Monthly Archives: October 2017

ASHG 2017 Summary

Featured Presentation
MNG Laboratories’ Chief Medical Officer, Dr. Peter L. Nagy, MD, PhD, gave an insightful presentation on exome use in carrier testing. In a review of our data, we found that over 40% of children born with catastrophic or severe disabilities that we diagnosed with rare autosomal recessive conditions carry pathogenic variants that would not have been detected using currently available targeted carrier tests. For those that were unable to attend the presentation, MNG Laboratories prepared a live webinar on this topic. To listen to the recording, click here.
Submitted Posters
“Mitochondrial genome sequencing in phenotype-based panels and exome sequencing increases test sensitivity.” Next-generation sequencing (NGS) allows rapid variant analysis for identifying disease causing variants. Exclusion of mitochondrial sequencing analysis in NGS disease screening panels limits their power by ignoring the potential of pathogenic mitochondrial variants. Initially thought to be rare, mitochondrial genetic diseases represent important and common sources of disorders. Recent genetic epidemiological studies quantifying the most common pathogenic mtDNA variants have shown the incidence of clinical mitochondrial diseases is about 1 in 5000. Additionally, a survey of newborn cord bloods revealed that 1 in 200 infants harbored common pathogenic mtDNA variants. Coupled with variant assessment and curation database software, the addition of mtDNA sequencing to phenotype-based panels and exomes increases the ability to discover variants of interest that aid in the determination of patient treatment. Upon including mtDNA sequencing with the panels, we have positively identified pathogenic or potentially pathogenic variants in patient samples having no definitively pathogenic nuclear genome variants. The effect of this inclusion has been particularly beneficial in NGS panels associated with neurological disorders. The increased sensitivity of the NGS panels and the ease of ordering a single test instead of two provides added value for both clinicians and their patients.

To view poster, click here.

“Combining repeat expansion testing with NGS phenotype based panels provides significant diagnostic benefit.” Targeted, phenotype-based next-generation sequencing (NGS) panels are a powerful tool for clinical diagnostics and have made variant calling cheaper, faster, and more accessible. The availability of targeted NGS panels has increased over the past few years to cover a range of conditions including inherited and rare diseases. A number of diseases assessed by NGS panels are known to have multiple genotypic causes, ranging from single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) to repeat expansions. While NGS panels can precisely identify SNPs and CNVs, due to the current limitations of sequencing technology, NGS cannot accurately detect large repeat expansions.  To date, more than 20 diseases have been found to be caused by repeat expansions, including Huntington’s, Friedreich’s Ataxia (FRDA), myotonic dystrophy, spinocerebellar ataxia (SCA), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Fragile X, and others. Research has shown that repeat expansions are responsible for as many as 1 in 3 cases familial of ALS and 1 in 4 cases of familial FTD. For other diseases, such as the rarer SCAs, the prevalence in the general population is currently unknown. By including repeat expansion testing with targeted phenotype-based NGS panels, we can increase the clinical-based sensitivity of the panels we offer. At MNG Laboratories, we currently perform repeat expansion testing for FRDA, C9ORF72, HTT, eleven SCAs, and Fragile X.  Initial findings suggest that repeat expansion testing with our neuromuscular and movement disorder panels increases our positive reports by 5-20%.

To view poster, click here.

“Single exon resolution copy number analysis significantly increases clinical sensitivity of NGS.’ The detection of copy number variants (CNVs) is essential to providing a comprehensive approach to reaching a differential diagnosis. Typically, a large-scale method such as array-based copy number analysis is used to detect larger variations across the genome. While these methods offer a more efficient approach to covering a wide genomic area, they often fail to identify smaller CNVs that may be causative of a patient’s phenotype. In our custom next generation sequencing (NGS) panels, we seek to provide a more comprehensive diagnosis through the detection of CNVs down to a single exon resolution. Using a custom designed capture reagent and the EXCAVATOR copy number analysis software, we are able to detect CNVs of greater than ten exons across all genes included in our panels. Additionally, we are able to detect CNVs at single exon resolution through the use of supplementary intronic probes for all genes with known pathogenic CNVs of ten exons or fewer. Since the inclusion of copy number analysis with our custom NGS panels in September 2016, we have seen a 1.6% increase in the total number of positive reports issued. Here we present multiple case studies in which single exon resolution copy number analysis was crucial in reaching a diagnosis across a variety of phenotypes.

To view poster, click here.

“Protocols to keep NGS gene panels and annotation content current.” With decreasing sequencing costs and growing numbers of out of the box bioinformatics solutions, the landscape of clinically relevant genes and variants is changing at an unprecedented rate. Staying at the forefront of clinical relevancy requires frequently scheduled curation and updating of both gene lists and annotation databases.  A two-fold approach is taken to keep data interpretation up to date.  Gene list classifications are updated quarterly and annotation databases are updated monthly, coinciding with ClinVar’s monthly release.  Gene classification is determined by the combined use of OMIM and ClinVar and review of the scientific literature.  Newly pathogenic or reclassified genes are individually examined to confirm correct placement for each panel based on multiple lines of independent scientific evidence.  This gene curation results in a quarterly custom capture redesign and NGS panel updates.  To ensure that annotations are precisely defined and up to date, our bioinformatics solution processes variant and gene annotation from external databases monthly through a normalization pipeline.  Frequently updating custom capture reagent in conjunction with updating annotation content on a monthly basis increases diagnostic sensitivity in NGS panels.

To view poster, click here.

Webinar: Exome Use in Carrier Testing

In a review of our data, we found that over 40% of children born with catastrophic or severe disabilities that we diagnosed with rare autosomal recessive conditions carry pathogenic variants that would not have been detected using currently available targeted carrier tests. Join MNG Laboratories’ CMO, Dr. Peter L. Nagy, MD, PhD, as he discusses how the MNG Carrier Exome™ can detect rare potentially pathogenic variants that could possibly manifest in offspring which would otherwise not be detected by standard screening panels.
Wednesday, November 1st 2:00 – 3:00PM EST
Click Here for Webinar Recording

Now Introducing RNA Sequencing Services

MNG Transcriptome™ is a cutting-edge, powerful analysis tool using RNA sequencing to determine what effect, if any, a VUS may have on the transcription of RNA from DNA, especially those found in splice site regions. This analysis is commonly used in cancer diagnostics, but can be applied to any phenotype to assess the functional impact of a variant on gene expression. MNG understands that our clients are looking for answers and sometimes the answer to the most challenging diagnostic cases require the most sophisticated tools. The MNG Transcriptome™ is now available and we believe will become a valuable added feature to our growing portfolio. There are three ways to use MNG’s expertise in RNA sequencing, all with 2-4 week turnaround time:
  1. MNG Transcriptome – Full Analysis: Complete RNA transcriptome sequencing that can be ordered at the time of initial testing as a reflex to any NGS panel, or in conjunction with our MNG ExomeTM.
  2. Gene-Specific RNA Sequencing: Analysis of one or up to five genes for variant investigation following a report with a VUS identified in a splice site or intronic region, or the variant is noted to have a potential effect on splicing.
Exclusive to MNG panels, we provide services to the following:
  1. Panel-Specific RNA Sequencing: Transcriptome analysis can be ordered as an add-on to any of our NGS panels and will only include the analysis of genes listed in the panel.
These tests have been validated on the following tissue types:
  • Blood
  • Muscle biopsies
  • Fibroblasts and lymphoid cell lines
Please call MNG Laboratories prior to ordering transcriptome testing due to its clinical relevance to the patient, which tissue type is required, and logistical coordination of sending a specimen for RNA extraction which requires a separate specimen collection process.

Webinar: Challenging Cases and the Need for Complementary Test Methods to Improve Clinical Sensitivity of Genetic Testing

Listen to Dr. Peter L. Nagy, MD, PhD, and Senior Genetic Counselor, Ymkje Cuperus, MS, as they present multple case studies in which comprehensive testing methods incorporated into our next-generation sequencing test offerings, such as copy number assessment, mitochondrial genome sequencing with depletion analysis, and repeat expansion expansion testing, can increase clinical sensitivity of genetic testing.

Click here for webinar recording