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TCAG Facilities

Statistical Consulting Services

Please see our terms of use.

1. Statistical Consulting Service Overview

The TCAG statistical consulting service can provide a wide range of advice and assistance:

• advice on study design and analytical planning
• sample size and power calculations
• statistical analysis of study data
• interpreting and summarizing results
• assistance for writing grant proposals.

We are always interested in expanding our knowledge into new data types.

2. Genetic Analysis

• Design and analysis of genetic linkage mapping studies
  • single gene disorders or complex diseases
  • discrete or quantitative traits
  • evaluation of covariate effects on linkage signals
  • mapping in natural or experimental crosses
• Association studies of quantitative and discrete traits
  • family-based control design
  • case-control design
  • population stratification
  • single marker or multi-marker associations
  • genome-wide association analysis
• Estimation of haplotypes in related or unrelated individuals
• Power calculations

3. Microarray Gene Expression Analysis

• Experimental design
  • sample size and power calculations
• Analysis of data from various platforms (e.g. Affymetrix, exon arrays, Illumina, others)
  • pre-processing (normalization, filtering, QC metrics, visualizations, etc.)
  • identification of differentially expressed genes
• time course studies
• multiple experimental factors and/or interactions
  • clustering and class prediction
  • limited pathway and gene function analysis
• Multiple hypothesis testing (e.g. control of false positive and false negative rates)
• MicroRNA data analysis
• Alternative splicing data analysis
• Data integration across platforms and laboratories

4. Copy Number Variation Analysis

• Analysis of data from different platforms (aCGH, BAC or Agilent oligonucleotide arrays, Affymetrix/Illumina SNP arrays)
• Identification of regions containing copy number changes
• Testing for differences in frequency of copy number changes between groups

5. Next Generation Sequence Data Analysis

• Alignment, genome assembly, genome annotation, etc.
• Variant detection (SNPs and structure variants)
• Identification of enriched regions
• Differential analysis of transcript read counts for expression profiling

6. Genome-wide Epigenetic and Epigenomic Analysis

• Design and power analysis of epigenetic/epigenomic studies
• Identification of epigenetic/epigenomic signatures
• Chromatin mapping
• Identification of small RNAs

7. Human Microbiome and Metagenomic Analysis

• Metagenomic assembly
• Function analysis of microbiome
• Biomarker discovery from microbiome data
• Association analysis of host genomic variants with its microbiome

8. Other Data Types

We can provide advice and perform analysis for a wide variety of other data types not listed above. Some examples are:

• Annotation of uncharacterized gene functions
• Enrichment analysis of gene sets
• Pathway analysis
• Proteomic data
• Epidemiological studies

Please contact the facility for details.

9. Statistical analysis tools/software

We use the tools and software which include state-of-the-art, well-compared, widely-adopted and transparent methods for data analysis. Examples of these can be found at www.bioconductor.org, http://www.nslij-genetics.org/soft/ and http://probability.ca/cran/.

We have installed Matlab on our cluster (http://ccm.sickkids.ca) with the following major toolboxes:

• Matlab
• Bioinformatics
• Statistics
• Optimization
• Parallel Computing
• 8 distributed Servers

Users who would like to use this software will be required to pay a project-based or an annual based fee. Pease contact the facility for details.

In addition, we have a series of commercial software for different types of data analysis: GeneSpring, SpotFire, Stratagene, Partek and Ingenuity Pathway Analysis, etc.

10. Statistical and Software Training

We provide statistical and software training primarily in one-to-one or small group (e.g. from a specific lab or project) settings. We provide tutorials or workshops for specific approaches and software to larger groups as needed. For more information, please contact the facility.

11. Statistical Analysis Pricing

The Statistical Analysis Facility provides consultative services at varying rates depending on project scope:

• hourly basis: $70 per hour
• Weekly or monthly basis. Applicable for long term projects requiring dedicated personnel (e.g. genome-wide association analysis). Please contact the facility for details.

Download the Statistical Analysis Consulting Form (Acrobat 39 KB)

For a free initial consultation and estimate, please contact the facility.

12. Support Letter

We will gladly provide investigators with a letter of support stating our willingness to assist you in grant applications. Please contact the facility.

• Study design
• Sample size and power calculation
• Write statistical analysis plans
• Provide a letter of support

13. Publications by Statistical Facility

• Selected methodology publications by Statistical Facility staff
• Selected publications by Statistical Facility users (Co-authored or Acknowledged)
• Conference abstracts and presentations

14. Facility Contact