Technology Overview
iScan BeadArray
Illumina iScan System utilizes BeadArray technology for a broad range of DNA analysis applications including genotyping and methylation studies. The 3-micron silica beads are assembled in microwells on slide with high density, enabling multi-sample analysis per slide. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in one of Illumina’s assays. Different combinations of probe design enable a wide range of applications on a whole-genome scale, including gene- and exon-level analysis, genotyping and resequencing.
The iScan platform at the Core can perform the following analyses:
- Whole genome SNP genotyping
- Whole genome methylation analysis
- Whole genome copy number variation (CNV) analysis
- Custom SNP genotyping
A typical iScan BeadChip experiment (Infinium) includes the following steps:
- Preparation of DNA isolated from specimens
- Hybridization of sample to BeadChips
- Stringent washes, single base extension, staining and imaging of BeadChips
- Analysis of scanned images and data extraction
For details of iScan BeadArrayTechnology and products, please visit Illumina iScan website.
Service Charges and Ordering
CPOS Genomics Core provides the following services
- Illumina Infinium Genotyping assay
- Illumina Infinium Methylation assay
Service charge will depend on sample size and analysis type. Please enquire.
Service charge usually includes
Pre-service advice and discussions
Sample processing, hybridization and scanning (consumables and labour included)
Data QC and delivery
Service Ordering
Please refer to Sample Preparation and Requirement section for sample requirements.
Please submit service request through iLab.
Sample Preparation and Requirements
Preparation of DNA samples for genotyping and methylation analysis
Please consult platform specialist before sample preparation.
For Genotyping
Isolate DNA using high quality purification reagents/kits and dissolve/elute DNA in TE buffer (10 mM Tris, 1 mM EDTA), pH 8.0.
DNA Sample Quality and Quantity requirements
- Double-stranded, non-degraded high quality DNA*
- Fragment sizes of at least 2 Kb
- A260/280 = 1.8-2.2
- Concentration MUST be normalized to 50 ng/uL**
- Minimum 15 uL**
- Dissolved in TE buffer(10 mM Tris, 1 mM EDTA), pH 8.0
* Whole Genome Amplified DNA is not recommended.
** Accurate quantification is critical.
Users are highly recommended to determine sample concentration by fluorometric assay, e.g. use picogreen assay or Qubit. Alternative indirect methods such as UV spectrometry/NanoDrop can incorrectly report the concentration of dsDNA in your sample when single-stranded DNA, oligonucleotides, RNA, and/or proteins carried over from DNA extraction are present in the samples. If these latter methods are used, it is safer to submit 20uL of DNA at 150 ng/uL for Qubit measurement.
Normalized samples should be stored at -80oC until sample submission.
For Methylation Analysis
Isolate DNA using high quality purification reagents/kits and dissolve/elute DNA in TE buffer (10 mM Tris, 1 mM EDTA), pH 8.0.
DNA Sample Quality and Quantity requirements
- Double-stranded, non-degraded high quality DNA*
- Fragment sizes of at least 2 Kb
- A260/280 = 1.8-2.2
- Dissolved in TE buffer(10 mM Tris, 1 mM EDTA), pH 8.0
* Whole Genome Amplified DNA is not recommended.
For methylation analysis, sample quantity requirement depends on sample size. Please consult.
For both genotyping and methylation analysis, please examine DNA quality also on 0.8% agarose gel along with proper size marker (with good resolution).
Retain a softcopy of gel photo to be emailed to platform specialist.
Below is an acceptable example of gel photo:
Sample Submission
Submission of DNA samples for genotyping and methylation analysis
**For custom Beadchip service, please contact Dr CHAN, Agnes (2831-5427) before sample submission.
For Genotyping Analysis
- Check that all samples meet requirements.
- Email sample information (sample ID, A260/280 ratio) and gel photos to platform specialist.
- When notified by platform specialist that all samples pass QC, download and fill in “iScan sample layout for genotyping“. Arrange samples down the column, i.e. if 8 samples/chip, use A1-H1; if 12 samples/per chip, use A1-D2; and continue in E2 and so on. Completely fill in sample layout, sample ID and A260/280 ratio.
- Submit service request through iLab. Attach iScan sample layout spreadsheet after creating the service request.
** Use 1 sample layout spreadsheet for each sample plate submitted.** - Transfer 15 uL of DNA samples (50 ng/uL) to 96-well skirted plate according to sample layout spreadsheet.
- Label CLEARLY on the side of the skirted 96-well PCR plate with your name, date and plate ID.
- Seal plate tightly with good adhesive film. Make sure there is no leakage.
- Contact platform specialist for sample submission arrangement.
- Bring the sample plate ON ICE to CPOS Genomics Core.
For Methylation Analysis
- Check that all samples meet requirements. (Sample quantity requirement depends on sample size. Please consult.)
- Download and fill in “iScan sample submission for methylation“.
- Submit service request through iLab. Attach iScan sample submission for methylation after creating the service request.
- Transfer DNA samples in tubes with clear labelling of sample ID.
- Contact platform specialist for sample submission arrangement.
- Bring the sample tubes ON ICE to CPOS Genomics Core.
Data Collection
Processing Time
Time for completion of service may vary depending on the number of samples submitted and the level of service demand at sample submission.
Samples will be put in a processing queue as soon as the samples, BeadChip kits and other reagents are all ready.
Estimated completion date will be informed at time of sample submission.
Data Delivery
Upon completion of your experiment, you will receive an email notification with procedure for online data download.
Please secure your own copy of data.
Data Analysis Support
Users of our iScan platform are entitled to use the Data Analysis Workstation for downstream data analysis at no extra cost.
In-person software tutorials are available.
GenomeStudio Software 2011.1 (for methylation analysis) and 2.0.5 (for genotyping analysis) license keys for all modules are now available on Illumina website for download.
Terms of Service
Special notes
- Centre for PanorOmic Sciences (CPOS) has no obligation for failure of experiments if users fail to follow the instructions given and/or provide sufficient information to our staff.
- Users have the responsibility to perform quality control on their DNA samples. Centre for PanorOmic Sciences (CPOS) has no obligation for failure of experiments due to sample mix up and/or degradation of DNA samples.
Turnaround time
Turnaround time will be informed at time of sample submission, dependent on job queue.
In case of unforseeable delay, users will be contacted immediately.
Leftover Samples
After the completion of the experiment, DNA samples will be kept for 30 days.
Users are welcome to collect any leftover materials during this period, after which, the materials will be discarded without further notice.
Please contact platform specialist for pick-up arrangement.
Useful Links
For more information
Contact
Ms FUNG, Joyce
Ms LAM, Levina
