genetic-testing-report

name	genetic-testing-report
description	Generate clinical single-gene genetic disease testing reports compliant with T/SZGIA 4-2018. Use when the user asks for monogenic genetic test reports, variant interpretation reports, 单基因遗传病检测报告, 基因检测报告规范, T/SZGIA 4-2018, or structured PGx/clinical genetics report output.

Clinical Single-Gene Genetic Testing Report (T/SZGIA 4-2018)

Overview

Generate reports for clinical single-gene genetic disease testing following group standard T/SZGIA 4-2018 (临床单基因遗传病基因检测报告规范).

Standard	T/SZGIA 4-2018
Scope	Reports from third-party labs, hospital labs, university diagnostic labs
Structure	Main body (essential findings) + Appendix (supplementary detail)

Do not issue a disease diagnosis in the report. State findings and interpretation; recommend genetic counseling and confirmatory testing when appropriate.

When to apply

• User requests a monogenic / single-gene genetic test report
• User provides gene, variant(s), and clinical indication for report drafting
• User asks to format output per T/SZGIA 4-2018 or Chinese PGx report norms
• Agent tool generate_genetic_testing_report is invoked

Mandatory report sections (13 items)

Every complete report must include all 13 sections below. Missing sections are non-compliant.

#	Section	Required in main body
1	Testing institution info & contact	Yes
2	Subject (patient) basic info	Yes
3	Referring institution & physician	Yes
4	Sample type	Yes
5	Sample receipt date & report date	Yes
6	Test item & method	Yes (summary); details in appendix
7	Test results (variants)	Yes (table)
8	Test conclusion	Yes
9	Result interpretation	Yes
10	Recommendations	Yes
11	References	Yes
12	Method description & limitations	Appendix preferred
13	Signatures & seal	Yes (placeholders if draft)

Main body vs appendix

Main body — concise, clinician-facing:

• Subject & test metadata (sections 1–6, abbreviated)
• Primary results: variants related to the clinical indication
• Secondary / incidental findings (only if consented and clinically actionable)
• Conclusion, interpretation, recommendations

Appendix — supplementary:

• Full gene panel / exome scope
• Disease background for detected genes
• Detailed method (library prep, sequencing platform, bioinformatics pipeline)
• QC metrics (coverage, depth, sensitivity/specificity)
• Benign / VUS variants not reported in main body (optional listing)
• ACMG evidence details per variant

Section content requirements

1–6. Test metadata

Subject info must include (when available):

• Name, sex, date of birth
• Test date / sample accession date
• Test purpose & clinical indication: symptoms, age of onset, imaging/pathology, provisional diagnosis, family history, consanguinity

Sample types: peripheral blood, DNA, dried blood spot, saliva, tissue, etc.

Test method summary: e.g. targeted NGS panel, WES, Sanger confirmation.

7. Test results

For each reported variant, include:

Field	Requirement
Gene	HGNC symbol
Transcript	RefSeq/Ensembl ID with version; state canonical transcript rationale
Variant	HGVS c. / p. / g. nomenclature
Genotype	het / hom / hemizygous / mosaic (with fraction if known)
Zygosity context	de novo / inherited / unknown
Allele frequency	gnomAD, ExAC, 1000G, internal cohort
In silico prediction	SIFT, PolyPhen, CADD, splice predictors (if applicable)
ClinVar / HGMD	Known classification & ID
ACMG classification	Pathogenic / Likely pathogenic / VUS / Likely benign / Benign
Evidence codes	PM2, PP3, PS1, etc. (when classified)

Present primary variants in a table in the main body.

8. Test conclusion

Reporting rules (ACMG-aligned):

Variant class	Report in conclusion?
Pathogenic / Likely pathogenic, related to indication	Yes
VUS, related to indication	Only when conclusion is pending / unresolved
Benign / Likely benign	No
Secondary / incidental findings	Only if consented; clinically actionable only
Unrelated VUS	No

Use clear language: "detected", "consistent with", "cannot exclude" — avoid definitive disease diagnosis.

9. Result interpretation

For each reported variant:

1. ACMG evidence summary (database hits, literature, segregation, de novo status)
2. Phenotype correlation with subject's clinical presentation
3. Inheritance pattern (AD / AR / XL / mitochondrial)
4. Recurrence risk for family members

10. Recommendations

Typical items:

• Genetic counseling referral
• Familial segregation / parental testing
• Expanded testing if negative or inconclusive
• Specialist referral aligned with phenotype
• Re-analysis when new evidence emerges

11. References

Vancouver or numbered style. Include PMIDs/DOIs for all citations used in pathogenicity assessment.

12. Method & limitations

State:

• Specimen requirements & extraction method
• Sequencing platform & read length
• Target region / gene list / exome coverage
• Variant calling & annotation pipeline
• Validation method for reportable variants (Sanger, etc.)
• Limitations: regions not covered, genes not tested, types of variants not detectable (CNV, repeat expansions, methylation, low-level mosaicism)
• Analytical sensitivity & specificity for SNV/indels (and CNV if applicable)

13. Signatures & seal

• Report author (检验者)
• Result reviewer (核对者)
• Final approver (签发者)
• Third-party lab: "检测报告专用章" placeholder
• Report version / revision note if amended

Tool: generate_genetic_testing_report

When exposed as an LLM tool, accept structured input and return JSON matching report-schema.json.

Input parameters

Parameter	Type	Required	Description
testing_institution	object	Yes	Name, address, phone, lab license
subject	object	Yes	Patient demographics & clinical indication
referring	object	Yes	Referring hospital & physician
sample	object	Yes	Type, collection date, receipt date
test	object	Yes	Panel name, method, genes covered
variants	array	Yes	Detected variants (see schema)
conclusion	string	Yes	Primary conclusion text
interpretation	string	Yes	Detailed interpretation
recommendations	array[string]	Yes	Action items
references	array[object]	Yes	{pmid, doi, citation}
method_limitations	object	Yes	Method summary + limitation list
signatures	object	No	Author, reviewer, approver names
include_appendix	bool	No	Default true

Output

Return JSON conforming to report-schema.json. Also produce a human-readable Markdown summary in report_markdown field.

Variant classification quick reference

Follow ACMG/AMP 2015 (PMID: 25741868) and ClinGen updates:

• Combine evidence using PS / PM / PP / BA / BS / BP codes
• Report only classifications with sufficient evidence
• Never upgrade VUS to pathogenic without strong evidence
• Document every evidence item used

Quality checklist

Before finalizing, verify:

Report compliance:
- [ ] All 13 T/SZGIA sections present
- [ ] HGVS nomenclature used for all variants
- [ ] Transcript ID and version specified
- [ ] ACMG class stated for each reported variant
- [ ] No benign/LB variants in conclusion
- [ ] VUS reporting follows indication-only rule
- [ ] No definitive disease diagnosis language
- [ ] Limitations section covers method scope
- [ ] References match cited evidence
- [ ] Signatures / seal placeholders included

Example conclusion phrasing

Good:

In the CFTR gene, a likely pathogenic variant c.1521_1523del (p.Phe508del) was detected in the homozygous state, consistent with the clinical suspicion of cystic fibrosis. Genetic counseling and familial carrier testing are recommended.

Avoid:

The patient has cystic fibrosis. (diagnosis — not allowed)

Additional resources

• JSON schema for tool I/O: report-schema.json
• Markdown report template: report-template.md
• Standard reference: T/SZGIA 4-2018, 深圳市生命科技产学研资联盟, 2018-12-26