Next Generation Sequencing (NGS)

TEST NAME:   Next Generation Sequencing

INDICATIONS FOR TESTING:   Next generation sequencing (NGS) is most helpful for patients who have findings suspicious of multiple potential genetic causes. This is generally the result of either clinical ambiguity due to marked phenotypic overlap between various syndromes or numerous genetic causes for a single disorder. Detailed information about the clinical indications for each of our gene panels can be found by accessing the indication-specific gene panel testing pages of our test menu.

TEST INFORMATION:   Next generation sequencing (NGS) is a technology that simultaneously analyzes multiple gene sequences. NGS is able to analyze a panel of potentially causative genes at the base-pair (DNA sequence) level in a cost-effective manner. This assay compares the patient’s DNA sequence of the targeted genes to a reference sequence. Any variant identified in the patient’s DNA sequence is screened against the most current versions of primary genomic databases and peer-reviewed literature, and pathogenic changes are confirmed by traditional Sanger sequencing or by another appropriate testing method.

TESTING NOTE: For comprehensive analysis of the genes of interest, it is often indicated to couple gene sequencing with Targeted Deletion/Duplication Testing.

ADVANTAGES:

  • Given the overlap of physical findings between many genetic conditions, especially those in related syndromes, NGS is a useful tool when a single syndrome is not clinically clear.
  • Similarly, NGS is a useful tool when mutations in one of many genes can cause a single syndrome.
  • Our systematic data analysis references the most current versions of primary genomic databases, which translates to better mutation classification (e.g., benign vs. pathogenic) for your patient.
  • NGS is a cost-effective method of testing many potentially causative genes simultaneously rather than ordering separate Sanger sequencing one gene at a time.
  • It allows for large scale testing on a small sample of blood.

LIMITATIONS:

  • NGS will identify sequence variations, but it will not identify large deletions or duplications. A complementary test such as whole genome microarray analysis or gene-specific deletion/duplication analysis is necessary to identify genetic dosage abnormalities.
  • NGS is NOT whole exome sequencing or whole genome sequencing. The test will only identify sequence-based mutations in the genes included on the panel ordered.

RESULTS:

Once a variant is confirmed, our laboratory team interprets this information in conjunction with the patient’s clinical findings and the scientific literature in order to classify a finding as a pathogenic mutation, benign variant, or variant of uncertain clinical significance. There are three possible results:

  • A normal result indicates that sequencing did not find any pathogenic mutations or variants of uncertain clinical significance in the genes analyzed.
  • An abnormal result indicates that a pathogenic mutation was identified. Any available information regarding the phenotype (physical, developmental, and cognitive findings) associated with that mutation will accompany the technical details on the report.
  • In some cases, the clinical significance of an identified sequence variant may not be well understood. These variants will be reported as variants of uncertain clinical significance. Any available information about the molecular characteristics of the genetic change and the relationship of the genetic change to phenotype will be included on the report.
  • Parental testing may be recommended in order to classify the result as de novo or familial for the purpose of recurrence risk calculation.

REQUIRED FORMS:   Postnatal Test Request Form

OTHER FORMS:   Request for Pre-Authorization for Genetic Testing (Postnatal Diagnoses on peripheral blood)


SPECIMEN COLLECTION & SHIPPING

SPECIMEN REQUIREMENTS:

  • Blood >3 mo of age: 3-5 ml in an EDTA tube (purple top) 
  • Blood (newborn minimum requirement): 1 ml in an EDTA tube (purple top)
  • Buccal swab*: kits available upon request
  • Extracted DNA: 5 µg

*Buccal swabs may not yield an adequate amount of DNA for next generation sequencing. Please contact our laboratory before sending buccal swabs for this testing methodology.


CPT CODES and PRICING:   Contact the laboratory billing staff for current codes and costs.


TURN-AROUND-TIME:   Results are typically available in 2-6 weeks.


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contact us
Phone:  402-559-5070 
1-800-656-3937 x95070
Fax:  402-559-7248
humangenetics@unmc.edu

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