Webinar: Real-World Examples of Efficiency Gains in the Analysis and Interpretation of Genomic Data


Dr. Eva Serra, PhD

Pre-registered Clinical Scientist
& Product Manager,


Dr. Mark Kiel, MD, PhD

Co-Founder & Chief Scientific Officer, Genomenon

In our most recent webinar, Dr. Mark Kiel welcomed our guest Dr. Eva Serra, who demonstrated Congenica, a way to overcome challenges in the analysis, interpretation and reporting of complex genomic data with an all-in-one solution that optimizes process efficiency from raw data to report.

We learned:

  • How to recognize the hidden costs and inefficiencies of NGS data analysis
  • How to maximize workflow efficiency and diagnostic yield using advanced clinical decision support software
  • How this method has been applied to real-life clinical cases
Webinar Q&A

Can Mastermind queries include 5′ UTR, 3’UTR, promoters, enhancers, etc.?

Yes, Mastermind captures each of these types of non-coding changes in addition to splice and intronic variants.

Are Mastermind queries confined to humans or include other species (model organisms)?

Mastermind is focused on human genetic variation but we have many results that use animal models of human disease.

You show a lot of tertiary and user interface benefits which are nice but could you comment on why congenica is superior than other tools in the secondary analysis?

Congenica secondary pipelines enable you to benefit from an optimized all-in-one software solution. Our platform reduces your requirement to invest in your own technology infrastructure and accelerates your result times to maximize overall efficiency. Our pipelines have been validated in-house, are compatible with GRCh37 and GRCh38 genome assemblies (primary sequence) and can process data from FASTQ/BAM or VCF from gene panels, exomes or full genomes. Congenica software integrates a suite of secondary analysis pipelines into a single solution, providing you with scalable alignment and variant detection of diverse variant types (SNVs, Indels and CNVs). We provide SNV and indel calling using Sentieon and CNV calling using ExomeDepth. Sentieon provides an optimized implementation of the standard BWA-GATK algorithms, benefiting from 2X speedup in alignment and consistent results to GATK HaplotypeCaller, 10X faster. ExomeDepth (PMID: 22942019), a read-depth based approach, increases the accuracy and detection of CNVs by controlling for technical biases that are known to affect CNV calling. ExomeDepth has the ability to detect hard to identify variants such as rare CNVs and heterozygous deletions through improved sensitivity, as well as detect CNVs of varying sizes (from few exons up to multiple contiguous genes).

What is the resolution of CNVs in whole exome?

Based in our internal validation, our CNV calling pipeline (ExomeDepth) is able to detect CNV events of varying sizes, detecting CNVs as small as 105bp (previously detected and confirmed by MLPA) to large multi-genic CNVs up to a size of at least 2.2Mb. A White Paper is available from support@congenica.com if you’re interested in learning more about the analytical performance of our CNV calling pipeline.

Are your filters already pre-set or do you have to set them for every case?

Congenica provides both project-level and dynamic filtering behaviour, helping you to define (preset) given filters and/or change filters on the fly when you are reviewing your case variants. This behaviour helps you to expand or narrow the scope of variants for review without being constrained to a specific/default filtering behaviour.

Curated variant lists – how many do you reference? How can we access them with your software? Can we search for variants in each one?

Congenica provides several curated variant lists for both SNVs, indels and CNVs (e.g. ClinVar, Decipher, DGV, ISCA). Users also have the ability to upload and use their own custom curated variant lists and surface associated information in the platform. Users are able to actively search for patient variants that are part of any of those lists. The benefit of supporting multiple resources in the form of curated lists in Congenica is that you won’t need to visit multiple resources outside of the platform, saving you analysis time and helping you to consolidate all of the relevant information in one single place.

What inheritance filters do you support?

Congenica supports all Mendelian inheritance filters used in rare disease analysis. We have inheritance filters for trio families and non-trio families and also filters for consistency with specific modes of inheritance (e.g. to detect compound heterozygous variants).

How are gene panels managed within your software? Do you provide your own panels or can a user make their own gene panels?

Congenica provides gene panels from international, community-curated resources, but the user also has the flexibility to create or upload their own gene panels in the platform, enabling you to leverage your clinical expertise when conducting analyses.

About the Webinar

Genomic data analysis is a time-consuming and intensive process. Transforming raw next-generation sequencing (NGS) data into meaningful information that can be incorporated into patient care for targeted therapy, disease diagnosis, and management requires immense scientific, clinical, and technical expertise.

In this webinar, Dr. Serra presented recent studies that detail the true time and cost implications of NGS data analysis, and provide clinical examples of where workflow efficiency has been optimized using the Congenica clinical decision support platform – an integrated solution for the analysis and interpretation of complex genomic data. Dr. Kiel demonstrated how the Mastermind Genomic Search Engine can be used within the Congenica platform to expedite the literature curation process for variant interpretation.

This webinar focused on actual clinical cases to explore how these efficiency savings can be adopted by your lab to increase case throughput, diagnostic yield, and confidence in every diagnosis.


Eva Serra, PhD, Pre-registered Clinical Scientist & Product Manager, Congenica
As part of the Congenica Clinical team, Eva contributed to the analysis of rare disease patients in the Genomics England 100,000 Genomes project, and is actively working on clinical interpretation of patient data from other projects. As a Product Manager, Eva drives the integration of new product features into Congenica’s platform.

Eva holds a MSc in Human Genetics from Imperial College London and a PhD in Human Genomics (Bioinformatics) from the Wellcome Sanger Institute and the University of Cambridge.

Eva’s PhD research focused on using large-scale exome and whole-genome sequencing to understand the genetic basis of rare and complex diseases, with particular interest in congenital hypothyroidism, very-early-onset inflammatory bowel disease (IBD) and adult IBD.

Mark Kiel, MD PhD, Chief Science Officer and Founder, Genomenon
Dr. Kiel is Founder and Chief Science Officer at Genomenon, where he oversees the company’s scientific direction and product development.

Prior to starting Genomenon, Mark completed his residency in Clinical Pathology in 2014 at the University of Michigan. While at Michigan, he completed a fellowship in Molecular Diagnostics and devised the informatics framework for clinical next-generation sequencing in the Molecular Diagnostics Laboratory.

During his doctoral studies, he made ground-breaking contributions to the study of hematopoietic stem cells, for which he was awarded the Weintraub International Graduate Student Award and the ProQuest Distinguished Dissertation Award.

While a post-doctoral researcher, he made significant contributions to the field of Hematopathology, including genomic profiling of lymphoid malignancies, for which he was awarded the Benjamin Castleman Award.

About Congenica

Congenica significantly improves the workflow efficiency of NGS secondary and tertiary pipelines, integrating a number of best-in-class tools into a single all-in-one solution.

Congenica simplifies your workflows and maximizes diagnostic yield and confidence, empowering you to accurately make important clinical decisions and provide patients with life-changing answers faster than ever before.

Genomics England selected Congenica as the exclusive clinical interpretation solution for the UK NHS’ ground-breaking national Genomic Medicine Service. This achievement followed the platform’s extensive validation as part of the 100,000 Genomes Project and a competitive tender process involving the leading global providers in genomic data analysis.

Congenica is now being adopted internationally as the gold standard in data analysis and interpretation, empowering healthcare professionals to deliver world-leading genomic medicine services at scale.


About Genomenon

Genomenon connects patient DNA with the billions of dollars spent on research to help doctors diagnose and cure cancer patients and babies with rare diseases.

Our flagship product, the Mastermind Genomic Search Engine is used by hundreds of genetic labs worldwide to accelerate diagnosis, increase diagnostic yield and assure repeatability in
reporting genetic testing results.

We license our Mastermind Curated Genomic Datasets to pharmaceutical and bio-pharma companies to inform precision medicine development, deliver genomic biomarkers for clinical trial target selection, and support CDx regulatory submissions with empirical evidence.