CLINICAL CAPABILITIES // Genetic testing
Nervous System
Identify genetic risk factors and causes of nervous system cancer and brain cancer.
Who Would Benefit from Nervous System and Brain Cancer Genetic Testing?
1
A person with a strong family history of certain types of cancer
Determine if they carry a gene mutation that increases their risk. If they do have an inherited mutation, they might want to have screening tests to look for cancer early, or even take steps to try to lower their risk.
2
A person already diagnosed with cancer
This is especially true if there are other factors to suggest the cancer might have been caused by an inherited mutation (such as a strong family history or if the cancer was diagnosed at a young age). Genetic testing might show if the person has a higher risk of developing cancer. It can also help other family members decide if they want to be tested for the mutation.
3
Family members of a person known to have an inherited gene mutation that increases their risk of cancer
Testing can help them know if they need screening tests to look for cancer early, or if they should take steps to try to lower their risk.
How Do I Order a Test?
A printed copy of the requisition form must be submitted with the specimen if you are not placing your order through the online portal. You can find and print a copy of the requisition form here. If you need to modify your order, please contact client services.
Nervous System & Brain Panel Best Practices
Preferred Specimen
2mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
Alternate Specimens
- Saliva
- Buccal swab
- gDNA
Let's get started!
How to Ship Your Samples
Follow IATA Regulations
Please note that Psomagen sample collection kits are built to protect the samples from being damaged during transport and to comply with the International Air Transport Association (IATA) regulation. If you are using packaging other than that provided by Psomagen, please make sure to follow the "three layers of packaging" rule to avoid the risk of having the package destroyed by the courier:
- A primary sample receptacle sealed (collection tube).
- A leak-proof specimen bag containing absorbent material.
- An outer packaging that meets the local postal regulations and is labeled as “Exempt Human Specimen.”
For more information please refer to page 187 of IATA Dangerous Goods Regulation.
Additional Shipment Requirements
For saliva, ship at room temperature (overnight shipping is not necessary).
For blood, we recommend using overnight shipping the same day that the blood is collected.
- Blood can be kept at room temperature for up to 48 hours.
- We request that blood is refrigerated no longer than two weeks.
- Please do not freeze blood as deletion/duplication analysis is not supported for frozen or partially frozen blood.
Please ship the specimen in a crush-proof container via FedEx Priority Overnight (in accordance with the FedEx Packaging Guidelines for Clinical Samples.
Our US Shipping Address
Attn: Clinical Laboratory Testing Personnel
Psomagen Inc.
1330 Piccard Drive, Ste 103
Rockville, MD 20850
Test for 27 related genes
Gene List
APC
ATM
DICER1
EPCAM
HRAS
MEN1
MLH1
MSH2
MSH6
NF1
PHOX2B
PMS2
POT1
PRKAR1A
PTEN
SMARCA4
SMARCB1
SMARCE1
TP53
TSC1
TSC2
VHL
Test Methodology and Limitations
DNA sequencing involves the extraction of genomic DNA from specimens collected in approved containers and provided the specimen meets required sample minimum quantity (e.g. volume, weight, etc). This is followed by quantification and qualification to ensure the adequacy of amount and purity for sequencing. Subsequently, whole exome sequencing is conducted on an IlluminaTM short read sequencing (SRS) platform (e.g., Novaseq X PlusTM) at Psomagen, Inc.’s laboratories (CLIA # 21D2062464, CAP # 8742212).
DNA sequence alignment, variant calling, and variant filtering are performed utilizing the Illumina DRAGENTM bioinformatics pipeline (version 4.2.4.) and various tool sets, which align reads to the human reference genome (GRCh38) and identify single nucleotide variants (SNVs) and small insertions/deletions (InDels). Variant annotations are performed using a pipeline available in Fabric Enterprise. Variant review and interpretation are conducted according to the standards and guidelines set forth by the American College of Medical Genetics and Genomics (Richards S, et al., Genet Med., 2015) by Fabric Clinical Labs (CLIA #45D2281059, CAP # 9619501). Only variants classified as pathogenic or likely pathogenic are reported. The following quality filters are applied to all variants: coverage <40x, allele balance outside 0.3-0.7.
Variants in the following genes are reported: ALK, APC, ATM, DICER1, EPCAM, HRAS, LZTR1, MEN1, MLH1, MSH2, MSH6, NF1, NF2, PHOX2B, PMS2, POT1, PRKAR1A, PTCH1, PTEN, SMARCA4, SMARCB1, SMARCE1, SUFU, TP53, TSC1, TSC2, VHL.
This test is designed to detect single nucleotide variants (SNVs) and small insertions/deletions (InDels). Next-Generation Sequencing (NGS) coverage may vary across the genome, potentially resulting in missed variants in regions with low coverage depth. Some genetic abnormalities may be undetectable with the current version of this test. While the DRAGEN bioinformatics pipeline demonstrates high accuracy for variant calling, there remains a possibility of false positive or false negative results due to variant interpretation which relies on current scientific knowledge and available databases. This may lead to the reclassification of reported variants as new information emerges from ongoing research and is updated in the ACMG guidelines. Furthermore, systematic chemical, computational, or human errors may contribute to false positives or false negatives of DNA variants. For any reported variants, confirmation by orthogonal technology and subsequent consultation with a genetic counselor or qualified healthcare provider can help to establish definitive risk. This result should be considered preliminary until such confirmation has been performed.
Clinical management for this individual should be based on personal and family history, along with other relevant information. If considered relevant to this individual’s clinical presentation and/or family history, targeted testing of appropriate family members of this individual for the reported variants may help to interpret these results. For assistance with the interpretation of these results, healthcare professionals may contact Psomagen directly at (301) 251-1007 or support@psomagen.com.
More Resources
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