From a7ea7c3bdfc76f7442dc9d0a8a3e3974b4708960 Mon Sep 17 00:00:00 2001 From: Kemal Yaylali Date: Mon, 28 Sep 2026 19:47:34 +0100 Subject: [PATCH] P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 360 GSA arrays (120 1000 Genomes individuals x 3 replicates): concordance 0.9934 vs NYGC 30x (0.9958 on sites in both sets), 0.9985 vs GIAB HG001 v4.2.1 (non-ref F1 0.997), replicate concordance 0.9966; allele-swap sites 0.016 %; 358/360 replicate pairs detected as duplicates. Plan §16.5 metrics in docs/validation/P8.md (K-024). --- README.md | 3 + docs/known_unknowns.md | 1 + docs/validation/P8.md | 106 ++ docs/validation/P8_gse165845_summary.json | 1616 +++++++++++++++++++++ 4 files changed, 1726 insertions(+) create mode 100644 docs/validation/P8.md create mode 100644 docs/validation/P8_gse165845_summary.json diff --git a/README.md b/README.md index 1a99fb6..7f70261 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,9 @@ On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained diff Phase **P7 (differential testing)** is complete: `simurg compare` (EXACT/NEAR/DISCREPANCY/UNKNOWN per field and locus class, every discrepancy listed, HTML dashboard) and a nightly run on the Pi (GSA vs gtc2vcf, Omni2.5 subset vs vendor GTCs, VCF regression) — `docs/validation/P7.md`. +Phase **P8 (scientific validation)** is complete: on GEO GSE165845 (360 GSA arrays, 120 1000 Genomes individuals × +3 replicates) genotype concordance is 0.9934 vs NYGC 30x WGS, 0.9985 vs GIAB HG001 v4.2.1 (non-ref F1 0.997), and +0.9966 between replicates — `docs/validation/P8.md`. Available commands: `simurg version`, `simurg inspect [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`, `simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`, `simurg gtc-to-vcf`, `simurg export plink|bedgraph|finalreport|locus-summary`, `simurg compare`. diff --git a/docs/known_unknowns.md b/docs/known_unknowns.md index 71714e6..953c3ff 100644 --- a/docs/known_unknowns.md +++ b/docs/known_unknowns.md @@ -4,6 +4,7 @@ Plan §20 lists the open questions; this file records what the implementation ha | ID | Date | Topic | Finding | Status | |---|---|---|---|---| +| K-024 | 2026-09-28 | GSE165845 (P8) | GSA-MD v1 chips have no public cluster file; the GSA v1 C1 EGT with the C2 build-38 BPM covers 99.996 % of bead addresses and gives median LogR deviation 0.246 (cluster mismatch, not noise). GSM5051309 (NA20362 rep 2) is a failed array (call rate 0.762, concordance 0.336 with its own replicates). 27 510 array records have no NYGC 30x record and are scored as hom-ref; 1444 of them are systematically called alt. | Recorded in `docs/validation/P8.md`; results reported with and without these. | | K-023 | 2026-09-28 | P6 optional outputs | Implemented and validated the same day: `--info-fields` (with `--egt`), `--extra-format`, `--merge-snv-indel`, `--auxiliary-loci`, PLINK 2 `.pgen`. Two decisions: OUT-035 rule (d) uses the MNV's last plus-strand base for minus-strand designs (spec amended); `--extra-format` writes NORMX/NORMY missing where the raw intensities are both 0, and THETA/R missing where both normalized intensities are 0 (148 values on 3 GSA samples; gtc2vcf writes 0). | resolved | | K-022 | 2026-09-28 | VCF oracles' limits (GSA v4 PGx, GRCh38) | gtc2vcf leaves 144 indel probes unresolved (`REF=I`/`D`) that SimurgArray resolves from `SourceSeq`; both leave 49 indels unresolved. GTCtoVCF (python-2.7 era) runs under Python 3 only with two local patches (pyvcf3 `Format` field; skip instead of crash on 3 CYP2D6 indels whose `SourceSeq` has the dash on the right, `[ALLELE/-]`, which SimurgArray handles), and needs the alt-contig loci filtered when the FASTA has no alts. Neither oracle applies ploidy (males' X/Y/MT hets stay diploid). | documented | | K-021 | 2026-09-28 | Control metrics on legacy Omni2.5 IDATs | (1) The Omni2.5 manifest lists two bead addresses per control (e.g. 27630314 and 127630314, two bead-pool versions); only one is on a given chip. Absent addresses were NaN and poisoned the bead mean → 1794/2141 samples falsely flagged on both staining metrics. Absent addresses are now skipped. (2) 1290 samples have Biotin (Bgnd) green = 0 exactly (background-subtracted), so staining green is signal/0; QC-008 now defines that as +Inf (pass) and only 0/0 as NaN (flag). | resolved (spec QC-008 amended) | diff --git a/docs/validation/P8.md b/docs/validation/P8.md new file mode 100644 index 0000000..076070c --- /dev/null +++ b/docs/validation/P8.md @@ -0,0 +1,106 @@ +# Phase P8 validation — scientific accuracy against whole-genome truth + +Date: 2026-09-28. One AWS spot run (m7g.4xlarge, 16 vCPU, 36 min; plus an aborted first attempt, see Notes). +Cost ≈ $0.33 in total. Full numbers: `docs/validation/P8_gse165845_summary.json`. + +## Data and method + +| Item | Source | +|---|---| +| Arrays | GEO **GSE165845**: 120 1000 Genomes individuals × 3 replicates = **360 samples** (GSA-MD v1 BeadChips, 27 chips), IDATs from GEO | +| Manifest / clusters | GSA-24v1-0 **C2 build 38** BPM + CSV, GSA v1 **C1** cluster file (the only public GSA v1 EGT; 99.996 % of the manifest's bead addresses are on the GSA-MD chips) | +| Calls | `simurg genotype` (defaults, 360 samples in 1 min 55 s) → `simurg gtc-to-vcf --merge --csv` (cohort BCF, 4 min) | +| Truth 1 | NYGC 1kGP 30x high-coverage phased panel (20220422, SNV/indel, GRCh38), all 120 individuals | +| Truth 2 | GIAB HG001 (NA12878) v4.2.1 GRCh38, inside its confident-region BED, chromosomes 1–22 | +| Reference | Ensembl GRCh38 release 110 primary assembly | + +Scripts: `scripts/p8/prepare.py` (GEO download, IDATs laid out by the barcode/position in their headers), +`scripts/cloud/tasks/p8.sh` (the whole run), `scripts/p8/validate_p8.py` (metrics). Both call sets are split to +biallelic records and left-normalised against the same FASTA (`bcftools norm -m-any`) and matched on +(CHROM, POS, REF, ALT). Chromosomes 1–22 and X (GIAB: 1–22). An array site absent from the WGS call set is +counted as homozygous reference (both call sets are complete for their individuals); a site where the WGS set has +*different* alleles at the same position is excluded and counted (871 of 617 144). Genotype classes are hom-ref / +het / hom-alt; a variant-level true positive needs the exact genotype. MAF comes from the NYGC AF over 3202 genomes. + +## Results (plan §16.5) + +### Against NYGC 30x — 360 samples, 617 144 array records, 219 M called genotypes + +| Metric | All sites | Sites in both sets | Excluding the one failed array (359 samples) | +|---|---|---|---| +| Genotype concordance | **0.99338** | 0.99580 | 0.99478 | +| Non-reference discordance (NRD) | 0.0245 | 0.0150 | — | +| No-call rate | 0.0108 | 0.0110 | 0.0102 | +| Non-ref sensitivity / precision / F1 | 0.9956 / 0.9768 / 0.9861 | 0.9956 / 0.9864 / 0.9910 | — | + +Per genotype class (sites in both sets): + +| Class | Truth genotypes | Sensitivity | Precision | Specificity | F1 | +|---|---|---|---|---|---| +| hom-ref | 151.6 M | 0.9959 | 0.9995 | 0.9986 | 0.9977 | +| het | 36.9 M | 0.9943 | 0.9905 | 0.9980 | 0.9924 | +| hom-alt | 21.2 M | 0.9979 | 0.9792 | 0.9976 | 0.9885 | + +Per MAF bin (sites in both sets; non-ref precision is low for rare variants, the usual array behaviour — most +"alt" calls of a very rare variant are false positives): + +| MAF | Genotypes | Concordance | NRD | Non-ref sensitivity | Non-ref precision | F1 | +|---|---|---|---|---|---|---| +| < 0.1 % | 3.9 M | 0.9959 | 0.799 | 0.993 | 0.201 | 0.334 | +| 0.1–1 % | 49.0 M | 0.9975 | 0.152 | 0.997 | 0.849 | 0.917 | +| 1–5 % | 38.9 M | 0.9959 | 0.074 | 0.995 | 0.927 | 0.960 | +| 5–10 % | 21.9 M | 0.9947 | 0.030 | 0.995 | 0.972 | 0.983 | +| 10–20 % | 32.8 M | 0.9951 | 0.013 | 0.995 | 0.988 | 0.992 | +| 20–50 % | 63.2 M | 0.9952 | 0.008 | 0.996 | 0.994 | 0.995 | + +SNVs: concordance 0.99336 (218.2 M genotypes). Indels: concordance 0.99754 (1.24 M genotypes), non-ref sensitivity +0.990, precision 0.828. Array sites absent from NYGC (27 510 records, 9.8 M genotypes): 94.2 % hom-ref calls; +the remaining alt calls there are the main source of the lower "all sites" precision. + +Per sample: median concordance 0.99485, median NRD 0.0189. Lowest: 0.3369 (the failed array below), then 0.9866. + +### Against GIAB HG001 v4.2.1 — NA12878 × 3 replicates, confident regions + +| Metric | Value | +|---|---| +| Array records inside the BED | 577 617 (150 671 in the GIAB VCF, 426 658 hom-ref by absence) | +| Genotype concordance | **0.99853** (replicates 0.99911, 0.99727, 0.99918) | +| NRD | 0.0056 | +| No-call rate | 0.0165 | +| Non-ref sensitivity / precision / F1 | 0.9992 / 0.9946 / **0.9969** | +| hom-ref / het / hom-alt F1 | 0.9991 / 0.9962 / 0.9981 | +| Indels (9371 genotypes) | concordance 0.99989, sensitivity 1.000, precision 0.991 | + +### Replicates, site errors, batch, relatedness + +| Metric | Result | +|---|---| +| Replicate concordance (360 pairs, both called) | pooled **0.99660**; median 0.99963; without the failed array (358 pairs) 0.99942 | +| Median non-ref discordance between replicates | 0.0014 | +| Systematically discordant sites (wrong in ≥ 50 % of ≥ 10 called samples) | 2419 of 616 221 (0.39 %); 1444 of them absent from NYGC | +| Allele-swap pattern (strand/allele error: array = 2 − truth at ≥ 80 % of the discordant calls) | **100 sites (0.016 %)**, 5 of them A/T or C/G | +| Per-chip batch (27 chips) | median call rate 0.9911, median LogR deviation 0.246; 4 chips flagged as call-rate outliers (3 × MAD): 203672270124 (holds the failed array; mean concordance 0.830), 203660990106 and 203660990145 (hold the 2nd and 3rd lowest-concordance arrays, chip means 0.992/0.993), 203660990061 (one array, call rate 0.980, concordance 0.994) | +| Replicates detected as duplicates by `simurg genotype` cohort relatedness | 358/360 pairs; the 2 missed pairs involve the failed array; 0 duplicates between different individuals | +| Mendelian error rate | not measurable here (no complete trio among the 120 individuals); P5: median 0.031 % over 335 Omni2.5 trios (`docs/validation/P5.md`) | + +Lists: `per_sample.tsv`, `replicate_pairs.tsv.gz`, `systematic_sites.tsv.gz` in the run's results +(`s3://…/run-20260928T180818Z/p8/`, kept out of the repository). + +## Notes + +* **One failed array.** GSM5051309 (NA20362 replicate 2, `203672270124_R12C02`) has call rate 0.762 and LogR + deviation 1.38; `simurg genotype` flags it `low_call_rate;high_lrr_sd;het_outlier`. Its genotypes agree with its own + replicates at only 0.336, so the sample itself (not the pipeline) is bad. The run used no QC profile, so the flag + did not set a FAIL status; with `--qc-profile genotyping` it would have been excluded. The headline numbers keep it. +* **Cluster file.** GSE165845 was run on GSA-MD v1 chips, for which no public cluster file exists; the GSA v1 C1 EGT + was used. The high median LogR deviation (0.246) reflects that mismatch, not intensity noise, and call rate and + concordance could only improve with a matching EGT. +* **Absent-as-hom-ref.** 27 510 array records (4.5 %) have no NYGC record. Most are called hom-ref in all samples; + the 1444 systematically "wrong" ones among them are array alt calls at sites NYGC does not report (filtered or + truly monomorphic). The "sites in both sets" column shows the numbers without this assumption. +* **First attempt aborted.** The first run downloaded the 40 GB NYGC VCFs before using them; EBI served ≈ 15 MB/s, + the CPU sat idle for 30 minutes and the idle alarm terminated the instance (as designed; ≈ $0.17). The task now + streams each chromosome through `bcftools view -T` (manifest positions ± 100 bp, 120 individuals) while + genotyping runs, which keeps the CPU busy and needs no disk for the truth set. +* **Deferred parts of §16.5.** CNV precision/recall and PGx diplotype concordance need the CN/LOH and PGx modules + (plan §18 "v2 modules"); they are measured when those modules exist. diff --git a/docs/validation/P8_gse165845_summary.json b/docs/validation/P8_gse165845_summary.json new file mode 100644 index 0000000..90cc501 --- /dev/null +++ b/docs/validation/P8_gse165845_summary.json @@ -0,0 +1,1616 @@ +{ + "array_samples": 360, + "individuals": 120, + "samples_without_truth": [], + "array_duplicate_keys": 0, + "nygc_30x": { + "sites": { + "array_records": 617144, + "matched": 588763, + "absent_in_truth_as_hom_ref": 27510, + "allele_mismatch_excluded": 871, + "outside_region": 0 + }, + "all": { + "n_called": 219454275, + "n_nocall": 2404005, + "concordance": 0.9933790626771796, + 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