43:["$","title",null,{"children":"23andMe Chip Classification | lorenasandoval88 | Observable"}] 4b:T14d3,

Workflow

23andMe File Collection → Chip Manifests → Overlap & Fingerprints →

Classification

This analysis identifies 23andMe chip versions by comparing genotype SNP coordinates against v2, v3, v4, and v5 Build 37 chip fingerprints.

900 Candidate genotype files

885 PGP participants

881 Processed 23andMe files

900 files were selected from Google Cloud Storage for classification, while the consolidated metadata contains 885 unique PGP participants. Some participants have multiple files. Of the 900 candidate files, 881 were processed and 19 were skipped or failed. Processed files can still receive an unknown or unsupported-build classification. The 900 and 881 counts represent files; 885 represents participants.

Chip assignments use a provisional 80% fingerprint match threshold. Build 36 and unknown-build files cannot be reliably classified using Build 37 fingerprints.

4c:T6b3,{ const exportData = filtered_chip_match_table.map(d => ({ participant: d.participant, fileName: d.fileName, build: d.build, variants: d.variants, v3_match: d.v3_match, v4_match: d.v4_match, v5_match: d.v5_match, classification: d.classification })); const csvBlob = new Blob( [d3.csvFormat(exportData)], {type: "text/csv;charset=utf-8"} ); const jsonBlob = new Blob( [JSON.stringify(exportData, null, 2)], {type: "application/json"} ); const csvUrl = URL.createObjectURL(csvBlob); const jsonUrl = URL.createObjectURL(jsonBlob); invalidation.then(() => { URL.revokeObjectURL(csvUrl); URL.revokeObjectURL(jsonUrl); }); return html`

Download CSV Download JSON ${exportData.length.toLocaleString()} filtered files

`; }4d:T790,chipUpdateTable = { const byId = new Map(participants.map(p => [p.id, p])); return matchedParticipantFiles.map(d => { const p = byId.get(d.id) ?? {}; const profile = p.profile ?? {}; const veritasFiles = getVeritasFiles(p); const original = d.originalChip ?? "Unknown"; const inferred = d.inferredChip ?? "Unknown"; const resolved = d.chipVersion ?? "Unknown"; let status; if (original === "Unknown" && resolved !== "Unknown") { status = "Newly assigned"; } else if (original !== "Unknown" && resolved !== original) { status = "Replaced"; } else if (original === inferred) { status = "Confirmed - unchanged"; } else if ( inferred !== "Unknown" && original !== "Unknown" && original.split("_").every(chip => inferred.split("_").includes(chip) ) ) { status = "Compatible - original retained"; } else if (inferred !== "Unknown") { status = "Disagreement - original retained"; } else { status = "Unchanged"; } const extra = Object.fromEntries( Object.entries(d).filter(([key]) => ![ "id", "participant", "filename", "originalChip", "inferredChip", "resolvedChip", "status", "profileUrl" ].includes(key) ) ); const profileFields = Object.fromEntries( Object.entries(profile) .filter(([key]) => key !== "hex") .map(([key, value]) => [`profile_${key}`, value]) ); return { participant: d.id, filename: d.filename, originalChip: original, inferredChip: inferred, resolvedChip: resolved, status, wgsFileAvailable: veritasFiles.length > 0 ? "Yes" : "No", ...extra, profileUrl: p.profileUrl ?? profile.public_profile_url ?? null, ...profileFields }; }); }4e:T48e,wgsInfoTable = { const byId = new Map(participants.map(p => [p.id, p])); return chipUpdateTable .filter(d => d.wgsFileAvailable === "Yes") .map(d => { const p = byId.get(d.participant) ?? {}; // Find Veritas files and remove duplicate references const veritasFiles = [ ...new Map( getVeritasFiles(p).map((f, i) => [ f.downloadUrl ?? f.download_url ?? f.filename ?? `${f.name ?? "file"}_${i}`, f ]) ).values() ]; return { participant: d.participant, filename: d.filename, originalChip: d.originalChip, inferredChip: d.inferredChip, resolvedChip: d.resolvedChip, status: d.status, wgsFileAvailable: "Yes", veritasFileCount: veritasFiles.length, veritasFileNames: veritasFiles .map(f => f.filename ?? f.name ?? "Unknown") .join("; "), veritasDownloadUrls: veritasFiles .map(f => f.downloadUrl ?? f.download_url) .filter(Boolean) .join("; "), profileUrl: p.profileUrl }; }); }4f:Tcf1,--- ## Run the Chip-Matching Script Create the working folder: ```bash mkdir -p ~/chip-match cd ~/chip-match ``` Initialize the Node.js project: ```bash npm init -y npm pkg set type=module npm install @google-cloud/storage unzipper ``` Place the updated `index.js` in: ```text ~/chip-match/index.js ``` The updated script loads the **v2, v3, v4, and v5 chip fingerprints** and compares them against the PGP 23andMe files in: ```text gs://all23_0710/geneticFiles/ ``` For a quick local test, you can run: ```bash node index.js ``` For the full production run, use a **Cloud Run Job** so the process continues even if Cloud Shell is closed. --- ## Create the Dockerfile From: ```bash cd ~/chip-match ``` create the Dockerfile with: ```bash cat > Dockerfile <<'EOF' FROM node:20-slim WORKDIR /app COPY package*.json ./ RUN npm ci --omit=dev COPY index.js ./ CMD ["node", "index.js"] EOF ``` Verify that the Dockerfile is correct: ```bash cat Dockerfile ``` It should begin with: ```text FROM node:20-slim ``` and should **not** contain `cat > Dockerfile` inside the file itself. --- ## Create `.dockerignore` This prevents `node_modules` and unnecessary local files from being uploaded during the Cloud Build. ```bash cat > .dockerignore <<'EOF' node_modules npm-debug.log *.log *_backup.js .git EOF ``` --- ## Set Google Cloud Variables ```bash export PROJECT_ID="nih-nci-dceg-episphere-dev" export REGION="us-east4" ``` Optional check: ```bash echo "PROJECT_ID=$PROJECT_ID" echo "REGION=$REGION" ``` --- ## Build the Container ```bash gcloud builds submit \ --project="$PROJECT_ID" \ --tag="gcr.io/$PROJECT_ID/chip-match:latest" \ . ``` Wait for the build to finish successfully before continuing. --- ## Deploy the Cloud Run Job ```bash gcloud run jobs deploy chip-match-v2v3v4v5 \ --image="gcr.io/$PROJECT_ID/chip-match:latest" \ --region="$REGION" \ --project="$PROJECT_ID" \ --tasks=1 \ --parallelism=1 \ --memory=4Gi \ --cpu=2 \ --task-timeout=3h \ --max-retries=1 \ --set-env-vars="BUCKET_NAME=all23_0710,INPUT_PREFIX=geneticFiles/,FINGERPRINT_PREFIX=chip_manifests/chip_fingerprints,OUTPUT_PREFIX=chip_manifests/chip_match_results,TARGET_BUILD=37,MATCH_THRESHOLD=0.80,FILE_LIMIT=0" ``` --- ## Execute the Job Run the job asynchronously: ```bash gcloud run jobs execute chip-match-v2v3v4v5 \ --region="$REGION" \ --project="$PROJECT_ID" \ --async ``` Once this command successfully starts the execution, **Cloud Shell can be closed**. The Cloud Run Job continues independently. --- ## Check Job Status Check the latest execution: ```bash gcloud run jobs executions describe-latest \ --job=chip-match-v2v3v4v5 \ --region="$REGION" ``` Or list recent executions: ```bash gcloud run jobs executions list \ --job=chip-match-v2v3v4v5 \ --region="$REGION" ``` --- ## Output Results are written to: ```text gs://all23_0710/chip_manifests/chip_match_results/ ``` Main output files: ```text chip_match_results.json chip_match_summary.json skipped_files.json failed_files.json ``` List the output files: ```bash gcloud storage ls \ gs://all23_0710/chip_manifests/chip_match_results/ ``` View the summary: ```bash gcloud storage cat \ gs://all23_0710/chip_manifests/chip_match_results/chip_match_summary.json ```50:T4e5,chip_match_table = v2v3v4v5_match_results.map(d => { const supported = d.genomeBuild === d.targetBuild; return { participant: d.fileName?.match(/^(hu[0-9A-F]+)/i)?.[1] ?? "", fileName: d.fileName, build: d.genomeBuild ?? "Unknown", variants: d.totalUniqueCoordinates, v2_match: supported ? d.matches?.v2?.matchPercent ?? 0 : null, v3_match: supported ? d.matches?.v3?.matchPercent ?? 0 : null, v4_match: supported ? d.matches?.v4?.matchPercent ?? 0 : null, v5_match: supported ? d.matches?.v5?.matchPercent ?? 0 : null, classification: d.classification, basis: d.classification === "unsupported_build" ? `Build ${d.genomeBuild}; fingerprints are Build ${d.targetBuild}` : d.basis }; }) // chip_match_table = v2v3v4v5_match_results.map(d => ({ // participant: d.fileName?.match(/^(hu[0-9A-F]+)/i)?.[1] ?? "", // fileName: d.fileName, // build: d.genomeBuild ?? "Unknown", // variants: d.totalUniqueCoordinates, // v2_match: d.matches?.v2?.matchPercent ?? 0, // v3_match: d.matches?.v3?.matchPercent ?? 0, // v4_match: d.matches?.v4?.matchPercent ?? 0, // v5_match: d.matches?.v5?.matchPercent ?? 0, // classification: d.classification, // basis: d.basis // 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Chip Classification","cells":[{"id":43,"value":"# 23andMe Chip Classification\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":142,"value":"$4b","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":223,"value":"","pinned":true,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":110,"value":"

\n \n

","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"v2v3v4v5_match_results = (await (await FileAttachment(\"v2v3v4v5_chip_match_results.json\").json()))\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":146,"value":"---\n#### Chip Classification Results by Genome Build and Chip Version","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":65,"value":"viewof buildFilter = Inputs.select(\n [\"All\", \"37\", \"36\", \"Unknown\"],\n {\n label: \"Genome Build\",\n value: \"All\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":68,"value":"viewof classificationFilter = Inputs.select(\n [\n \"All\",\n ...new Set(\n v2v3v4v5_match_results\n .map(d => d.classification)\n .filter(Boolean)\n )].sort(),\n {\n label: \"Classification\",\n multiple: true,\n value: [\"v5\"]\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":79,"value":"${filtered_chip_match_table.length.toLocaleString()} files shown","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":113,"value":"filtered_chip_match_table = chip_match_table.filter(d => {\n\n const buildMatch =\n buildFilter === \"All\" ||\n d.build === buildFilter;\n\n const classificationMatch =\n classificationFilter.length === 0 ||\n classificationFilter.includes(\"All\") ||\n classificationFilter.includes(d.classification);\n\n return buildMatch && classificationMatch;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":66,"value":"Inputs.table(filtered_chip_match_table, {\n columns: [\n \"participant\",\n \"fileName\",\n \"build\",\n \"variants\",\n \"v2_match\",\n \"v3_match\",\n \"v4_match\",\n \"v5_match\",\n \"classification\"\n ],\n\n header: {\n participant: \"Participant\",\n fileName: \"Filename\",\n build: \"Build\",\n variants: \"Coordinates\",\n v2_match: \"v2 Match %\",\n v3_match: \"v3 Match %\",\n v4_match: \"v4 Match %\",\n v5_match: \"v5 Match %\",\n classification: \"Classification\"\n },\n\n width: {\n participant: 80,\n fileName: 300,\n build: 45,\n variants: 100,\n v2_match: 90,\n v3_match: 90,\n v4_match: 90,\n v5_match: 90,\n classification: 130\n },\n\n format: {\n variants: d3.format(\",\"),\n v2_match: d => d == null ? \"—\" : `${d.toFixed(2)}%`,\n v3_match: d => d == null ? \"—\" : `${d.toFixed(2)}%`,\n v4_match: d => d == null ? \"—\" : `${d.toFixed(2)}%`,\n v5_match: d => d == null ? \"—\" : `${d.toFixed(2)}%`\n },\n\n rows: 10\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":120,"value":"$4c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":186,"value":"---\n#### Chip Classification Updates — ${chipUpdateTable.length} Files (${[...new Set(chipUpdateTable.map(d => d.inferredChip))].join(\", \")})\n\nOf the **${chipUpdateTable.length} files** analyzed:\n\n- **${chipUpdateTable.filter(d => d.originalChip === d.inferredChip && d.inferredChip !== \"Unknown\").length} confirmed:** Original chip version matched the SNP fingerprint classification.\n- **${chipUpdateTable.filter(d => d.status === \"Newly assigned\").length} newly assigned:** Previously classified as **Unknown**, now assigned a chip version using SNP fingerprints.\n- **${chipUpdateTable.filter(d => d.status === \"Disagreement - original retained\").length} disagreements:** Original and inferred chip versions differ; the original was retained.\n- **${chipUpdateTable.filter(d => d.status === \"Replaced\").length} replaced:** Original chip version was updated to the inferred version.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":183,"value":"$4d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":191,"value":"Inputs.table(chipUpdateTable, {\n rows: 15,\n columns: Object.keys(chipUpdateTable[0] ?? {}),\n\n format: {\n filename: d =>\n d?.length > 20 ? d.slice(0, 20) + \"…\" : d,\n\n ...Object.fromEntries(\n Object.keys(chipUpdateTable[0] ?? {})\n .filter(key => key.startsWith(\"profile_\"))\n .map(key => [\n key,\n d => {\n const s = typeof d === \"string\"\n ? d\n : JSON.stringify(d ?? \"\");\n\n return s.length > 20\n ? s.slice(0, 20) + \"…\"\n : s;\n }\n ])\n )\n },\n\n width: {\n ...Object.fromEntries(\n Object.keys(chipUpdateTable[0] ?? {})\n .map(key => [key, 110])\n ),\n\n participant: 90,\n filename: 160,\n originalChip: 100,\n inferredChip: 100,\n resolvedChip: 100,\n status: 170,\n wgsFileAvailable: 110,\n profileUrl: 110\n },\n\n maxWidth: 850,\n layout: \"fixed\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":217,"value":"---\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":222,"value":"

\n \n

\n\n---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"$4e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":214,"value":"Inputs.table(wgsInfoTable, {\n rows: 11,\n\n columns: Object.keys(wgsInfoTable[0] ?? {}),\n\n format: {\n filename: d =>\n d?.length > 22 ? d.slice(0, 22) + \"…\" : d,\n\n veritasFileNames: d =>\n d?.length > 35 ? d.slice(0, 35) + \"…\" : d\n },\n\n width: {\n participant: 90,\n filename: 170,\n originalChip: 100,\n inferredChip: 100,\n resolvedChip: 100,\n status: 170,\n wgsFileAvailable: 90,\n veritasFileCount: 90,\n veritasFileNames: 200,\n veritasDownloadUrls: 150,\n profileUrl: 140\n },\n\n maxWidth: 900,\n layout: \"fixed\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"---\n## Results","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"Of **900 candidate objects**, **881 23andMe files were successfully processed**, **19 objects were skipped**, and **0 files failed**.\n\n| Classification | Files | Interpretation |\n|---|---:|---|\n| v3 | 265 | Classified as 23andMe v3 |\n| v4 | 231 | Classified as 23andMe v4 |\n| v5 | 74 | Classified as 23andMe v5 |\n| v3 + v5 | 6 | Matched fingerprints from both v3 and v5 |\n| v3 + v4 + v5 | 1 | Matched fingerprints from all three chip versions |\n| Unknown | 34 | Did not meet the ≥80% fingerprint-match threshold |\n| Unsupported build | 257 | Genome Build 36; fingerprints were defined for Build 37 |\n| Unknown build | 13 | Genome build could not be determined |\n| **Total processed** | **881** | **23andMe files successfully processed** |\n| **Skipped** | **19** | **Candidate objects not processed as 23andMe files** |\n| **Failed** | **0** | **No processing failures** |","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2,"value":"$4f","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":39,"value":"","pinned":true,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":116,"value":"---\n\n## Helper Functions/variables","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"$50","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":181,"value":"participants = FileAttachment(\n \"NEW_participants_1020_consolidated_with_build_and_profile_07102026_2053.json\"\n).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":210,"value":"getVeritasFiles = p =>\n [\n ...(p.files ?? []),\n ...(p.profile?.files ?? [])\n ].filter(f =>\n [\n f.filename,\n f.name,\n f.dataType,\n f.data_type,\n f.description,\n f.downloadUrl,\n f.download_url\n ]\n .filter(Boolean)\n .join(\" \")\n .toLowerCase()\n .includes(\"veritas\")\n )","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"matchedParticipantFiles = {\n const selectedNames = new Set(\n filtered_chip_match_table.map(d => d.fileName)\n );\n\n return participants.flatMap(p =>\n (p.files ?? []).flatMap(f =>\n (f.genomeBuildFiles ?? [])\n .filter(g => selectedNames.has(g.gcsfilename))\n .map(g => ({\n id: p.id,\n filename: g.gcsfilename,\n genomeBuild: f.genomeBuild,\n chipVersion: f.chipVersionResolved,\n originalChip: f.chipVersionOriginal,\n inferredChip: f.chipVersionInferred,\n valid23File: f.valid23File,\n v5Match: f.chipMatchPercentages?.v5 ?? null,\n classification: f.chipClassification,\n profileUrl: p.profileUrl\n }))\n )\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W51","stdlib":"2"}} 42:null