Description
Material provided: data
Unit definition: bioinformatics support for raw sequencing data for 15 samples – ca 15M per sample
Short Description: Since May 2022, cases of Mpox have been reported in several countries where the disease is not endemic. The etiological agent is the Mpox virus (MPXV) and the disease is reported to be similar to the smallpox. Between the 2018 and the current outbreak, MPXV whole genome sequences have shown on average 100 nucleotide sequences. Therefore, whole genome sequencing allows a fast and low-cost method to investigate known mutations and to discover emerging and novel variants, that can be of important to the European and global health. The data obtained can be applied to variant calling and phylogenetic/prevalence studies.
The Experiment and the Product
The Whole Genome sequencing analysis service for Mpox Virus (Ref-SKU: S.1.13.3.IT.149.41) is based on Illumina DNA prep protocol and includes the following steps for each sample:
- Tagmentation;
- Amplification of tagmented DNA
- Pool of libraries;
- Library Validation by Fragment Analyzer;
- Normalization to 4nM for cluster generation;
- Sequencing: 2×150 PE NextSeq
Figure: Fragment analyzer trace for the library validation step
The service for the bioinformatics analysis of Mpox virus Whole Genome Illumina Sequencing (Ref-SKU: S.1.13.3.IT.149.45) includes:
- Quality check, removal of adapter sequences and filtering of raw reads;
- Genome assembly by mapping the reads to the reference genomes (RefSeq: NC_003310; MT903344; MT903343);
- Variant calling;
- Reconstruction of consensus sequence;
- Phylogenetic analyses.
END-USER RESPONSIBILITIES
Biological material to be provided by the end-users and described in the dedicated request form.
– DNA INPUT RECOMMENDATIONS
For the library preparation, the Polo d’Innovazione Genomica Genetica Biologia, follows the library preparation protocol from Illumina DNA Prep resources. The kit protocol has been optimized for total genomic DNA.
Please, provide at least 50 µl with 1-500ng of total DNA.
– REMARKS:
- If the provided sample doesn’t comply with the above requested specifications for “DNA INPUT RECOMMENDATIONS”, the customer will be contacted for a re-sampling.
- In case of failure of the sequencing run, the service will be repeated.
– DESPATCH OF SAMPLES
- Safe-lock 1.5 – 2 ml tubes properly capped to be used to avoid accidental evaporation or sample contamination during shipping.
- Samples to be labelled correctly.
- Correct temperature must be ensured during the shipment to avoid sample degradation.
- Complete the enclosed Sample Submission form and return together with the samples to: orders@pologgb.com.
SUPPLIER RESPONSIBILITIES:
– STORAGE OF BIOLOGICAL SAMPLES
Polo d’Innovazione Genomica Genetica Biologia will store the analysed samples only for 1 month after delivery. Extended storage time is available for a maximum of 4 months and must be requested in advance of the experiments in the service request application.
– STORAGE OF DATA
Polo d’Innovazione Genomica Genetica Biologia waives any responsibility for the storage and backup of the supplied project and sequencing data after delivery to the end-user. Polo d’Innovazione Genomica Genetica Biologia will store the project data only for 1 month after delivery. After expiration of this period, all data are removed from our servers and archived (unless otherwise agreed with the end-user). Your data might be re-imported at an extra cost within the period of 1 year after delivery of the final data. After 1 year, all project data will be deleted permanently from our systems. Extended data storage is available on request at an extra cost and must be requested at project start.
– DELIVERY OF RESULTS
The bioinformatics results will be sent according to the Modalities of Transfer with a Bioinformatic Reports PDF Files. The bioinformatic analysis will be executed in 45 days from the generated sequencing data.
Modalities of transfer:
- by “WeTransfer” platform for data of up to 2Gb
- by “MegaSync” platform for data ranging from 2Gb to 15Gb
- by HD for data over 15 Gb
Please note that the cost of HD driver is not included. Where requested, the end-user must provide the HD.
For further details on the description of the experiment, please consult the Illumina DNA Prep prep Reference Guide.
For more information, please contact us.
For technical assistance, contact Polo GGB Technical Support:
Email: techsupport@pologgb.com
Telephone: 0039 0577 381310