Laboratory for Molecular Pediatric Pathology (LaMPP) | Current Offerings

Nucleic acid extraction and quantitation

DNA, RNA and TNA purification from various sources (listed below), using the Promega Maxwell automated purification platform, followed by fluorescence based quantitation via the Promega Quantus.

Acceptable sample sources:

  • FFPE tissue sections or scrolls
  • Fresh/frozen tissue
  • Whole blood
  • Bone marrow
  • Bone marrow aspirate smears

Variant detection by droplet digital (dd) PCR:

Droplet digital (dd) PCR is designed for the detection of a sequence variant present at low allele frequency (rare mutation) in a pool of wild type DNA. Samples are run on the Bio-Rad QX200 digital droplet system.

We currently test for the following mutations:

  • PIK3CA (C420R, E542K, E545K, H1047L and H1047R)
  • BRAF (V600E)
  • Histone H3 (HIST1H3B and H3F3A)

Coming soon: Fusion detection by next-generation sequencing (NGS):

The ArcherDX FusionPlex assays are RNA-based targeted sequencing assays which detect and identify gene fusions. These assays are designed to sequence from a known translocation partner into an unknown partner, using a small quantity of RNA extracted from FFPE or fresh tissue. Archer’s proprietary Anchored Multiplex PCR™-based enrichment detects fusion partners or breakpoints. Libraries are run on the Illumin MiSeq instrument. Full gene lists provided upon request.

We currently offer the following panels:

  • ArcherDX Heme v2 (87 genes associated with hematological malignancies)
  • Boston Children’s Hospital custom solid tumor/neuro (65 genes associated with soft tissue sarcomas and brain cancers)

Coming soon: Affymetrix OncoScan for loss-of-heterozygosity (LOH) and genome-wide copy number assessment,