Molecular Pathology Report (Somatic Tumor NGS)

Patient Name: [Patient Name]

Medical Record Number: [Medical Record Number]

Date of Birth: [Date of Birth]

Ordering Provider: [Ordering Provider]

Report Date: [Report Date]

Accession Number: [Accession Number]

Performing Laboratory: [Performing Laboratory Name]

Laboratory Address: [Laboratory Address]

Specimen Source/Site: [Specimen Source/Site]

Specimen Type: [Specimen Type]

Collection Date: [Collection Date]

Pathology Case/Block ID: [Pathology Case/Block ID]

Results Summary

Assay: [Assay name and version]

Specimen: [Specimen source/site and type]

Adequacy: [Acceptable / Suboptimal but tested / Failed] (If suboptimal, briefly state reason and estimated tumor cellularity; if any component was not performed, state here)

Tier I Variants (Strong Clinical Significance):

• [Gene]: [Protein change], VAF [VAF %] (Add additional items for each variant; if none detected, state "No Tier I variants detected.")

Tier II Variants (Potential Clinical Significance):

• [Gene]: [Protein change], VAF [VAF %] (Add additional items for each variant; if none detected, state "No Tier II variants detected.")

MSI Status: [MSI-High / MSI-Stable / Indeterminate / Not assessed]

TMB: [Numeric value] mut/Mb (Include categorical interpretation [High / Intermediate / Low] only if laboratory has validated cutoffs)

Critical Limitations: [Brief description of critical limitations impacting interpretation] (Include only if present—e.g., tumor content below validated minimum, key regions failed coverage, fusion analysis not performed; otherwise omit this line entirely)

Clinical Indication

• [Reason for testing, e.g., tumor genomic profiling for therapy-relevant variants]
• [Histologic diagnosis and anatomic site] (If not provided, state "Diagnosis not provided")
• [Relevant clinical context, stage, or prior molecular testing if available]

Specimen Adequacy

Overall Assessment: [Acceptable / Suboptimal but tested / Failed] (If suboptimal, specify reason: low tumor content, degraded DNA/RNA, decalcification, necrosis, scant tissue)

Estimated Tumor Cellularity: [Tumor %] (Include enrichment method if performed, e.g., macrodissection; use "Not provided" if unavailable)

Component Performance: DNA analysis: [Performed / Not performed / Failed]; RNA fusion analysis: [Performed / Not performed / Failed] (If a component was not performed, state reason)

(If tumor % is unknown or below assay's validated minimum, include caveat regarding potential reduced sensitivity for low-VAF variants)

Detailed Molecular Results

Tier I Variants

(Include only if Tier I variants detected; otherwise omit this subsection)

Gene	Variant (protein and coding DNA)	Variant Type	VAF (%)	Depth	Clinical Significance Category	Evidence Summary
[Gene]	[p.ProteinChange; c.CodingChange]	[SNV / Indel / Splice]	[VAF %]	[Depth]	[Therapeutic / Diagnostic / Prognostic / Resistance]	[Concise evidence summary]

Reference sequence(s): [Transcript, e.g., NM_XXXXX.X] | Genome build: [GRCh37 / GRCh38]

[Interpretive paragraph for each Tier I variant: explain significance in tumor context, therapeutic and resistance implications using general language such as "may be associated with sensitivity to..."]

Tier II Variants

(Include only if Tier II variants detected; otherwise omit this subsection)

Gene	Variant (protein and coding DNA)	Variant Type	VAF (%)	Depth	Clinical Significance Category	Evidence Summary
[Gene]	[p.ProteinChange; c.CodingChange]	[SNV / Indel / Splice]	[VAF %]	[Depth]	[Therapeutic / Diagnostic / Prognostic / Resistance]	[Brief note]

[Short interpretive note for Tier II variants if clinically helpful]

Tier III Variants (Variants of Uncertain Significance)

(Do not overstate actionability; if large volume, filter to genes relevant to indication and state filtering policy)

Gene	Variant (protein and coding DNA)	Variant Type	VAF (%)	Depth
[Gene]	[p.ProteinChange; c.CodingChange]	[SNV / Indel / Splice]	[VAF %]	[Depth]

(If filtering applied, state VUS reporting policy and criteria used)

Copy Number Alterations

(Include only if assessed by assay)

Gene/Locus	Copy Number Call	Quantitative Estimate	Tier	Interpretation
[Gene/Locus]	[Gain / Loss / Amplification / Deletion]	[Copy number or log2 ratio]	[Tier I / II / III]	[Brief interpretive note]

Note: CNV calling from targeted panels may have reduced reliability in low-purity samples.

Gene Fusions/Rearrangements

(Include only if assessed by assay)

Fusion/Rearrangement	Detection Method	Transcript Details	Supporting Evidence	Tier/Interpretation
[PartnerA–PartnerB]	[DNA-based / RNA-based]	[Breakpoints/transcripts if available]	[Read counts if available]	[Tier and brief note]

Pertinent Negatives

(Report only when tumor type is known and relevant regions had adequate coverage)

• [Gene/Region]: Not detected (Adequate coverage)
• [Gene/Region]: Indeterminate (Inadequate coverage)

Biomarker Details

Microsatellite Instability (MSI)

Result: [MSI-High / MSI-Stable / Indeterminate / Not assessed]

[Clinical interpretation in tumor context] (If assay validation is tumor-type-limited, state this; if neoplastic cell content is unknown or below validated minimum, recommend orthogonal testing such as MMR IHC or PCR-based MSI)

Tumor Mutational Burden (TMB)

Result: [Numeric value] mut/Mb [High / Intermediate / Low] (Include categorical interpretation only if laboratory has validated cutoffs)

Method: [Assay name/version]; [Sequencing platform]; Genomic territory: [size in Mb]; Variants included: [coding SNVs, indels, etc.]; Enrichment: [Amplicon / Hybrid capture]. TMB values may differ across assays due to territory and filtering differences.

Clinical Interpretation

(Organize by finding in descending order of clinical significance: Tier I variants first, then Tier II, then biomarkers)

[Finding 1: Gene/Alteration]: [What was found and why it matters—predictive, prognostic, or diagnostic significance]. [Therapeutic implications using general language, e.g., "may be associated with sensitivity to..."]. [Resistance considerations if applicable].

[Finding 2]: [Interpretation as above]

(For tumor-only testing, include:) Somatic versus germline origin cannot be definitively determined without paired normal analysis. (If any finding is suspicious for germline origin based on VAF ~50%, gene, or clinical context, explicitly label as "possible germline" and recommend confirmatory germline testing from a non-tumor specimen with genetic counseling referral.)

Test Performance Summary

Panel: [Panel name with reference to gene list or appendix]

Alteration Types Assessed: SNVs, Indels, CNVs, Fusions (Specify DNA vs. RNA components)

Minimum Coverage Threshold: [Coverage cutoff for variant calling]

Failed Regions: [List genes/regions below threshold, or state "All targeted regions met coverage thresholds"]

(Include QC metrics—mean depth, uniformity, tumor purity estimate—only if abnormal or materially affecting interpretation)

Limitations

Analytic: [Variant classes not detected or poorly detected, e.g., large structural variants, repeat expansions, low-level subclonal variants below limit of detection; known problematic regions if relevant]

Specimen-related: [Impact of tumor content, fixation, or DNA/RNA quality on this specific case if applicable]

Interpretive: Clinical actionability reflects knowledge as of report date; treatment decisions require integration with full clinical context.

References

(Optional: 3–5 key guideline or drug label references supporting major interpretive claims)

• [Reference 1]
• [Reference 2]
• [Reference 3]

Amendments

(Include only for corrected or appended reports; omit entirely for original reports)

Amendment Date: [Date] | Reason: [Reason] | Sections Updated: [Sections] | Description: [What changed and why]

Sign-out

Interpreting Pathologist: [Name]

Credentials: [Credentials]

Date/Time: [Date and Time]

Documentation standards: Use consistent terminology (Detected, Not detected, Indeterminate, Failed, Not assessed). For missing required fields, use "Not provided." Exclude Tier IV (benign/likely benign) variants unless specifically indicated. Do not infer somatic vs. germline status without paired normal. Do not infer or recompute MSI/TMB from individual variants.