Frequently Asked Questions

 

Clinical Genomics

 

 

SOMATIC CANCER

  • How are the multiplexed Seraseq materials made?

In short, when building these contrived samples, we synthesize 600-800 bp constructs, each containing an engineered variant at the center. The constructs are then combined and blended into a background of gDNA GM24385 at the desired allele fraction, which is confirmed by digital PCR.

  • How do you quantitate the allelic fractions of the introduced variants?

The quality control of allelic frequencies is performed using digital droplet PCR with assays for each variant. The results are provided in the Product Report, which is available online.

  • How should I use Seraseq samples in my assay?

Seraseq samples should be treated as a regular specimen. Please see product package insert for further details.

  • What is the difference between Mutation Mix and Reference Material?

Mutation Mix and Reference Material are two different sample formats. Mutation Mix is provided as purified DNA or RNA, whereas Reference Material is a full-process sample, allowing for evaluating the complete workflow from sample purification to result.

 

INHERITED DISEASE

  • How do you generate multiplexed reference samples with a single genetic background?

In short, when building these contrived samples for inherited disease, we synthesize 600 bp constructs, each containing an engineered variant at the center. The constructs are then combined and blended into a background of gDNA GM24385 at the desired allele fraction, which is confirmed by digital PCR.

  • How do you quantitate the allelic fractions of the introduced variants?

The quality control of allelic frequencies is performed using digital droplet PCR. The results are provided in the Product Report, which is available online.

  • How do I use these materials with my assay?

Seraseq samples are provided as purified HMW DNA, and can enter the workflow as a regular specimen, after extraction step. Please see the package insert for further details.

 

REPRODUCTIVE HEALTH

  • What NIPT Reference materials are available?

SeraCare® offers two types of NIPT Reference Materials: Matched Maternal-fetal NIPT Reference Materials and Unmatched NIPT Reference Materials.

  • How are these products built?

Maternal-fetal matched NIPT Reference Materials are produced from cfDNA extracted from plasma of a pregnant patient. This source sample is either from a euploid (normal) pregnancy or a one with confirmed aneuploidy. Material is further processed but maintains natural cfDNA size profile of both fetal and maternal cfDNA of approximately 170bp on average. This DNA is then stabilized and introduced into a dilution of SeraCare's SeraCon Matribase(simulated plasma).

Unmatched NIPT Reference Materials are created from male fetal DNA derived from placental trophoblast cells with a confirmed trisomy and then blended with genomic DNA obtained from an unrelated, non-pregnant female.

Both types of materials are intended for a full process validation and run control.

  • How is ploidy status verified (quality control) for the Seraseq aneuploidy products?

The ploidy status is verified using one or more of the standard NIPT assays offered in the market.

  • How do you quantitate the fetal fraction?

Matched Maternal-Fetal: Fetal fraction is verified by a standard NIPT assay and indicated in the Product Report.

Unmatched NIPT reference materials: Fetal fraction is verified and controlled to the desired level using digital PCR (dPCR).

  • How do I use these materials with my assay?

The NIPT Reference Material is an encapsulated (plasma-like) cfDNA sample which may be used in a manner consistent with clinical plasma samples prior to extraction, in parallel with test specimens, in a target enrichment NGS or Digital PCR workflow following the protocol as described by the assay vendor. Depending on cfDNA extraction methodology recovery yield of around 80% can be expected.

This material can be used to develop a new test, validate an assay, monitor routine performance, troubleshoot problems across the entire workflow and ensure overall proficiency with the same sustainable product.

  • Are these products customizable?

Yes. We offer various custom options. Please contact us on info@seracare.com to discuss your specific needs.

  • What is the NIPT test compatibility of these products?

The Seraseq Maternal-fetal matched NIPT Reference Materials have been tested with a broad range of counting and pair end methods, such as VeriSeq, Harmony, Panorama and Iona.

The Seraseq Unmatched NIPT Reference Materials are suitable for chromosome counting tests or amplification assays that don’t require maternal-fetal samples to be matched (or related).

Note that neither of the current products are suitable for methylation-based assays.

NIPT test compatibility

 

NGS: PURIFIED DNA OR RNA PRODUCTS

  • What buffer is used for the purified DNA/RNA products?

Seraseq purified DNA or RNA is provided in 0.1x TE, which is a low salt (1 mM Tris, 0.1 mM EDTA) buffer.

  • What is the composition of the plasma matrix used in your Reference Material products?

Seracon Matribase is manufactured from human plasma which is collected in 4% sodium citrate solution. This product is not treated and is 0.2µm filtered.

  • Would it be possible to get the sequence file for the background cell line - GM24385?

For the sequence file, click here.

  • Is it possible to purchase just the background genomic DNA from GM24385?

Unfortunately, no. Coriell sells the GM24385 cells or NA24385 purified genomic DNA from these cells.

  • Where can I find the exact sequences of the RNA Fusion?

For the RNA Fusion sequence, click here.

  • Is there a BED file (.BED) or vcf (.vcf) file for each product?

Please contact technicalsupport@seracare.com for assistance.

  • Can I use any library kit with these reference materials?

Our products are designed to perform as patient samples. We and our customers have used a variety of different library kits and sequencing platforms. In general, we recommend that you follow the manufacturer's protocol in using any kits or equipment.

  • Does the Fusion RNA Mix or FFPE version contain any DNA?

No. Our Fusion RNA products contain the RNA fusion fragments blended with total RNA from GM24385. There is no DNA present.

 

iQ NGS QC Management

  • How will iQ™ NGS QC Management software help me track quality control (QC) metrics of my assays?

iQ NGS QC Management software allows you to automate data collection and tracking, as well as gather insights by analyzing QC metrics trends. These metrics are generated by running reference materials such as the Seraseq™ line of products.

Using iQ NGS QC Management to track and trend the data generated by Seraseq reference materials, you can be more confident in the performance of your assay, save costs on reagents, monitor instrument performance over time, and improve overall lab efficiency.

  • How do I gain insights into the performance of my assays?

Because iQ NGS QC Management works with reference materials such as the Seraseq™ line of products, QC data from each run is tracked and analyzed for trends using the informative run dashboard and the Levey-Jennings charts, at both the metric and variant level; data is automatically assessed as passed, warned, or failed.

  • How can I report the QC results for a run to lab management and external inspectors?

iQ NGS QC Management makes it easy to review and sign off on each metric in a run, and assess the run as passing or failing. At a moment’s notice, a final run QC report can be generated with the charts and value tables that were reviewed and signed off on, along with the reviewer’s name and review date. These reports can be easily shared with any key stakeholder such as a lab director or external inspector.

  • I’ve been using spreadsheets to track QC metrics, can I import my historical data?

Yes, iQ NGS QC Management has simple-to-use import tools that can take your historical data and automatically import it into the software. This frees you from wrangling with spreadsheets and to spend more time learning insights about your assay’s performance.

  • I use a LIMS (Lab Information Management System) to track my samples and wet lab processes, can I connect it to iQ NGS QC Management?

The iQ Connector REST API allows you to interface with your existing LIMS/LIS system so that you can take advantage of your historical data and hook into your existing processes, making it possible to quickly scale the QC throughput of your assays.

  • Can I track run, sample, or variant level metrics? How will I know if a metric failed?

When you define your custom QC workflow, you easily establish the critical QC metrics you track across all the steps in the workflow at the run, sample, and variant levels. Additionally, iQ NGS QC Management gives you tools to set acceptance criteria for automatically passing, warning, and failing a metric.

  • How secure and robust is iQ NGS QC Management?

iQ NGS QC Management runs on Amazon Web Services using best in class security protocols to protect your data at rest and in transport using HTTPS. To ensure only authorized users can access the system, iQ NGS QC Management employs the enterprise-grade identity management system Auth0 for user authentication.

Contact a member of the SeraCare sales team or sign up for a customized demo and free software trial.