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

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  1. Whole Exome Sequencing

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 rates.

Why Choose CentoXome®?

High diagnostic rates

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
  • No mitochondria encoded genes
  • Highly uniform coverage of the whole exome
  • Mean depth 70-100x
  • 98% of targeted bases covered at 20x*
  • Detects SNVs and InDels
  • Sensitivity >99.6%
  • Confirmation of potentially relevant low quality SNVs and InDels by Sanger
Additional option
  • NGS-based detection of CNVs
  • Exon-level homozygous deletions, heterozygous deletions and homozygous duplications 3 subsequent exons
  • Sensitivity >80.0%
  • Confirmation of 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: 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: 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 1

    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 pre-conceptional counseling.


Tailored Services to Your Patient's Needs

Options and Packages
Turnaround time
Regular≤30 business days

≤15 business days
PrenatalPrenatal workflow
  • Reduced turnaround time, up to 15 business days
  • Prioritization and expediting at each stage of the process
  • Includes cell culture and maternal contamination
Number of samplesSolo, Duo and TrioYes
    Trio plusYes
    Reanalysis and reinterpretationAt low cost in case of uncertain or negative results Yes
    Additional testing

    CentoArray® 750K or HD

      CentoMito® GenomeYes

      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 rate of >31% by detecting SNVs and InDels even without additional CNV analysis1 . 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 (optional)

      Scientific articles

      • Understanding DNA Alterations in Colorectal Cancer

        Germline and somatic DNA alterations may cause inherited diseases and/or cancer. While CENTOGENE’s routine diagnostic focus is on the former, we frequently address oncological questions in research settings. Deep sequencing of colorectal tumors in one such project provided unprecedented insights…

      • Characterization of an Ultra-Rare Disorder

        Novel gene-disease associations are continuously being proposed, but the underlying evidence is frequently based on only a few patients from a single family. CENTOGENE’s focus on rare disease diagnostics has enabled us to internally confirm many pertinent observations. For a rare form of…

      • An Unorthodox Disease Mechanism

        Essential proteins are defined as those that are necessary for living. In theory, homozygous loss-of-function variants that only affect certain isoforms may still be found in living individuals. A recent study involving patients that were identified at CENTOGENE presents one of the first examples of…

      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 rate improved from about 26% when using few clinical information to about 40% as compared when we received detailed clinical information1.

      Incidental findings

      CENTOGENE does report on findings not directly related to the cause of a disease only upon request and only for genes listed in the ACMG guidelines3.


      1. Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, et al. (2017). Clinical exome sequencing: Results from 2819 samples reflecting 1000 families. Eur J Hum Genet. 25(2):176-182. doi:10.1038/ejhg.2016.146
      2. Kalia SS, Adelman K, Bale SJ, et al. (2017). Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): A policy statement of the American College of Medical Genetics and Genomics. Genet Med. 19(2):249-255. doi:10.1038/gim.2016.190
      3. Green RC, Berg JS, Grody WW, et al. (2013). ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 15(7):565-574. doi:10.1038/gim.2013.73

      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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