Contact Information

Primary Contact

Kristen Pike
Associate Scientist II


8560 Progress Drive
Frederick, Maryland 21701


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. We perform traditional polymerase chain reaction and Sanger sequencing for the discovery of de novo mutations, as well as for the confirmation of whole exome sequencing data, next-generation sequencing data, or whole genome sequencing data. Assays for more than 90 genes have been developed for diseases such as dyskeratosis congenita, melanoma, colorectal cancer, xeroderma pigmentosum, and kidney disease.


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. We also provide a companion diagnostic assay with fragment analysis of the UGT1A1 gene.

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; microsatellite 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, buffy coats, platelet-depleted whole blood, plasma, FFPE blocks, microscope slides, hair, nails, 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.

Droplet digital PCR:

Assays have been developed to detect and quantify Epstein–Barr virus in relation to Burkitt lymphoma, as well as for a pseudogene associated with Chronic Granulomatous Disease, and the EPAS1 gene for mosaicism related to paragangliomas in patients. The Bio-Rad QX200 system is utilized. Assays for confirming known variants via other technologies such as qPCR can be implemented as well.

Core Sanger sequencing:

Plasmids and PCR products can be purified, cycle sequenced, and run on ABI 3730XL instruments. High-quality results in the form of .ab1 files are uploaded to a secure LIMS typically within 24-48 hours of sample receipt.


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.

Other Capabilities/Instruments:

Illumina MiSeqDx for next-generation sequencing

Leica BondRx stainer for RNAScope assays

Thermo Fisher QuantStudio for qPCR

Illumina NextSeq for next-generation sequencing

Beckman FXp robotic liquid handler and Hamilton Microlab Prep for automation

Microm Microtome for sectioning formalin-fixed paraffin-embedded (FFPE) tissues

Future additions:

We have installed 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 2024.

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

Other Capabilities/Instruments:

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
  • 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
  • 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

To request services from this NCI Frederick core facility, you must submit your requisition through: NAS.

Major Instrumentation

  • Illumina MiSeqDx
  • Leica BondRx stainer
  • Thermo Fisher QuantStudio
  • Illumina NextSeq
  • BioRad QX200
  • Beckman FXp robotic liquid handler
  • Hamilton Microlab Preps
  • Microm Microtome
  • NanoString nCounter Flex Dx
  • GeneTitan MC
  • ABI 3730XL sequencers
  • Agilent Bioanalyzer 2100's

User Guidelines

NIH Investigators may place a formal request for our lab's services at


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  • Maria Concetia Fargnoli, Kris Pike, Ruth M. Pfeiffer, Shirley Tsang, Ester Rozenblum, David J. Munroe, Yelena Golubeva, Donato Calista, Stefania Seidenari, Daniela Massi, Paolo Carli, Juergen Bauer, David E. Elder, Boris C. Bastian, Ketty Peris, and Maria T. Landi: MC1R Variants Increase Risk of Melanomas Harboring BRAF Mutations. Journal of Investigative Dermatology 128: 2485-2490, 2008.
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  • Mesothelioma Mouse Models with Mixed Genomic States of Chromosome and Microsatellite Instability. Yurong Song, Shaneen S. Baxter , Lisheng Dai, Chelsea Sanders, Sandra Burkett, Ryan N. Baugher , Stephanie D. Mellott, Todd B. Young, Heidi E. Lawhorn, Simone Difilippantonio, Baktiar Karim, Yuwaraj Kadariya, Ligia A. Pinto, Joseph R. Testa and Robert H. Shoemaker. Cancers 2022, 14, 3108. Published: 24 June 2022
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