OSTR | Office of Science and Technology Resources

Sequencing Facility

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.

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.

Our lab currently employs the following sequencing platforms:


HiSeq 6000

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  NovaSeq6000,  NextSeq500,  Hiseq4000, and MiSeq sequencer

PacBio RS

Long-Reads/PacBio Sequencing

PacBio Sequel II Sequencing

  • Amplification-free sequencing via single-molecule real-time (SMRT) technology enables rapid identification of long nucleotide chains, with average yields of 100-120 Gb per SMRT Cell for Continuous Long Reads (CLR – long insert libraries > 20 kb) or 200-400 Gb per SMRT cell for highly accurate Circular Consensus Sequence (CCS – short insert libraries < 20 kb).
  • Polymerase read lengths averaging greater than 120,000 bases per molecule, with maximum read lengths > 200,000 bases, facilitate genome assembly and mapping of repetitive regions with high fidelity circular consensus reads.
  • The option of 10 to 30 hour run times depending on desired data yield and accuracy, as well as project type.
  • Project flexibility with production protocols that include large and small genome sequencing, whole and targeted transcriptome sequencing (Iso-Seq), and amplicon sequencing, either single or multiplexed.

Single Cell

10X Genomics

  • 10X Genomics Chromium System, powered by GemCode Technology, provides a precisely engineered reagent delivery method that enables thousands of micro-reactions in parallel.
  • Incorporation of identifying barcodes enables reads generated by short read sequencing mapped back to their original HMW DNA, single cell, or single nucleus of origin.
  • Genome and exome sequencing using Linked-Reads resolves genic phasing, reveals structural variation and detects variants in complex regions of the genome.
  • Chromium Single Cell Gene Expression Solution enables cell characterization and gene expression profiling of thousands of cells, while Single Cell Immune Profiling enables simultaneous analysis
  • Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) and Single Cell CNV Solutions reveal the heterogeneity and regulatory landscape of the genome, providing insights into cell variability and clonal evolution.

Bionano Genomics

Bionano Genomics 

  • Bionano’s non-sequencing-based genome mapping technology images and analyzes extremely long, high-molecular-weight DNA 
  • Felicitates identification of structural variants and creation of de novo genome assemblies

Services

SF Services

To request services from the CCR Sequencing Facility
Submit a Sequencing Facility Request
Prior to filling out a NAS request, you are advised to consult with Dr. Maggie Cam and/or Mr. Bao Tran to discuss your project design and bioinformatics approach to data analysis:

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

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

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.

Long-reads/PacBio sequencing:

If you want more information on long reads technologies, please contact us at LongReadInfo@mail.nih.gov

  • Whole Genome Sequencing – de novo assembly, haplotype resolution, structural variant detection, DNA epigenetic modification detection.
  • RNA Sequencing – full-length transcript sequencing for whole-transcriptome or gene-specific targets.
  • Targeted Sequencing – long amplicon sequencing; full-length viral sequencing, full-length vector sequencing, targeted enrichment, and multiplexing strategies.
  • HLA Typing – amplification of full gene for HLA class I, other HLA genes target available.

Others:

  • Whole Genome Sequencing using 10X Genomics Linked-Reads: Long-range information from short-read sequencing, to resolve genic phasing, reveal structural variation and detect variants in complex genomic regions. 
  • Exome Sequencing using 10X Genomics Linked-Reads: Large scale structural variants detection across the entire exome.
  • Optical mapping using Bionano Technology: Imaging and analysis of extremely long, high-molecular-weight DNA felicitates identification of structural variants and creation of de novo genome assemblies

Single-cell sequencing:

  • Single Cell Transcriptomics: 3’ and 5’ gene expression profiling to uncover cell-to-cell gene expression variability
  • Single Cell Immune Profiling: simultaneous analysis of the cellular context of the adaptive immune response and immune repertoires of thousands of T and B cells
  • Single Cell ATAC-seq: chromatin profiling of thousands of single cells to provide insights into the regulatory landscape of the genome
  • Single Cell CNV analysis: single cell CNV calls at 2 Mb resolution for revealing genome heterogeneity

R&D resources:

New applications, new protocols, new platforms etc.  

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.

Bioinformatics Support:

CCR-SF bioinformatics group provides coordinated joint consultation services for sequencing technology selection,  project design,  and data analysis for next generation sequencing projects. We support analysis for Whole Genome/Exome sequencing,  ATAC-seq, ChIP-seq, RNA-seq, miRNA-seq and analysis for new data types from single cell sequencing, long-read sequencing and optical mapping.  We work collaboratively with the CCR Collaborative Bioinformatics Resource (CCBR) and provide a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. 

Pricing

Illumina Library Construction CCR NIAID Other Divisions
Project Type Library Prep Per Sample Library Prep Per Sample Library Prep Per Sample
ChIP-Seq $50 + (Sequencing Cost) $108 + (Sequencing Cost) $94 + (Sequencing Cost)
gDNA-Seq $29 + (Sequencing Cost) $77 + (Sequencing Cost) $55 + (Sequencing Cost)
Nextera DNA Flex $38 + (Sequencing Cost) $90 + (Sequencing Cost) $71 + (Sequencing Cost)
Whole Genome Methyl-Seq $58 + (Sequencing Cost) $120 + (Sequencing Cost) $109 + (Sequencing Cost)
Total RNA-Seq $106 + (Sequencing Cost) $191 + (Sequencing Cost) $198 + (Sequencing Cost)
mRNA-Seq $80 + (Sequencing Cost) $152 + (Sequencing Cost) $149 + (Sequencing Cost)
miRNA-Seq $56 + (Sequencing Cost) $117 + (Sequencing Cost) $105 + (Sequencing Cost)
10XChromium Library Construction CCR NIAID Other Divisions
Project Type Library Prep Per Sample Library Prep Per Sample Library Prep Per Sample
10XChromium Single Cell 3′ RNA-Seq (v3) $1500 + (Sequencing Cost) $1533 + (Sequencing Cost) $1875 + (Sequencing Cost)
10XChromium Single Cell 3′ RNA-Seq + feature barcode $1550 + (Sequencing Cost) $1583 + (Sequencing Cost) $1938 + (Sequencing Cost)
10XChromium Single Cell 5′ RNA-Seq $1500 + (Sequencing Cost) $1533 + (Sequencing Cost) $1875 + (Sequencing Cost)
10XChromium Single Cell VDJ $1500 + (Sequencing Cost) $1533 + (Sequencing Cost) $1875 + (Sequencing Cost)
10XChromium Single Cell VDJ 5′ GEX $1600 + (Sequencing Cost) $1633 + (Sequencing Cost) $2000 + (Sequencing Cost)
10XChromium Single Cell ATAC-seq $1375 + (Sequencing Cost) $1408 + (Sequencing Cost) $1719 + (Sequencing Cost)
10XChromium Single Cell CNV (16 Reaction Kit) $1500 + (Sequencing Cost) $1533 + (Sequencing Cost) $1875 + (Sequencing Cost)
10XChromium Single Cell CNV (4 Reaction Kit) $1600 + (Sequencing Cost) $1633 + (Sequencing Cost) $2000 + (Sequencing Cost)
Illumina NovaSeq CCR NIAID Other Divisions
Run Type Cost Per Lane Cost Per Lane Cost Per Lane
S1 x 100 bp $3310 + (Lib. Prep) $4940 + (Lib. Prep) $6175 + (Lib. Prep)
S1 x 200 bp $4248 + (Lib. Prep) $6340 + (Lib. Prep) $7925 + (Lib. Prep)
S1 x 300 bp $4985 + (Lib. Prep) $7440 + (Lib. Prep) $9300 + (Lib. Prep)
S2 x 100 bp $6928 + (Lib. Prep) $10340 + (Lib. Prep) $12925 + (Lib. Prep)
S2 x 200 bp $9273 + (Lib. Prep) $13840 + (Lib. Prep) $17300 + (Lib. Prep)
S2 x 300 bp $10780 + (Lib. Prep) $16090 + (Lib. Prep) $20113 + (Lib. Prep)
S4 x 200 bp $18452 + (Lib. Prep) $27540 + (Lib. Prep) $34425 + (Lib. Prep)
S4 x 300 bp $21185 + (Lib. Prep) $31620 + (Lib. Prep) $39525 + (Lib. Prep)
SP x 100 bp $2070 + (Lib. Prep) $3090 + (Lib. Prep) $3863 + (Lib. Prep)
SP x 300 bp $3142 + (Lib. Prep) $4690 + (Lib. Prep) $5863 + (Lib. Prep)
SP x 500 bp $4248 + (Lib. Prep) $6340 + (Lib. Prep) $7925 + (Lib. Prep)
XP 2-Lane Kit $299 + (Lib. Prep) $299 + (Lib. Prep) $299 + (Lib. Prep)
XP 4-Lane Kit $999 + (Lib. Prep) $999 + (Lib. Prep) $999 + (Lib. Prep)
MiSeq CCR NIAID Other Divisions
Run Type Cost Cost Cost
SR 1 x 50 bp (V2) $563 + (Lib. Prep) $840 + (Lib. Prep) $1050 + (Lib. Prep)
PE 2 x 150 bp (V2) $723 + (Lib. Prep) $1080 + (Lib. Prep) $1350 + (Lib. Prep)
PE 2 x 250 bp (V2) $811 + (Lib. Prep) $1210 + (Lib. Prep) $1513 + (Lib. Prep)
PE 2 x 75 bp (V3) $623 + (Lib. Prep) $930 + (Lib. Prep) $1163 + (Lib. Prep)
PE 2 x 300 bp (V3) $1058 + (Lib. Prep) $1580 + (Lib. Prep) $1975 + (Lib. Prep)
Illumina NextSeq High Output CCR NIAID Other Divisions
Run Type Cost Cost Cost
1 x 75 bp (V2) $1022 + (Lib. Prep) $1525 + (Lib. Prep) $1906 + (Lib. Prep)
2 x 75 bp (V2) $1956 + (Lib. Prep) $2920 + (Lib. Prep) $3650 + (Lib. Prep)
2 x 150 bp (V2) $3136 + (Lib. Prep) $4680 + (Lib. Prep) $5850 + (Lib. Prep)
Pacbio Sequel Sample Prep CCR NIAID Other Divisions
Project Type Library Prep Per Sample Library Prep Per Sample Library Prep Per Sample
gDNA $94 + (Sequencing Cost) $143 + (Sequencing Cost) $179 + (Sequencing Cost)
gDNA Low Input $57 + (Sequencing Cost) $86 + (Sequencing Cost) $108 + (Sequencing Cost)
Microbial, Multiplexed $53 + (Sequencing Cost) $81 + (Sequencing Cost) $101 + (Sequencing Cost)
Amplicon, Single or Multiplexed $18 + (Sequencing Cost) $27 + (Sequencing Cost) $34 + (Sequencing Cost)
Iso-Seq, Single $84 + (Sequencing Cost) $127 + (Sequencing Cost) $159 + (Sequencing Cost)
Iso-Seq, Multiplexed $37 (Multiplexing Per Library) + (Sequencing Cost) $56 (Multiplexing Per Library) + (Sequencing Cost) $70 (Multiplexing Per Library) + (Sequencing Cost)
HLA Sequencing $25 + (Sequencing Cost) $38 + (Sequencing Cost) $48 + (Sequencing Cost)
*Note: All prices above are per sample

**Note: Iso-Seq price is based on whole transcriptome amplification and sequencing; estimates for targeted Iso-Seq will be determined individually
Pacbio Sequel Sequencing CCR NIAID Other Divisions
Run Type Cost Cost Cost
SMRT Cell 1M V2 $589 + (Lib. Prep) $892 + (Lib. Prep) $1115 + (Lib. Prep)
SMRT Cell 1M V2 LongRead (LR) $589 + (Lib. Prep) $892 + (Lib. Prep) $1115 + (Lib. Prep)

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 Resources
Illumina PacBio

Bioinformatics Information

Specialized in NGS data analysis and quality control, CCR-SF bioinformatics team works closely with CCR researchers to provide support services such as sequencing technology consultation, experimental design, and data analysis and management. Please visit the Frequently Asked Questions for more information.

Bioinformatics Resources and FAQ

Publications

Publications

2019

Zhao Y*, Mehta M*, Walton A*, Talsania K*, Levin Y, Shetty J, Gillanders EM, Tran B, Carrick DM. Robustness of RNA sequencing on older formalin-fixedparaffin-embedded tissue from high-grade ovarian serous adenocarcinomas. PLoS  2019 May 6;14(5): e0216050.

Levin Y†, Talsania K†, Tran B, Shetty J*, Zhao Y*, Mehta M*. Optimization for sequencing and analysis of degraded FFPE-RNA samples. JoVE, In Press. († Co-first authors; * Co-corresponding authors)

Magen A, Nie J, Ciucci T, Tamoutounour S, Zhao Y, Mehta M, Tran B, McGavern DB, Hannenhalli S, Bosselut R. Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+T Cells. Cell Reports, 2019, 29(10):  3019-3032.e6

The Somatic Mutation Working Group of the SEQC-II consortium, Xiao W, Kusko R, Ren L, Fang F, Shen T, Talsania K, Kriga Y, Shetty J, Tran B, Zhao Y, et al. Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing.  Nat Biotechnol, 2019. Accepted

Ma L, Hernandez M, Zhao Y, Mehta M, Tran B, Kelly M, Rae Z, Hernandez J, Davis J, Martin S, Kleiner D, Hewitt S, Ylaya K, Wood B, Greten T, Wang X. Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer.  Cancer Cell. 2019 Oct 03.

Jiao X, Sui H, Lyons C, Tran B, Sherman BT, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 1 Strain McKrae. Microbiol Resour Announc. 2019 Sep 26;8(39).

Jiao X, Sui H, Lyons C, Tran B, Sherman BT, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 1 Strain MacIntyre. Microbiol Resour Announc. 2019 Sep 12;8(37).

Vacchio MS, Ciucci T, Gao Y, Watanabe M, Balmaceno-Criss M, McGinty MT, Huang A, Xiao Q, McConkey C, Zhao Y, Shetty J, Tran B, Pepper M, Vahedi G, Jenkins MK,  McGavern DB, Bosselut R. A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation. Immunity.  2019 Sep 17;51(3):465-478.e6. Epub 2019 Aug 15.

Talsania K, Mehta M, Raley C, Kriga Y, Gowda S, Grose C, Drew M, Roberts V, Tai Cheng K, Burkett S, Oeser S, Stephens R, Soppet D, Chen X, Kumar P, German O, Smirnova T, Hautman C, Shetty J, Tran B, Zhao Y, & Esposito D. Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies. Gene, 2019, 10 (2). pii: E79.

Ciucci T, Vacchio MS, Gao Y, Ardori FT, Candia J, Mehta M, Zhao Y, Tran B, Tessarollo L, McGavern D, & Bosselut R. Emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok. Immunity, 2019, 50(1): 91-105.e4.

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, 68(1): 127-140.

Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W,  Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407.

Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M:De Novo assembly and phasing of dikaryotic genomes from two isolates of puccinia coronata f. sp. avenae, the causal agent of oat crown rust. MBio, 9(1):2018.

Greer YE, Porat-Shliom N, Nagashima K, Stuelten C, Crooks D, Koparde VN, Gilbert SF, Islam C, Ubaldini A, Ji Y, Gattinoni L, Soheilian F, Wang X, Hafner M, Shetty J, Tran B, Jailwala P, Cam M, Lang M, Voeller D, Reinhold WC, Rajapakse V, Pommier Y, Weigert R, Linehan WM, Lipkowitz S. ONC201 kills breast cancer cells in vitro by targeting mitochondria. Oncotarget. 2018 Apr 6;9(26):18454-18479.

Cramer SD, Hixon JA, Andrews C, Porter RJ, Rodrigues GOL, Wu X, Back T, Czarra K, Michael H, Cam M, Chen J, Esposito D, Senkevitch E, Negi V, Aplan PD, Li W, Durum SK. Mutant IL-7Rα and mutant NRas are sufficient to induce murine T cell acute lymphoblastic leukemia. Leukemia. 2018 Aug;32(8):1795-1882.

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

Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R. Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF.   J Immunol. 2017 Sep 1;199(5): 1716-1728.

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.

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X,  Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW. Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min. 2016 Apr 5; 9:13.

Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.   J Data Mining Genomics Proteomics. 2016 Jan;7(1). pii: 182. Epub 2015 Nov 8.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun. 2016 Feb 22;7:10740.

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. 

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.

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. 

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.

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. 

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.

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 6:6746. 2015.

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.

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.

Collaborative Publications 

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)

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. 

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.

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.

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.

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

R&D Scientist

ATRF Room D-3010
301-846-7068
monika.mehta@nih.gov
Caroline Fromont

Acting PacBio Lab Manager

ATRF Room D-3039
301-228-4799
caroline.fromont@nih.gov
Oksana German

Illumina QA Specialist

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

R&D/Coming Soon


Oxford Napore

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
  • 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