Embgenix product FAQs
Embgenix reagent kits and analysis software enable streamlined assessment of copy number variations (CNVs) from embryo biopsies and spent media samples. Provided below are answers to frequently asked questions about Embgenix products and applications. Please contact us if you have questions that are not addressed by product documentation or web content.
Are Embgenix kits and software compatible with Illumina platforms other than MiSeq® and NextSeq®?
Yes. Embgenix kits are broadly compatible with most Illumina platforms. Takara Bio has validated the kits on MiSeq and NextSeq and we provide supporting documentation for these platforms, but the kits have been used successfully with other platforms (e.g., NovaSeq™, MiniSeq™, etc.), including those with patterned flow cells. Regardless of which platform is used, the validated protocols call for sequencing with 2 x 75-bp paired-end reads.
Whom should I contact for technical support?
For inquiries involving the wet lab portion of the Embgenix workflow (e.g., WGA, library preparation, Illumina sequencing), please contact Takara Bio Technical Support using the contact information on this page. For inquiries involving Embgenix Analysis Software, please send an email to firstname.lastname@example.org.
What are the detection limits of Embgenix assays?
The assays have been validated to reliably detect CNVs ≥10 Mb and mosaicisms ≥30%.
What samples were used in validating the Embgenix PGT-A Kit and analysis software?
The Embgenix PGT-A Kit and analysis software were validated using trophectoderm (TE) biopsy and genomic DNA samples representing euploids, aneuploids, and mosaics.
Can Embgenix assays detect phenomena such as polyploidy or uniparental disomy?
Embgenix assays are not currently able to detect polypoloidy or uniparental disomy.
Questions about Embgenix kits
What is the recommended quantity of cells that should be processed for each sample using the Embgenix PGT-A Kit?
The Embgenix PGT-A Kit can successfully process inputs of 3–10 trophectoderm (TE) biopsy cells.
What are the recommended read length and sequencing depth for analysis of libraries generated with the Embgenix PGT-A Kit?
Libraries should be sequenced using 2 x 75-bp paired-end reads. The recommended sequencing depth is 2 million paired-end reads per sample, though the Embgenix PGT-A Kit has been validated at a depth of 1.5 million paired-end reads.
Can AMPure beads be used with the Embgenix PGT-A Kit instead of NucleoMag NGS Clean-up and Size Select?
Yes. NucleoMag and AMPure beads were confirmed to be functionally interchangable.
Do Illumina sequencing reagents need to be purchased separately?
Yes. Illumina reagent kits are required for sequencing of Embgenix NGS libraries. Please refer to the corresponding Embgenix kit user manual for specific guidelines.
Can WGA products from PicoPLEX kits be incorporated into Embgenix library prep and data analysis workflows?
We don't recommend incorporating PicoPLEX WGA products into the Embgenix workflow. Even though Embgenix employs PicoPLEX WGA technology, there are some differences in the chemistries and priming sequences used in the v1, v2, and v3 PicoPLEX WGA kits that could impact their compatibility with the Embgenix workflow.
Whom should I contact for technical support with the wet-lab portion of the workflow?
Questions about Embgenix software
Does Embgenix Analysis Software need to be purchased separately?
No. Access to the cloud-based software is freely provided upon purchase of Embgenix kits.
What is the process for obtaining access to Embgenix Analysis Software?
Access to Embgenix software is only provided to those who have purchased an Embgenix kit. The process for obtaining access is as follows:
- Purchase an Embgenix kit
- Fill out a request form for the software package corresponding to the kit that was purchased
- Embgenix Support will confirm the purchase, create an account for your group, and provide you with login credentials (including a temporary password) and a login page URL via email
- Log in to your new account, update your password, and add additional users from your group to your account
How is Embgenix Analysis Software provided (e.g., local installation vs. cloud-based deployment)?
At this time, Embgenix Analysis Software is provided via the cloud and cannot be installed locally. Access to the software is freely provided upon purchase of an Embgenix kit and completion of a request form on the corresponding signup page.
Whom should I contact for technical support with the software?
Please submit technical support inquiries involving Embgenix software to the following email address (provided within the software interface): email@example.com
What is the typical workflow for responses to technical support inquiries involving Embgenix Analysis Software?
When a new inquiry is submitted to firstname.lastname@example.org, a ticket will be created and a notification will be sent to a specialized support team for the software. The user who submitted the inquiry will receive an email confirming creation of the ticket and including a link to view its status. Followup notification emails will be sent as the team responds to the inquiry until the matter is resolved and the ticket is closed. Users should expect to receive a response within one business day following submission of a new inquiry, but response times may be much faster depending on the timing of the inquiry.
How have data security concerns been addressed for cloud-based Embgenix Analysis Software?
Embgenix Analysis Software is compliant with the Health Insurance Portability and Accountability Act (HIPAA) to protect ePHI, and appropriate security measures are in place by the cloud service provider to ensure security. We also have a Data Processing Agreement (DPA) with the cloud service provider to ensure the security of ePHI from EU residents as required by the General Data Protection Regulation (GDPR).
How does the software analyze sequencing data to perform CNV calling?
NGS reads are aligned to the human reference genome and assigned to corresponding bins. Binned read counts are compared to a set of internally configured references to determine calculated copy numbers. Additional steps performed prior to copy number calling include read trimming and GC bias correction.
What are the thresholds for detection and classification of aneuploidies and mosaicisms?
Samples are called according to the following ranges (expressed as percentages of full gains/losses):
- 0–30% - euploid
- 30–50% - low mosaic
- 50–70% - high mosaic
- 70–100% - aneuploid
Is it possible to adjust the parameters of the analysis performed by the software (e.g., the thresholds used to call abnormalities)?
At this time it is not possible for users of Embgenix Analysis Software to adjust the thresholds used for automated CNV calling. The software does include manual annotation features to allow for calling of CNVs not detected by the automated analysis and exclusion of CNVs called automatically by the software.
What do the solid and dotted lines represent in the CNV plots?
The solid lines correspond to full gains/losses, while the dotted lines correspond to mosaic gains/losses at frequencies of +/–50% and +/–70%, respectively.
Can analysis reports be customized?
Yes. The software provides a variety of different options for customization of the report, including exclusion of X/Y chromosome information, customization of the report footer, inclusion of a logo and address information for the laboratory, adjustment of CNV call types, etc.
How long does it take to complete the data analysis workflow with Embgenix Analysis Software?
It typically takes 10–15 minutes to process samples via the software workflow, but there can be some variability in processing times for the upload and analysis steps depending on factors such as internet bandwidth and physical proximity to the cloud server.
Can the software support scenarios where samples are spread across multiple sequencing lanes, yielding more than two files per sample?
Yes. Embgenix software can process data obtained from multiple lanes for a given sample. This may require revising the naming of the files containing the sequencing data to match Illumina's convention as follows: [sample name]_S[sample number]_L[lane number]_R[read number]_001.fastq.
Lane numbers are typically specified as "L001", "L002", "L003", etc., in the name of each corresponding sequence file for a given sample.
Are any additional charges assessed for the use of data analysis or reporting features in the software?
No. All features of Embgenix Analysis Software are freely provided to customers using Embgenix kits.
Are any data analysis services offered?
All Embgenix analysis capabilities currently available are included in the software and provided via the interface.
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