Services

We are able to deliver you extracted samples, high throughput genotyping data, high throughput sequencing data, biostatistics and NGS bioinformatics analyses. We are Illumina Service Provider (CSPro) for sequencing on NGS equipments.

Extractions

  • DNA extractions on Qiagen Autopure LS : Available volumes to be extract : 1-5ml ; 5-10ml ; 10-20ml
  • RNA extractions on Qiagen QiaCubbe

Jellyfish of DNA in suspension © F.Viala/CNRS Photothèque

Genotyping / Expression

  • Taqman Probes SNP genotyping on Roche LightCycler 1536 or Lifescience Viia7
  • SNP Genotyping on Fluidigm Biomark with SNPtype assays
  • Highthrouput genotyping on Illumina IScan
  • Taqman Probes for expression study on Lifescience Viia7
  • Solaris Probes for expression study on Fluidigm Biomark

Illumina chips for genotyping or expression studies.

SNP genotyping scatter plot : genotype distribution as clusters after analysis

NGS Sequencing

Libraries preparation for High throughput sequencing:

  • Whole Exome libraries using NimbleGen kits (SeqCap EZ MedExome Roche) and automation on Starlet (Hamilton)
  • Genome libraries for sequencing on Illumina HiSeq4000
  • Targeted sequencing libraries for sequencing on Roche GS Junior, Illumina HiSeq, Illumina NextSeq, Illumina Miseq
  • Other kinds of libtraries on demand.

Profiles obtained via Bioanalyzer, DNA1000 chip – These libraries were fragmented on Bioruptor (Diagenode) and prepared via the T-Storm (Raindance). They are ready for targeted sequencing via Hiseq2500 or Miseq.

Next Generation Sequencing (NGS) using Illumina HiSeq4000, NextSeq500, HiSeq2500, MiSeq

From a few months, we have added new NGS equipments in our lab : HiSeq4000 and NextSeq500, Illumina. These equipments allow us to offer you three sequencing modes: the ultra high, the high and the medium throughput sequencing modes. Whatever the method chosen, any types of libraries are susceptible to be sequenced on the HiSeq: Exomes, small RNA, total RNA, mRNA, MethylSeq, ChipSeq, amplicons, genomes, RAD… We are certified for sequencing on Illumina NGS equipments.

illumina-propel

 

The Sequencing Analysis Viewer tool (Illumina) allows the visualization of the sequencing quality parameters during a run or at the end of a run on HiSeq, NextSeq or MiMeq.

A 1: flow cell chart displays color-coded quality metrics per tile for the entire flow cell (8 lanes in this picture); 2: Cycle plot displays plots that allows to follow the progression of quality metrics during a run, each base is color-coded; 3: QScore distribution: allows to visualize the number of reads by quality score. The quality score is cumulative for current cycle and previous cycles and only reads that pass the quality filter are included; 4: Lane plot: the data by lane pane displays plots that allows to view quality metrics per lane; 5: QScore Heatmap : displays plots that allows to view the QScore by cycle. B Imaging tab: displays in detail a section of a flow cell. Various quality parameters can be analyzed (density of clusters pass clusters, error rate (determined by alignment with PhiX)…).

 

Overview of a sequencing run on Hiseq / Image of a section of a flow cell

Bioinformatic and bio-statistics analyzes

  • Bioinformatics analysis of high-throughput sequencing data :
    Whole exome :
    We offer different levels of analysis :
    • Level 1: Data FastQ and reporting.
    • Level 2: Data FastQ, List of SNPs and Indels with a depth filter of 8, BAM file, statistical reporting.
    • Level 3:
      • FastQ and BAM Files,
      • List of the SNPs with additional notes: gene, consequence (missense, stop lost, etc…), id swissprot, amino acid change, description of the gene, dbSNP hg19 (rs), frequencies with Complete Genomics, frequencies with 1000 Genomes, functional predictions for non-synonyms coding SNPs, MIM disease, pathway, expression, interactions,
      • List of the Indels with additional notes: concerned gene, consequence (frameshift, etc…), id swissprot, amino acid change, description of the gene, dbSNP hg19 ( rs ), frequency Complete Genomics
      • Statistics, report
    • Level 4: ON REQUEST (ex: comparative study between individuals, compared with genotyping data, segregation studies …).
  • Bio-statistical analyses:
    We offer you different analyzes that can be chosen independently each other :
    • RNA seq data:
      • 1: Analysis of differential expression (normalization and comparison of two or more conditions) + results annotation.
      • 2: Identification of (alternative) splicing sites.
    • SNP array data:
      • 1: Genome-wide association study, results annotation (gene + literature).
      • 2: Imputation of genotypes from a reference panel.
      • 3: Study enrichment of association signal in a set of genes (metabolic pathway, candidate genes, list of differentially expressed genes, etc.).
      • 4: Detection of chromosomal alterations (duplication, deletion and homozygosity mosaics regions, etc.).
    • NanoString data:
      • 1: Data quality control (raw, standardized data and reporting).
      • 2: Differential expression analysis.
         

 

 

 

 

Sequence alignment from high throughput sequencers after use of Integrative Genomics Viewer tool