Polymorphism analysis by DNA chip
The platform offers a single nucleotide polymorphism (SNP) analysis service based on Illumina’s BeadArray technology. This technology allows the genotyping of the entire genome as well as the profiling of genes and exons.
A wide choice of genotyping chips is available in humans based on the size, number of samples, location of genetic variation and allele frequency. The Illumina’s BeadChip with customized or standard contents are designed to interrogate simultaneous 300,000 to 5 million loci (SNPs and indels) in format of 4, 8 or 24 samples.
These chips not only provide information on the genotype of the SNP but also on the copy number variation (CNV) which may reveal chromosomal abnormalities.
The average genotype detection success rate is 98% or higher.
- DNA quantification and validation
- Hybridization on Illumina’s chips (according to the projects)
- Quality controls of the generated data
- Raw intensity file (.idat format)
- Final report of genotyped SNPs per sample (.txt format)
- GenomeStudio project report (.bsc format)
- Sample sheet corresponding to the sample repartition on the chip (.csv format)
- Chip decoding file (.dmap format)
- Manifest corresponding to the SNP analysis probes on the chip (.bpm format)
Illumina’s chips catalog : https://emea.illumina.com/products/by-type/microarray-kits.html
Methylation analysis by DNA chip
The platform offers methylation analysis services based on Illumina’s BeadArray technology.
The purpose of this analysis is to measure, after bisulfite conversion, the methylation levels of CpG sites distributed throughout the genome by quantitative genotyping using Illumina Infinium Methylation EPIC (850K) chips. The number of samples analyzed in parallel by this chip is 8 samples.
These Bead chips are compatible for an analysis from the genomic DNA or DNA coming from paraffin’s blocks (FFPE) and require 500 ng DNA measured by fluorimetric assay and not amplified samples.
In the case of FFPE tissues, methylome’s study remains a challenge. Indeed, the extracted DNA from these tissues are often degraded due the fixation and inclusion condition. In order to make this source of material compatible with Illumina chips, a protocol optimization is introduced to improve the quality of FFPE DNAs and therefore the reproducibility of the method.
The CpG detection success rate is on average equal to or higher than 96 % in the case of genomics DNA. The rate is higher than 90 % for DNA extracted from non-tumor FFPE tissues.
- DNA quantification and validation
- Bisulfite treatment, quantity controls after conversion
- DNA restauration in the case of FFPE tissues
- Hybridization on Illumina’s Infinium methylation EPIC (850 K) array
- Quality controls of the generated data
- Raw intensity file (.idat format)
- Final report of methylated and non-methylated cytosines (.txt format)
- GenomeStudio project report (.bsc format)
- Sample sheet corresponding to the sample repartition on the chip (.csv format)
- Chip decoding file (.dmap format)
- Manifeste de répartition des sondes de méthylation sur la puce (format .bmp)
Infinium Methylation EPIC array https://emea.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html
In practice: don’t hesitate to contact us to learn more at medecine-p3s@sorbonne-universite.fr or at 01.40.77.81.32