NATIONAL CANCER INSTITUTE - CANCER.GOV

Contact Information


Primary Contact

Kristen Pike
Associate Scientist II

Location

8560 Progress Drive
Frederick, Maryland 21701

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. We perform traditional polymerase chain reaction and Sanger sequencing for the discovery of de novo mutations, as well as for the confirmation of many forms of next-generation 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.

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 MC 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.

Next-Generation Sequencing:

Next-generation sequencing capabilities utilizing Illumina MiSeq, NextSeq, and NovaSeq platforms are at the forefront of new assay requests at the CMDL. Work with custom-designed panels as well as larger workflows such as whole genome sequencing are currently in development, with CLIA validation of a custom amplicon panel for HLA loss of heterozygosity underway and a future validation of a panel targeting Lynch Syndrome mononucleotide repeats planned. The CMDL also offers custom assays targeting both human and mouse p53, and has experience in targeted sequencing, RNA sequencing, whole exome sequencing, and whole genome sequencing to help aid any research efforts.

Mass Spectrometry:

The CMDL is currently striding towards a new frontier with clinical proteomics via mass spectrometry. Utilizing an FDA-registered AB Sciex Citrine high sensitivity triple quad MS general purpose reader, the CMDL is nearing completion of validation for their first MS assay targeting Thyroglobulin in support of DCTD clinical trial efforts through an immune-enrichment multiple reaction monitoring approach. Talks are also currently underway to identify additional clinically actionable targets that would best serve NCI efforts and clinical trials. The integration of this information with genomics assays will allow us to offer proteogenomic interpretation, leading to deeper understanding of how genotypes support phenotypic presentation clinically.

CLIA 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. as well as RNA extraction from FFPE slides and blocks 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 or utilized for downstream efforts within the CMDL. Several extraction methods have been automated as well to increase throughput while reducing cost impact to customers.

Droplet digital PCR:

Assays have been developed to detect and quantify Epstein–Barr virus in relation to Burkitt lymphoma, as well as for NCF1 and its pseudogene associated with Chronic Granulomatous Disease, and the EPAS1 gene for somatic 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.

Other Capabilities/Instruments:

  • Leica BondRx stainer for RNAScope assays
  • Thermo Fisher QuantStudio for qPCR
  • Beckman FXp, KingFisher Flex, and Hamilton Microlab Prep robotics for automation
  • Microm Microtome for sectioning formalin-fixed paraffin-embedded (FFPE) tissues

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

Major Instrumentation

  • Illumina MiSeq
  • Illumina NextSeq2000
  • NovaSeq6000
  • NovaSeq X Plus
  • Qiagen QIAcuity multiplex ddPCR
  • Thermo SeqStudio
  • Qubit and Nanodrop
  • Leica BondRx stainer
  • Thermo Fisher QuantStudio
  • Illumina NextSeq
  • BioRad QX200
  • Beckman FXp robotic liquid handler
  • Hamilton Microlab Preps
  • Microm Microtome
  • GeneTitan MC
  • ABI 3730XL sequencers
  • Agilent Bioanalyzer 2100's

User Guidelines

NIH Investigators may place a formal request for our lab's services at https://ncifrederick.cancer.gov/services/accessioning/Home/SignIn?ReturnUrl=%2fservices%2faccessioning%2f..

Publications

  • Frameshift mutations in peripheral blood as a biomarker for surveillance of Lynch syndrome. https://doi.org/10.1093/jnci/djae060. Yurong Song, Holli Loomans-Kropp, Ryan N Baugher, Brandon Somerville, Shaneen S Baxter, Travis D Kerr, Teri M Plona, Stephanie D Mellott, Todd B Young, Heidi E Lawhorn, Lei Wei, Qiang Hu, Song Liu, Alan Hutson, Ligia Pinto, John D Potter, Shizuko Sei, Ozkan Gelincik, Steven M Lipkin, Johannes Gebert, Matthias Kloor, Robert H Shoemaker. JNCI: Journal of the National Cancer Institute, Volume 116, Issue 6, Pages 957–965. Published: 11 March 2024
  • Organoids and metastatic orthotopic mouse model for mismatch repair-deficient colorectal cancer. https://doi.org/10.3389/fonc.2023.1223915. Yurong Song, Travis D. Kerr, Chelsea Sanders, Lisheng Dai, Shaneen S. Baxter, Brandon Somerville, Ryan N. Baugher, Stephanie D. Mellott, Todd B. Young, Heidi E. Lawhorn, Teri M. Plona, Bingfang Xu, Lei Wei, Qiang Hu, Song Liu, Alan Hutson, Baktiar Karim, Sandra Burkett, Simone Difilippantonio, Ligia Pinto, Johannes Gebert, Matthias Kloor, Steven M. Lipkin, Shizuko Sei and Robert H. Shoemaker. Frontiers in Oncology 2023, 13, 1-17. Published: 08 September 2023.
  • Mesothelioma Mouse Models with Mixed Genomic States of Chromosome and Microsatellite Instability. https://doi.org/10.3390/cancers14133108. 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
  • Kajal Biswas, Martin Couillard, Luca Cavallone, Sandra Burkett, Stacey Stauffer, Betty Martin, Eileen Southon, Susan Reid, Teri Plona, Ryan Baugher, Stephanie Mellott, Kristen Pike, Mary Albaugh, Chelsea Maedler-Kron, Nancy Hamel, Lino Tessarollo, Victoria Marcus, William Foulkes, and Shyam Sharan: A Novel Mouse Model of PMS2 Founder Mutation that Causes Mismatch Repair Defect Due to Aberrant Splicing. Cell Death & Disease, DOI 10.1038/s41419-021-04130-8 Paper #CDDIS-21-1697RR], September 6, 2021.
  • Tristan M. Sissung, Roberto H. Barbier, Douglas K. Price, Teri M. Plona, Kristen M. Pike, Stephanie D. Mellott, Ryan N. Baugher, Gordon R. Whiteley, Daniel R. Soppet, David Venzon, Arlene Berman, Arun Rajan, Giuseppe Giaccone, Paul Meltzer, and William D. Figg: Comparison of Eight Technologies to Determine Genotype at the UGT1A1 (TA)n Repeat Polymorphism: Potential Clinical Consequences of Genotyping Errors? International Journal of Molecular Sciences, 2020.
  • Tristan M. Sissung, Ph.D., M.S., Jon W McKeeby, D.Sc., Jharana Patel, PharmD, Juan J. Lertora, M.D., Ph.D., Parag Kumar, PharmD, Willy A Flegel, M.D., Sharon D. Adams, M.D., Ellen J Eckes, MSN, ARNP, FNP-BC, Frank Mickey, MBA, Teri M. Plona, BA, Stephanie D. Mellott, BS, Ryan N. Baugher, BA, Xiaolin Wu, PhD, Daniel R. Soppet, PhD, Mary E. Barcus, MD, Vivekananda Datta, MD, PhD, Kristen M. Pike, MS, Gary DiPatrizio, PharmD, William D. Figg, PharmD, MBA, and Barry R. Goldspiel, PharmD: PHARMACOGENOMICS IMPLEMENTATION AT THE NATIONAL INSTITUTES OF HEALTH CLINICAL CENTER. THE JOURNAL OF CLINICAL PHARMACOLOGY, 2017.
  • Tychele N. Turner, Kamal Sharma, Edwin C. Oh, Yangfan P. Liu, Ryan L. Collins, Maria X. Sosa, Dallas R. Auer, Harrison Brand, Stephan J. Sanders, Daniel Moreno-De-Luca, Vasyl Pihur, Teri Plona, Kristen Pike, Daniel R. Soppet, Michael W. Smith, Sau Wai Cheung, Christa Lese Martin, Matthew W. State, Michael E. Talkowski, Edwin Cook, Richard Huganir, Nicholas Katsanis, and Aravinda Chakravarti: Loss of δ-catenin function in severe autism. Nature 520: 51-56, 2015.
  • Zuoxiang Xiao, Qun Jiang, Jami Willette-Brown, Sichuan Xi, Feng Zhu, Sandra Burkett, Timothy Back, Na-Young Song, Mahesh Datla, Zhonghe Sun, Romina Goldszmid, Fanching Lin, Travis Cohoon, Kristen Pike, Xioalin Wu, David S. Schrump, Kwok-Kin Wong, Howard A. Young, Giorgio Trinchieri, Robert H. Wiltrout, and Yinling Hu: The Pivotal Role of IKKά in the Development of Spontaneous Lung Squamous Cell Carcinomas. Cancer Cell 23: 527-540, 2013.
  • Sharon A Savage, Neelam Giri, Lea Jessop, Kristen Pike, Teri Plona, Laurie Burdett, and Blanche P Alter: Sequence analysis of the shelterin telomere protection complex genes in dyskeratosis congenita. Journal of Medical Genetics 48: 285-288, 2011.
  • Xiaohong R. Yang, Lea Jessop, Timothy Myers, Laufey Amundadottir, Ruth M. Pfeiffer, William Wheeler, Kristen M. Pike, Jeff Yuenger, Laurie Burdett, Meredith Yeager, Stephen J. Chanock, Margaret A. Tucker, Alisa M. Goldstein: Lack of Germline PALB2 mutations in melanoma-prone families with CDKN2A mutations and pancreatic cancer. Familial Cancer 10:545-548, 2011.
  • Porcia T Bradford, Alisa M Goldstein, Deborah Tamura, Sikander G Khan, Takahiro Ueda, Jennifer Boyle, Kyu-Seon Oh, Kyoko Imoto, Hiroki Inui, Shin-Ichi Moriwaki, Steffen Emmert, Kristen M Pike, Arati Raziuddin, Teri M Plona, John J DiGiovanna, Margaret A Tucker, Kenneth H Kraemer: Cancer and neurologic degeneration in xeroderma pigmentosum: long term follow-up characterizes the role of DNA repair. Journal of Medical Genetics 48: 168-176, 2010.
  • Douglas B. Kuhns, W. Gregory Alvord, Theo Heller, Jordan J. Feld, Kristen M. Pike, Beatriz E. Marciano, Gulbu Uzel, Suk See DeRavin, Debra Long-Priel, Benjamin P. Soule, Kol A. Zarember, Harry L. Malech, Steven M. Holland, and John I. Gallin: Residual NADPH Oxidase and Survival in Chronic Granulomatous Disease. The New England Journal of Medicine 363: 2600-2610, 2010.
  • 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.
  • Haines DC, Gorelick PL, Battles JK, Pike KM, Anderson RJ, Fox JG, Taylor NS, Shen Z, Dewhirst FE, Anver MR, Ward JM: Inflammatory large bowel disease in immunodeficient rats naturally and experimentally infected with Helicobacter bilis. Vet Pathol 35: 202-208, 1998.
  • Battles JK, Williamson JC , Pike KM, Gorelick PL, Ward JM, Gonda MA: Diagnostic assay for Helicobacter hepaticus based on nucleotide sequence of its 16S rRNA gene. J Clin Microbiol 33: 1344-1347, 1995.

Keywords

ACD geneACVR2AAIM2AKT1 geneAPCAPOL1 geneASTE1ATR geneBAK1 geneBHD Exons 1-14BRAF gene Exons 11 & 15BRCA1 geneBRCA2 geneCARD 15 (NOD2) Exons 1-12CARD9CD18 gene Exons 1-16CDK4 geneCDKN2A gene Exons 1-3 & promoter regionCLIACLIC1CXCR4 Exons 1-2CYBA (p22phox) Exons 1-6CYBB(gp91phox) Exons 1-13CYBC1DAMSDEFB1 geneDEFB103 geneDKC1 geneDNA extractionDectin 2 (CLEC6A)Dectin-1 gene (CLEC7A)ELANE exons 1-5FBXW7 geneFH Exons 1-10FoxP3 Exons 1-12G6PDG6pc3 geneH-ras exons 2-5HAX1 geneIDH1 geneIL8RB (CXCR2) Exons 1-3IRAK4 geneJAGN1 Exons 1K-ras exons 2-5K-ras gene codon 12LIMK2 geneLMAN1LSTMARCKSMC1R geneMITF Exons 1-13MPO geneMSHMSH2 geneMSH3MTAP Exons 1-8N-ras exons 2-5NCF1 (p47phox) Exons 1-11NCF2 (p67phox) Exons 1-16NCF4NF1 geneNOLA2 geneNOLA3 geneP14 geneP53 (human) genePADI4PARP1 genePARP2 genePIK3CA genePOT1 genePTCH1PTEN geneRNASET2RNAScopeRNF43SMAD4 geneSTMN1 Exons 1-4Sanger SequencingTAF1BTCF4TEP1 geneTERC geneTERF1 geneTERF2 geneTERF2IP geneTERT geneTGFBR2TINF2 geneTPP1 geneUGT1A1VHL gene Exons 1-3WDR1 geneanalysisClinical Research Supportmass specmass spectrometrymutation detectionnci-coreqPCRPharmacoscanfragment analysisPCRddPCRDroplet digital PCRNGS (next generation sequencingpharmacogenomicsRNA extractionbloodbuffy coatplasmaFFPEbuccal swabsalivafragment analysisCYP3A4*6EPAS1 genemBAT30mBAT37mBAT59mBAT64mBAT67mL24372mPMS2mU12235RUNX1TSPOplatelet-depleted whole bloodDNA extraction from hair and nails