Embgenix product FAQs

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.

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 takara-support@basepairtech.com.

The assays have been validated to reliably detect CNVs ≥10 Mb and mosaicisms ≥30%.

The Embgenix PGT-A Kit and analysis software were validated using trophectoderm (TE) biopsy and genomic DNA samples representing euploids, aneuploids, and mosaics.

Embgenix assays are not currently able to detect polypoloidy or uniparental disomy.

The Embgenix PGT-A Kit can successfully process inputs of 3–10 trophectoderm (TE) biopsy cells.

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.

Yes. NucleoMag and AMPure beads were confirmed to be functionally interchangable.

Yes. Illumina reagent kits are required for sequencing of Embgenix NGS libraries. Please refer to the corresponding Embgenix kit user manual for specific guidelines.

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.

For support with the wet-lab worfklow (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 takara-support@basepairtech.com.

No. Access to the cloud-based software is freely provided upon purchase of Embgenix kits.

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

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.

Please submit technical support inquiries involving Embgenix software to the following email address (provided within the software interface): takara-support@basepairtech.com

When a new inquiry is submitted to takara-support@basepairtech.com, 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.

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).

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.

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

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.

The solid lines correspond to full gains/losses, while the dotted lines correspond to mosaic gains/losses at frequencies of +/–50% and +/–70%, respectively.

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.

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.

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.

No. All features of Embgenix Analysis Software are freely provided to customers using Embgenix kits.

All Embgenix analysis capabilities currently available are included in the software and provided via the interface.