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Overview

Mutation Detection:  For PCR and Sanger sequencing both testing and bioinformatics interpretation are conducted. This method is currently being used in patients with chronic granulomatous disease (CGD), WHIM syndrome, and other autoimmune disorders. Because Sanger is a “general method,” it can also be and has been used for other mutation detection, including assays for inherited diseases and cancer-related genes, as well as verification of next-generation sequencing discoveries. Assays can be optimized for any new gene(s) of interest.

Pharmacoscan:  The Pharmacoscan assay is used by several investigators at the NIH Clinical Center Pharmacy Department to test for genetic variations affecting the absorption, distribution, metabolism, and excretion of drugs. 4,627 ADME markers within approximately 1,200 genes are included in a single assay. Pharmacoscan is considered one of the panels that provide personalized medicine. Currently, there are only a limited number of genes of interest that are being used in the clinic, although the results of all are reported. The Applied Biosystems GeneTitan system is used for processing the Pharmacoscan assay. Other assays can also be developed on this multi-channel automated array instrument.

Fragment Analysis:  As a companion to the Pharmacoscan assay, fragment analysis is used to more accurately genotype the UGT1A1 gene TA repeat region. This technique can also be used for other genes if needed; microsattelite instability testing and analysis is one example. This platform is precise, with easily interpretable plot and sizing data, and the run time is quick, allowing for rapid turnaround times if needed. The Applied Biosystems 3730XL DNA sequencers are used for processing fragment analysis samples.

DNA Extraction:  DNA extraction from saliva, whole blood, FFPE tissues, buccal swabs, etc. has been performed under CLIA regulations. The high-quality nucleic acid can then be aliquoted, barcode labeled, and stored at the NCI-Frederick Repository for future studies and downstream applications, such as whole exome sequencing and whole genome sequencing.

LST/NanoString:  The Lymphoma Subtyping Test (LST) was developed to run on the NanoString platform and used to subtype patients as a companion diagnostic in a large clinical trial (NCT02285062) to identify patients of the ABC type who will respond to the drug lenalidomide. It is a highly complex test involving extraction of RNA from biopsy tissue specimens and requires a technician to “cut” material from slides to capture tumor sample. Other RNA assays can be developed as well, utilizing the Nanostring nCounter Flex Dx instrument in our clean room facility.

Future additions:  We are currently in the process of installing and validating a Sciex Citrine Mass spectrometer to expand our capabilities in the area of proteomics. This instrument is a high sensitivity triple quad mass spectrometer that has been FDA registered as a general-purpose reader so it can be used for a variety of assays. We are working closely with NCI collaborators to validate a number of LC MS/MS and immunoMRM assays. The integration of this information with genomics assays will allow us to enter the new field of proteogenomics offering genomic guided proteomics. The CLIA lab anticipates this capability to be added later in 2021.

*Please note: Custom assays can be developed and CLIA validated as needed. Contact us for more information!

LIMS page: https://ncifrederick.cancer.gov/Crtp/Cmdl/Order/JobType.aspx.

Sanger sequencing LIMS page:  https://crtpfm1.ncifcrf.gov/fmi/webd/ATP%20Work%20Requests. 

Website: https://frederick.cancer.gov/science/laboratories/moleculardiagnosticslab.

FNL Department Spotlight: https://frederick.cancer.gov/science/moleculardiagnosticslab/spotlight.

 

List of genes optimized for traditional PCR and Sanger sequencing:

ACD gene

ACVR2A

AIM2

AKT1 gene

APC

APOL1 gene

ASTE1

ATR gene

BAK1 gene

BHD Exons 1-14

BRAF gene Exons 11 & 15

BRCA1 gene

BRCA2 gene

CARD 15 (NOD2) Exons 1-12

CARD9

CD18 gene Exons 1-16

CDK4 gene

CDKN2A gene Exons 1-3 & promoter region

CLIC1

CXCR4 Exons 1-2

CYBA (p22phox) Exons 1-6

CYBB(gp91phox) Exons 1-13

CYBC1

DAMS

Dectin 2 (CLEC6A)

Dectin-1 gene (CLEC7A)

DEFB1 gene

DEFB103 gene

DKC1 gene

ELANE exons 1-5

FBXW7 gene

FH Exons 1-10

FoxP3 Exons 1-12

G6pc3 gene

G6PD

HAX1 gene

H-ras exons 2-5

IDH1 gene

IL8RB (CXCR2) Exons 1-3

IRAK4 gene

JAGN1 Exons 1,2

K-ras exons 2-5

K-ras gene codon 12

LIMK2 gene

LMAN1

MARCKS

MC1R gene

MITF Exons 1-13

MPO gene

MSH

MSH2 gene

MSH3

MTAP Exons 1-8

NCF1 (p47phox) Exons 1-11

NCF2 (p67phox) Exons 1-16

NCF4

NF1 gene

NOLA2 gene

NOLA3 gene

N-ras exons 2-5

P14 gene

P53 (human) gene

PADI4

PARP1 gene

PARP2 gene

PIK3CA gene

POT1 gene

PTCH1

PTEN gene

RNASET2

RNF43

SMAD4 gene

STMN1 Exons 1-4

TAF1B

TCF4

TEP1 gene

TERC gene

TERF1 gene

TERF2 gene

TERF2IP gene

TERT gene

TGFBR2

TINF2 gene

TPP1 gene

UGT1A1

VHL gene Exons 1-3

WDR1 gene

WDR1 gene, exons 4 for FFPE/short degraded DNA

WDR1 gene, exons 8 for FFPE/short degraded DNA


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