Skip to main content
An official website of the United States government
Email

NCLN Genomics Biomarker Assays

NCLN’s genomics assays are performed by the Molecular Characterization (MoCha) Laboratory at Frederick National Laboratory for Cancer Research (FNLCR).

Download the NCLN Assay Menu for assay information that has been formatted to copy-paste into the Biomarker Table of your CTEP LOI or protocol document.

Whole Exome Sequencing (WES)

Library prep method: customized KAPA Biosystems Hyper Prep

Hybrid capture/enrichment: Agilent SureSelect Capture Baits (V6+ COSMIC); 80 MB reportable region

Example Capabilities:

  • SNV and Indels calling (single nucleotide variants and insertions/deletions)
  • Copy number variants
  • Microsatellite instability (MSI)
  • Loss of heterozygosity (LOH); HLA typing
  • Homologous recombination deficiency (HRD)
  • Tumor mutational burden (TMB)
  • Neoantigen prediction

Note: WES requires the submission of a matched germline control specimen (typically blood for solid tumors or buccal swab for hematological malignancies). If matched germline specimens are not available, NCLN still has the ability to call somatic mutations; however, confidence in the results for some somatic variant calls may be lowered.

RNAseq

Library prep method: Illumina TruSeq RNA Exome

Example Capabilities:

  • Gene expression analysis
  • Gene fusion calling, including intragenic fusion events

Oncomine Panel

Library prep method: Ion Torrent AmpliSeq Oncomine v3 Kit

Example Capabilities:

The oncomine panel detects more than 8000 genomic alterations (including SNVs, Indels, CNV, and fusions) in 161 cancer-related genes across all major cancer types. Examples of variants in the oncomine panel include:

  • Full coverage of kinase domains in critical receptor tyrosine kinases such as BRAF, EGFR, and KIT.
  • 31 genes in DNA repair pathways
  • MAPK, PI3K, and cell cycle pathway genes.

For a full list of genes included in the panel, please see the Oncomine v3 product data sheet from ThermoFisher.

Circulating Tumor DNA (ctDNA)

Library prep method: Illumina TruSight Oncology 500 ctDNA v2 ("TSO500 ctDNA v2")

Example Capabilities:

Interrogates over 500 genes across all cancer types, including established clinically significant cancer biomarkers as well as promising candidates supported by clinical trial research and novel variations in top cancer-related genes.

For a full list of the 523 included genes, please see the TSO500 product data sheet from Illumina.

  • SNV and indels calling
  • Clinically relevant translocations
  • Copy number variants (CNVs)
  • Blood-based tumor mutational burden (bTMB)
  • Microsatellite instability (MSI)
  • Updated:

If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. In the case of permitted digital reproduction, please credit the National Cancer Institute as the source and link to the original NCI product using the original product's title; e.g., “NCLN Genomics Biomarker Assays was originally published by the National Cancer Institute.”

Email