Yale Cancer Center Bioinformatics Services

Purpose and Scope
The bioinformatics service is a function of YCAS which serves as the Biostatistics Shared Resource for the Yale Cancer Center (YCC). The services encompass bioinformatics support to YCC members on study designs, analysis, and grant and manuscript preparations. We aim to provide high-quality, cutting-edge and custom data analyses, as well as consultation and training/education for high throughput genomics, transcriptomics, proteomics, and other high-throughput data sets.

Services

• Array-based platforms, including genotyping arrays, gene expression arrays, copy number arrays, methylation arrays, and ChIP-on-chip arrays
• Analysis of next-generation sequencing data, including:
  • DNA-sequencing analysis, such as single nucleotide variations, indels, copy number variations, translocations and inversions from whole-exome and whole-genome DNA sequencing (DNA-seq)
  • Gene expression, splice variants, gene-set, and pathway analysis from RNA sequencing (RNA-seq)
  • microRNA expression from microRNA sequencing (miRNA-seq)
  • DNA methylation and differential methylation identification from methylation sequencing (methyl-seq)
  • Transcription factor binding sites and chromatin modifications from ChIP sequencing (ChIP-seq)
  • RNA binding sites identification from CLIP sequencing (CLIP-seq)
• Proteomics data analysis
• Data annotation, visualization, and database integration
• User training in bioinformatics software and tools

Fees
We provide supports for cancer-related projects. All Yale Cancer Center (YCC) members are entitled to receive free support for all non-billable services, and a maximum of 4 hours free support per year. Non-YCC members receive free support for non-billable activities, but need to pay for all billable activities. YCC members receive priority over nonmembers.
Non-billable activities: work on grant preparation, including analysis of pilot studies, provided the member of the YCAS Bioinformatics Core is written into the grant as percent FTE.
Billable activities: include all other services
Fees: $121/hour for FY15.

Time estimation

• The following estimation assumes no complications (e.g., quality issues) with the data. The actual analysis time heavily depends on data complexity.
• Turn-around time will depend on the work load.
• For sequencing data, the service is divided into two parts: hands-on time and computer time. The computer time is estimated with moderate coverage data based on an 8-CPU server. Actual computing time will vary from days to weeks depending on sequencing depth and server condition.

Array-based

	gene/miRNA expression	Chip-on-chip	Methylation array
Array-based	4 hours/comparison	4 hours/sample	4 hours/sample

DNA-seq

		Mapping	Indel/SNP calling	CNV
Whole-exom	Hands-on time	2 hours/sample	2 hours/sample	2 hours/sample
	Computer time	6-8 hours/sample	3-4 hours/sample	4 hours/sample
Whole-genome	Hands-on time	3 hours/sample	3 hours/sample	3 hours/sample
	Computer time	200 hours/sample	100 hours/sample	100 hours/sample

Methyl-seq

		Mapping	Methylation calling	Differential methyaltion
Targeted (RRBS)	Hands-on time	2 hours/sample	2 hours/sample	2 hours/sample
	Computer time	6-8 hours/sample	3-4 hours/sample	4 hours/sample
Whole-genome	Hands-on time	3 hours/sample	3 hours/sample	3 hours/sample
	Computer time	200 hours/sample	100 hours/sample	20 hours/sample

RNA-seq

	Mapping	Gene expression	Pathway/gene-set	Splice analysis
Hands-on time	4 hours/comparison	2 hours/comparison	1 hours/comparison	2 hours/sample
Computer time	1-2 days/comparison	10 hours/comparison	1 hour/comparison	4 hours/sample

Chip-seq

	Mapping	Peak calling	Differential binding analysis	Motif analysis
Hands-on time	2 hours/sample	2 hours/sample	2 hours/comparison	2 hours/sample
Computer time	5 hours/sample	2 hours/sample	4 hour/comparison	2 hours/sample

CLIP-seq

	Mapping	Differential binding analysis	Motif analysis
Hands-on time	2 hours/sample	2 hours/comparison	2 hours/sample
Computer time	5 hours/sample	4 hour/comparison	2 hours/sample