Whole-genome sequencing (WGS) data analysis for pathogenic mutations in cancer predisposition genes.
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├── your_file.vcf.gz # Raw WGS VCF (DeepVariant v1.5.0, GRCh37)
├── src/
│ └── analyze.py # VEP annotation pipeline script
├── BRCA2/
├── TP53/
├── RB1/
├── APC/
├── PTEN/
├── KRAS/
├── EGFR/
├── ATM/
├── CHEK2/
├── PALB2/
├── NAFLD/
├── NAFLD_extended/
└── CLINICAL_REPORT/ # Consolidated clinical-style summary (EN + zh-TW)
Each gene folder contains README.md (English) and README_zh-TW.md (Traditional Chinese).
A consolidated, clinical-style summary of all findings is available in CLINICAL_REPORT/:
index.md— landing page with headline findingscancer.md— 10-gene hereditary cancer screen (negative)nafld.md— NAFLD/metabolic panel (high genetic risk; APOE ε4/ε4)
Each report follows a clinical structure: Specimen & Method → Results → Interpretation → Limitations → Recommendations → Considerations for Your Clinician. Recommendations are generic referrals; Considerations are data-framed observations, not medical directives.
| Gene | Chromosome | Region (GRCh37) | PASS Variants | Coding Variants | Pathogenic |
|---|---|---|---|---|---|
| BRCA2 | chr13 | 32,889,611–32,973,805 | 68 | 2 (both benign) | None |
| TP53 | chr17 | 7,571,720–7,590,868 | 38 | 0 | None |
| RB1 | chr13 | 48,877,887–49,056,122 | 226 | 0 | None |
| APC | chr5 | 112,073,554–112,181,936 | 164 | 1 (benign) | None |
| PTEN | chr10 | 89,622,870–89,731,687 | 35 | 0 | None |
| KRAS | chr12 | 25,357,723–25,403,870 | 84 | 0 | None |
| EGFR | chr7 | 55,086,714–55,324,313 | 359 | 1 (benign) | None |
| ATM | chr11 | 108,093,211–108,239,829 | 55 | 1 (benign) | None |
| CHEK2 | chr22 | 29,083,731–29,138,410 | 108 | 0 | None |
| PALB2 | chr16 | 23,614,488–23,652,631 | 13 | 0 | None |
No pathogenic mutations detected across all 10 genes.
| Gene | rsID | Location (GRCh37) | Variant | Genotype | Result |
|---|---|---|---|---|---|
| PNPLA3 | rs738409 | chr22:44324727 | I148M (C>G) | HOM (G/G) | Homozygous risk allele ×2 |
| TM6SF2 | rs58542926 | chr19:19379549 | E167K (C>T) | HOM (T/T) | Homozygous risk allele ×2 |
| MBOAT7 | rs641738 | chr19:54676763 | T>C (intronic) | HET (C/T) | Heterozygous risk allele ×1 |
| HSD17B13 | rs72613567 | chr4:88231394 | TA-insertion | wild-type | No protective allele |
High NAFLD genetic risk profile — homozygous PNPLA3 I148M and TM6SF2 E167K, plus heterozygous MBOAT7. See NAFLD/ for full details.
| Gene | rsID | Variant | Genotype | Result |
|---|---|---|---|---|
| GCKR | rs1260326 | P446L | HET (T/C) | Risk-modifier (population-dependent) |
| MTARC1 | rs2642438 | A165T | HOM (G/G) | Protective ×2 (favourable) |
| APOE | rs429358+rs7412 | ε2/ε3/ε4 | ε4/ε4 | Homozygous ε4 — clinically relevant |
| LYPLAL1 | rs12137855 | C>T | wild-type | No risk allele |
| GPAM | rs2792751 | I43V | wild-type | No risk allele |
| PNPLA2 | rs1138693 | L481P | HET | Common benign polymorphism |
| CIDEB | (full gene scan) | — | no coding variants | No protective LoF variants |
| TRIB1 | rs2954021/17321515/2954029 | A>G/T | wild-type | No risk allele |
| MERTK | rs34943572 | N329S | HET | Rare, VUS |
| PEMT | rs7946 | V175M | wild-type | No risk allele |
Notable: APOE ε4/ε4 (homozygous). See NAFLD_extended/ for full details.
| Gene | Variant (GRCh37) | Genotype | Protein | ClinVar | gnomAD AF | Classification |
|---|---|---|---|---|---|---|
| BRCA2 | chr13:32906729 A>C (rs144848) | HET | p.Asn372His | Benign (expert panel) | ~24% | Common polymorphism |
| BRCA2 | chr13:32929387 T>C (rs169547) | HOM | p.Val2466Ala | Benign | ~98% | Near-fixed polymorphism |
| APC | chr5:112176756 T>A | HET | p.Val2355Asp | Not in ClinVar | Low | Likely benign |
| EGFR | chr7:55229255 G>A | HET | p.Arg451Lys | Not in ClinVar | Common | Common polymorphism |
| ATM | chr11:108183167 A>G | HOM | p.Asn1497Ser | Not in ClinVar | Common | Common polymorphism |
| Gene | Total PASS | Intronic | UTR | Upstream/Downstream | Synonymous | Splice-adjacent |
|---|---|---|---|---|---|---|
| BRCA2 | 68 | ~50 | ~5 | ~10 | 3 | 0 |
| TP53 | 38 | ~25 | ~1 | ~12 | 0 | 0 |
| RB1 | 226 | ~180 | ~20 | ~25 | 0 | 1 |
| APC | 164 | ~120 | ~5 | ~35 | 4 | 0 |
| PTEN | 35 | ~25 | ~3 | ~7 | 0 | 0 |
| KRAS | 84 | ~60 | ~5 | ~18 | 1 | 0 |
| EGFR | 359 | ~280 | ~15 | ~50 | 4 | 0 |
| ATM | 55 | ~40 | ~5 | ~10 | 0 | 1 |
| CHEK2 | 108 | ~85 | ~5 | ~18 | 0 | 0 |
| PALB2 | 13 | ~10 | ~1 | ~2 | 0 | 0 |
- Extract PASS-quality variants from VCF using
awk - Annotate via Ensembl VEP REST API (GRCh37 HGVS endpoint)
- Cross-reference with ClinVar and gnomAD for clinical significance
python src/analyze.py <GENE> <CHROM> <START> <END> your_file.vcf.gzTools: bcftools, Python 3, Ensembl VEP REST API, NCBI E-utilities
- File:
your_file.vcf.gz(173 MB) - Caller: DeepVariant v1.5.0
- Reference: GRCh37 (hg19)
- Sample: ULMEDCBB3A73_ULMEDCBB3A73
| Tag | Description |
|---|---|
| v1.0 | Initial BRCA2 analysis |
| v1.1 | Traditional Chinese README added |
| v1.2 | Session export log added |
| v1.3 | Docs reorganized into gene folders |
| TP53 | TP53 analysis added |
| RB1 | RB1 analysis added |
| APC | APC analysis added |
| PTEN | PTEN analysis added |
| KRAS | KRAS analysis added |
| EGFR | EGFR analysis added |
| ATM | ATM analysis added |
| CHEK2 | CHEK2 analysis added |
| PALB2 | PALB2 analysis added |
| v2.0 | Full 10-gene summary tables added |
| rc-1 | Session export log added |
| NAFLD | NAFLD core 4-locus panel |
| NAFLD_extended | Extended NAFLD panel (10 loci) |
| NAFLD_corrected | Core panel corrected (chr-prefix bug fix) |
| v3.0 | Clinical report added (CLINICAL_REPORT/) |
This is a computational analysis, not a clinical-grade variant interpretation. For medical decisions, consult a certified genetic counselor or clinical genetics laboratory.