NEW CentoXome®


It takes approx. 7 years to diagnose a patient with a rare disease. With NEW CentoXome®, we can turn those years into days – powered by our best-in-class insights based on superior technology, our extensive clinical experience, and wealth of genetic data in rare diseases.

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CENTOGENE’s New and Improved Whole Exome Sequencing Service

Whole Exome Sequencing (WES) is a comprehensive genetic test that identifies changes in a patient's DNA that are causative or related to their medical concerns. By focusing on the entire protein-coding regions of the genome – the exome – WES offers you the coverage you need to diagnose patients rapidly and reliably.

Overcoming the Obstacles of Rare Disease Diagnostics with NEW CentoXome

With more than 7,000 identified rare diseases and approximately 80% being linked to genetic causes, diagnosing rare disease patients can often be difficult – resulting in lengthy, expensive, and emotional diagnostic odysseys.1,2

With WES, this doesn’t have to be the case. Containing the majority (~85%) of known disease-causing changes, WES uncovers the cause of rare diseases in less time and at a lower overall cost – leading to better patient outcomes. With NEW CentoXome, we’ve taken WES to the next level. Enhanced to provide unparallel clinical coverage and diagnostic power in a single test, our product design and medical interpretation utilizes the world’s largest rare disease Bio/Databank containing >31 million unique variants from over 120 countries.

The Results: Diagnosing complex and unsolved patient cases – quicker and with the highest levels of certainty.

We Think It's Time For a Change

Why Choose CentoXome?

Turn Our Expertise Into Your Advantage

Best-in-class insights from the leader & trusted partner in rare disease diagnostics

Turn Your Open Questions Into Answers

Superior technology from the experts in omics testing for rare diseases

Turn Our Commitment Into Your Promise

Life-long support by a team dedicated to improving the lives of patients with rare diseases

Superior Technology With Unmatched Clinical Coverage and Diagnostic Power in a Single Test

The NEW CentoXome design and service delivers the ideal quality and performance from the world leader and trusted partner in rare disease diagnostics, with outstanding clinical coverage and unmatched clinical diagnostic power in a single test. Coupling insights from our extensive Bio/Databank in rare diseases with superior omics technology, patients and physicians benefit from a unique approach that increases diagnostic yield by up to 20% compared to routine WES3-8 via enhanced coverage of the exome, full mitochondrial genome, and known medically-associated genes and variants.

  • Mean depth ≥100 x 
  • Highly uniform coverage of the entire exome (~20,000 genes) and mitochondrial genome (37 genes); ≥98.0% target regions covered at ≥20 x
  • All protein coding regions of nuclear genes, +/- 10 bp exon-intron boundaries, and complete mitochondrial genome

  • ~8,000 disease-associated genes; ≥99.5 % target regions covered at ≥20x
  • 99% of all known clinically relevant variants in coding and non-coding regions extracted from HGMD®, ClinVar, and CENTOGENE's Bio/Databank for rare diseases
  • Highly sensitive and specific detection of SNVs, InDels, CNVs of exon-level to cytogenomic-level changes, UPD*, and mtDNA variants with heteroplasmy ≥15%
  • Sensitivity
  • SNVs and InDels (≤55 bp) >99.6%
    CNVs (≥3 exons)** >95.0%
  • Specificity of >99.9% is guaranteed for all reported variants***

SNVs: single nucleotide variants; InDels: small insertions/deletions; CNVs: copy number variations; UPD: uniparental disomy; mtDNA: variants in mitochondrial DNA
UPD screening is performed using an in-house specific algorithm for the following well-known clinically relevant chromosomal regions: 6q24, 7, 11p15.5, 14q32, 15q11q13, 20q13 and 20
CNV detection software has a sensitivity >95.0% for all homozygous/hemizygous and mitochondrial deletions, as well as heterozygous deletions/duplications and homozygous/hemizygous duplications spanning at least three consecutive exons
Variants with low quality and/or unclear zygosity are confirmed by orthogonal methods (i.e., SNVs and InDels by Sanger sequencing; CNVs by Multiplex ligation-dependent probe amplification, MPLA; quantitative polymerase chain reaction, qPCR; or chromosomal microarray, CMA)

When Is WES Recommended?

We recommend WES for complex and undiagnosed cases with suspicion of genetic causes.

WES is conventionally recommended when patients present complex, heterogeneous phenotypes that are suggestive of multiple conditions or are otherwise unclear or atypical. WES may also be recommended when a prior genetic test was unsuccessful. The latest clinical evidence also supports WES as a first-line test when a patient’s symptoms or family history suggests a genetic cause of the diseases. This is especially true for neurodevelopmental disorders, including intellectual disability, global developmental delay, and autism spectrum disorder due to the high diagnostic yield.9,10 The test results from WES 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.9,11,12

NEW CentoXome can help you tackle challenging and undiagnosed patient cases across all stages of life and covers a broad spectrum of disorders encompassing >7,000 rare diseases. We particularly recommend CentoXome for patients when:

  • Symptoms are very broad, complex, or unspecific, not pointing towards specific disease or typical phenotype
    e.g., patients with developmental delay, intellectual disability, autism spectrum disorder, epilepsy
  • Suspicion of chromosomal imbalances, microdeletion, or microduplication syndromes
    e.g., children with global development delay, and/or multiple congenital anomalies, DiGeorge syndrome
  • Clinical suspicion of mitochondrial disease
    e.g., patients with muscular weakness, cardiomyopathy, visual problems
  • A severe presentation in the neonatal or childhood period
    e.g., neonate babies and infants critically ill in Neonatal and Pediatric Intensive Care Units (NICU and PICU, respectively)
  • Prior genetic testing did not provide a conclusive diagnosis
    e.g., patient with neurodevelopmental delay, with similarly affected siblings, and negative testing with microarrays
  • Need a cost-conscious alternative to Whole Genome Sequencing (WGS)

Tailored Services Paired With Life-Long Support

We offer flexible testing options and additional services to provide a NEW CentoXome analysis tailored to patients’ needs, such as for ongoing pregnancies with fetal abnormalities, for prenatal diagnostics, and expedited WES for critically ill patients that need rapid and precise genetic diagnosis.

Committed to improving the lives of patients with rare diseases, NEW CentoXome is paired with life-long diagnostic support via a free-of-charge and proactive reclassification program, as well as an affordable case-level reanalysis in case of uncertain or negative results. WES diagnostic yield is continuously increasing due to the rapid rate of new gene-disease discoveries, and it is estimated that about 10-20% of undiagnosed patients can be diagnosed by reclassification and genomic data reanalysis.13

TURNAROUND TIME Regular ≤30 business days
Fast ≤15 business days
TESTING DESIGN Solo, Duo, Trio, and Trio Plus
ADDITIONAL SERVICES** Prenatal testing*
  • Prioritization and expediting at each stage of the process
  • Reduced turnaround time, up to ≤15 business days
  • Includes cell culture and maternal contamination testing
Genome-wide high-resolution analysis of SVs/large CNVs
  • CentoLCV (sWGS)
  • CentoArrayCyto® 750K or HD (CMA)
Lifelong diagnostic support
  • Proactive variant-level re-evaluation and reclassification at no extra cost***
  • Case-level reanalysis and medical reinterpretation at an affordable cost in case of uncertain or negative results

Solo: only the affected index patient is tested; Duo: index patient and affected or unaffected family member are tested; Trio: index patient and two family members, affected or unaffected are tested; PLUS: additional family member beyond Trio is tested; SVs: structural variants; CNVs: copy number variants; sWGS, shallow whole genome sequencing; CMA: chromosomal microarray analysis
More details at Prenatal Testing
We also offer raw data free of charge for download, along with filtered and annotated variant table for further research.
More details at Variant Reclassification Program

Best-in-Class Insights by the Leader & Trusted Partner in Rare Disease Diagnostics

When choosing our WES service, physicians, patients, and partners can feel confident that they will receive high-quality sequencing combined with best data analysis and interpretation, documented in comprehensive medical reports. By combining deep phenotype data with high quality genotype data using our advanced bioinformatics pipeline and artificial intelligence (AI), we accurately identify and prioritize disease-causing variants to deliver best-in-class clinical interpretation and reporting.

NEW CentoXome always includes medical reporting based on our clinical interpretation expertise, best-in-class curated variant data from our Bio/Databank, and international best-practice guidelines. A team of highly trained clinical geneticists and scientists interpret the data and cross-check every medical report. When applicable, we use our complementary omics testing platform and in-house data from our Bio/Databank to confirm results and validate the pathogenicity of variants found. All historical high-quality classifications are curated and codified in our Bio/Databank, which is a reference for diagnostic decisions and classifications. This data repository covers a wide range of ethnicities, unique variant data, and multiomic data from more than 120 countries.

Test reports always contain clear actionable clinical results, recommendations, and follow-up options. They are phenotype-driven and focused on reporting findings related to the patient’s clinical presentation/patient’s indications.

  • Clearly structured, conclusive, and concise reports
  • Detailed evaluation of patient’s family history and clinical information
  • Clear results of identified variants that can explain the phenotype following international best-practice guidelines (ACMG)14,15
  • Recommendations for differential diagnoses or follow-up analyses for specific diseases
  • References to publications supporting the medical and scientific results and detailed method description
  • Optional research findings related to phenotype if the diagnostic results are negative, and/or secondary findings based on ACMG guidelines14
  • CENTOGENE’s ‘Tabular List’ variant section for the index patient, which includes known genetic variants in our Bio/Databank classified as pathogenic/likely pathogenic. Our list makes often unreachable information accessible to physicians/genetic counselors, which may lead to further diagnostics and medical management of the patient and/or their family

For more information, please consult the Medical Reporting webpage and CENTOGENE’s ‘Tabular List’ variant section webpage.


1RARE Facts - Global Genes; 2NIH Genetics and Rare Disease (GARD); 3Clark et al. 2018, PMID: 30002876; 4Gross et al. 2018, PMID: 30293986; 5Wagner et al. 2019, PMID: 31059585; 6Schon et al. 2020, PMID: 3267494; 7Cheema et al. 2020, PMID: 3308301; 8Trujillano et al. 2017, PMID: 27848944; 9Stark et al. 2016, PMID: 26938784; 10Srivastava et al. 2019, PMID: 31182824; 11Smith. et al.2019, PMID: 29760485; 12Vissers et al. 2017, PMID: 28333917; 13Liu et al. 2019, PMID: 31216405; 14Miller et al. 2021, PMID: 34012069; 15Richards et al. 2015, PMID: 25741868;

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Product Resources

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.


Sample Reports

  • New CentoXome® Trio - index, positive mitDNA variant

  • New CentoXome® Trio - mother, carrier status confirmed


Scientific Papers

  • Scientific Study about Exome Sequencing

  • Results from Genomic Testing in 1019 Individuals

  • Utilization of Our Bio/Databank in Scientific Settings


Additional Resources


Posters & Whitepapers


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