Biostatistics and Bioinformatics Core

Biostatistics and Bioinformatics Core

Mission of the Core

Biostatistics and Bioinformatics Core members

The Biostatistics and Bioinformatics Core is a resource for Karmanos members in basic (in vitro and in vivo), clinical, population and translational sciences. Biostatistics is important in the design of cancer research studies to ensure that the scientific questions are framed so that they can be answered precisely and efficiently and in the analysis of these studies to ensure that the conclusions are accurate and valid. Bioinformatics is important to ensure computationally efficient and informative analyses.

The Biostatistics and Bioinformatics Core is supported, in part, by NIH Center grant P30 CA022453 to the Karmanos Cancer Institute at Wayne State University.

Core Services Available

Specifically, members of the Core:

  • Develop experimental designs for clinical, laboratory, intervention, and observational studies
  • Conduct statistical and bioinformatic analyses and collaborate on interpretation of results
  • Process raw genomic data (e.g., RNA-seq, exome sequencing) for use in statistical analyses
  • Conduct downstream bioinformatics analyses, including pathway, differential expression, and network analyses
  • Conduct statistical analyses of in vitro, in vivo, clinical and epidemiologic data
  • Write statistical reports and make statistical presentations
  • Write statistical and bioinformatic sections for grant proposals and manuscripts in collaboration with investigators
  • Provide instruction in biostatistics to cancer researchers in journal clubs, seminar series and grand rounds presentations
  • Evaluate new and conventional statistical and bioinformatic methodology for applicability to cancer research projects and for application or adaptation of methods as required
  • When current methods are inadequate, develop biostatics and bioinformatics methods for specific cancer research projects
  • Provide instruction in biostatistics to cancer researchers in journal clubs, seminar series and grand rounds presentations

Software, Servers & Grid

Bioinformatics software includes ANNOVAR, Bioconductor, GATK, Ingenuity and Oncomine, among others. The Core continuously reviews and updates processes to follow and maintain best practices when designing custom computational pipelines for all stages of bioinformatics analysis from data pre-processing to variant discovery. Statistical applications include general-purpose software R, SAS and Stata/MP. Software for calculating statistical power includes PASS and nQuery Advisor.

MS Windows based application software resides on a Dell PowerEdge 2950 III, which has two quad core Intel Xeon 5460 3.16 MHz processors, each with 2x6 MB cache, 32GB memory and two 300 GB disk drives and a Dell R820 with 4 Xeon E5-4650 2.70GHz processors, each with eight cores, 128GB memory, four 600GB and two 146GB disk drives. The backup unit is a 4 DAT drive running Veritas Backup Exec. Incremental backup of data files is performed nightly.

Full back-ups are performed weekly and the data tapes are maintained off-site in a secure, fireproof storage facility. Access to the server is restricted to members of the Biostatistics Core and authorized guests.

Linux based application software may be run on the Wayne State University high-performance grid system. The Wayne State University Grid is a tightly networked system of 400+ nodes and over 8000 processing cores.

Integrated into the Wayne State University high-performance grid computing facility are two PowerEdge R710 computers, each with 48GB RAM; dual 6 core Intel Xeon X5680 3.33 GHz processors and 1TB hard drives that run under the Linux operating system. Those computers were purchased by Karmanos for the use of Core members, but are accessible to other authorized Karmanos members whose research requires high performance computing capabilities.

The Core uses the Google Cloud Platform for computationally intensive analyses, analyses that require large memory, are highly distributed or CPU intensive, particularly pre-processing raw sequence data. Cloud resources will also be utilized for medium and long-term storage of raw data, processed data and associated procedures and pipelines. All third-party resources are HIPAA compliant.

Biostatistics Core Selected Publications

Beebe-Dimmer JL, Albrecht TL, Baird TE, Ruterbusch JJ, Hastert T, Harper FWK, Simon MS, Abrams J, Schwartz KL, Schwartz AG. The Detroit Research on Cancer Survivors (ROCS) Pilot Study: A Focus on Outcomes after Cancer in a Racially Diverse Patient Population Cancer Epidemiol Biomarkers Prev. 28(4):666-674. 2019 PMID: 30482875; PMCID: PMC6449184.

Chammaa M, Malysa A, Redondo C, Jang H, Chen W, Bepler G, Fernandez-Valdivia R. RUMI is a novel negative prognostic marker and therapeutic target in non-small-cell lung cancer. J Cell Physiol. 233(12):9548-9562. 2018 PMID: 29953591; PMCID: PMC6185790.  

Dekhne AS, Shah K, Ducker GS, Katinas JM, Wong-Roushar J, Nayeen MJ, Doshi A, Ning C, Bao X, Frühauf J, Liu J, Wallace-Povirk A, O'Connor C, Dzinic SH, White K, Kushner J, Kim S, Hüttemann M, Polin L, Rabinowitz JD, Li J, Hou Z, Dann CE 3rd, Gangjee A, Matherly LH. Novel Pyrrolo[3,2-d]pyrimidine Compounds Target Mitochondrial and Cytosolic One-carbon Metabolism with Broad-spectrum Antitumor Efficacy. Mol Cancer Ther. 18(10):1787-1799. 2019. PMID: 31289137; PMCID: PMC6774887.

Farran B, Albayrak S, Abrams J, Tainsky MA, Levin NK, Morris R, Matherly LH, Ratnam M, Winer I. Serum folate receptor α (sFR) in ovarian cancer diagnosis and surveillance. Cancer Med. 8(3):920-927. 2019 PMID: 30761774;  PMCID: PMC6434204.

Gadgeel SM, Ventimiglia J, Kalemkerian GP, Fidler MJ, Chen W, Sukari A, Halmos B Boerner J, Wozniak A, , Galasso C, Pennell NA, ,. Phase II Study of Maintenance Pembrolizumab in Patients with Extensive-Stage Small Cell Lung Cancer (SCLC). J Thorac Oncol. 13(9):1393-1399. 2017 PubMed PMID: 29775808.

Heath EI,  Heilbrun LK, Mannuel HD,  Liu G,  Lara PN,  Monk JP, Flaig TW,  Zurita- Saavedra AJ,  Mack PC,  Vaishampayan U,  Stella PJ,  Smith D, Bolton S,  Hussain A,         l-Janadi A,  Silbiger DR ,  Usman M ,  Ivy SP. Phase II Multicenter Randomized Trial of Docetaxel Plus Prednisone With or Without Cediranib in Men with Chemotherapy- Naive Metastatic Castrate-Resistant Prostate Cancer. The Oncologist, 24(9):1149-e807,

Heyza JR, Lei W, Watza D, Zhang H, Chen W, Back JB, Schwartz AG, Bepler G, Patrick SM. Identification and Characterization of Synthetic Viability with ERCC1 Deficiency in Response to Interstrand Crosslinks in Lung Cancer. Clin Cancer Res. 15;25(8):2523-2536. 2019  PMID: 30538112; PMC6467763.

Lusk CM, Watza D, Dyson G, Craig DB, Ratliff V, Wenzlaff AS, Lonardo F, Bollig-Fischer A, Bepler G, Purrington KS, Gadgeel S, Schwartz AG. (2019) Profiling the mutational landscape in known driver genes and novel genes in African American non-small, cell lung cancer patients. Clin Cancer Res. 2019 Apr 12. pii: clincanres.2439.2018. PMID: 30979741.

Modi D, Surapaneni M, Kim S, Ayash L, Alavi A, Ratanatharathorn V, Deol A, Uberti JP. Allogeneic stem cell transplant provides durable response in peripheral T-cell lymphoma. Leuk Res. Article 106171. 2019. PMID: 31228653;  PMCID: PMC6849390.

Paul AG, Nalichowski A, Abrams J, Paximadis P, Zhuang L, Miller S. Dosimetric evaluation of Point A and volume-based high-dose-rate plans: a single institution study on adaptive brachytherapy planning for cervical cancer J Contemp Brachytherapy. 10(3):202-210. 2018 PMID: 30038639;  PMCID: PMC6052381.

Teslow EA, Mitrea C, Bao B, Mohammad RM, Polin LA, Dyson G, Purrington KS, Bollig-Fischer A. (2019) Obesity-induced MBD2_v2 expression promotes tumor-initiating triple-negative breast cancer stem cells. Mol Oncol. 2019 Apr;13(4):894-908. PMID: 30636104.

Tien AC, Li J, Bao X, DeRogatis A, Kim S, Mehta S, Sanai N. A Phase 0 Trial of Ribociclib in Recurrent Glioblastoma Patients Incorporating a Tumor Pharmacodynamic- and Pharmacokinetic-Guided Expansion Cohort. Clin Cancer Res.25(19):5777-5786. 2019 PMID: 31285369.

Vaishampayan U, Podgorski I,  Heilbrun L, Lawhorn-Crews J,  Dobson K,  Boerner J, Stark K,  Smith D,  Heath E,  Fontana J, Shields A. Biomarkers and Bone Imaging Dynamics Associated with Clinical Outcomes of Oral Cabozantinib Therapy in Metastatic Castrate Resistant Prostate Cancer. Clinical Cancer Research, 25(2):652-662,. PMID: 30327304 PMCID: PMC6335157

Contact

Judith Abrams, Ph.D.
Director, Biostatistics and Bioinformatics Core
abramsj@karmanos.org

Wei Chen, Ph.D.
Biostatistician
chenw@karmanos.org

Greg Dyson, Ph.D.
Biostatistician
dysong@karmanos.org

Lance Heilbrun, Ph.D.
Assistant Director
heilbrun@karmanos.org

Seong Ho Kim, Ph.D.
Biostatistician
kimse@karmanos.org

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