Tackling the diagnostic challenge with whole exome sequencing. CentoXome® is the best choice when you need a fast, accurate, and cost-effective one-step solution to complete the diagnostic process of complex and unsolved cases.

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Whole Exome Sequencing

For certain patients the combination of symptoms does not allow the clinician to pinpoint a potential diagnosis. In such challenging cases, often a stepwise diagnostic strategy is chosen, which makes the testing complex, time consuming, costly and often not even conclusive. Furthermore, a delayed diagnosis may have a significant impact on the patient’s treatment and quality of life.

For these cases, the use of broad, whole exome sequencing (WES) has advantages over initially more targeted genetic testing. Whereas such targeted genetic testing focuses on a single gene or on a limited set of predetermined genes, WES testing examines all the protein coding regions in the genome (exons) simultaneously. It is estimated that most of the disease-causing mutations (about 85%) are located within the exons. This lack of bias allows to also identify disease causing mutations in unexpected genes that would be missed by targeted approaches.

CentoXome®, CENTOGENE’s whole exome sequencing service, offers an accurate and cost-effective one-step solution, with high diagnostic yield.

Why Choose CentoXome®?

High diagnostic power in a single test

Excellent exome coverage and uniformity

Shorter time to results by avoiding step-wise testing


Best-in-class clinical reports

Whole Exome Sequencing at CENTOGENE – CentoXome®

Excellent exome coverage and uniformity

End-to-end bioinformatics analysis

Validation of the sequencing results

Detailed clinical reports

CentoXome® – Key Features

  • >20,000 genes
  • All protein-coding regions and intron-exon boundary regions
  • Highly uniform coverage of the whole exome
  • Mean depth ≥70-100x
  • ≥98% of targeted bases covered at ≥20x*
Variants Default
  • Detects SNVs and InDels
  • Sensitivity >99.6%
  • Confirmation of potentially relevant low quality SNVs and InDels by Sanger
Additional testing option
  • High resolution NGS-based detection of CNVs
  • CNVs of ≥3 with >90% sensitivity
  • Confirmation of unclear SVs and CNVs by an orthogonal method

*Typically, CentoXome® reaches 20x coverage or higher for 98.5% to 99.5% of targeted regions. However, the minimum guaranteed coverage for every CentoXome® sample is ≥98% of targeted regions ≥20x.

The CentoXome® offers a highly uniform coverage of the complete exome and detects single nucleotide variants (SNVs) and small insertion and deletions (InDels) with high sensitivity.

As additional option for all CentoXome® tests, we offer also NGS-based detection of copy number variations (CNVs). The inclusion of this option allows not only the detection of previously described CNVs throughout the exome but also de novo CNVs and small CNVs (below <50kb) that might escape detection for example by chromosomal microarray analysis. This is possible due to the higher resolution of our NGS-based CNV analysis.

My positive diagnostic rate has gone up from 15% using just CGH microarray to 80% using targeted sequencing and whole exome sequencing. I am now able to do proper, informed genetic counselling.

Prof. Rose-Mary Boustany

Professor of Pediatrics and Adolescent Medicine, Beirut

When is WES Required?

For many patients the combination of symptoms does not allow suspecting specific genetic causes with a sufficiently high certainty. It is unclear which genes to look at.

Therefore, WES may be an affordable first test when the clinical spectrum is diverse and diagnostic answers are likely to be obtained only through sequencing the complete coding region, i.e. the whole exome. WES is also a good follow-on approach after more targeted approaches have been tried already and no causative variant was identified.

We particularly recommend WES for patients:

  • With clinical or genetic heterogeneity
  • Examples: Epilepsy, epileptic encephalopathies, muscular dystrophies/muscular disorders, ataxia, neuropathies, cardiomyopathies, skeletal dysplasias, immunodeficiency, deafness, blindness

  • With atypical clinical presentations or phenotypes
  • Example: A patient presenting with intracranial aneurysm (due to PKD1 gene - polycystic kidney disease)

  • With “blended” clinical presentations and clinical suspicion of dual diagnosis
  • Examples: Intellectual disability and severe immunodeficiency

  • With clearly genetic disease, but previous genetic testing having been negative.
  • Example: A patient with autosomal dominant spastic paraplegia and with a negative result for the gene panel

  • Who need a cost-conscious alternative to whole genome sequencing

CentoXome® Case Studies

  • CentoXome® - Case study

    Patient diagnosed with primary coenzyme Q10 deficiency type 4 after detecting two pathogenic variants in the COQ8A gene. This ended the diagnostic odyssey, allowed appropriate treatment, and helped the patient and his partner with preconception counseling.


Tailored Services to Your Patient's Needs

Options and Packages
Turnaround time
Regular≤30 business days
Fast≤15 business days
Prenatal testing
  • Reduced turnaround time, up to ≤15 business days
  • Prioritization and expediting at each stage of the process
  • Includes cell culture and maternal contamination
Testing design
Solo, Duo, Trio, and Trio Plus
Reanalysis and reinterpretationAt low cost in case of uncertain or negative results
Additional testing options

High resolution large copy number variation analysis with CentoLCV, CentoArrayCyto® 750K, or HD

Comprehensive mitochondrial genome analysis with CentoMito® Genome

We provide different options and packages to tailor the CentoXome® analysis to your patient’s needs, which improves even more the clinical utility of CentoXome® for the patients we test in our laboratory.

For example, CentoXome® already presents a high diagnostic yield of >31% by detecting SNVs and InDels even without additional CNV analysis.1 This can be further boosted by including the CNV option.

The test results from CentoXome® may also lead to more rapid diagnoses, improved prevention of symptomatic illness, more targeted treatments or even end the need for some costly or invasive procedures.

Downloads for whole exome sequencing

Clinical Anamnesis and Reporting

Conclusive clinical reports

High-quality reporting is an essential element for building a partnership of trust. Our philosophy is more than just producing technical data. The extensive interpretation of clinical and testing data delivered with our comprehensive medical reports includes differential diagnostic approaches as well as a detailed interpretation of key findings.

CENTOGENE’s large mutation database of rare genetic diseases, CentoMD®, that includes the systematic documentation of curated genetic variants, with detailed clinical information, frequency and geographic origin, coming from a worldwide cohort of patients, strongly strengthens the clinical interpretation of our CentoXome® results and warrants best diagnostic yields. It significantly improves the quality and consistency of the diagnosis, ultimately affecting your patients' treatment path.

  • Detailed evaluation of patient’s clinical information and family history
  • Clear results of identified variants that can explain the phenotype
  • Variant classification following international best-practice guidelines (ACMG)2,3
  • Comprehensive medical interpretation
  • Recommendations for differential diagnoses or follow-up analyses for specific diseases
  • References to publications supporting the medical and scientific results
  • Detailed description of the genetic testing method, and coverage of reported genes
  • Report of research variants or incidental findings based on ACMG guidelines (optional) and additional information on pathogenic and likely pathogenic variants listed in CentoMD®, which are known to be related to severe and early-onset diseases (for more information, see details and the list of genes covered).

Scientific articles

  • Six Novel Gene-Disease Associations

    While technology has advanced over the past ten years, more than half of patients with genetic diseases remain undiagnosed, even after applying genome-wide diagnostic approaches. By performing deep genetic analyses and Bio/Databank mining, CENTOGENE discovered six novel gene-disease associations and…

  • Recognition of CENTOGENE's Scientific Expertise

    Review articles constitute a unique type of scientific publication, as they summarize, rather than present, observations and interpretations. In prestigious journals, they are commonly provided by the most recognized experts in the field. A pertinent example involving CENTOGENE authorship was…

  • A Genetic Cause for Infectious Disease

    While infectious diseases are commonly connected to environmental factors, genetic defects in some genes can strongly increase a person’s susceptibility to infections. Data generated at CENTOGENE helped to identify yet another example of this rare phenomenon. The findings, which revealed a novel…

Clinical anamnesis

One consequence of WES is the increased amount, complexity, and variety of results that need to be interpreted. Therefore, it is of utmost importance to obtain specific and detailed clinical information from the index patient and the parents when performing exome sequencing.

Withholding any clinical information, including your patient's family history, may affect test results and their interpretation. Missing clinical information could lead to exclusion of genetic variants that might be relevant for the patient. For example, the CentoXome® diagnostic yield improved from about 26% when using few clinical information to about 40% as compared when we received detailed clinical information.1

REFERENCES: 1Trujillano et al. 2017, PMID: 27848944; 2Richards et al. 2015, PMID: 25741868; 3Kalia et al. 2017, PMID: 27854360

Downloads for CentoXome® sample reports

  • CentoXome® Solo - Sample report, positive

  • CentoXome® Trio - Sample report, positive index

  • CentoXome® Trio - Sample report, positive parent 1


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