{"id":11317,"date":"2022-03-30T10:07:29","date_gmt":"2022-03-30T01:07:29","guid":{"rendered":"https:\/\/admin.acceleratingscience.com\/learning-at-the-bench\/?p=11317"},"modified":"2025-04-23T14:11:42","modified_gmt":"2025-04-23T05:11:42","slug":"mutation_analysis_snp_ngs_gsd_ts_1","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/learning-at-the-bench\/mutation_analysis_snp_ngs_gsd_ts_1\/","title":{"rendered":"NGS\u5909\u7570\u89e3\u6790\u306b\u65e5\u672c\u4eba\u591a\u578b\uff08SNP\uff09\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u3092\u8ffd\u52a0\u3057\u3088\u3046\uff01"},"content":{"rendered":"

\u25bc\u3053\u3093\u306a\u65b9\u306b\u304a\u3059\u3059\u3081\u3067\u3059\uff01
\n\u30fbIon Torrent\u2122 \u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u3067\u30d2\u30c8\u306e\u907a\u4f1d\u5b50\u5909\u7570\u89e3\u6790\u3092\u5b9f\u65bd\u3057\u3066\u3044\u308b\u3001\u3082\u3057\u304f\u306f\u5b9f\u65bd\u3057\u305f\u3044
\n\u30fbIon Reporter\u2122 \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u3092\u4f7f\u7528\u3057\u3066\u30c7\u30fc\u30bf\u89e3\u6790\u3092\u5b9f\u65bd\u3057\u3066\u3044\u308b
\n\u30fbIon Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306e\u89e3\u6790\u3092\u30ab\u30b9\u30bf\u30e0\u3057\u305f\u3044<\/p>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u3068\u306f\uff1f<\/h2>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2<\/a>\u306f\u3001\u5f53\u793e\u304c\u63d0\u4f9b\u3059\u308b\u30af\u30e9\u30a6\u30c9\u30d9\u30fc\u30b9\u306e\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\uff08NGS\uff09 \u30c7\u30fc\u30bf\u89e3\u6790\u7528\u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u3067\u3059\u3002Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306f\u30d2\u30c8\u907a\u4f1d\u5b50\u5909\u7570\u89e3\u6790\u306e\u6a5f\u80fd\u304c\u5145\u5b9f\u3057\u3066\u304a\u308a\u3001\u30b2\u30ce\u30e0\u4e0a\u306e\u5909\u7570\u3084\u878d\u5408\u907a\u4f1d\u5b50\u3092\u691c\u51fa\u3059\u308b\u3060\u3051\u3067\u306a\u304f\u3001\u691c\u51fa\u3057\u305f\u5909\u7570\u306b\u5bfe\u3057\u3066\u3055\u307e\u3056\u307e\u306a\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u3092\u4ed8\u52a0\u3057\u305f\u308a\u3001\u305d\u306e\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u3092\u57fa\u306b\u3057\u305f\u30d5\u30a3\u30eb\u30bf\u30ea\u30f3\u30b0\u6a5f\u80fd\u306a\u3069\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u304c\u53ef\u80fd\u3067\u3059\u3002Web\u30d6\u30e9\u30a6\u30b6\u306e\u64cd\u4f5c\u306e\u307f\u3067\u30c7\u30fc\u30bf\u89e3\u6790\u304c\u5b9f\u884c\u3067\u304d\u3001\u7279\u5225\u306a\u30d0\u30a4\u30aa\u30a4\u30f3\u30d5\u30a9\u30de\u30c6\u30a3\u30af\u30b9\u306e\u77e5\u8b58\u3092\u6301\u305f\u306a\u304f\u3066\u3082\u3001\u8208\u5473\u306e\u3042\u308b\u5909\u7570\u3092\u5c11\u306a\u3044\u64cd\u4f5c\u30b9\u30c6\u30c3\u30d7\u3067\u7d5e\u308a\u8fbc\u3080\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002\u307e\u305f\u3001\u30d2\u30c8\u306e\u5909\u7570\u89e3\u6790\u4ee5\u5916\u306b\u3082\u3001\u514d\u75ab\u30ec\u30d1\u30fc\u30c8\u30ea\u30fc\u89e3\u6790\u308416S rRNA \u30b7\u30fc\u30b1\u30f3\u30b9\uff08\u7d30\u83cc\u53e2\uff09\u89e3\u6790\u306e\u305f\u3081\u306e\u6a5f\u80fd\u304c\u5099\u308f\u3063\u3066\u3044\u307e\u3059\u3002\u89e3\u6790\u65b9\u6cd5\u306f\u3001\u300cIon Reporter \u57fa\u672c\u64cd\u4f5c\u65b9\u6cd5<\/a>\u300d\u8cc7\u6599\u3092\u3054\u89a7\u304f\u3060\u3055\u3044\u3002<\/p>\n

\u521d\u671f\u8a2d\u5b9a\u3067\u5099\u308f\u3063\u3066\u3044\u308b\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831<\/h2>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306b\u306f\u3001\u4f8b\u3048\u3070\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u5909\u7570\u3084\u591a\u578b\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u53d6\u5f97\u3055\u308c\u305f\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u304c\u642d\u8f09\u3055\u308c\u3066\u304a\u308a\u3001\u691c\u51fa\u3057\u305f\u5909\u7570\u306e\u8a55\u4fa1\u306b\u5f79\u7acb\u3061\u307e\u3059\u3002
\n\u30fbCOSMIC<\/a>
\n\u30fbClinVar<\/a>
\n\u30fbdbSNP<\/a>
\n\u30fb1000 Genomes<\/a>
\n\u30fbNHLBI ESP<\/a>
\n\u30fbExAC<\/a>
\n\u30fbgnomAD<\/a><\/p>\n

\u4ee3\u8868\u7684\u306a\u65e5\u672c\u4eba\u591a\u578b\uff08SNP\u3001INDEL\uff09\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9<\/h2>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306b\u306f\u5148\u8ff0\u306e\u3088\u3046\u306b\u3055\u307e\u3056\u307e\u306a\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u304c\u642d\u8f09\u3055\u308c\u3066\u3044\u307e\u3059\u304c\u3001\u65e5\u672c\u4eba\u3092\u542b\u3080\u3001\u7279\u5b9a\u306e\u4eba\u7a2e\u306e\u307f\u306b\u591a\u304f\u898b\u3089\u308c\u308b\u591a\u578b\u60c5\u5831\u307e\u3067\u306f\u7db2\u7f85\u3055\u308c\u3066\u3044\u306a\u3044\u3053\u3068\u304c\u3042\u308a\u307e\u3059\u3002\u4ee5\u4e0b\u306b\u4e00\u822c\u306b\u516c\u958b\u3055\u308c\u3066\u3044\u308b\u4ee3\u8868\u7684\u306a\u65e5\u672c\u4eba\u591a\u578b\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u3054\u7d39\u4ecb\u3057\u307e\u3059\u3002\u3053\u308c\u3089\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306e\u60c5\u5831\u3092\u5229\u7528\u3067\u304d\u308c\u3070\u3001\u65e5\u672c\u4eba\u306e\u30b2\u30ce\u30e0\u89e3\u6790\u306b\u304a\u3044\u3066\u75c5\u7684\u5909\u7570\u306e\u7d5e\u308a\u8fbc\u307f\u306e\u7cbe\u5ea6\u3084\u4f5c\u696d\u52b9\u7387\u3092\u4e0a\u3052\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u3068\u8003\u3048\u3089\u308c\u307e\u3059\u3002<\/p>\n

\u3010\u4ee3\u8868\u7684\u306a\u65e5\u672c\u4eba\u591a\u578b\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3011
\n\u30fbHuman Genetic Variation Database\uff08HGVD\uff09<\/a>
\n\u4eac\u90fd\u5927\u5b66\u304c\u4e3b\u5c0e\u3057\u3066\u4f5c\u6210\u3055\u308c\u305f\u591a\u578b\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3002\u65e5\u672c\u4eba\u5065\u5e38\u8005\u306e\u30a8\u30af\u30bd\u30fc\u30e0\u89e3\u6790\u7d50\u679c1,000\u4f8b\u4ee5\u4e0a\u3068\u30b3\u30db\u30fc\u30c8\u7814\u7a76\u7d50\u679c3,000\u4f8b\u4ee5\u4e0a\u306e\u30c7\u30fc\u30bf\u3092\u57fa\u306b\u3057\u3066\u3044\u308b\u3002<\/p>\n

\u30fbJapanese Multi Omics Reference Panel\uff08jMorp\uff09<\/a>
\n\u6771\u5317\u30e1\u30c7\u30a3\u30ab\u30eb\u30fb\u30e1\u30ac\u30d0\u30f3\u30af\u6a5f\u69cb\uff08ToMMo\u2122\uff09\u304c\u7ba1\u7406\u3057\u3066\u3044\u308b\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3002\u65e5\u672c\u4eba\u5065\u5e38\u8005\u7d0414,000\u4f8b\uff082022\u5e741\u6708\u6642\u70b9\uff09\u306e\u5168\u30b2\u30ce\u30e0\u89e3\u6790\u7d50\u679c\u3092\u57fa\u306b\u3057\u3066\u3044\u308b\u3002<\/p>\n

\u30ab\u30b9\u30bf\u30e0\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u306e\u8ffd\u52a0<\/h2>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306b\u306f\u5916\u90e8\u30c7\u30fc\u30bf\u3092\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u3068\u3057\u3066\u767b\u9332\u3067\u304d\u308b\u6a5f\u80fd\u304c\u5099\u308f\u3063\u3066\u304a\u308a\u3001\u65e5\u672c\u4eba\u591a\u578b\u3092\u542b\u3081\u305f\u5916\u90e8\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306e\u60c5\u5831\u3092\u5909\u7570\u89e3\u6790\u306b\u7d44\u307f\u8fbc\u3080\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002\u5916\u90e8\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306e\u60c5\u5831\u306f\u4e00\u822c\u7684\u306b\u30c6\u30ad\u30b9\u30c8\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u306e\u3067\u3001\u591a\u304f\u306e\u5834\u5408Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u3067\u306e\u5229\u7528\u304c\u53ef\u80fd\u3067\u3059\u3002\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u306f\u3001VCF\uff08Variant Call Format\uff09\u3068\u3044\u3046NGS\u306e\u30c7\u30fc\u30bf\u89e3\u6790\u3067\u4e00\u822c\u7684\u306b\u4f7f\u7528\u3055\u308c\u308b\u5f62\u5f0f\u3067\u767b\u9332\u3057\u307e\u3059\u3002\u3082\u3057\u767b\u9332\u3057\u305f\u3044\u30c7\u30fc\u30bf\u304cVCF\u3068\u306a\u3063\u3066\u3044\u306a\u3044\u5834\u5408\u306f\u3001\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u30fc\u306a\u3069\u3092\u4f7f\u7528\u3057\u3066\u30d5\u30a1\u30a4\u30eb\u3092\u52a0\u5de5\u3057\u307e\u3059\u3002<\/p>\n

\u3010VCF\u30d5\u30a1\u30a4\u30eb\u306e\u4f8b\uff08Excel\u2122\u3067\u958b\u3044\u305f\u3068\u3053\u308d\uff09\u3011
\n\"\"
\n\uff08\u4e0a\u8a18\u30c7\u30fc\u30bf\u306f\u7279\u5b9a\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u53d6\u5f97\u3055\u308c\u305f\u3082\u306e\u3067\u306f\u3042\u308a\u307e\u305b\u3093\u3002\uff09<\/p>\n

\u3010\u89e3\u6790\u7d50\u679c\u306e\u4f8b\u3011
\n\"\"
\n\u8fd1\u5e74\u306f\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u4e0a\u306e\u60c5\u5831\u304c\u81a8\u5927\u306b\u306a\u308a\u3001\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u53ef\u80fd\u306a\u591a\u578b\u30c7\u30fc\u30bf\u306e\u30d5\u30a1\u30a4\u30eb\u30b5\u30a4\u30ba\u304c\u6570\u30ae\u30ac\u30d0\u30a4\u30c8\u306b\u9054\u3057\u3066\u3057\u307e\u3046\u3053\u3068\u3082\u3042\u308a\u307e\u3059\u3002\u3053\u306e\u3088\u3046\u306a\u30d5\u30a1\u30a4\u30eb\u3092Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306b\u767b\u9332\u3057\u3088\u3046\u3068\u3057\u3066\u3082\u3001\u30cd\u30c3\u30c8\u30ef\u30fc\u30af\u74b0\u5883\u3084\u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u306e\u5236\u9650\u306b\u3088\u308a\u767b\u9332\u304c\u3067\u304d\u306a\u3044\u5834\u5408\u304c\u3042\u308a\u307e\u3059\u3002\u305d\u306e\u3088\u3046\u306a\u6642\u306b\u306f\u3001\u4f8b\u3048\u3070\u4e0b\u8a18\u306e\u3088\u3046\u306bbedtools\u306a\u3069\u306e\u30c4\u30fc\u30eb\u3092\u7528\u3044\u3066\u89e3\u6790\u5bfe\u8c61\u306e\u907a\u4f1d\u5b50\u30d1\u30cd\u30eb\u306e\u30bf\u30fc\u30b2\u30c3\u30c8\u9818\u57df\u306b\u542b\u307e\u308c\u308b\u591a\u578b\u60c5\u5831\u306e\u307f\u3092\u62bd\u51fa\u3057\u3001\u767b\u9332\u3059\u308bVCF\u30d5\u30a1\u30a4\u30eb\u306e\u30b5\u30a4\u30ba\u3092\u5c0f\u3055\u304f\u3059\u308b\u3053\u3068\u304c\u6709\u52b9\u3067\u3059\u3002\u305f\u3060\u3057\u3001\u64cd\u4f5c\u306b\u306fLinux\u2122 OS\u3092\u642d\u8f09\u3057\u305f\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u30fc\u304c\u5fc5\u8981\u3068\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
bedtools intersect -a JapaneseSNPs_whole_genome.vcf -b AmpliSeq_designed.bed -wb
\n\uff08VCF\u30d5\u30a1\u30a4\u30eb\u3068BED\u30d5\u30a1\u30a4\u30eb\u306e\u540d\u79f0\u306f\u4f8b\uff09<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

<\/h2>\n

\u307e\u3068\u3081<\/h2>\n

Ion Reporter \u30bd\u30d5\u30c8\u30a6\u30a8\u30a2\u3067\u306f\u3001\u3055\u307e\u3056\u307e\u306a\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u3092\u8ffd\u52a0\u3057\u3066\u30d2\u30c8\u306e\u5909\u7570\u89e3\u6790\u306e\u7cbe\u5ea6\u3092\u4e0a\u3052\u308b\u3053\u3068\u304c\u53ef\u80fd\u3067\u3059\u3002\u30ab\u30b9\u30bf\u30e0\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u306e\u8ffd\u52a0\u306b\u3064\u3044\u3066\u3001\u3054\u4e0d\u660e\u306a\u70b9\u304c\u3054\u3056\u3044\u307e\u3057\u305f\u3089\u5f53\u793e\u30c6\u30af\u30cb\u30ab\u30eb\u30b5\u30dd\u30fc\u30c8<\/a>\u307e\u3067\u304a\u554f\u3044\u5408\u308f\u305b\u304f\u3060\u3055\u3044\u3002
\n\u307e\u305f\u3001\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b9\uff08NGS\uff09\u30c7\u30fc\u30bf\u89e3\u6790\u30b3\u30f3\u30b5\u30eb\u30c6\u30a3\u30f3\u30b0\u30b5\u30fc\u30d3\u30b9<\/a>\u3067\u306f\u3001\u30ab\u30b9\u30bf\u30e0\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u306e\u4f5c\u6210\u304b\u3089\u89e3\u6790\u7d50\u679c\u306e\u8a55\u4fa1\u307e\u3067\u3001\u5f53\u793e\u306e\u30d0\u30a4\u30aa\u30a4\u30f3\u30d5\u30a9\u30de\u30c6\u30a3\u30b7\u30e3\u30f3\u304c\u304a\u5ba2\u3055\u307e\u3092\u30c8\u30fc\u30bf\u30eb\u3067\u30b5\u30dd\u30fc\u30c8\u81f4\u3057\u307e\u3059\u3002\u30b5\u30fc\u30d3\u30b9\u306e\u5185\u5bb9\u306b\u3064\u3044\u3066\u3054\u8208\u5473\u304c\u3042\u308a\u307e\u3057\u305f\u3089\u3001\u5f53\u793e\u30c6\u30af\u30cb\u30ab\u30eb\u30b5\u30dd\u30fc\u30c8\u307e\u3067\u304a\u554f\u3044\u5408\u308f\u305b\u304f\u3060\u3055\u3044\u3002<\/p>\n

\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\uff08NGS\uff09\u5165\u9580<\/h2>\n

\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b9\u306e\u539f\u7406\u3084\u4f55\u304c\u3067\u304d\u308b\u304b\u3088\u304f\u308f\u304b\u3089\u306a\u3044\u3001\u307e\u305f\u306f\u81ea\u5206\u306e\u7814\u7a76\u9818\u57df\u306b\u3069\u306e\u3088\u3046\u306b\u6d3b\u7528\u3067\u304d\u308b\u304b\u308f\u304b\u3089\u306a\u3044\u3068\u3044\u3046\u65b9\u5411\u3051\u306b\u3001\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b9\u306e\u57fa\u672c\u3084\u5404\u7814\u7a76\u9818\u57df\u306b\u7279\u5316\u3057\u305f\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u3092\u307e\u3068\u3081\u307e\u3057\u305f\u3002\u30ea\u30f3\u30af\u5148\u304b\u3089\u3001\u305d\u308c\u305e\u308c\u306e\u9818\u57df\u306b\u5fdc\u3058\u305f\u30da\u30fc\u30b8\u3092\u3054\u89a7\u3044\u305f\u3060\u3051\u307e\u3059\u3002<\/p>\n

\u8a73\u7d30\u3092\u898b\u308b<\/a><\/p>\n

\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b9 \u30c7\u30fc\u30bf\u89e3\u6790\u30aa\u30f3\u30e9\u30a4\u30f3\u500b\u5225\u76f8\u8ac7<\/h2>\n

IonTorrent\u30e6\u30fc\u30b6\u3067\u30c7\u30fc\u30bf\u89e3\u6790\u306b\u95a2\u3059\u308b\u5177\u4f53\u7684\u306a\u8ab2\u984c\u3092\u304a\u6301\u3061\u306e\u65b9\u306b\u306f\u3001\u7121\u6599\u306e\u500b\u5225\u76f8\u8ac7\u306e\u6642\u9593\u3092\u958b\u8a2d\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n

\u8a73\u7d30\u3092\u898b\u308b<\/a><\/p>\n

 <\/p>\n

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ToMMo is a trademark of Tohoku University.
\nExcel is a trademark of Microsoft Corporation.
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