How to Obtain Services & User Fees

Services and User Fees

NextGen sequencing analysis
Advanced Ingenuity/Biological Network analysis

For all questions regarding analyses and charges, please contact Andrew Kossenkov, Ph.D., 215-495-6898.


CC Members & Affiliates

Non-Wistar Academic


Customized Bioinformatics Service

- High level analysis

- Paper/grant support

- Algorithm development

- Web applications

- Any additional/custom analyses



Sequencing data preprocessing

Raw data transfer/management



DNA-seq (CHIP,SNP: Exon, Whole-genome)






Microarray data preprocessing

Raw data transfer/management



Quality control/normalization




Data analysis

Statistical differences between conditions, functional enrichments, etc.


2 groups

- e.g. control vs. experimental




3 groups

- Pairwise comparisons, overlaps between results




4 groups or more

- Multi-group clustering




NextGen Sequencing Data Analysis

Sample quality is assessed using Illumina base call summary, IVC plots, error graphs, etc.

Sequence data analysis will include:

  1. Primary Analysis: Sequence file in fastq format with base call summary and quality assessment.
  2. Secondary Analysis: Alignment file in bed format with summary of alignment, including quality of alignment.
  3. Tertiary Analysis (single or two sample analysis with background statistical model): UCSC browser up-loadable Peak file in bed format, wiggle file in wiggle file format, enrich region in bed format with summary of peaks.
  4. Genomic Annotation: 
  • Peaks annotate to genes; each peak is annotated to closest up and downstream gene.
  • Peaks annotate to any other binding sites; each peak is annotated to any other customer suggested binding sites. For this purpose, data will be downloaded from NCBI short read archive and processed as required.
  • Two samples’ peak comparison also provided.

All analyses will include detailed description of each stage and summary. At different stages of the analysis, customers will be contacted to discuss the progress.


Microarray Data Analysis

Pre-analysis consult (email/in person) is required before analysis is started.

Microarray data analysis and report include:

  1. Preprocessing: Data extraction, normalization, filtering
  1. Quality control: Data issues, technical and sample outlier detection, experimental genes check
  1. Group comparisons:
  • Significant genes
  • Heatmaps
  • DAVID functional analysis
  • Basic core Ingenuity pathway analysis
  • Gene overlap between multi-comparisons
  1. Result files delivered:
  • Raw expression data file
  • Normalized expression data file      
  • Gene list files
  • P-values, fold changes, etc.
  • Function/pathway enrichment files
  • PowerPoint report with results and all steps of the analysis
  • Post-analysis meeting to discuss/explain the results 

Advanced Pathway Analyses

Advanced pathway analyses include but are not limited to:

  • Biomarkers, toxicity, comparison, new pathway, metabolite analyses
  • Search and network growth by target name, drug, or disease
  • Integration of transcription factors with gene regulation (available late 2011)
  • Combined mRNA and miRNA expression analyses using validated (TarBase) and non-validated targets
  • Comprehensive literature overview with molecular relationships by target
  • Comprehensive clinical trial matrix within specific target/disease area

Basic training in use of Ingenuity and DAVID will be offered depending on interest.


For all questions regarding analyses and charges, please contact Andrew Kossenkov, Ph.D., 215-495-6898.