Learning to use

Genome-Phenome Analyzer FAQs

Do referring physicians need to change what they do today?

No. The referring physicians can continue to use paper-based forms to submit the clinical history and the lab can enter the clinical data into the integrated Genome-Phenome Analyzer. However, SimulConsult enables clinicians to submit a SimulConsult Patient Summary to the lab directly, saving additional time, and typically capturing the history with greater precision. This allows labs to leverage the fact that thousands of clinicians around the world are familiar with SimulConsult and use it in their clinical practice.

How sophisticated is the interpretation?

The integrated Genome-Phenome Analyzer reads “variant table” information resulting from the initial bioinformatics analysis, and imports the HGNC code for the gene, the severity of the variant, and the zygosity of the variant (heterozygous or homozygous). It is able to handle not only autosomal dominant and autosomal recessive diseases, but also other modes of inheritance (e.g., X-linked) and deal with complex situations such as compound heterozygosity and two pathogenic genes. It considers not only genetic diseases detectable on “next generation” sequence analysis, but also genetic diseases not well detected (e.g., trinucleotide repeats and large copy number variants), and nongenetic diseases. 

How large a variant file can be uploaded?

Variant tables with tens of thousands of variants upload in a few seconds.

How can I focus on de novo variants?

Variants known to be de novo are important to consider in genomic analysis since they have a high likelihood of being pathogenic. Although the gene zygosities that result from these de novo variants are important to review, they are not labeled as de novo in the software. This is because there is a simple way to recognize them.

It is possible to identify causative de novo variants if DNA from both parents is sequenced, and the parents are unaffected. But under such circumstances all monoallelic zygosities displayed will result from de novo variants. So to find the de novo variants, just look for the monoallelic zygosities. This applies both in the genome-phenome analysis and the discovery gene analysis.

Is the Genome-Phenome Analyzer useful in research to discovery new genome-phenome association?

In addition to identifying known genetic diseases, the integrated Genome-Phenome Analyzer is also useful in gene discovery. Even if the condition is a new channelopathy or ciliopathy, for example, the suggestions in the differential diagnosis of many diseases in such categories provides hints of the type of disease to expect and has been useful in prioritizing gene candidates to study in greater detail. 

Can SimulConsult output be customized to our lab reporting system?

APIs are customizable by request.

How does the analysis take into account change in HGNC gene symbols?

The software and database recognize old HGNC gene symbols going back to the start of 2010. Accordingly, the analysis of a genomic variant table should work regardless of whether you have the new or old HGNC symbol for a gene. The main displays use the new gene, with the old gene name also displayed when appropriate.