The Cancer Genomics Shared Resource (CGSR) of the Wake Forest Baptist Comprehensive Cancer Center is a National Cancer Institute (NCI)-supported laboratory that provides comprehensive genomic, transcriptomic and epigenomic profiling analyses for research and diagnostic purposes.
The CGSR provides users with a coordinated approach to conduct research, working closely with other WFBCCC Shared Resources, including:
- Tumor Tissue and Pathology Shared Resource
- Proteomics and Metabolomics Shared Resource
- Biostatistics Shared Resource
- Bioinformatics Shared Resource
The Mission of the CGSR is to provide technical and analytical expertise in genomics research to facilitate high-impact translational science, basic research and clinical diagnostics.
We provide faculty with comprehensive and cost-competitive genetic analyses focused on:
- Next-generation sequencing (NGS)
- DNA microarray technologies
- Bioinformatics solutions
The CGSR has a modern infrastructure that includes:
- Illumina NextSeq 500 NGS
- Illumina MiSeq NGS
- Agilent 2100 Bioanalyzer
- Custom scripts for data processing (R coding)
The CGSR performs nucleic acid (RNA and DNA) purification and quantification, microarray analysis and comprehensive next-generation DNA sequencing, including whole genome sequencing (WGS), whole exome sequencing (WES), RNAseq, small RNAseq, Single-cell RNAseq, ChIPseq and methylation-based sequencing.
In collaboration with the departments of medical genetics and pathology, the NGS sequencing facility is maintained under Clinical Laboratory Improvement Amendments (CLIA) compliance to permit the development and implementation of clinical DNA sequencing.
Co-directors Lance Miller, PhD, and Greg Hawkins, PhD, have vast experience in developing strategies and implementing new genomic methodologies for genomic analysis. Each is available for consultation or collaboration for experimental design, data analysis, and manuscript and grant preparation.
The technical staff—Lou Craddock (lab manager), Wei Cui, Jamie Haywood, Cynthia Van Horn, PhD, and Pam Smitherman—are highly skilled, bringing more than 60 combined years of genomics research experience. Jeff Chou, PhD, is a highly experienced bioinformaticist/biostatistician who provides basic QC/QA analysis for NGS and microarray data.
- Genome sequencing (NGS, array)
- whole genome, whole exome, targeted panels: SNP, mutation, copy number alteration, methylation, ChIP-Seq
- Expression profiling (NGS, array)
- Whole transcriptome (RNAseq), targeted gene panels: mRNA/microRNA/small RNA/single-cell RNA/lncRNA, splice variants, gene fusions, allele specific expression, genetic variants
- RNA/DNA extraction (for downstream profiling)
- FFPEs, FNAs, core Bx, frozen sections
- RNA/DNA integrity analysis (Bioanalysis)
- Project design
- Data processing and “level 1” QC/QA analysis
- RNAseq- data normalization and differential expression
- DNAseq- standard variant and peak calling (ChIPseq, methylation)
- Custom analysis for additional statistics and visualization methods (in conjunction with bioinformatics core)
- Pardee, TS, Anderson, RG, Pladna KM, Isom S, Ghiraldeli LP, Miller LD, Chou JW, Jin G, Zhang W, Ellis LR, Berenzon D, Howard DS, Hurd DD, Manuel M, Dralle S, Lyerly S, Powell BL. A Phase I Study of CPI-613 in Combination with High-Dose Cytarabine and Mitoxantrone for Relapsed or Refractory Acute Myeloid Leukemia. Clin Cancer Res. 2018 Feb 6. doi: 10.1158/1078-0432 CCR-17-2282 [Epub ahead of print].
- Ma L, Chou JW, Snipes JA, Bharadwaj MS, Craddock AL, Cheng D, Weckerle A, Petrovic S, Hicks PJ, Hemal AK, Hawkins GA, Miller LD, Molina AJ, Langefeld CD, Murea M, Parks JS, Freedman BI. APOL1 Renal-Risk Variants Induce Mitochondrial Dysfunction. J Am Soc Nephrol. 2017 Apr;28 (4):1093-1105
- Miller LD, Chou JA, Black MA, Print C, Chifman J, Alistar A, Putti T, Zhou X, Bedognetti D, Hendrickx W, Pulikuth A, Rennhack J, Andrechek ER, Demaria S, Wang E, Marincola FM. Immunogenic Subtypes of Breast Cancer Delineated by Gene Classifiers of Immune Responsiveness. Cancer Immunol Res. 2016 Jul;4(7):600-10.
- Dewi FN, Wood CE, Willson CJ, REigster TC, Lees CJ, Howard TD, Huang Z, Murphy SK, Tooze JA, Chou JW, Miller LD, Cline JM. Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques. Cancer Prev Res (Phila). 2016 May;9(5):385-95.
- Levine EA, Votanopoulos KI, Qasem SA, Philip J, Cummins KA, Chou JW, Ruiz J, D'Agostino R, Shen P, Miller JD. Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix. J. Am Coll Surg. 2016 Apr;222(4): 493-503.