High-resolution molecular karyotyping with around 750,000 markers; detects CNVs, ROH and mosaicism.
Direct
About this service
PlatformAffymetrix GeneChip (CytoScan)
Data provided
Original signal intensities (CEL file), experiment file (ARR file) and QC report.
CYCHP files (generated by Chromosome Analysis Suite).
Standard report with significant segments (hg38): minimum genomic segment size 1 Mb for losses, 2 Mb for gains; Whole Genome View; KaryoView; segments table.
Upon request further bioinformatic analyses are available (additional cost will apply).
Workflow
Quality and quantity control of each DNA sample by gel electrophoresis and Nanodrop.
Sample preparation including restriction digestion, adapter ligation, PCR, fragmentation and labeling. During processing, success of the PCR and fragmentation is assessed by gel electrophoresis (QC gel 1 and 2). A positive control per batch ensures process quality; a negative control excludes DNA contamination.
Hybridization, dyeing, washing, and scanning of the appropriate ThermoFisher/Affymetrix microarray.
Generation of CYCHP files using the Affymetrix software Chromosome Analysis Suite.
Service-specific terms
If DNA samples do not pass the QC, a set-up fee of 25.- EUR per sample will be charged.
If the extracted DNA does not meet the sample requirements for the service, only the cost of DNA isolation will be charged. Further agreements and additional costs may apply.
Additional costs for data media (e.g. hard drives or usb drives) and delivery are not included and will be charged accordingly.
The assay requires at least 50 ng/µL, recommended input 250 ng; please send at least 500 ng at 50 ng/µL or above.
The cartridge CytoScan assay requires a concentration of at least 50 ng/µL; the recommended input is 250 ng, i.e. 5 µL at 50 ng/µL (Thermo Fisher, CytoScan Assay User Guide).
Please send at least 500 ng per sample at 50 ng/µL or above, i.e. at least 10 µL. The surplus covers intake QC and allows a repeat run without resubmission.
Dissolved in reduced-EDTA TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). High EDTA and residual salts inhibit the enzymatic steps.
Concentration determined fluorometrically (Qubit or PicoGreen). DNA must be double-stranded -- no boiling or strong denaturants. RNase treatment during extraction is recommended, as RNA distorts photometric readings.
Not degraded: a strong main band at roughly 10 to 20 kb on an agarose gel.
Free of polymerase inhibitors, in particular heme from blood and chelating agents. OD260/280 between 1.8 and 2.0, OD260/230 above 1.5; please clean up samples below these values before shipping.
Ship chilled or at ambient temperature; dry ice is not required for purified DNA.