Molecular Testing

Name, Description Units DFCI Fee PHS Fee Non-PHS Academic Fee Non-PHS Industry Fee
OncoPanel – Tumor

OncoPanel is a cancer genomic assay to detect somatic mutations, copy number variations, and structural variants in tumor DNA extracted from fresh, frozen or formalin-fixed paraffin-embedded samples.The OncoPanel assay surveys exonic DNA sequences of 447 cancer genes and 191 regions across 60 genes for rearrangement detection. DNA is isolated from tissue containing at least 20% tumor nuclei and analyzed by massively parallel sequencing using a solution-phase Agilent SureSelect hybrid capture kit and an Illumina HiSeq 2500 sequencer. This service can be performed on many sample types including blood, bone marrow, FFPE, cell pellets and fresh frozen tissue. The full OncoPanel service includes initial slide review to determine tumor area and percentage as well pathologist interpretation with an OncoPanel report.

each $875.00 $875.00 $1,260.00 $1,739.06
OncoPanel - Tumor Without Pathology Sign Out

This service offers the same test as “OncoPanel-Tumor”, but does not include pathologist review/sign out of the test results.

each $785.00 $785.00 $1,130.40 $1,560.19
Oncopanel - Germline

OncoPanel germline is a genomic assay designed to detect germline mutations and copy number variations in germline DNA extracted from peripheral blood samples. The OncoPanel germline assay surveys the exonic DNA sequences of 147 genes associated with hereditary cancer predisposition. The OncoPanel germline gene list is a subset of the genes included in the OncoPanel tumor test. DNA is isolated from leukocytes in peripheral blood and analyzed by massively parallel sequencing using a solution-phase Agilent SureSelect hybrid capture kit and an Illumina HiSeq 2500 sequencer. The service can be performed on both peripheral blood samples and DNA previously extracted from peripheral blood leukocytes. The full OncoPanel germline service includes pathologist interpretation with a germline report focused on hereditary cancer predisposition.

1 Min $875.00 $875.00 $1,260.00 $1,739.06
Rapid Heme Panel

The BWH Rapid Heme Panel Assay (RHP) is an amplification-based, next generation sequencing assay that analyzes 95 genes frequently mutated in myeloid and lymphoid malignancies. This assay can detect nucleotide substitutions, small insertions and deletions, and a limited number of copy number changes. It cannot detect structural variants and the ability to detect copy number changes is limited. RHP testing requires 500 ng of DNA isolated from peripheral blood, bone marrow, body fluids or fresh/frozen tissue samples.

each $460.00 $460.00 $663.00 $914.00

Molecular barcoding technology enables researchers to digitally count the number of unique transcripts in a single tube. The multiplexing power allows for measuring up to 800 mRNA, DNA, miRNA or protein molecules in a single tube without any enzymatic steps and it is compatible with difficult sample types like FFPE. Nanostring testing can be performed with multiple available panels or custom-designed panels.

each $42.00 $42.00 $60.48 $83.48

EGFR c.2369C>T (p.T790M) assay is a digital droplet PCR (ddPCR) assay validated for use on formalin fixed paraffin-embedded (FFPE) and fresh frozen tissues including surgical biopsies, cytology cell blocks and fine needle aspirate smears. This quantitative assay is sensitive to 1% mutant allele fraction.

each $160.00 $160.00 $230.40 $318.00
MGMT Promoter Methylation Analysis each $300.00 $300.00 $432.00 $596.25
HPV Genotyping each $200.00 $200.00 $288.00 $397.50
EGFR ddPCR (plasma)

This assay has been designed to detect EGFR mutations in cell-free DNA from plasma samples. Droplet Digital™ PCR (ddPCR™) provides an absolute quantitation of target DNA molecules with accuracy, precision, and sensitivity. ddPCR applications include measurement of copy number variation, rare sequence detection, mutation detection, and gene expression analysis. Cell free DNA (cfDNA) is extracted from a plasma specimen and emulsified with oil into ~20,000 droplets, each containing approximately 0-1 molecules of target DNA. PCR is performed to endpoint in each droplet. These droplets are run through a flow cytometer, where droplets containing mutant and wildtype DNA emit different colored signals. The count of these signals allows quantification of allelic prevalence. This assay can detect mutations with allelic frequency of > 1%.

each $175.00 $175.00 $252.00 $347.81

This qualitative assay is designed to detect the derivative 22 chromosome of the reciprocal translocation t(9;22)(q34;q11) known as the Philadelphia chromosome (Ph).

each $150.00 $150.00 $216.00 $298.13
Microsatellite Instability Assay (MSI)

DNA is separately prepared from microdissected normal and tumor cells and analyzed by a PCR based assay using fluorescent-labeled primers to 10 different microsatellite DNA loci (4 mononucleotide repeats – BAT 25, BAT 26, BAT 40, BAT 34c4, 4 dinucleotide repeats – D17S250, D5S346, D18S55, D10S197, ACTC and a penta-tetra-mononucleotide marker, MYCL1). The alteration in the length of the repetitive sequences is detected by sizing the PCR products by capillary gel electrophoresis. The normal and tumor allele patterns are compared for each marker. The number of DNA loci analyzed was reduced to 5 (BAT 25, BAT 26, BAT40, BAT34, and D18S55).

each $260.00 $260.00 $374.40 $516.75
BRAF ddPCR v600E each $150.00 $150.00 $216.00 $298.13
16S rRNA Sequencing for the identification of Bacterial Isolates

The 5S, 16S, and 23S rRNA genes are unique to bacteria and can be used for taxonomic differentiation. The 16S gene is 1540 bp in length and consists of 9 variable regions, which can be used for identification, flanked by constant regions, which can be used as binding spots for amplification and sequencing primers. The first 500bp of the gene is commonly used for identification purposes, but additional discrimination can be gained from determining the full-length sequence. 16S sequences can allow for the identification of many bacteria down to the species level; however, some isolates cannot be identified past the genus level without including alternate targets such as recA, rpoB, tuf, gyrA, and gyrB.

The use of 16S sequencing for bacterial identification is appropriate in several situations. First and foremost, it can provide valuable information for hard-to-identify isolates. In addition, it can provide confirmation for very unusual isolates which have been identified by traditional methods. Furthermore, it can be very helpful for slow-growing (often anaerobic) isolates, which can be identified by traditional methods but for which a clinical answer is sought urgently. It can also be used for identification of isolates from both FFPE specimens and surgical specimens, though those applications are not included in this protocol. Importantly, 16S is only a means of identification, and cannot give information about properties such as antibiotic resistance of isolates.

$234.00 $234.00 $336.00 $464.00

Cytogenetics Services

Name, Description Units DFCI Fee PHS Fee Non-PHS Academic Fee Non-PHS Industry Fee
FISH - 5 micron section

Fluorescence in situ hybridization (FISH) can be used to answer specific questions about the cytogenetic status of patients, using metaphase or interphase cells under various conditions. FISH is most commonly used to investigate the presence of gene fusions, rearrangements or amplifications in neoplastic specimens, to detect microdeletions at a submicroscopic level, and to determine the makeup of derivative or extra marker specimens. The 5 micron section assay is performed using FFPE slides. The FISH probes are charged separately from the chemistry. Contact the CAMD Core for pricing.

each $135.00 $135.00 $194.40 $268.31
Microarray - Agilent 1x1M CGH Array

The Agilent 1×1M array platform is a high density, whole genome, comparative genomic hybridization (CGH) array that contains 963,029 probes spaced across the human genome with a 2.1 kb overall median probe spacing and a 1.8 kb probe spacing in RefSeq genes. This array permits the detection of copy number changes relative to a co-hybridized reference DNA specimen.
Array type: CGH, high density
Minimum DNA requirement: ~1ug DNA.
Sample type: fresh, frozen or FFPE

each $575.00 $575.00 $828.00 $1,142.81
Microarray - Oncoscan

The Affymetrix Oncoscan assay is a SNP-based microarray with 220,000 molecular inversion probes (MIPs) with an average genome-wide spacing of 16kb, and increased resolution (1 probe per 5 kb) in ~900 well-described cancer genes This array permits the detection of both copy number changes and allelic imbalances. Similarly, certain ploidy states can be identified using this platform.
Array type: SNP + CN
Minimum DNA requirement: 80ng
Sample type: fresh, frozen or FFPE

each $825.00 $825.00 $1,188.00 $1,639.69
Microarray - Cytoscan HD Array

The Affymetrix Cytoscan HD assay is a high density, whole genome microarray with 2,696,550 probes (1,953,246 non-polymorphic regions and 743,304 single-nucleotide polymorphisms), with an average genome-wide spacing of 1.1 kb. This array permits the detection of both copy number changes, allelic imbalances and certain ploidy states can be identified using this platform.
Array type: SNP + CN, high density
Minimum DNA requirement: 250ng
Sample type: fresh or frozen

each $750.00 $750.00 $1,080.00 $1,490.63
EGFR FISH Probe each $63.62 $63.62 $91.61 $0.00
HER2 FISH Probe each $117.00 $117.00 $168.48 $247.16
BRAF FISH Probe $60.00 $60.00 $86.40 $0.00
ALK FISH Probe each $165.00 $165.00 $237.60 $348.50
TFE3 FISH Probe each $60.00 $60.00 $86.40 $0.00
ETV6 FISH Probe $40.00 $40.00 $57.60 $0.00
NUT BRD4 FISH Probe ea $60.00 $60.00 $86.40 $0.00


Name, Description Units DFCI Fee PHS Fee Non-PHS Academic Fee Non-PHS Industry Fee
Specimen Retrieval

Investigators can request retrieval and nucleic acid quantification of previously tested CAMD samples. Oncopanel samples must have approval from the 11-104 user committee before a service request can be processed.

each $15.00 $15.00 $10.00 $0.00
Project Management Fee each $25.00 $25.00 $0.00 $0.00

Nucleic Acid Preparation

Name, Description Units DFCI Fee PHS Fee Non-PHS Academic Fee Non-PHS Industry Fee
DNA Isolation from Blood/Bone Marrow

DNA is isolated from blood and bone marrow using Qiagen reagents.

each $30.00 $30.00 $43.20 $59.63
DNA Isolation from FFPE

DNA isolation from FFPE or fresh frozen tissue is performed using the Qiagen QIAamp DNA mini kit and quantified by spectrophotometry (Nanodrop).

each $30.00 $30.00 $43.20 $59.63
RNA Isolation from Blood/Bone Marrow

RNA is extracted from blood or bone marrow using a Trizol protocol and quantified using Nanodrop.

each $30.00 $30.00 $43.20 $59.63
RNA Concentration with Zymo Kit

RNA is cleaned and concentrated with a Zymo kit by removing proteins, enzymes, salts, detergents and more from any impure RNA sample, as well as to increase the RNA concentration of dilute preparations.

each $30.00 $30.00 $43.20 $59.63
DNA Isolation from Plasma

Free-circulating cell free (cf) DNA is solated from plasma using the Qiagen QIAamp Circulating Nucleic Acid Kit.

each $40.00 $40.00 $57.60 $79.50
RNA Isolationfrom FFPE

RNA is extracted using the Qiagen RNEasy Kit and quantified by Nanodrop.

each $30.00 $30.00 $43.20 $59.63
DNA/RNA Nanodrop Quantification each $2.00 $2.00 $2.88 $3.18
DNA/RNA Qubit Quantification each $3.00 $3.00 $4.32 $4.77