MNG Genome MaNaGer® Pipeline

The MNG Genome MaNaGer® is our proprietary process for evaluating the significance of genetic changes. This unique approach centers on the concept of genetic disorders as diseases of molecular systems, rather than individual genes. We also improve our decision-making by including functional information about genes obtained from model organisms. Our proprietary database incorporates this “system related phenotype interpretation” approach into our analysis and thus ensures delivery of first-in-class specificity and sensitivity in our reporting.

15 Years of Sequencing Experience Over 15,000 patients sequenced
Proprietary Neurogenetic Database MNG Genome MaNaGer® Pipeline ensures high specificity & sensitivity of variant detection and interpretation
Expert Decision Making Functional information about genes and variants obtained from model organisms and in silico modeling
First-In-Class Reporting Reporting variants that are either certain or likely to cause the condition based on available scientific evidence

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MNG’s Reporting Process

The value of next-generation sequencing (NGS) depends on the sensitivity and specificity of the testing as well as clear, user-friendly interpretation and reporting of results. Our customized reporting process helps us stay at the forefront of the evolving genetics field with our regularly-updated NGS panels. We focus on identifying the cause of the disease and only report variants that are actionable and either certain or likely to cause the condition based on available scientific evidence. The NGS reporting team thoroughly assesses the most up-to-date literature as well as our in-house curated database consisting of over 10,000 data sets from patients with neurological and muscular disorders, providing clinically relevant variant classification and producing first-in-class result reports. We employ a wide variety of clinical and predictive tools in order to deliver accurate and responsible calls for variants identified through the use of our powerful Genome MaNaGer®. Only the most up to date databases are included in our variant and gene annotation (see table).
Integrating a multi-angled interpretative approach in conjunction with clinical information, the NGS reporting team provides the most relevant results, affording greater detailed reporting. By adhering to the most current ACMG guidelines for reporting criteria, patient reports are structured to be clear and concise, ensuring a client focused structure. MNG adheres to the strict guidelines of CLIA, CAP, and ACMG. Our reports focus on single nucleotide changes and small (<100bp) insertions and deletions found in the exome and mitochondrial DNA. We can report incidental findings based on ACMG guidelines if the patient or the patient’s guardian chooses to receive such results. We do not report carrier status, parental data, copy number changes, or repeat expansion disorders. We can offer a reevaluation of reports upon request. Whole exome sequencing requires the submission of a signed consent form. The consent form must be signed by all parties.

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Quality Assurance

At MNG Laboratories, high quality data and results are paramount to our process in delivering first-in-class NGS clinical reporting.

To ensure that only the highest quality data and results are utilized in our bioinformatics pipeline, we use the definitions of performance characteristics adapted for NGS by the “next-generation sequencing: Standardization of Clinical Testing (Nex-StoCT)” workgroup (Gargis AS, 2012). Their proposed metrics were adapted and expanded to establish, monitor, and assure high-quality NGS analytical results throughout our data analysis (see table). MNG’s analytical Genome MaNaGer® pipeline automatically monitors all important quality metrics to ensure robust and reproducible results. These metrics include the total number of reads obtained, percentage of reads mapping to the desired target regions, and the completeness of the coverage for regions of interest (guaranteed greater than 99% in all NGS tests), among others.
In addition, we monitor the transition-to-transversion ratio among the variants detected, the ratio of homozygous to heterozygous changes, as well as the ratio of low confidence calls to high confidence calls. An extensive coverage analysis is performed for all NGS samples to ensure that no pathogenic variants in sequencing regions of interest are left without complete coverage. If a known pathogenic or likely pathogenic variant is identified as not covered by the Agilent capture, it is amplified by targeted PCR and sequenced by Sanger sequencing. Gender is independently established by examining Y chromosome alignment statistics and from the ratio of heterozygous and homozygous calls on the X chromosome. We also monitor the percentage of rare variants shared between the proband and additional tested family members to ensure sample and familial connection. For this same reason, we also confirm all disease causing variants with an independent methodology using the original DNA sample.

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