Pre-processing & Quality Control of Raw Data

  • Pre-processing includes de-multiplexing of raw sequence data into the fastq format. Quality assessment of raw sequence reads, including per base-quality check, replication and adapter content control.
  • If needed, we also offer further data pre-processing steps, including adapter clipping, quality trimming and read filtering
  • Diagnostic plots and quality statistics are provided with each analysis

DNA Re-Sequencing (Genome, Exome, Diagnostic Exome, Amplicon-Based Panels)

  • The standard data analysis of DNA resequencing projects includes:
    • Pre-processing of reads (adapter trimming, quality trimming)
    • Mapping of reads to the reference genome
    • Variant calling and genotyping (single nucleotide variants and small insertions/deletions)
    • Annotation of variants with information from public databases
    • Basic filtering of variant lists based on annotated information from public databases and our in-house variant database
    • Quality control of raw data, mapped reads and variant lists
  • Data delivery:
    • Raw data (fastq format)
    • Mapped reads (bam format)
    • Variant lists (VCF format)
  • Upon request we can perform these secondary data analyses:
    • Somatic variant calling from tumor or from tumor-normal pairs
    • Trio analysis
    • Analysis of large insertions/deletions by copy number
    • Other custom secondary analyses

Mate-Pair Sequencing

  • The analysis of mate-pair sequenced reads includes mapping of the pre-processed sequencing reads to a desired reference genome
  • Filtering of high-quality uniquely mapping reads
  • Detection of small insertions and deletions as well as single nucleotide variations
  • Detection of structural variations, such as large insertions, deletions, or other structural rearrangements
  • Data delivery
    • Raw sequencing data in fastq format
    • Pre-processed sequencing data in fastq format
    • Structural variant lists in text-based format
    • List of small variants (small insertions/deletions and single nucleotide variations) in the VCF file format
    • For each analysis a report in PDF format is provided with detailed information on the different analysis steps, tools used in the processing and results from the applied methods.

RNA Sequencing

  • Mapping of pre-processed sequencing reads to a predefined reference genome
  • Read counting of mapped reads based on predefined genome annotations
  • Normalization of read counts for comparative analyses, applying RPKM, FPKM or CPM normalization
  • Additional quality assessment of normalized read counts, including sample correlation analysis, read count distribution analysis, as well as principal component analysis
  • Fold-change based identification of differentially expressed transcripts/genes
  • Statistical assessment of differential expression with subsequent multiple testing correction
  • Time Series Data Analysis
    • Statistical assessment of differences between time points as well as between different time series
    • Visualization of time series data
  • Data Mining
    • Supervised and unsupervised clustering as well as cluster quality assessment
    • Gene mining
  • Gene Ontology (GO) Enrichment Analysis
    • Annotation of transcripts/genes with GO IDs and GO terms
    • Statistical assessment of overrepresented GO categories
    • Visualization of overrepresented GO categories and their hierarchical relationships
  • Ingenuity based Pathway Analysis (IPA)
    • Identification of canonical pathways
    • Upstream regulator analysis
    • Analysis of biofunction and impact on disease status
  • Detection of alternative splicing events and differential expression of alternatively spliced transcripts
  • Detection of gene fusion events
  • Data delivery
    • Raw sequencing data in fastq format
    • Pre-processed sequencing data in fastq format
    • Quality control package, including diagnostic visualizations and statistics in text-based format
    • Mapped sequencing reads in bam format
    • Raw and normalized read count tables in text-based format
    • Lists of differentially expressed transcripts/genes in text-based format
    • Data package for data mining applications, including lists of transcripts/genes as well as high quality visualizations
    • Lists of enriched GO categories and the contained differentially expressed transcripts/genes in text-based format
    • Data package for pathway analysis, including lists of genes and high quality plots
    • List of alternatively spliced and differentially expressed transcripts and visualization and annotation of potentially new splice sites
    • List of detected gene fusion sites in text-based format
    • For each analysis a report in PDF format is provided with detailed information on the different analysis steps, tools used in the processing and results from the applied methods.

Whole Genome Methylation Sequencing / Reduced Representation Bisulfite Sequencing

  • Extraction of methylated sites
  • Filtering for static methylation differences between sample groups
  • Statistical assessment of differential methylation as well as multiple testing correction
  • Association of methylation sites with their respective genes
  • Gene Ontology (GO) Enrichment Analysis of differentially methylated genes
    • Annotation of differentially methylated genes with GO IDs and GO terms
    • Statistical evaluation of overrepresented GO terms
    • Visualization of overrepresented GO group hierarchies
  • Ingenuity based Pathway Analysis (IPA)
    • Identification of canonical pathways
    • Upstream regulator analysis
    • Analysis of biofunction and impact on disease status
  • Data delivery
    • Raw sequencing data in fastq format
    • Pre-processed sequencing data in fastq format
    • Quality control data package, including diagnostic plots as well as quality statistics in text-based format
    • Mapping results in bam format
    • List of methylation sites in text-based format
    • List of differentially methylated sites with gene annotations in text-based format
    • Data package for GO enrichment analysis, including lists of enriched GO categories contained differentially methylated genes
    • Data package, including lists and plots for pathway based analyses
    • For each analysis a report in PDF format is provided with detailed information on the different analysis steps, tools used in the processing and results from the applied methods.