarifying the genetic cause of diseases. It offers an unbeatable combination of cost efficiency and diagnostic precision: Its unique design provides deep, uniform coverage across almost all disease-relevant regions, resulting in high sensitivity and clinically meaningful findings. Performed as a trio analysis, ExomeXtra® achieves highest diagnostic yields and solves most patient cases.
Whole genome diagnostics is offered as a second-tier option for the rare unsolved cases in which, e.g., structural mechanisms are suspected. It is available after a negative exome diagnostics result.
What We Offer with This Service
Our Promise to You
Service Details
- PCR-free WGS, meaning reduced library bias and improved uniform coverage
- 120 Gb of sequencing data generated for each patient
- Analysis of SNVs, indels, and the complete mitochondrial genome
- Genome-wide coverage of structural variants, including CNVs (also mosaic variants), inversions, insertions, and translocations
- Genome-wide detection of loss of heterozygosity (LOH)
- Screening for certain repeat expansions, including AFF2, AR, ARX, ATN1, ATXN1 (SCA1), ATXN2 (SCA2), ATXN3 (SCA3), ATXN7 (SCA7), ATXN8 (SCA8), C9orf72, CACNA1A (SCA6), CNBP, COMP, DIP2B, DMD, DMPK, FGF14 (SCA27B), FMR1, FOXL2, FXN, GIPC1, GLS, HOXD13, HTT, JPH3, LRP12, NIPA1, NOP56, NOTCH2NLC, NUTM2B-AS1, PABPN1, PHOX2B, PPP2R2B, PRDM12, PRNP, RUNX2, SOX3, TBP, TBX1, TNRC6A, VWA1, XYLT1, YEATS2, ZIC2, ZIC3 *
- Detection and reporting of deep intronic variants if predicted to have a splicing effect, and variants 1000 kb upstream or downstream of known genes
- High evidence pharmacogenetic variants
- Screening for certain infections & pathogens, including Toxoplasmosis, Varicella, Cytomegalovirus, Fifth disease, Syphilis, Herpes Simplex 1 & 2
* In the context of SCA27B, we are examining a common 5’-flanking variant in FGF14, which is predominantly found in alleles that do not have a pathogenic expansion.1
Sample Report
Our Standard Sample Requirements
- 1 ml–2 ml EDTA blood (recommended sample type, min. 1-2 ml EDTA-blood)
- Genomic DNA (> 2 μg DNA, concentr. ≥ 50 ng/μl)
Information for transplant (bone marrow, tissue, stem cells) patient:
If you have previously had a stem cell transplant, please contact us.
We will then let you know which sample type is appropriate.
Here you can find more information on how to ship your sample safely.
Other sample material sources are possible on request. Please note: In case of insufficient sample quality, the analysis might fail. If you have more than one option of samples, please contact us (diagnostic-support@cegat.com) and we will assist you in choosing the optimal sample for your patient.
Why Trio ExomeXtra® Remains the Front-Line Test
ExomeXtra® covers all known disease-causing coding and non-coding regions with deep, uniform coverage (>100×). Its unique design enables the detection of SNVs, indels, CNVs, UPDs, mitochondrial variants, mosaicism, repeat expansions, and selected infections. These variant types account for the vast majority of genetically determined disorders.
Trio analyses further increase the likelihood of identifying the underlying cause. Compared with index-only analyses, trio diagnostics achieves substantially higher solution rates, with multiple cohorts showing a 5–15 percentage-point increase in diagnostic yield2,3,4. Introducing parental data, and therefore inheritance information, greatly improves variant interpretation, especially in complex or unspecific phenotypes. In contrast, switching from exome to genome diagnostics typically provides only a 1–5 percentage-point increase in diagnostic yield5.
This comparison shows that Trio ExomeXtra® is the most suitable approach for the first diagnostic step. A genome-based approach is less effective because its broader coverage seldom translates into meaningful clinical findings: many additional variants fall into the category of uncertain significance, and the reduced depth limits sensitivity in relevant regions.
For these reasons, whole genome diagnostics is strongly recommended as a second-line test. A high-quality exome such as ExomeXtra® offers the strongest combination of genetic precision and cost efficiency for initial testing. Only specific variant types – such as inversions, translocations or complex genomic rearrangements – may require genome-wide analysis after a negative exome-based analysis.
References
1 Pellerin, D. et al. A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus. Nat Genet 56, 1366–1370; 10.1038/s41588-024-01808-5 (2024).
2 Malmgren H, Kvarnung M, et al. (2025) Diagnostic yield of 1000 trio analyses with exome and genome sequencing in a clinical setting. Front. Genet. 16:1580879. doi: 10.3389/fgene.2025.1580879
3 Farwell, Kelly D. et al. (2015) Enhanced utility of family-centered diagnostic exome sequencing with inheritance model–based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genetics in Medicine (2015), Volume 17, Issue 7, 578 – 586
4 Retterer, Kyle et al. (2016) Clinical application of whole-exome sequencing across clinical indications. Genetics in Medicine, Volume 18, Issue 7, 696 – 704
5 Battke, F., Schulze, M., & Schulte, B. (2024). What Is the Real Diagnostic Benefit of Whole-Genome Sequencing?. Preprints. https://doi.org/10.20944/preprints202412.0023.v1
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Diagnostic Support
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