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Particulars

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Service:

NGS Endometrial Cancer Panel – Technical Requirements

1. Test Details- NGS Endometrial Cancer Panel

· Sequencing Platforms: Illumina/Thermo Fisher platforms

· Testing must be performed using the provided FFPE tissue samples and exclusively by Next-Generation Sequencing (NGS) methodology, except for MSI testing, which shall be performed separately by IHC.

2. Scope of Work and Technical Requirements

• Turnaround Time (TAT):

The complete testing process, including sequencing, bioinformatics analysis, interpretation, and reporting, must be completed within a strict turnaround time of less than 15 calendar days from receipt of the sample.

3. Sequencing Depth:

· Each reportable variant must be supported by a minimum sequencing depth of >1,000×.

· At least 80% of the target bases must achieve a minimum coverage depth of 500×.

4. Accreditation:

The service provider must hold NABL accreditation for the relevant/ specific test or scope of testing along with DSIR, and ISO certifications.

5. Required Gene/Marker Coverage:

The NGS panel must include, at minimum:

o POLE

o TP53

6. MSI Testing: MSI assessment must be performed separately using Immunohistochemistry (IHC).

7. Bioinformatics and Variant Analysis Requirements-

The service provider shall perform comprehensive bioinformatics analysis using validated and appropriate NGS pipelines.

The analysis should include:

●Comprehensive variant detection and annotation relevant to the tested genes/regions.

●Identification and characterization of clinically relevant genomic variants.

●Variant annotation using established clinical and disease databases, including but not limited to: OMIM and ClinVar

●Population frequency assessment using appropriate population databases, including: 1000 Genomes, ExAC, gnomAD, ESP

●Population frequency information should be used to assist in distinguishing common germline polymorphisms from potentially clinically relevant variants.

8. Reporting Requirements-

The final report must provide comprehensive genomic findings and clinical interpretation.

A. Genomic Findings

For each reported variant, the report should include, at minimum:

● Gene

● Genomic finding / variant

● Variant Allele Frequency (VAF)

● Read depth / sequencing depth

● Exonic location

● Predicted functional impact

● Variant classification

● Oncogenicity / genomic classification

● Tier classification

● Relevant transcript and variant nomenclature, where applicable

B. Genomic Findings with Clinical Evidence

For each clinically relevant reported variant, the report should provide evidence-based clinical interpretation, including, where applicable:

● FDA-approved therapies for the patient's tumor type

● Therapies of potential clinical significance

● Potential therapeutic resistance implications

● Relevant and potentially applicable clinical trials

● Drug/therapy indications supported by available clinical-trial or other established clinical evidence

Clinical interpretation should clearly distinguish between established clinical evidence, potential therapeutic relevance, and investigational options.

9. Service Provider Qualifications and Certifications

The service provider must possess valid and applicable:

● NABL accreditation

● DSIR recognition/certification, where applicable

● ISO certification(s) relevant to the testing laboratory and quality management system; Copies of relevant certificates/accreditations may be requested for verification.

10. Non-Outsourcing Requirement

The complete testing workflow must be performed in-house by the service provider (appropriate documentation should be provided in support of this). No part of the testing process shall be outsourced to a third party, including:

● Sample processing

● DNA extraction/pre-analytical processing

● Library preparation

● Sequencing

● Primary data analysis

● Bioinformatics analysis

● Variant annotation

● Clinical interpretation

● Report generation

11. Laboratory Visit and Audit

The service provider shall permit an on-site laboratory visit by the client's authorized team and/or students for the purpose of:

● Reviewing laboratory infrastructure

● Verifying sequencing platforms

● Reviewing sample-processing and library-preparation facilities

● Understanding sequencing and bioinformatics workflows

● Reviewing quality-control procedures

● Verifying accreditation and quality-management practices

● Assessing the overall testing workflow and laboratory capabilities

The provision for such a laboratory visit shall be mandatory.

10 samples