Advanced Bioinformatics Solutions

With our broad expertise in the life sciences, Ambry’s bioinformatics offers state-of-the-art computational solutions to help our clients manage and interpret large clinical and research datasets, including those from next-generation sequencing, microarray, and protein assays. Our comprehensive and highly customizable services include many aspects of the research process from study design and initial data collection, to quality control and data management, to advanced interpretation using approaches such as computational modelling and machine learning.

Genomics, Transcriptomics and Epigenomics Solutions

Employing cutting edge bioinformatics tools, machine-learning methods and human genetic databases, the bioinformatics team offers end-to-end solutions for genomic, transcriptomic and epigenomic data analysis including:

• Raw sequencing data quality analysis
• Data management
• Variant detection from targeted, whole-exome and whole-genome sequencing data
• Microsatellite instability (MSI) analysis
• Differential gene expression (Figure 1A)
• Gene ontology (GO) and pathway analysis (Figure 1B and 1C)
• Gene network analysis
• Alternative splicing detection (Figure 2)
• Novel transcript discovery
• Long non-coding RNA (lncRNA) detection
• Chromatin immunoprecipitation sequencing (ChIP-Seq) analysis (Figure 3)
• Whole genome bisulfite sequencing (WGBS) analysis

Figure 1. (A) Heatmap representation of differentially expressed genes in ER/PR/HER2 triple negative (ER-/PR-/HER2-), ER/PR/HER2 positive (ER+/PR+/HER2+) and HER2+ positive breast cancers when compared with normal breast tissues. GO analysis of (B) highly expressed (cluster 1) and (C) lowly expressed (cluster 2) genes as shown in Figure 1A.

Figure 2. Exon skipping in the SPAG9 gene in HER2+ positive breast cancer. SPAG9 transcripts are shown on the bottom.

Figure 3. Histone H3K4me3 and H3K27ac profiles at HOXA locus in normal breast cells, ER negative (ER-) and ER positive (ER+) breast cancer cells.

Statistical Genetics Solution

Our highly trained statistical and clinical research scientists bring more than two decades of combined experience in study design and statistical analysis. Our highly skilled team provides a broad range of statistical services including personalized expert review and consultation for study design, data analysis and report generation.

• Experimental and observational design
• Technology selection
• Feasibility assessment
• Power and sample size calculation
• Protocol preparation
• Clinical data analysis
• Data consolidation, curation, annotation and visualization
• Summary of results and report generation

Proteomics Solutions

Ambry Genetics offers proteomics solutions by characterizing and analyzing genetic data in the context of protein structures. Structural analysis can be used to screen potential biomarkers for susceptibility to genetic variations in general populations and disease cohorts. Combining with genomics and statistics solutions, we offer the competitive edge in patient stratification, pharmacogenomic associations, and biomarker discovery.