{"id":10777,"date":"2024-02-29T01:01:04","date_gmt":"2024-02-28T22:01:04","guid":{"rendered":"https:\/\/f-genetics.com\/?p=10777"},"modified":"2024-05-15T23:55:37","modified_gmt":"2024-05-15T20:55:37","slug":"nipt-bioinformaticheskij-analiz","status":"publish","type":"post","link":"https:\/\/f-genetics.com\/en\/nipt-bioinformaticheskij-analiz\/","title":{"rendered":"NIPT. Bioinformatic analysis"},"content":{"rendered":"<p>The algorithm consists of&nbsp;processing raw sequencing data (fastq). Processing is&nbsp;performed by&nbsp;demultiplexing samples (separation by&nbsp;index sequences), then trimming (cutting off index and adapter sequences), marking PCR duplicates, mapping to&nbsp;the reference genome, and calculating the number of&nbsp;reads mapped to&nbsp;individual genome regions. After mapping, the level of&nbsp;deviation is&nbsp;estimated to&nbsp;determine the karyotype.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Bioinformatics analysis algorithm<\/strong><\/h2>\n\n\n\n<p>The resulting raw data on&nbsp;the&nbsp;fluorescence of&nbsp;DNA fragments is&nbsp;subjected to&nbsp;basecalling to&nbsp;get fastq files containing information about the&nbsp;genetic sequence and phred-score sequencing quality. The&nbsp;data carries information about the&nbsp;index sequence, which allows demultiplexing, that&nbsp;is, assigning the&nbsp;information obtained for&nbsp;each individual nanosphere to&nbsp;the test sample.<\/p>\n\n\n\n<p>After basecalling and demultiplexing, index and adapter sequences are trimmed. Trimming consists of&nbsp;cutting off the service parts of&nbsp;the read in&nbsp;order not to&nbsp;disrupt further analysis. Trimming is&nbsp;also carried out according to&nbsp;quality not to&nbsp;use the part of&nbsp;the read characterized by&nbsp;low sequencing quality in&nbsp;further analysis.<\/p>\n\n\n\n<p>Next, the reads are mapped to&nbsp;the reference genome of&nbsp;the human hg19. This sequence is&nbsp;characterized by&nbsp;the absence of&nbsp;alternative contigs and parts of&nbsp;chromosomes, which makes it&nbsp;possible to&nbsp;more accurately estimate the amount of&nbsp;reads mapped to&nbsp;each individual chromosome. Mapping is&nbsp;performed using the Barrows-Wheeler transform. Data on&nbsp;the mapping of&nbsp;each individual sample is&nbsp;in&nbsp;the .sam format file.<\/p>\n\n\n\n<p>After mapping, the format . sam is&nbsp;converted to&nbsp;binary format . bam, which significantly speeds up&nbsp;the work of&nbsp;further algorithms. The file is&nbsp;sorted in&nbsp;such a&nbsp;way that at&nbsp;the beginning of&nbsp;the file there are reads mapped to&nbsp;each of&nbsp;the contigs (in&nbsp;the case of&nbsp;this document, chromosomes) in&nbsp;alphabetical order, and inside the contig&nbsp;&mdash; by&nbsp;increasing the coordinate of&nbsp;the read start. PCR labeling of&nbsp;duplicates is&nbsp;performed, which makes it&nbsp;possible to&nbsp;exclude from the analysis reads that are exact duplicates of&nbsp;other reads.<\/p>\n\n\n\n<p>Then, the number of&nbsp;reads mapped to&nbsp;each of&nbsp;the individual sections of&nbsp;the chromosome of&nbsp;equal size, called bin, is&nbsp;estimated. For each bin a&nbsp;standardized assessment is&nbsp;performed, it&nbsp;consists in&nbsp;estimating the number of&nbsp;standard deviations of&nbsp;the bin coverage for a&nbsp;sample of&nbsp;all bin coverages. In&nbsp;the case of&nbsp;a&nbsp;high z-score, it&nbsp;is&nbsp;concluded that there is&nbsp;a&nbsp;trisomy on&nbsp;the chromosome under study.<\/p>\n\n\n\n<p class=\"is-style-purple\"><strong>The algorithm is&nbsp;implemented in&nbsp;Python using object-oriented programming approaches.<\/strong><\/p>","protected":false},"excerpt":{"rendered":"<p>\u0410\u043b\u0433\u043e\u0440\u0438\u0442\u043c \u0437\u0430\u043a\u043b\u044e\u0447\u0430\u0435\u0442\u0441\u044f \u0432\u00a0\u043e\u0431\u0440\u0430\u0431\u043e\u0442\u043a\u0435 \u043f\u0435\u0440\u0432\u0438\u0447\u043d\u044b\u0445 \u0434\u0430\u043d\u043d\u044b\u0445 \u0441\u0435\u043a\u0432\u0435\u043d\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u044f (fastq). \u041e\u0431\u0440\u0430\u0431\u043e\u0442\u043a\u0430 \u043f\u0440\u043e\u0438\u0437\u0432\u043e\u0434\u0438\u0442\u0441\u044f \u043f\u0443\u0442\u0435\u043c \u0434\u0435\u043c\u0443\u043b\u044c\u0442\u0438\u043f\u043b\u0435\u043a\u0441\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u044f \u043e\u0431\u0440\u0430\u0437\u0446\u043e\u0432 (\u0440\u0430\u0437\u0434\u0435\u043b\u0435\u043d\u0438\u044f \u043f\u043e\u00a0\u0438\u043d\u0434\u0435\u043a\u0441\u043d\u044b\u043c \u043f\u043e\u0441\u043b\u0435\u0434\u043e\u0432\u0430\u0442\u0435\u043b\u044c\u043d\u043e\u0441\u0442\u044f\u043c), \u0437\u0430\u0442\u0435\u043c \u043f\u0440\u043e\u0432\u043e\u0434\u0438\u0442\u0441\u044f \u0442\u0440\u0438\u043c\u043c\u0438\u043d\u0433 (\u043e\u0442\u0440\u0435\u0437\u0430\u043d\u0438\u0435 \u0438\u043d\u0434\u0435\u043a\u0441\u043d\u044b\u0445 \u0438\u00a0\u0430\u0434\u0430\u043f\u0442\u0435\u0440\u043d\u044b\u0445 \u043f\u043e\u0441\u043b\u0435\u0434\u043e\u0432\u0430\u0442\u0435\u043b\u044c\u043d\u043e\u0441\u0442\u0435\u0439), \u043c\u0430\u0440\u043a\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u0435 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\u043f\u043e\u0437\u0432\u043e\u043b\u044f\u044e\u0449\u0435\u0433\u043e \u043e\u043f\u0440\u0435\u0434\u0435\u043b\u0438\u0442\u044c \u043a\u0430\u0440\u0438\u043e\u0442\u0438\u043f. \u0410\u043b\u0433\u043e\u0440\u0438\u0442\u043c \u0431\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0433\u043e \u0430\u043d\u0430\u043b\u0438\u0437\u0430 \u041f\u043e\u043b\u0443\u0447\u0435\u043d\u043d\u044b\u0435 \u043f\u0435\u0440\u0432\u0438\u0447\u043d\u044b\u0435 \u0434\u0430\u043d\u043d\u044b\u0435 \u043e&nbsp;\u0444\u043b\u0443\u043e\u0440\u0435\u0441\u0446\u0435\u043d\u0446\u0438\u0438 \u0414\u041d\u041a-\u0444\u0440\u0430\u0433\u043c\u0435\u043d\u0442\u043e\u0432 \u043f\u043e\u0434\u0432\u0435\u0440\u0433\u0430\u044e\u0442\u0441\u044f basecalling \u0441&nbsp;\u043f\u043e\u043b\u0443\u0447\u0435\u043d\u0438\u0435\u043c fastq \u0444\u0430\u0439\u043b\u043e\u0432,&hellip;<\/p>","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"inline_featured_image":false,"footnotes":""},"categories":[4],"tags":[],"class_list":["post-10777","post","type-post","status-publish","format-standard","hentry","category-articles"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.8 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>\u041d\u0418\u041f\u0422. \u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0439 \u0430\u043d\u0430\u043b\u0438\u0437 - First Genetics<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/f-genetics.com\/en\/nipt-bioinformaticheskij-analiz\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta 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