The only difference is that CLIA-Validated Service includes a Lab Director Signature and QA Oversight whereas CLIA Environment does not. In addition, the CLIA Environment service level allows greater flexibility in experimental design, such as custom starting materials, and offers a range of sequencing coverage options.

Yes, we do. Click here to request a quote.

Whole genome sequencing requires an extremely high amount of sequencing throughput to generate a moderate depth of coverage. The data generated, while comprehensive, does not allow detection of mutations with as much sensitivity as a targeted approach. Exome sequencing is the most cost-effective and efficient solution.

A large portion of relevant mutations occur in the exome. In fact, the exome contains as many as 85% of disease-related mutations. Covering less than 2% of the whole genome, exome sequencing requires only 1/50th of the sequencing throughput to generate the same depth of coverage. This approach provides flexible experimental options:

• Maintain the same depth of coverage and multiplex more samples into the same sequencing lane, significantly decreasing total project cost
• Increase the depth of coverage to facilitate the detection of rare, low-frequency mutation

The answer depends on the goals of your sequencing project. Our CLIA-Validated service is only available with ~50x coverage, which is ideal for germline variant detection. In contrast, our CLIA Environment service provides a wide range of coverage options to meet your needs for a variety of applications, as outlined below:

• Germline/frequent variants: 50-100x
• Somatic/rare variants: ≥200x
• Tumor vs Normal: ≥200x tumor, ≥100x normal
• Population studies: 50-100x

We provide raw data as FASTQ files for all projects. We also offer mapping and variant calling through BAM and VCF files, respectively. Please note that no variant annotation or interpretation is offered at this time.

Azenta‘s CLIA team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation to answer any questions. For any form questions that require support, please contact the CLIA team at CLIA@Azenta.com, toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 ext. 1.

We have proven our steadfast commitment to superior service throughout the years, becoming established as a global leader in DNA sequencing and genomics. Further, we have extensive experience and expertise in next generation sequencing techniques, including population-scale sequencing. Our CLIA NGS services build upon our RUO services, utilizing the same optimized workflows but within a CLIA-certified and CAP-accredited laboratory.

Yes, our laboratory is both CLIA-certified and CAP-accredited. Our CLIA and CAP license numbers are 31D2038673 and 8015683, respectively.

CLIA PCR and Sanger Sequencing is PCR and Sanger sequencing processed in a CLIA-licensed/CAP-accredited laboratory. All work is performed under a CLIA-compliant workflow that utilizes CLIA-trained personnel on CLIA-qualified equipment.  

Yes, Azenta is licensed by CMS (Centers for Medicare and Medicaid Services) under the Clinical Laboratory Improvement Amendments of 1998 as qualified to perform high complexity clinical laboratory testing. Azenta holds clinical lab licenses from NJ, PA, CA, RI and MD.

Yes, Azenta is CAP (College of American Pathologists) accredited. 

Choose “CLIA Environment” if you need CLIA lab, CLIA personnel, CLIA workflow, without QA oversight or lab director (Azenta does not make claims to the clinical significance of the data).

Choose “CLIA Workflow” if you need CLIA lab, CLIA personnel, CLIA workflow, QA oversight, assay performed in triplicate at the assay development stage, no test registration, no clinical outcome reporting, and lab director signature to ensure CLIA-compliant sequencing. This uses the workflow and activities of the validated CLIA test but does not use a registered test from the test roster.

Choose “CLIA” if you need CLIA lab, CLIA personnel, CLIA workflow, QA oversight, assay validation (to assess accuracy, sensitivity, reproducibility), test registration, clinical outcome reporting, and lab director signature.

Click here for a visual summary of CLIA Environment, CLIA Workflow, and CLIA full service.

Please email Regulatory@azenta.com to discuss further.

Please email Regulatory@azenta.com to discuss sample acceptance criteria.

Please email Regulatory@azenta.com to discuss PCR assay design.

CLIA Sanger sequencing is performed in the CLIA-certified/CAP-accredited laboratory by CLIA-trained personnel on CLIA-qualified equipment. Sample and reagent tracking for each order with a review of the final documentation by Quality Assurance and our lab director is also provided.

You will receive the original sequencing results in a chromatogram (.ab1 files), the sequence files (.seq files), and the quality files (.phd files) along with a quality report which contains the quality score and contiguous read length per trace. For an additional fee, you can request a lab director signed report which will indicate that the order was processed within a CLIA-compliant workflow.

This report includes the exact nucleotide base calls for any mutations found within the region of interest. Two-fold sequencing is necessary to obtain this report.

Yes, you can request a lab director signed report which will indicate that the order was processed within a CLIA-compliant workflow for an additional fee per trace.

Yes, please see the service offerings here.

Azenta Life Sciences, formerly GENEWIZ, can accept sample types from which high-quality genomic DNA (gDNA) can be extracted. We have extensive experience working with all sample types including cells, cell pellets, PBMCs, whole blood, and fresh frozen tissue. The sample requirements for the most common sample types are > 500 ng for genomic DNA and 10-30 mg of fresh frozen tissue.

We offer two analytically validated NGS-based assays, leveraging targeted approaches to identify, quantify, and monitor viral vector integration events across the genome. Both assays generate information on insertion site location and frequency as well as offer the following unique capabilities:

 

Target Enrichment Sequencing (TES)

A Hybridization-Capture TES Assay that generates information on insertion site location and frequency, and additionally allows for insertion/transgene integrity study, which is important to resolve mutations or rearrangements.

 

Quantitative Shearing Linear Amplification Mediated-PCR (qsLAM-PCR)

A Targeted qsLAM-PCR Sequencing Assay that focuses on identifying insertion site location and frequency, offering superior sensitivity on insertion site detection.

Both of our analytically validated NGS-based assays are efficient at generating information about where the viral vector has inserted into the host genome:

 

Linear Amplification-Mediated-PCR (LAM-PCR) focuses on insertion site location and frequency, offering superior sensitivity on insertion site detection;

 

Hybrid Capture Targeted Enrichment Sequencing (TES) generates information on insertion site location and frequency, and additionally allows for insertion/transgene integrity study, which is important to resolve mutations or rearrangements.

Standard turnaround time is 3-4 weeks; Expedited options are also available. 

Lentiviral vectors are efficient gene delivery vehicles suitable for delivering long-term transgene expression in various cell types over time. A drawback of the lentiviral vector include the risk of insertional mutagenesis due to the semi-random integration of genes.

 

Guidance from the FDA and other regulatory authorities, is that patients treated with cell or gene therapies utilizing viral vectors be monitored for 5 – 15 years for safety. This monitoring includes, but not limited to, vector integration studies of patient samples to ensure stability.

Per the FDA, “LTFU observations are extended assessments that continue some of the scheduled observations of a clinical trial past the active follow-up period and are an integral portion of the study of some investigational GT products.  LTFU observations are important to monitor long term safety of GT products.  For GT products that present long term risks to subjects, LTFU/surveillance plan(s) should also be put in place post-licensure for monitoring of delayed adverse events (for details we refer you to section VI. of this document).”

 

Guidelines from the FDA suggest 15 years of long-term follow up after gene therapy treatment with integrating vectors such as lentiviral vectors. Analysis should be performed to determine the site of vector integration if the analysis of a subject’s surrogate cells suggests a predominant clone (e.g., oligoclonal pattern of vector insertions) or monoclonality. In addition, if you detect a predominant integration site, test for persistence by performing another analysis for clonality no more than three months later.

 

Source: https://www.fda.gov/regulatory-information/search-fda-guidance-documents/long-term-follow-after-administration-human-gene-therapy-products

Lentiviral vectors are well known for their ability to effectively deliver genetic material for long-term transgene expression over time. There is also potential for unintended consequences resulting from random viral integrations into the host genome. Azenta has developed detection methods to study clonal outgrowths of transduced cell populations after gene therapy administration.

When lentiviral integration happens near oncogenes or within key genes, it may affect important cellular functions. For this reason, it is important to identify the exact site(s) of integration in target cells, post-infection. The selected integration site has important consequences for both the expression of the transgene and the phenotype of the host cell.

1) Insertion site location, frequency, abundance

2) Integration hotspots & CPG islands

3) Oncogenic gene annotation of Integration Site

4) Longtitudinal profiling (clonal expansion)

5) Vector integrity (TES)

 

Custom analysis support options are also available upon consultation.

Microarrays offer a high throughput technology to examine genotyping, gene expression, and/or methylation data for samples. Targets are printed or synthesized on a solid substrate, which is interrogated by a probe derived from samples of interest. Detection is typically done using a high-density scanner after hybridization and staining.

• ThermoFisher manufactures microarrays by synthesizing targets in situ. Arrays are offered in a 96-well plate and may contain 800,000+ targets in each well. Microarrays are scanned on a ThermoFisher GeneTitan instrument with analysis using the Axiom Analysis Suite Software. ThermoFisher offers microarrays for genotyping and gene expression analysis.
• Illumina utilizes silica microbeads adorned with hundreds of thousands to millions of genotypes. These beads are housed in etched microwells and coated with multiple copies of an oligonucleotide probe targeting a specific genomic locus. The beads contain one extra base which enables incorporation of a labeled nucleotide, which can be detected on Illumina’s iScan instrument, and analyzed using GenomeStudio software. Illumina offers bead chip arrays for genotyping or methylation analysis.

We can accept many sample types, including, but not limited to, whole blood, PBMCs, tissue, saliva, FFPE blocks or curls, laser microdissections, or extracted nucleic acids (DNA or RNA).

• For ThermoFisher Axiom arrays, 96 samples are genotyped per plate. For ThermoFisher GO Screen (gene expression) arrays, 384 samples are processed per plate.
• For Illumina bead chip arrays, the number of samples depends on the bead chip array of interest. Typically, these are processed as 8, 16, 24, 32, or 96 samples.

Kindly note that for either microarray supplier, you will be charged for a full plate/bead chip, including all necessary controls.

Our microarray service is offered at a regulatory level appropriate for exploratory research. This offers quality oversight in a regulated environment consisting of instrument maintenance and calibration logs, reagent lot tracking, staff training logs, chain-of-custody audit trails, IT systems maintenance and back-up logs, and the ability to audit the facility and process. Note that we can offer this as a clinically validated service; please inquire for additional details.

• ThermoFisher microarrays: Both positive (HapMap) and negative (no template) controls, provided by ThermoFisher, are used in the Axiom (genotyping) arrays. For a ThermoFisher Axiom array (96-wells), only 94 samples are available for customer samples as 2 positions are required for these controls. For ThermoFisher GO Screen (384-wells), one NTC and one positive control are used per plate.
• Illumina bead chips: A single positive control, provided by Illumina, is used per run, regardless of the number of bead chips in the run.

Yes, please email clia@azenta.com and we’d be delighted to arrange a meeting to consult about the details of your project with one of our PhD-level study managers.