Overview

CCR Sequencing Facility

Mission:

The mission of the Center for Cancer Research Sequencing Facility (CCR-SF) is to utilize high-throughput sequencing technologies to enrich cancer research and ensure that the NCI community can leverage the leading-edge of Next-Generation Sequencing technology.

Submit a Sequencing Facility Request

CCR Sequencing Facility: Overview

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at previously unthinkable speeds and a fraction of their former cost. At the Sequencing Facility, NCI researchers are provided access to the latest technologies, with consultation and Q&A services available throughout the design and execution of sequencing projects. Please click here for more detailed information on sequencing applications and supported projects.

Our lab currently employs the following sequencing platforms:


HiSeq 2000

Illumina (Short Read) Sequencing Technology

  • Illumina sequencing utilizes reversible terminator chemistry optimized to achieve high levels of cost-effectiveness and throughput
  • Millions of reads produced per sample lane at 50 bp to 300 bp read lengths
  • Support for the multiplexing of 96 bar-coded samples into a single lane
  • Available resources include one NovaSeq6000, three NextSeq500, one Hiseq4000, and one MiSeq sequencer
PacBio RS

Long-Read Sequencing and Mapping Technologies

PacBio Sequel Sequencing

  • Sequencing via single-molecule, real-time (SMRT) technology enables rapid identification of long nucleotide chains, with average yields 10 – 20 Gb per SMRT Cell (Detailed description)
  • Read lengths averaging greater than 20,000 bases per molecule, with maximum read lengths > 100,000 bases, facilitate genome assembly and mapping of repetitive regions
  • The highly accurate circular consensus reads up to 10,000 base pairs
  • Amplification-free direct sequencing of individual molecules precludes PCR bias and artifacts
  • A low-input protocol developed by the Sequencing Facility enables sequencing of as little as 500 picograms of starting material for many applications
  • Minimal machine turnaround time provides flexibility in experimental and run design

Oxford Nanopore Technologies MinIon Sequencing

  • Sequencing via nanopore technology enables rapid identification of ultra-long reads, with average yields 0.5 – 10 Gb per flow cell, depending on which application utilizes (Detailed description)
  • Read lengths averaging greater than 100,000 bases per molecule, with maximum read lengths > 1,000,000 bases, facilitate genome assembly and mapping of repetitive regions
  • Amplification-free direct sequencing of individual DNA and RNA molecules precludes PCR bias and artifacts
  • Minimal machine turnaround time provides flexibility in experimental and run design

Bionano Genomics Irys Next-Generation Genome Mapping

  • Non-sequencing-based genome mapping technology images and analyzes extremely long, high-molecular-weight DNA molecules to create de novogenome assemblies and detect large structural variants (> 100kb) missed by long-read sequencing technologies (Detailed description)
  • Can be used to scaffold sequencing data with genome maps to assemble genomes with the greatest contiguity in correct order and orientation
  • Requires cellular input as the starting material for DNA extraction

Single Cell Sequencing

  • The Chromium system from 10X Genomics uses the 10X Gemcode technology to provide comprehensive solutions for DNA and RNA analysis
  • Single cell 3’ mRNA-Seq provides gene expression profiles of thousands of individual cells
  • Single cell V(D)J solution profiles full-length paired V(D)J transcripts from thousands of cells

Services

SF Services

The mission of the Center for Cancer Research Sequencing Facility (CCR-SF) is to utilize high-throughput sequencing technologies to enrich cancer research and ensure that the NCI community can leverage the leading-edge of Next-Generation Sequencing technology.

The Sequencing Facility is available to provide support and assistance through each stage of the sequencing process:

 

We currently offer sequencing services on the Illumina HiSeq4000 and NextSeq instruments, and the PacBio RS. Each sequencer conveys different advantages depending on the desired application; please visit the Protocols and Resources page for more details about the sequencing chemistry and technology utilized by each platform. We encourage you to contact us so we can provide you with the most current information and help you plan your project to meet your sequencing needs.

Short-reads/Illumina sequencing:

1. ChIP DNA sequencing

2. Genomic DNA sequencing

3. Methylated DNA sequencing (bisulfite)

4. Whole exome sequencing

5. Total RNA sequencing

6. mRNA sequencing

7. miRNA sequencing

Long-reads/PacBio sequencing:

1. Whole Genome Sequencing – de novo assembly, haplotype resolution structural variant detection, DNA epigenetic modification detection

2. RNA Sequencing – full-length transcript sequencing for whole-transcriptome or gene-specific targets

3. Targeted Sequencing – long amplicon sequencing; full-length viral sequencing full-length vector sequencing, targeted enrichment, and multiplexing strategies

Long-reads/Oxford Nanopore sequencing:

1. Whole Genome Sequencing – ultra-long reads, structural variant detection

2. RNA Sequencing – full-length transcript sequencing (cDNA or RNA)

Others:

1. Single cell 3’ mRNA sequencing (10X Genomics)

2. Single cell Immune profiling (10X Genomics)

3. Structure variation analysis using linked reads – whole genome and whole exome sequencing (10X Genomics)

4. Optical mapping using Bionano Irys

5. R&D projects: new applications, new protocols, new platforms etc Please visit the Protocols and Resources page for more details about the sequencing chemistry and technology utilized by each platform. We encourage you to contact us so we can provide you with the most current information and help you plan your project to meet your sequencing needs.

Request Services

Request Services

To request services from the CCR Sequencing Facility, you must visit the NCI at Frederick Accessioning System (NAS).  Prior to filling out a NAS request, you are advised to consult with Dr. Maggie Cam and Mr. Bao Tran to discuss your project design and bioinformatics approach to data analysis:

Maggie Cam, Ph.D.
maggie.cam@nih.gov
301-443-2965

Bao Tran
Director, Sequencing Facility
tranb2@mail.nih.gov
301-360-3460

 

Pricing

Pricing for different sequencing platforms
*CCR investigators will receive an additional 33% subsidy on the sequencing cost and Investigators outside of CCR will pay 25% overhead cost.

 

Pricing for Library Construction
Project Type Lib. Prep Per Sample
ChIP-Seq $54 + Sequencing
gDNA-Seq $30 + Sequencing
Nextera® XT gDNA-Seq $40 + Sequencing
Whole Genome Methyl-Seq $65 + Sequencing
Total RNA-Seq $108 + Sequencing
mRNA-Seq $91 + Sequencing
miRNA-Seq $71 + Sequencing
10XChromium Single cell 3′-RNA-Seq $1396 + Sequencing
10XChromium Genome $541 + Sequencing
HiSeq 2500 v4 Pricing
Run Type Cost Per Lane
PE 2 x 125bp (v4) $2143 + (Lib. Prep)
HiSeq 4000 Pricing
PE 2 x 150 bp $2100 + (Lib. Prep)
NextSeq High Output Pricing
Run Type Cost
1 x 75 bp (v2) $1334 + (Lib. Prep)
2 x 75 bp (v2) $2558 + (Lib. Prep)
2 x 150 bp (v2) $4094 + (Lib. Prep)
MiSeq Pricing
SR 1 x 50 bp (v2) $755 + (Lib. Prep)
PE 2 x 150 bp (v2) $962 + (Lib. Prep)
PE 2 x 250 bp (v2) $1077 + (Lib. Prep)
PE 2 x 75 bp (v2) $828 + (Lib. Prep)
PE 2 x 300 bp (v2) $1408 + (Lib. Prep)
Pacbio Sequel Pricing
Standard Library Prep $187
Express Library Prep (>15 kb) $205
8-plex Barcoded Adapter Library Prep $207
16-plex Barcoded Adapter Library Prep $227
SMRT Cell 1M v2 (10 Hour) $866
SMRT Cell 1M v2 LR (20 Hour) $983
Oxford Nanopore Pricing
Ligation Sequencing Library Prep $151
Rapid Sequencing Library Prep $146
1D2 Sequencing Library Prep $151
Direct RNA Sequencing Library Prep $202
Flow Cell (R9.4 or R9.5) $900
Oxford Nanopore Pricing
Standard Sample Prep $596
IrysChip V2 $765

Protocols and Resources

SF Protocols and Resources

Here you will find all the forms necessary for submitting your sequencing proposal and samples to the laboratory. To aid in project planning, we have also provided handouts of the technical details of each sequencing platform as well as the sample preparation protocols used by our laboratory. Do you have additional questions about the Sequencing Facility? Check out our sequencing FAQs, containing the most common questions we receive!

Laboratory Forms and Information

Illumina PacBio

Protocols and Workflows

Illumina PacBio

Supplemental Documentation

Publications

CCR Sequencing Facility Presented Posters

Monika Mehta, Parimal Kumar, Vicky Chen, John Bettridge, Yongmei Zhao, Jyoti Shetty, Bao Tran. Single Cell Sequencing at CCR-Sequencing Facility. Molecular Biology in Single Cells Symposium, NCI, April 2018 & NCI Frederick Spring Research Festival, May 2018.

Keyur Talsania, Jack Chen, Tsai-wei Shen, Vicky Chen, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis for Genome Assembly and Structural Variant Detection. National Interagency Confederation for Biological Research Spring Research Festival at Fort Detrick and the National Cancer Institute, May 2018.

Vicky Chen, Tsai-wei Shen, Keyur Talsania, John Bettridge, Monika Mehta, Michael Kelly, Xiaolin Wu, Bao Tran, Jack Collins, Yongmei Zhao. High throughput Single Cell Transcriptome Sequencing Data Analysis. NIH Single Cell Symposium, April 2018.

Jack Chen, Oksana German, Sujatha Gowda, Yuliya Kriga, Christopher Hautman, Yelena Levin, Monika Mehta, Castle Raley, Jyoti Shetty, Tatyana Smirnova, Heidi Smith, Keyur Talsania, Vicky Chen, Tsai-wei Shen, Yongmei Zhao and Bao Tran. Innovative Sequencing Resources in the CCR Sequencing Facility. March 2018.

Wenming Xiao, Yongmei Zhao. A comprehensive investigation of factors impacting the accuracy of mutation detection using next-generation sequencing technology. 18-A-4219-AACR 2018.

Monika Mehta, Yongmei Zhao, Keyur Talsania, Ashley Walton, Yelena Levin, Jyoti Shetty, Elizabeth Gillanders, Bao Tran, Danielle Carrick. RNA Sequencing from Archived FFPE Tissues. AGBT Meeting, Feb 2018.

Yongmei Zhao, Keyur Talsania, Castle Raley, Monika Mehta, Jyoti Shetty, Yuliya Kriga, Sujatha Gowda, Jack Chen, Carissa Grose, Matthew Drew, Veronica Roberts, Kwong Tai Cheng, Sandra Burkett, Steffen Oeser, Robert Stephens, Daniel Soppet, Jack Collins, Bao Tran, Dominic Esposito. Draft Genome Assembly and Annotation of the Trichoplusia ni Insect Cell Line Tni-FNL. AGBT Conference 2018.

Cristobal Vera, Keyur Talsania, Ashley Walton, Sucheta Godbole, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis for Structural Variation Detection and Genome Assembly. National Interagency Confederation for Biological Research Spring Research Festival, May 2017.

Keyur Talsania, Sucheta Godbole, Ashley Walton, J. Cristobal Vera, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis Pipelines for Transcriptome Sequence Analysis. National Interagency Confederation for Biological Research Spring Research Festival, May 2017.

Monika Mehta, Yongmei Zhao, Jyoti Shetty, Castle Raley, Bao Tran. New Advancements in Next-Generation Sequencing Approaches to Address a Variety of Biological Questions. Advances in Genome Biology and Technology (AGBT) Meeting, Feb 2017.

Keyur Talsania, Sucheta Godbole, J. Cristobal Vera, Thomas Skelly, Jack Chen, Robert Stephens, Jack Collins, Bao Tran, Yongmei Zhao. Bioinformatics Support for Next-Generation Sequencing and Data Analysis at CCR-SF. National Interagency Confederation for Biological Research Spring Research Festival, May 2016.

Brenda Ho, Ashley Walton, Monika Mehta.  Analysis of Illumina library preparation protocols for NGS analysis of FFPE RNA samples in cancer research. NIH Summer Intern Poster Day at NIH Bethesda campus.  July 29th, 2016.

Monika Mehta, Castle Raley, Yongmei Zhao, Jyoti Shetty, Bao Tran.  New Advances In Studying Cellular RNA By Next-generation Sequencing. Presented at: CCR RNA Biology Workshop at NCI Shady Grove. November 1, 2016.

CCR Investigator Publications –Acknowledging 

2018

Zheng H, Pomyen Y, Hernandez MO, Li C, Livak F, Tang W, Dang H, Greten T, Zhao Y, Mehta M, Levin Y, Shetty J, Tran B, Budhu A, and Wang XW. Single cell analysis reveals cancer stem cell heterogeneities in hepatocellular carcinoma. Hepatology, 2018 (accepted for publication).

Zhao Y, Mehta M, Walton A, Talsania K, Levin Y, Shetty J, Gillanders EM, Tran B, and Carrick D. Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas. Manuscript under preparation.

2017

Shukla A, Zhu J, Kim SY, Hager G, Ruan Y and Hunter KW (2017) Identification of a core inherited metastatic susceptibility network by integrated epigenetic, genetic and chromosomal interaction analysis.  Manuscript in preparation

2016

Hodson DJ, Shaffer AL, Xiao W, Wright GW, Schmitz R, Phelan JD, Yang Y, Webster DE, Rui L, Kohlhammer H, Nakagawa M, Waldmann TA, Staudt LM.  Regulation of normal B cell differentiation and malignant B cell survival by OCT2.  Proc Natl Acad Sci 2016 113:E2039-E2046.

Thompson, Bethtrice; Varticovski, Lyuba; Baek, Songjoon; et al. Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLOS ONE   Volume: 11   Issue: 2

Yang Y, Kelly P, Shaffer AL, Schmitz R, Liu X, Huang DW, Webster D, Young RM, Yoo H, Nakagawa M, Ceribelli M, Wright GW, Yang Y, Zhao H, Yu X, Xu W, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Targeting non-proteolytic protein ubiquitination for the treatment of diffuse large B cell lymphoma.  Cancer Cell 2016 29:494-507.

Kuschal C, Botta E, Orioli D, Digiovanna JJ, Seneca S, Keymolen K, Tamura D, Heller E, Khan SG, Caligiuri G, Lanzafame M, Nardo T, Ricotti R, Peverali FA, Stephens R, Zhao Y, Lehmann AR, Baranello L, Levens D, Kraemer KH, Stefanini M. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy.Am J Hum Genet. 2016 Apr 7;98(4):627-42.

Rui L, Drennan AC, Ceribelli M, Zhu F, Wright GW, Xiao W, Grindle KM, Lu L, Hodson DJ, Zhao H, Xu W, Yang Y, Staudt LM.  Epigenetic gene regulation by Janus kinase 1 in diffuse large B cell lymphoma. Proc Natl Acad Sci, in press, 2016.

Smith OK, Kim RG, Fu H, Martin M, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlaine S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WC, Aladjem MI. Distinct Epigenetic Features of Differentiation-Regulated Replication Origins. Epigenetics and Chromatin 9:18. 2016.

Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan  M, Kim RG, You Y, Hanna H, Boisclair  Y, Long  Q, Aladjem  MI. A Replicator-Specific Binding Protein Essential For Site-Specific Initiation of DNA Replication in Mammalian Cells. Nat. Commun. 7:11748. 2016.

Ceribelli M, Hou EZ, Kelly PN, Huang DW, Ganapathi K, Evbuomwan MO, Pittaluga S, Shaffer AL, Wright G, Marcucci G, Forman SJ, Xiao W, Guha R, Zhang X, Ferrer M, Chaperot L, Plumas L, Jaffe ES, Thomas CJ, Reizis B, Staudt LM.  A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm.  Cancer Cell 2016, in press.

Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Jermusyk A, Zhang X, Rost L, Collins I, Jia J, Parikh H, Zhang T, Song L, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Bamlet WR, TCGA Research Network, Chanock S, Chatterjee N, Wolpin BM, Smith J, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterizing cis-regulatory variation in the transcriptome of histologically normal and tumor-derived pancreatic tissues. 2016: Gut

Doran AG, Wong K, Flint J, Adams DJ, Hunter KW* and Keane TM* (2016) Deep genome sequencing and variation analysis of 13 inbred mouse strains find novel missense mutations in essential DNA repair pathway genes.  Genome Biology, 17:167.

Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M.  HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. doi: 10.1093/nar/gkw323.

Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res. 2015 Sep;25(9):1295-308. doi: 10.1101/gr.192229.115.PMID:26156321

Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M. HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol. 2013 Aug;33(16):3377-89. doi: 10.1128/MCB.00435-13.

Bai L, Yang H, Hu Y, Shukla, A, Ha, N-H, Doran A, Faraji F, Goldberger N, Lee M, Keane T and Hunter KW. (2016) An integrated genome-wide systems genetics screen for breast cancer susceptibility genes.  PLoS Genetics, doi 10.1371/journal.pgen.1005989

Ha N-H, Long J, Cai Q, Shu X-O and Hunter KW. The circadian rhythm gene Arntl2 is a metastasis susceptibility gene for estrogen receptor-negative breast cancer.  PLoS Genetics, 12(9) e1006267.  The article highlighted by the journal (Siracusa and Bussard, PLoS Genetics 12(9) e1006299).

Kim J, Sturgill D, Tran AD, Sinclair DA, Oberdoerffer P. Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability. Nucleic Acids Res. 2016 Apr 20;44(7):e64. doi: 10.1093/nar/gkv1482.

Khurana S, Kruhlak MJ, Kim J, Tran AD, Liu J, Nyswaner K, Shi L, Jailwala P, Sung MH, Hakim O, Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Nucleic Acids Res. 2016 Apr 20;44(7):e64. doi: 10.1093/nar/gkv1482.

2015

Young RM, Wu T, Schmitz T, Dawood M, Xiao W, Phelan JD, Xu W, Menard L, Meffre E, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Survival of human lymphoma cells requires B cell receptor engagement by self-antigens.  Proc Natl Acad Sci 2015 112:13447-54.

Manna S, Kim JK, Baugé C, Cam M, Zhao Y, Shetty J, Vacchio MS, Castro E, Tran B, Tessarollo L, Bosselut R. Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation. Nat Commun. 2015;6:8152

Miles, George; Zhao, Yongmei; Levin, Yelena; et al. Multiplex Tissue and Clinical Proteomics By Next-Generation Sequencing Conference: 104th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Location: Boston, MA Date: MAR 21-27, 2015

Fu H, Martin MM, Regairaz M, Huang L, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, Aladjem MI. The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage. Nature Communications 6:67462015.

Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE. Allele-specific analysis of DNA replication origins in mammalian cells. Nat Commun.6:7051. 2015.

2014

Schmitz R, Ceribelli M, Pitaluga S, Wright G, and Staudt LM.  Oncogenic mechanisms in Burkitt lymphoma. Cold Spring Harb Perspect Med. 2014 4:1-13.

Yang Y, Schmitz R, Mitala J, Whiting A, Xiao W, Ceribelli M, Wright G, Zhao H, Yang Y, Xu W, Rosenwald A, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Wiestner A, Kruhlak MJ, Iwai K, Bernal F, Staudt LM.  Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms.  Cancer Discovery 2014 4:480-93.

Yudkin D, Hayward B, Aladjem MI, Kumari D, Usdin K. Chromosome fragility and the abnormal replication of the FMR1 locus in Fragile X syndrome. Hum Mol Genet, 23:2940-52. 2014.

Mukhopadhyay R, Lajugie J, Fourel N, Selzer A, Schizas M, Bartholdy B, Mar J, Lin CM, Martin MM, Ryan M, Aladjem MI, Bouhassira EE. Allele-specific genome-wide profiling in human primary erythroblasts reveals replication program organization. PLoS Genetics 10(5): e1004319. 2014.

Hoskins JW, Jia J, Flandez M, Parikh H, Xiao W, Collins I, Emmanuel MA, Ibrahim A, Powell J, Zhang L, Malats N, Bamlet WR, Petersen GM, Real FX, Amundadottir LT. Transcriptome analysis of pancreatic cancer reveals a tumor suppressor function for HNF1A. Carcinogenesis 2014; 35(12): 2670-2678.

Yi, Ming; Zhao, Yongmei; Jia, Li; et al. Performance comparison of SNP detection tools with Illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. NAR Volume: 42   Issue: 12     Article Number: e101

Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM*, Cyster JG*.  Loss of signaling via Gα13 in germinal center B cell-derived lymphoma.  Nature 2014 516: 254-8.

Ceribelli M, Kelly P, Shaffer AL, Wright G, Yang Y, Mathews-Griner LA, Guha R, Shinn P, Keller JM, Liu D, Patel PR, Ferrer M, Joshi S, Nerle S, Sandy P, Normant E, Thomas CJ, Staudt LM.  Blockade of oncogenic IkB kinase activity in ABC DLBCL by small molecule BET protein inhibitors.  Proc Natl Acad Sci 2014 111:11365-70.

Nakagawa M, Schmitz R, Xiao W, Goldman CK, Xu W, Yang Y, Yu X, Waldmann TA, Staudt LM.  Gain-of-function CCR4 mutations in adult T-cell leukemia/lymphoma.  J Exp Med 2014 211:2497-2505.

2013

Xiao W, Tran B, Staudt LM, Schmitz R. High-throughput RNA sequencing in B-cell lymphomas. Methods Mol Biol 2013 971:295-312.

Jia J, Parikh H, Xiao W, Hoskins JW, Pflicke H, Liu X, Collins I, Zhou W, Wang Z, Powell J, Thorgeirsson SS, Rudloff U, Petersen GM, Amundadottir LT.  An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. BMC Med Genomics 2013; 6:33.

Fu YP, Kohaar I, Rothman N, Earl J, Figueroa JD, Ye Y, Malats N, Tang W, Liu L, Garcia-Closas M, Muchmore B, Chatterjee N, Tarway M, Kogevinas M, Porter-Gill P, Baris D, Mumy A, Albanes D, Purdue MP, Hutchinson A, Carrato A, Tardón A, Serra C, García-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Diver WR, Gapstur SM, Thun MJ, Virtamo J, Chanock SJ, Fraumeni JF Jr, Silverman DT, Wu X, Real FX, Prokunina-Olsson L. Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4974-9. doi: 10.1073/pnas.1202189109

Swaminathan, Sanjay; Hu, Xiaojun; Zheng, Xin; et al. Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   Volume: 434   Issue: 2   Pages: 228-234.

Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet. 9:e1003542. 2013.

2012

Snow AL, Xiao W, Stinson JR, Lu W, Chaigne-Delalande B, Zheng L, Pittaluga S, Matthews HF, Schmitz R, Jhavar S, Kuchen S, Kardava L, Wang W, Lamborn IT, Jing H, Raffeld M, Moir S, Fleisher TA, Staudt LM, Su HC, Lenardo MJ.  Congenital B cell lymphocytosis explained by novel germline CARD11 mutations.  J Exp Med 2012 209:2247-61.

Grontved L, Hager GL. Impact of chromatin structure on PR signaling: Transition from local to global analysis. Mol Cell Endocrinol. 357, 30-36.

Li M1, He Y, Dubois W, Wu X, Shi J, Huang J.  Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells, Molecular Cell (2012), doi:10.1016/j.molcel. 2012. 01.020

Yang Y, Shaffer AL, Emre NCT, Ceribelli M, Wright G, Xiao W, Powell J, Platig J, Kohlhammer H, Young RM, Zhao H, Yang Y, Xu W, Balasubramanian S, Buggy JJ, Mathews LA, Shinn P, Guha R, Ferrer M, Thomas C, Staudt LM. Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma.  Cancer Cell 2012 21:723–737.

Koh Y, Wu X, Ferris AL, Matreyek KA, Smith SJ, Lee K, KewalRamani VN, Hughes SH, Engelman A:  Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and ledgf/p75 on the efficiency and specificity of viral DNA integration. Journal of virology. 2012. doi: 10.1128/jvi.01148-12.

Wang H, Jurado KA, Wu X, Shun MC, Li X, Ferris AL, Smith SJ, Patel PA, Fuchs JR, Cherepanov P, Kvaratskheila M, Hughes SH, Engelman A: Hrp2 determines the efficiency and specificity of hiv-1 integration in ledgf/p75 knockout cells but does not contribute to the antiviral activity of a potent ledgf/p75-binding site integrase inhibitor. Nucleic acids research. 2012.

Schmitz R, Young RM, Cerribeli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson D, Buras E, Lu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM.  Pathogenetic mechanisms and therapeutic targets in Burkitt lymphoma from structural and functional genomics. Nature 2012 490:116-20.

Grontved L, Bandle R, John S, Baek S, Chung H-J, Liu Y, Aguilera G, Oberholtzer C, Hager GL, Levens D: Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin 2012 Jun 26;5(1):10. doi: 10.1186/1756-8935-5-10.

2011

Ngo VN, Young RM, Schmitz R, Jhavar S, Xiao W, Lim KH, Kohlhammer H, Xu W, Yang Y, Zhao H, Shaffer AL, Romesser P, Wright G, Powell J, Rosenwald A, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Staudt LM.  Oncogenically active MYD88 mutations in human lymphoma.  Nature 2011 470:115-119.

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Research 21: 1822-1832.  2011.

Contacts

Contacts

For questions concerning the Sequencing Facility, proposal submission and funding, and project status, please contact:

Bao Tran

Bao Tran

Laboratory Director

ATRF Room D-3047
301-360-3460
301-360-3465
tranb2@mail.nih.gov

Jyoti Shetty

Jyoti Shetty

Illumina Lab Manager

ATRF Room D-3038
301-360-3454
shettyju@mail.nih.gov

Yongmei Zhao

Yongmei Zhao

Bioinformatics Manager

ATRF Room D-3048
301-360-3455
yongmei.zhao@nih.gov

Monika Mehta

Mehta Monika

R&D Scientist

ATRF Room D-3042
301-846-7068
monika.mehta@nih.gov

Castle Raley

Christopher Lyons (Hautman)

Acting PacBio Lab Manager

ATRF Room D-3037
301-846-5662
hautmancj@mail.nih.gov

Oksana German

Illumina QA Specialist

ATRF Room D-3037
301-360-3457
oksana.german@fnlcr.nih.gov