{"id":2996,"date":"2024-09-25T12:04:54","date_gmt":"2024-09-25T09:04:54","guid":{"rendered":"https:\/\/marmarapatoloji.com\/?p=2996"},"modified":"2026-05-07T04:00:44","modified_gmt":"2026-05-07T04:00:44","slug":"yeni-nesil-dizileme-ngs","status":"publish","type":"post","link":"https:\/\/marmarapatoloji.com\/en\/2024\/09\/25\/yeni-nesil-dizileme-ngs\/","title":{"rendered":"Next Generation Sequencing (NGS)"},"content":{"rendered":"\n<h4 class=\"wp-block-heading\">Yeni nesil dizileme (NGS), milyonlarca n\u00fckleik asidin ayn\u0131 anda paralel olarak dizilenmesine olanak tan\u0131yan y\u00fcksek verimli bir tekniktir.<\/h4>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>Temel \u00f6zellikler<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/>Klinik kullan\u0131m\u0131 kolayla\u015ft\u0131ran y\u00fcksek verimli ve uygun maliyetli dizilemeye olanak tan\u0131r.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Yeni nesil dizilemenin farkl\u0131 y\u00f6ntemleri temel olarak k\u0131sa okuma (pirosekanslama, sentezle dizileme, ligasyonla dizileme, iyon sel) ve uzun okuma (tek molek\u00fcl ger\u00e7ek zamanl\u0131 dizileme, nanog\u00f6zenek dizileme) olarak ikiye ayr\u0131l\u0131r.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Klinik uygulamalara \u00f6ncelikle onkoloji panelleri ve germ hatt\u0131 panelleri ile birlikte yeni ortaya \u00e7\u0131kan t\u00fcm ekzom dizilemesi\/t\u00fcm genom dizilemesi dahildir.<\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>Terminoloji<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/>Yeni nesil dizileme (NGS), b\u00fcy\u00fck oranda paralel dizileme, t\u00fcm genom dizilemesi (WGS), t\u00fcm ekzom dizilemesi (WES), RNA dizilemesi (RNA seq), metilasyon dizilemesi (metil seq) ve kromatin imm\u00fcno\u00e7\u00f6kt\u00fcrme dizilemesi (ChIP seq)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img fetchpriority=\"high\" decoding=\"async\" width=\"473\" height=\"600\" class=\"wp-image-3000\" src=\"https:\/\/marmarapatoloji.com\/wp-content\/uploads\/2024\/09\/yeni-nesil-dizileme-gorsel.jpg\" alt=\"\" srcset=\"https:\/\/marmarapatoloji.com\/wp-content\/uploads\/2024\/09\/yeni-nesil-dizileme-gorsel.jpg 473w, https:\/\/marmarapatoloji.com\/wp-content\/uploads\/2024\/09\/yeni-nesil-dizileme-gorsel-237x300.jpg 237w\" sizes=\"(max-width: 473px) 100vw, 473px\" \/><\/figure>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>Tarih\u00e7e<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\">20. y\u00fczy\u0131l\u0131n ba\u015flar\u0131nda, bir\u00e7ok ara\u015ft\u0131rma h\u00fccre sinyal yollar\u0131n\u0131 ve h\u00fccresel yap\u0131 ta\u015flar\u0131n\u0131 ayd\u0131nlatmaya \u00e7al\u0131\u015ft\u0131. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20212918\/\" target=\"_blank\" rel=\"noreferrer noopener\">Biomark Insights 2010;5:9<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31277491\/\" target=\"_blank\" rel=\"noreferrer noopener\">Int J Mol Sci 2019;20:3292<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29019985\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nature 2017;550:345<\/a>\u00a0)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>1921 &#8211; 1922:<\/strong> Frederick Banting ve Charles Best, peptit hormonu ins\u00fclini ke\u015ffetti.<\/li>\n\n\n\n<li><strong>1953:<\/strong> Fred Sanger ins\u00fclinin amino asit dizisini yay\u0131nlad\u0131 ve di\u011fer proteinlerin amino asit dizilerini belirleme \u00e7abalar\u0131n\u0131 ba\u015flatt\u0131.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/>Proteinlerin amino asit dizilerinin belirlenmesindeki ba\u015far\u0131, genetik materyalin dizilenmesine y\u00f6nelik \u00e7abalara ilham kayna\u011f\u0131 oldu (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29019985\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nature 2017;550:345<\/a>\u00a0)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>1965:<\/strong> \u0130lk RNA dizileri belirlendi ve yay\u0131nland\u0131 (tan\u0131mlanan ilk dizi alanin tRNA&#8217;s\u0131yd\u0131)<\/li>\n\n\n\n<li>DNA dizilimi, Sanger ve Coulson ile Maxam ve Gilbert&#8217;in 1976 &#8211; 1977 y\u0131llar\u0131nda daha y\u00fcksek verimli DNA dizilimi y\u00f6ntemlerini yay\u0131nlamas\u0131na kadar daha zorlu ve zahmetli oldu\u011fu kan\u0131tland\u0131\n<ul class=\"wp-block-list\">\n<li>Sanger ve Coulson y\u00f6ntemi: DNA primerleri ve DNA polimeraz kullan\u0131larak zincir sonland\u0131rma<\/li>\n\n\n\n<li>Maxam ve Gilbert y\u00f6ntemi: restriksiyon par\u00e7alanmas\u0131 ve baz spesifik kimyasal b\u00f6l\u00fcnme<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Hem Sanger ve Coulson&#8217;un (Sanger dizilemesi) hem de Maxam ve Gilbert&#8217;in y\u00f6ntemleri hemen kullan\u0131ld\u0131 ve yeni DNA dizileme projelerinin \u00fcstel b\u00fcy\u00fcmesini te\u015fvik etti (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29019985\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nature 2017;550:345<\/a>\u00a0)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Her iki DNA dizileme y\u00f6ntemi de yay\u0131nland\u0131ktan k\u0131sa bir s\u00fcre sonra, shotgun dizileme y\u00f6ntemleri (dizilerin \u00f6rt\u00fc\u015fmesiyle belirlenen birle\u015fimlerle rastgele klonlar\u0131n dizilenmesi) 1979 &#8211; 1980 y\u0131llar\u0131nda yay\u0131nland\u0131.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">DNA dizileme \u00e7abalar\u0131n\u0131n b\u00fcy\u00fcmesi, veri tabanlar\u0131 ve arama ara\u00e7lar\u0131 (\u00f6rne\u011fin NCBI BLAST, GenBank, vb.) dahil olmak \u00fczere biyoenformatik teknolojisi ve kaynaklar\u0131ndaki ilerlemeleri m\u00fcjdeledi (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29019985\/\">Nature 2017;550:345<\/a>\u00a0)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>1980 &#8211; 1990&#8217;lar:<\/strong> b\u00fcy\u00fck \u00f6l\u00e7\u00fcde paralel dizileme y\u00f6ntemleri tan\u0131mland\u0131<\/li>\n\n\n\n<li><strong>1990 &#8211; 2004:<\/strong> O d\u00f6nemde y\u00fcr\u00fct\u00fclen en iddial\u0131 dizileme projesi oldu\u011fu d\u00fc\u015f\u00fcn\u00fclen \u0130nsan Genomu Projesi ger\u00e7ekle\u015ftirildi ve insan genomunun b\u00fcy\u00fck bir k\u0131sm\u0131n\u0131n nihai dizisi 2004 y\u0131l\u0131nda yay\u0131nland\u0131\n<ul class=\"wp-block-list\">\n<li>Projenin iddial\u0131 yap\u0131s\u0131 biyoenformatik ve genetik teknolojilerinde geli\u015fmelere yol a\u00e7t\u0131 (daha y\u00fcksek verim ve do\u011frulukla daha verimli s\u00fcre\u00e7ler gerektirdi, vb.)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>2000&#8217;ler &#8211; 2010:<\/strong> B\u00fcy\u00fck \u00f6l\u00e7\u00fcde paralel dizileme y\u00f6ntemleri Sanger dizileme y\u00f6ntemlerinin yerini ald\u0131 ve ilk NGS makineleri ticari olarak piyasaya sunuldu.<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>Sanger dizilemesi<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Alt\u0131n standart<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Uzun okumalarda y\u00fcksek do\u011fruluk sa\u011flayan tarihi alt\u0131n standart; ancak NGS y\u00f6ntemlerinin do\u011frulu\u011fu (%99,965 do\u011frulama oran\u0131), verimlili\u011fi ve maliyet etkinli\u011fi klinik ve ara\u015ft\u0131rma ortamlar\u0131nda Sanger dizilemesini b\u00fcy\u00fck \u00f6l\u00e7\u00fcde g\u00f6lgede b\u0131rakm\u0131\u015ft\u0131r (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/26847218\/\" target=\"_blank\" rel=\"noreferrer noopener\">Clin Chem 2016;62:647<\/a>\u00a0)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Y\u00f6ntem:<\/strong> Diziyi belirlemek i\u00e7in modifiye dideoksin\u00fckleotidlerle zincir sonland\u0131rmay\u0131 kullan\u0131r.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Avantajlar\u0131:<\/strong> Herhangi bir hedefi (DNA, RNA, epigenetik de\u011fi\u015fiklikler) s\u0131ralayabilir, y\u00fcksek kalite, uzun okuma uzunluklar\u0131.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Dezavantajlar\u0131:<\/strong> y\u00fcksek maliyet (\u00f6zellikle daha uzun dizilerde ve birden fazla gen\/lokus dizilenirken), d\u00fc\u015f\u00fck verim, zaman al\u0131c\u0131 ve t\u00fcm\u00f6r \u00f6rneklerinde somatik varyantlar\u0131 ve yap\u0131sal varyantlar\u0131 tan\u0131mlamak i\u00e7in yetersiz duyarl\u0131l\u0131k, primer tasar\u0131m\u0131 ve amplifikasyonu i\u00e7in ilgi duyulan dizileri bilmek gerekir.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Kullan\u0131m:<\/strong> NGS verileri i\u00e7in do\u011frulama arac\u0131; klinik ve ara\u015ft\u0131rma ortamlar\u0131nda birincil dizileme y\u00f6ntemi olarak kullan\u0131m\u0131 azal\u0131yor.<\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>NGS metodolojisine genel bak\u0131\u015f<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/>K\u00fct\u00fcphane haz\u0131rlama, \u00e7o\u011faltma ve dizilemeden olu\u015fan b\u00fcy\u00fck \u00e7apl\u0131 paralel dizileme y\u00f6ntemlerini kullan\u0131r.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>K\u00fct\u00fcphane (\u00f6rnek) haz\u0131rlama:<\/strong> DNA&#8217;n\u0131n rastgele par\u00e7alanmas\u0131 ve ard\u0131ndan ortak adapt\u00f6r dizilerinin ba\u011flanmas\u0131<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\u00d6rnek giri\u015fi: DNA molek\u00fclleri (kandan, kemik ili\u011finden, yanak s\u00fcr\u00fcnt\u00fcs\u00fcnden, t\u00fck\u00fcr\u00fckten, formalinle fikse edilmi\u015f parafine g\u00f6m\u00fcl\u00fc dokudan, vb.)<\/li>\n\n\n\n<li>Par\u00e7alanma: DNA&#8217;y\u0131 enzimatik olarak (restriksiyon enzimi, transpozaz), sonik olarak veya mekanik olarak rastgele boyutlara par\u00e7alay\u0131n (genellikle k\u0131sa okuma dizilemesi i\u00e7in 200 &#8211; 300 n\u00fckleotid)<\/li>\n\n\n\n<li>Hedef DNA&#8217;n\u0131n modifikasyonu\n<ul class=\"wp-block-list\">\n<li>Adapt\u00f6rler: Par\u00e7alanm\u0131\u015f DNA \u00f6rneklerinin u\u00e7lar\u0131na birden fazla i\u015flevi yerine getiren benzersiz DNA dizileri eklenir\n<ul class=\"wp-block-list\">\n<li>Ayn\u0131 \u00e7al\u0131\u015fmada farkl\u0131 \u00f6rneklerin \u00e7oklu olarak i\u015flenmesi i\u00e7in hasta tan\u0131mlay\u0131c\u0131lar\u0131n\u0131 i\u00e7eren bir barkod (indeks) sa\u011flay\u0131n<\/li>\n\n\n\n<li>Dizilerin dizileme \u00e7iplerine\/boncuklar\u0131na hibridizasyonuna izin verin<\/li>\n\n\n\n<li>Amplifikasyon ve dizileme primerleri i\u00e7in evrensel astarlama noktalar\u0131 olarak hizmet eder<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Zenginle\u015ftirme: Bu ad\u0131m yaln\u0131zca belirli genomik b\u00f6lgelerin (hastal\u0131k gen panelleri, ekzomlar, vb.) analiz edilmesi durumunda gereklidir.\n<ul class=\"wp-block-list\">\n<li>PCR amplifikasyonu (amplikon)\n<ul class=\"wp-block-list\">\n<li>Avantajlar\u0131: daha k\u00fc\u00e7\u00fck genomik b\u00f6lgeler i\u00e7in idealdir<\/li>\n\n\n\n<li>Dezavantajlar\u0131: \u0130lgi duyulan hedefi ka\u00e7\u0131rabilir (daha d\u00fc\u015f\u00fck hassasiyet)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Dizi yakalama \/ hibridizasyon\n<ul class=\"wp-block-list\">\n<li>Yemler (biyotinlenmi\u015f RNA veya DNA oligon\u00fckleotidleri) DNA&#8217;n\u0131n belirli b\u00f6lgelerine ba\u011flan\u0131r<\/li>\n\n\n\n<li>Avantajlar\u0131: daha b\u00fcy\u00fck genomik b\u00f6lgeler i\u00e7in idealdir<\/li>\n\n\n\n<li>Dezavantajlar\u0131: hedef d\u0131\u015f\u0131 yakalama nedeniyle hedef b\u00f6lgeler i\u00e7in daha d\u00fc\u015f\u00fck zenginle\u015ftirme (daha d\u00fc\u015f\u00fck \u00f6zg\u00fcll\u00fck)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Amplifikasyon ve k\u00fcme olu\u015fturma<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Her molek\u00fcl, tek bir \u015fablon par\u00e7as\u0131ndan t\u00fcretilen PCR amplikonlar\u0131n\u0131n orijinal molek\u00fcle yak\u0131n bir mesafede k\u00fcmelenmesini sa\u011flayan multipleks PCR kullan\u0131larak bir y\u00fczey (\u00e7ip, ak\u0131\u015f h\u00fccresi, boncuklar, nano k\u00fcre, vb.) \u00fczerinde immobilize edilir ve \u00e7o\u011falt\u0131l\u0131r (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333\u00a0<\/a>)\n<ul class=\"wp-block-list\">\n<li>Boncuk tabanl\u0131 sistemler: Belirli bir oligon\u00fckleotid par\u00e7as\u0131na tamamlay\u0131c\u0131 1 adapt\u00f6r bir boncu\u011fa sabitlenir ve milyonlarca klonal DNA par\u00e7as\u0131n\u0131n tek bir boncuk \u00fczerine sabitlendi\u011fi em\u00fclsiyon PCR yoluyla amplifikasyon ger\u00e7ekle\u015fir<\/li>\n\n\n\n<li>Kat\u0131 y\u00fczey sistemleri: adapt\u00f6r, oligon\u00fckleotidi \u00e7ipe belirli bir konumda sabitler\n<ul class=\"wp-block-list\">\n<li>Amplifikasyon, do\u011frudan slayt \u00fczerinde k\u00f6pr\u00fc PCR yoluyla ger\u00e7ekle\u015fir; burada ileri ve geri primerler y\u00fczeye ba\u011flan\u0131r ve bu da tamamlay\u0131c\u0131 tek zincirli DNA par\u00e7alar\u0131 i\u00e7in ba\u011flanma yerleri sa\u011flar<\/li>\n\n\n\n<li>Ak\u0131\u015f h\u00fccreleri: Slayt \u00fczerindeki primerlerin kesin konumunu tan\u0131mlayan ve daha y\u00fcksek verim sa\u011flayan desenli kat\u0131 y\u00fczey sistemi<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>DNA nanoball&#8217;lar\u0131: \u00e7\u00f6zeltide, DNA tekrar tekrar ba\u011flan\u0131r, daireselle\u015ftirilir ve 4 benzersiz adapt\u00f6r b\u00f6lgesi ile kesilir<\/li>\n\n\n\n<li>Daha sonra, desenli bir slayt \u00fczerine da\u011f\u0131t\u0131lan DNA nano k\u00fcreleri olu\u015fturmak i\u00e7in yuvarlanan daire amplifikasyonu kullan\u0131l\u0131r<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Dizileme<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Her k\u00fcme, ayr\u0131 bir dizileme reaksiyonu olarak hareket edecek ve birden fazla numuneden gelen k\u00fct\u00fcphaneler paralel olarak ayn\u0131 anda dizilenebilecek<\/li>\n\n\n\n<li>Okunuyor: dizileme \u00e7\u0131kt\u0131s\u0131; orijinal \u015fablon molek\u00fcl\u00fcn\u00fcn dizisini temsil eden n\u00fckleotid dizisi<\/li>\n\n\n\n<li>\u00c7ift u\u00e7 okumalar\u0131: DNA \u015fablonu her iki u\u00e7tan dizilenir ve hem ileri hem de geri okumalar geli\u015fmi\u015f haritalama, kapsama ve verime olanak tan\u0131r (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333<\/a>\u00a0)\n<ul class=\"wp-block-list\">\n<li>\u0130leri ve geri okumalar aras\u0131nda asimetri varsa yap\u0131sal d\u00fczenlemelerin tan\u0131mlanmas\u0131na yard\u0131mc\u0131 olabilir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>NGS platformlar\u0131n\u0131n kategorilendirilmesi (\u00a0Platform i\u015flevleri ve y\u00f6ntemleri hakk\u0131nda bilgi i\u00e7in\u00a0<a href=\"https:\/\/www.pathologyoutlines.com\/topic\/molecularnextgensequencing.html#platformsforngssection\" target=\"_blank\" rel=\"noreferrer noopener\">NGS i\u00e7in Platformlar b\u00f6l\u00fcm\u00fcne bak\u0131n<\/a>)\n<ul class=\"wp-block-list\">\n<li>Nesiller (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333\u00a0<\/a>)\n<ul class=\"wp-block-list\">\n<li>\u0130kinci nesil: PCR&#8217;ye ba\u011f\u0131ml\u0131\n<ul class=\"wp-block-list\">\n<li>Pirosekanslama (Roche 454 sistemi)<\/li>\n\n\n\n<li>Ligasyonla dizileme (AB SOLiD sistemi, Complete Genomics, Polonator G.007, vb.)<\/li>\n\n\n\n<li>Sentez yoluyla dizileme (Illumina, Qiagen GeneReader)<\/li>\n\n\n\n<li>\u0130yon yar\u0131 iletken dizilemesi (Thermo Fisher&#8217;dan Ion Torrent)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00dc\u00e7\u00fcnc\u00fc nesil: PCR&#8217;ye gerek kalmadan ger\u00e7ek zamanl\u0131 dizileme\n<ul class=\"wp-block-list\">\n<li>Tek molek\u00fcl ger\u00e7ek zamanl\u0131 (SMRT) (PacBio, Roche)<\/li>\n\n\n\n<li>Nanopore (Oxford Nanopore Teknolojileri)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>K\u0131sa okuma ve uzun okuma (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28146134\/\" target=\"_blank\" rel=\"noreferrer noopener\">Int J Mol Sci 2017;18:E308\u00a0<\/a>)\n<ul class=\"wp-block-list\">\n<li>K\u0131sa okuma: &lt; 300 baz \u00e7iftini okur \n<ul class=\"wp-block-list\">\n<li>\u00d6rnekler: sentez yoluyla dizileme, ligasyon yoluyla dizileme, pirosekanslama<\/li>\n\n\n\n<li>Avantajlar: Gb ba\u015f\u0131na d\u00fc\u015f\u00fck maliyet, y\u00fcksek do\u011fruluk<\/li>\n\n\n\n<li>Dezavantajlar\u0131: Azalm\u0131\u015f hizalama, yap\u0131sal d\u00fczenlemelerin s\u0131n\u0131rl\u0131 tespiti ve \u00e7\u00f6z\u00fcm\u00fc<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Uzun okuma: 2,5 Kb&#8217;den b\u00fcy\u00fck okunur. \n<ul class=\"wp-block-list\">\n<li>\u00d6rnekler: tek molek\u00fcl ger\u00e7ek zamanl\u0131 (SMRT), nanopore<\/li>\n\n\n\n<li>Avantajlar: iyile\u015ftirilmi\u015f hizalama, yap\u0131sal varyasyonlar\u0131n ve b\u00fcy\u00fck yeniden d\u00fczenlemelerin tespiti, tekrarlayan b\u00f6lgelerin dizilenmesi, yeni RNA transkript izoformlar\u0131n\u0131n ke\u015ffi, PCR&#8217;ye g\u00fcvenilmemesi ta\u015f\u0131nabilirli\u011fi ve i\u015flem s\u00fcresini iyile\u015ftirir.<\/li>\n\n\n\n<li>Dezavantajlar\u0131: Gb ba\u015f\u0131na y\u00fcksek maliyet, d\u00fc\u015f\u00fck do\u011fruluk \n<ul class=\"wp-block-list\">\n<li>Okuma derinli\u011fini art\u0131rmay\u0131 da i\u00e7eren y\u00f6ntem ve biyoenformatik algoritma iyile\u015ftirmesi, maliyeti hala k\u0131sa okuma y\u00f6ntemlerinden daha fazla olmas\u0131na ra\u011fmen do\u011frulu\u011fu %98&#8217;e kadar art\u0131rm\u0131\u015ft\u0131r (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2020;21:597<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\">Formalinle sabitlenmi\u015f parafine g\u00f6m\u00fcl\u00fc doku (FFPE)<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\">Genetik test i\u00e7in kullan\u0131lan en yayg\u0131n \u00f6rnek t\u00fcrlerinden biridir. <em><strong>Mutlaka \u00f6rnek patoloji laboratuvar\u0131nda ve Patolog taraf\u0131ndan se\u00e7ilmelidir. Yeteri kadar t\u00fcm\u00f6r dokusu i\u00e7ermeyen \u00f6rnekler yanl\u0131\u015f pozitif ya da yanl\u0131\u015f negatif sonu\u00e7lara neden olabilir. \u00d6rne\u011fin t\u00fcm\u00f6r dokusundan yeteri kadar i\u00e7erip-i\u00e7ermedi\u011fini. Mikroskop alt\u0131nda inceleme yapan Patolog karar verebilir. FFPE, NGS testi i\u00e7in klinik olarak uygun bir \u00f6rnek t\u00fcr\u00fc sa\u011flar. <\/strong><\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Genel i\u015f ak\u0131\u015f\u0131<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Tru-cut biyopsiler ve ince i\u011fne aspirasyonlar\u0131 (FNA) genellikle birincil t\u00fcm\u00f6r tan\u0131s\u0131 i\u00e7in doku elde etmek amac\u0131yla kullan\u0131l\u0131r.\n<ul class=\"wp-block-list\">\n<li>Eksizyonel biyopsiler ve rezeksiyonlar gibi daha b\u00fcy\u00fck cerrahi \u00f6rnekler, ilk tan\u0131 i\u00e7in daha az s\u0131kl\u0131kla elde edilir.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Doku formalinle sabitlenir ve histopatolojik de\u011ferlendirme i\u00e7in parafin bloka g\u00f6m\u00fcl\u00fcr.<\/li>\n\n\n\n<li>Kesitli doku, tan\u0131 koymak i\u00e7in morfoloji veya imm\u00fcnofenotip a\u00e7\u0131s\u0131ndan de\u011ferlendirilir.<\/li>\n\n\n\n<li>Parafin blo\u011funda kalan doku, NGS ile molek\u00fcler analiz de dahil olmak \u00fczere yard\u0131mc\u0131 testler i\u00e7in kullan\u0131labilir.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Bu i\u015f ak\u0131\u015f\u0131yla, yeni bir kanser tan\u0131s\u0131 i\u00e7in gerekli t\u00fcm tan\u0131 testleri, tek bir k\u00fc\u00e7\u00fck biyopsiden elde edilen materyal \u00fczerinde tamamlanabilir ve bu sayede hastan\u0131n daha invaziv cerrahi prosed\u00fcrlere maruz kalmas\u0131 en aza indirilirken, klinisyenlerin terap\u00f6tik y\u00f6netimi optimize etmesine yard\u0131mc\u0131 olunur.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">NGS testleri i\u00e7in FFPE&#8217;nin avantajlar\u0131<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Ar\u015fivlenebilir doku \n<ul class=\"wp-block-list\">\n<li>FFPE dokusundaki DNA nispeten stabildir ve t\u00fcm\u00f6rlerin retrospektif analizine olanak tan\u0131r.<\/li>\n\n\n\n<li>DNA miktar\u0131 ve canl\u0131l\u0131\u011f\u0131 ortam ko\u015fullar\u0131nda zamanla azal\u0131r (baz\u0131 \u00e7al\u0131\u015fmalarda miktar %50&#8217;nin alt\u0131na d\u00fc\u015fm\u00fc\u015ft\u00fcr ve 4-6 y\u0131l sonra sadece %11&#8217;i \u00e7o\u011falt\u0131labilmektedir) (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n\n\n\n<li>FFPE&#8217;yi daha d\u00fc\u015f\u00fck s\u0131cakl\u0131klarda saklamak veya FFPE dokusunu dondurmak, FFPE&#8217;deki genetik materyali daha iyi korumak i\u00e7in bir yol olarak \u00f6nerilmi\u015ftir (ancak bu \u00f6neriyi de\u011ferlendirmek i\u00e7in daha fazla veriye ihtiya\u00e7 vard\u0131r ve bu muhtemelen FFPE&#8217;yi saklaman\u0131n maliyetini art\u0131racakt\u0131r) (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750\u00a0<\/a>)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Histolojik analiz \n<ul class=\"wp-block-list\">\n<li>Tan\u0131ya ek olarak, \u00f6rneklerin morfolojik analizi, NGS \u00f6rne\u011findeki son t\u00fcm\u00f6r y\u00fczdesini en \u00fcst d\u00fczeye \u00e7\u0131karmak i\u00e7in t\u00fcm\u00f6r d\u0131\u015f\u0131 \u00f6rne\u011fin geri kalan\u0131ndan t\u00fcm\u00f6r\u00fcn makrodiseksiyonuna da olanak tan\u0131r.<\/li>\n\n\n\n<li>Baz\u0131 yeni ara\u015ft\u0131rmalar, farkl\u0131 imm\u00fcnohistokimyasal profillere sahip t\u00fcm\u00f6r b\u00f6lgelerinde NGS uygulayarak farkl\u0131 imm\u00fcnofenotiplere sahip t\u00fcm\u00f6r b\u00f6lgeleri aras\u0131ndaki genomik farkl\u0131l\u0131klar\u0131 ay\u0131rt etmenin m\u00fcmk\u00fcn olabilece\u011fini belirtmektedir; ancak baz\u0131 ara\u015ft\u0131rmalarda imm\u00fcnboyama i\u00e7in gereken ek i\u015flem ad\u0131mlar\u0131n\u0131n DNA miktar\u0131n\u0131 ve kalitesini azaltt\u0131\u011f\u0131 g\u00f6sterilmi\u015ftir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28498833\/\" target=\"_blank\" rel=\"noreferrer noopener\">PLoS One 2017;12:e0176280<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Ta\u015f\u0131ma kolayl\u0131\u011f\u0131 \n<ul class=\"wp-block-list\">\n<li>Bloklar halinde veya slaytlar \u00fczerinde kesilmi\u015f FFPE doku, ortam ko\u015fullar\u0131nda ta\u015f\u0131nabilir ve \u00f6nemli biyolojik tehlikeler olu\u015fturmaz (taze doku, kan, kemik ili\u011fi, beyin-omurilik s\u0131v\u0131s\u0131 vb. gibi numunelerin i\u015flenmesiyle ili\u015fkili daha s\u0131k\u0131 ta\u015f\u0131ma gereksinimleri ve potansiyel enfeksiyon tehlikeleriyle kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131nda).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">\u0130deal FFPE numunesini elde etmeyle ili\u015fkili zorluklar<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Analiz \u00f6ncesi hatalar\u0131n azalt\u0131lmas\u0131 \n<ul class=\"wp-block-list\">\n<li>S\u0131cak ve so\u011fuk iskemik s\u00fcreleri azaltmak i\u00e7in \u00f6rnekler m\u00fcmk\u00fcn olan en k\u0131sa s\u00fcrede hastadan al\u0131nmal\u0131 ve formalin i\u00e7ine yerle\u015ftirilmelidir (formalinin daha fazla ve daha e\u015fit \u015fekilde n\u00fcfuz etmesini sa\u011flamak i\u00e7in uygun kesitlerle). \n<ul class=\"wp-block-list\">\n<li>Uzun s\u00fcreli s\u0131cak iskemi (numunenin hastadan \u00e7\u0131kar\u0131l\u0131rken perf\u00fczyonunun azalmas\u0131yla olu\u015fur) ve so\u011fuk iskemi (numunenin formalin i\u00e7ine yerle\u015ftirilmesi\/saklanmas\u0131 s\u0131ras\u0131nda olu\u015fur) genetik materyalin bozulmas\u0131 ve belirli transkriptlerde potansiyel art\u0131\u015flar ve azalmalar dahil olmak \u00fczere bir dizi genetik de\u011fi\u015fiklikle ili\u015fkilidir (RNA, DNA&#8217;ya k\u0131yasla daha karars\u0131z oldu\u011fundan, potansiyel bozulma etkilerine \u00f6zellikle e\u011filimlidir) (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnekleme s\u0131ras\u0131nda t\u00fcm\u00f6r hacmi ve t\u00fcm\u00f6r y\u00fczdesi optimize edilmelidir.\n<ul class=\"wp-block-list\">\n<li>Bir numunede analiz i\u00e7in mevcut t\u00fcm\u00f6r miktar\u0131, NGS testinin ba\u015far\u0131s\u0131n\u0131 \u00f6nemli \u00f6l\u00e7\u00fcde etkileyen \u00f6n analitik fakt\u00f6rlerden biridir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222\u00a0<\/a>)<\/li>\n\n\n\n<li>Genellikle, test i\u00e7in g\u00f6nderilen numunenin en az %20&#8217;sinin t\u00fcm\u00f6r olmas\u0131 \u00f6nerilir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222<\/a>\u00a0)<\/li>\n\n\n\n<li>Bir\u00e7ok \u00fcretici, NGS testinde en b\u00fcy\u00fck ba\u015far\u0131y\u0131 elde etmek i\u00e7in en az 10 ng t\u00fcm\u00f6r DNA&#8217;s\u0131n\u0131n \u00e7\u0131kar\u0131lmas\u0131n\u0131 da \u00f6nermektedir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222<\/a>\u00a0)\n<ul class=\"wp-block-list\">\n<li>Illumina gibi platformlar, hibrit yakalama testleri i\u00e7in numune ba\u015f\u0131na en az 15.000 t\u00fcm\u00f6r h\u00fccresi \u00f6nermektedir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n\n\n\n<li>Ion Torrent platformu, deney ba\u015f\u0131na 100 &#8211; 1000 t\u00fcm\u00f6r h\u00fccresi gerektirir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Daha b\u00fcy\u00fck \u00f6rnekler (eksizyonlar ve rezeksiyonlar) \u00e7ekirdek biyopsiler ve FNA \u00f6rneklerine k\u0131yasla daha b\u00fcy\u00fck t\u00fcm\u00f6r hacmi ve t\u00fcm\u00f6r y\u00fczdesi elde etme olas\u0131l\u0131\u011f\u0131 daha y\u00fcksektir. \n<ul class=\"wp-block-list\">\n<li>Rezeksiyon \u00f6rnekleri ve eksizyonel biyopsiler daha y\u00fcksek NGS ba\u015far\u0131 oranlar\u0131yla ili\u015fkilidir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Tru-cut biyopsiler ve ince i\u011fne aspirasyon biyopsileri t\u00fcm\u00f6rden yetersiz par\u00e7alar\/t\u00fcm\u00f6r h\u00fccresi k\u00fcmeleri verebilir veya t\u00fcm\u00f6r d\u0131\u015f\u0131 h\u00fccrelere (\u00f6rne\u011fin iltihapl\u0131 h\u00fccreler ve normal \u00e7evreleyen doku) k\u0131yasla d\u00fc\u015f\u00fck oranda t\u00fcm\u00f6r h\u00fccresi i\u00e7eren \u00f6rneklerle sonu\u00e7lanabilir. \n<ul class=\"wp-block-list\">\n<li>D\u00fc\u015f\u00fck t\u00fcm\u00f6r h\u00fccreselli\u011fi, t\u00fcm\u00f6r h\u00fccrelerine \u00f6zg\u00fc anlaml\u0131 genetik analizleri engelleyebilir.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Tru-cut biyopsiler ve ince i\u011fne aspirasyon biyopsisi \u00f6rnekleri gibi daha k\u00fc\u00e7\u00fck veya daha s\u0131n\u0131rl\u0131 \u00f6rnekler elde edildi\u011finde, biyopsi materyalinin h\u0131zl\u0131 yerinde de\u011ferlendirilmesi (ROSE) gibi s\u00fcre\u00e7ler, hem morfolojik hem de yard\u0131mc\u0131 testler (NGS analizi gibi) i\u00e7in son \u00f6rnekteki t\u00fcm\u00f6r hacmini en \u00fcst d\u00fczeye \u00e7\u0131karmak amac\u0131yla \u00f6rnek \u00f6rneklemesinin s\u0131n\u0131fland\u0131r\u0131lmas\u0131na yard\u0131mc\u0131 olabilir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>NGS \u00e7al\u0131\u015fmalar\u0131 i\u00e7in genetik materyalin optimum kalitesini ve miktar\u0131n\u0131 sa\u011flamak i\u00e7in yeterli formalin fiksasyonu kritik \u00f6neme sahiptir. \n<ul class=\"wp-block-list\">\n<li>Morfoloji ve NGS gibi yard\u0131mc\u0131 \u00e7al\u0131\u015fmalara g\u00f6re numunelerin analizi i\u00e7in %10 formalinde 12 &#8211; 24 saatlik fiksasyon \u00f6nerilir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27657050\/\" target=\"_blank\" rel=\"noreferrer noopener\">Int J Mol Sci 2016;17:1579<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28498833\/\" target=\"_blank\" rel=\"noreferrer noopener\">PLoS One 2017;12:e0176280<\/a>\u00a0)<\/li>\n\n\n\n<li>Yetersiz fiksasyon, dokular\u0131n ve genetik materyalin enzimatik bozulmas\u0131na neden olabilir.<\/li>\n\n\n\n<li>A\u015f\u0131r\u0131 fiksasyon, daha fazla formalin fiksasyonuna ba\u011fl\u0131 eserlerin (500 bazda 1 modifikasyona kadar) olu\u015fumuna yol a\u00e7abilir.<\/li>\n\n\n\n<li>Genetik materyalin \u00e7\u0131kar\u0131lmas\u0131 ve NGS k\u00fct\u00fcphanelerinin olu\u015fturulmas\u0131 s\u0131ras\u0131nda, DNA&#8217;dan \u00e7apraz ba\u011flar\u0131 ve urasil bazlar\u0131n\u0131 \u00e7\u0131karmak ve y\u00fcksek hacimli ssDNA par\u00e7alar\u0131n\u0131 azaltmak i\u00e7in enzimatik i\u015flemler gibi ek ad\u0131mlar, fiksasyon eserlerini ve CNV&#8217;lerin ve tek n\u00fckleotid varyantlar\u0131n\u0131n (SNV&#8217;ler) yanl\u0131\u015f tespitlerini azaltmaya yard\u0131mc\u0131 olabilir.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>M\u00fcmk\u00fcnse ek doku i\u015fleme ad\u0131mlar\u0131 (\u00f6rne\u011fin kalsifikasyon giderme) atlanmal\u0131d\u0131r. \n<ul class=\"wp-block-list\">\n<li>Kemik ve di\u011fer \u00f6nemli \u00f6l\u00e7\u00fcde kalsifiye olmu\u015f dokular daha d\u00fc\u015f\u00fck NGS ba\u015far\u0131s\u0131yla ili\u015fkilidir. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222<\/a>\u00a0)<\/li>\n\n\n\n<li>Kire\u00e7 \u00e7\u00f6zme (dekalsifkasyon), genetik materyali par\u00e7alayan g\u00fc\u00e7l\u00fc (hidroklorik ve nitrik) veya zay\u0131f (pikrik, formin, asetik) asitlerin veya \u015felat olu\u015fturucu ajanlar\u0131n (EDTA) kullan\u0131m\u0131n\u0131 gerektirir. \n<ul class=\"wp-block-list\">\n<li>Zay\u0131f asitlere ve EDTA&#8217;ya k\u0131sa s\u00fcreli maruz kalma, SNV&#8217;lerin, CNV&#8217;lerin ve f\u00fczyon transkriptlerinin tespiti i\u00e7in yeterli DNA&#8217;n\u0131n \u00e7\u0131kar\u0131lmas\u0131na hala izin verebilir. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35629172\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Pers Med 2022;12:750<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Genel olarak, birincil t\u00fcm\u00f6r\u00fcn biyopsisi zorsa ve kemik ve di\u011fer dokulara \u00e7ok say\u0131da metastaz\u0131 varsa, kemik d\u0131\u015f\u0131 metastazlardan biyopsi al\u0131nmas\u0131, NGS yoluyla ba\u015far\u0131l\u0131 bir \u015fekilde analiz edilme olas\u0131l\u0131\u011f\u0131 daha y\u00fcksek olan dokular\u0131n elde edilmesiyle sonu\u00e7lanabilir. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27124905\/\" target=\"_blank\" rel=\"noreferrer noopener\">Am J Clin Pathol 2016;145:222<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>FFPE&#8217;den genetik materyal \u00e7\u0131karma y\u00f6ntemleri, NGS i\u00e7in kullan\u0131lan materyalin miktar\u0131n\u0131 ve kalitesini de \u00f6nemli \u00f6l\u00e7\u00fcde etkileyebilir.\n<ul class=\"wp-block-list\">\n<li>\u00c7al\u0131\u015fmalar, farkl\u0131 ekstraksiyon kitlerinin (kolonlar, manyetik boncuklar vb. gibi farkl\u0131 reaktifler veya safla\u015ft\u0131rma y\u00f6ntemleri kullan\u0131larak) ekstrakte edilen materyalin nihai verimi, safl\u0131\u011f\u0131 ve kalitesi a\u00e7\u0131s\u0131ndan farkl\u0131l\u0131k g\u00f6sterdi\u011fini g\u00f6stermi\u015ftir. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27657050\/\" target=\"_blank\" rel=\"noreferrer noopener\">Int J Mol Sci 2016;17:1579<\/a>\u00a0)<\/li>\n\n\n\n<li>\u00d6zellikle d\u00fc\u015f\u00fck t\u00fcm\u00f6r hacmi\/y\u00fczdesine sahip k\u00fc\u00e7\u00fck \u00f6rneklerle \u00e7al\u0131\u015f\u0131ld\u0131\u011f\u0131nda, \u00e7\u0131karma i\u015fleminin verimlili\u011fini, kalitesini ve verimini en \u00fcst d\u00fczeye \u00e7\u0131karmak esast\u0131r. (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27657050\/\" target=\"_blank\" rel=\"noreferrer noopener\">Int J Mol Sci 2016;17:1579<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\">Veri \u00e7\u0131kt\u0131s\u0131 ve analizi<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Demultipleksleme:<\/strong> E\u015f zamanl\u0131 olarak dizilenen birle\u015ftirilmi\u015f hasta \u00f6rnekleri (\u00f6rnek k\u00fct\u00fcphaneleri) daha sonra her hasta \u00f6rne\u011fine \u00f6zg\u00fc barkodlarla (indeksler) ayr\u0131l\u0131r<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Okumalar<\/strong>, dizi benzerli\u011fine g\u00f6re fiziksel olarak k\u00fcmelenir ve ileri ve geri okumalar hizalan\u0131r (e\u015fle\u015ftirilir)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Hizalama<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Yeniden dizileme: Dizi okumalar\u0131 referans diziye (bir bireyin referans genomuna) g\u00f6re hizalan\u0131r.<\/li>\n\n\n\n<li>De novo: diziler birbirine hizalanm\u0131\u015f \u015fekilde okunur.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Yorum:<\/strong> patojenik, muhtemelen patojenik, belirsiz \u00f6neme sahip varyant, muhtemelen iyi huylu, iyi huylu (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27993330\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Mol Diagn 2017;19:4<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25741868\/\" target=\"_blank\" rel=\"noreferrer noopener\">Genet Med 2015;17:405<\/a>\u00a0)<\/p>\n\n\n\n<h5 class=\"wp-block-heading\">NGS&#8217;nin avantajlar\u0131 (Sanger dizilemesiyle kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131nda)<\/h5>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Y\u00fcksek verim\/\u00e7\u0131kt\u0131<\/li>\n\n\n\n<li>\u0130yile\u015ftirilmi\u015f \u00e7\u00f6z\u00fcn\u00fcrl\u00fck<\/li>\n\n\n\n<li>Maliyet etkin<\/li>\n\n\n\n<li>Yap\u0131sal farkl\u0131l\u0131klar\u0131 tespit edebilen algoritmalar mevcuttur<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\">NGS&#8217;nin dezavantajlar\u0131 (Sanger dizilemesiyle kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131nda)<\/h5>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Daha k\u0131sa okuma uzunluklar\u0131<\/li>\n\n\n\n<li>Homoloji alanlar\u0131nda (ps\u00f6dogenler gibi), tekrar geni\u015flemelerinde, b\u00fcy\u00fck eklemelerde, kopya say\u0131s\u0131 varyantlar\u0131nda (CNV&#8217;ler) veya di\u011fer yap\u0131sal varyantlarda ham do\u011frulukta azalma \n<ul class=\"wp-block-list\">\n<li>Genetik olaylar genellikle benzersiz olmayan dizilerde (sentromerik DNA, tekrarlayan elemanlar, vb.) meydana gelir ve bu da NGS ile tan\u0131mlamay\u0131 zorla\u015ft\u0131r\u0131r<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Y\u00fcksek ba\u015flang\u0131\u00e7 \u200b\u200bmaliyetleri<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\">NGS i\u00e7in Platformlar<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Pirosekanslama<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Ticari olarak ba\u015far\u0131l\u0131 ilk NGS sistemi<\/li>\n\n\n\n<li>Dizileme mekanizmas\u0131 \n<ul class=\"wp-block-list\">\n<li>\u015eablonla ba\u011flanan boncuklar, enzim i\u00e7eren boncuklar\u0131n bulundu\u011fu bir taba\u011fa da\u011f\u0131t\u0131l\u0131r.<\/li>\n\n\n\n<li>4 n\u00fckleotidin her birinden 1 tanesi dizileme reaksiyonuna iteratif olarak eklenir.<\/li>\n\n\n\n<li>N\u00fckleotid kat\u0131l\u0131m\u0131 s\u0131ras\u0131nda pirofosfat (Ppi) sal\u0131n\u0131r ve Ppi sal\u0131n\u0131m\u0131, kat\u0131lan n\u00fckleotid miktar\u0131na e\u015fittir.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnek: 454 sistemi (Roche)<\/li>\n\n\n\n<li>Avantajlar\u0131: h\u0131zl\u0131, uzun okuma uzunlu\u011fu<\/li>\n\n\n\n<li>Dezavantajlar\u0131: reaktiflerin y\u00fcksek maliyeti, polibaz &gt; 6 ile nispeten y\u00fcksek hata oran\u0131, d\u00fc\u015f\u00fck verim (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22829749\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Biomed Biotechnol 2012;2012:251364<\/a>\u00a0)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Ligasyonla dizileme<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Dizileme mekanizmas\u0131: Etiketli probun DNA ipli\u011fine hibridizasyonu ve ba\u011flanmas\u0131\n<ul class=\"wp-block-list\">\n<li>2 prob spesifik baz ve 6 dejenerat baz i\u00e7eren oktamer oligon\u00fckleotid problar\u0131n\u0131 kullan\u0131r<\/li>\n\n\n\n<li>Her bir prob, son baza ba\u011fl\u0131 4 floresan boyadan birine, birinci bazda bir ligasyon alan\u0131na ve be\u015finci bazda bir ayr\u0131lma alan\u0131na sahip olacak<\/li>\n\n\n\n<li>Dizileme, prob ve \u015fablon aras\u0131ndaki tamamlay\u0131c\u0131 ba\u011flanma ile ger\u00e7ekle\u015fir ve ankraj k\u00f6rleri adapt\u00f6re tamamlay\u0131c\u0131 olarak ba\u011flan\u0131r ve ligasyon i\u00e7in bir ba\u015flatma noktas\u0131 g\u00f6revi g\u00f6r\u00fcr<\/li>\n\n\n\n<li>Daha sonra serbest b\u0131rak\u0131lan floresans g\u00f6r\u00fcnt\u00fclenir<\/li>\n\n\n\n<li>Floresan sinyali ve oktamerin son 4 n\u00fckleotidi kopar\u0131l\u0131r ve d\u00f6ng\u00fc devam eder<\/li>\n\n\n\n<li>Birka\u00e7 hibridizasyon, ligasyon ve kesme d\u00f6ng\u00fcs\u00fcnden sonra, DNA zinciri denat\u00fcre edilir ve reaksiyonu tekrarlamak i\u00e7in 1 bazla kayd\u0131r\u0131lm\u0131\u015f ba\u015fka bir dizileme primeri kullan\u0131l\u0131r<\/li>\n\n\n\n<li>Toplamda 5 dizileme primeri kullan\u0131l\u0131r ve par\u00e7an\u0131n dizisi yakla\u015f\u0131k 5 dizileme turundan sonra \u00e7\u0131kar\u0131labilir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnek: AB SOLiD sistemi (Thermo Fisher)<\/li>\n\n\n\n<li>Avantajlar\u0131: \u0130kinci nesil NGS&#8217;nin en y\u00fcksek do\u011frulu\u011fu, polimeraza ba\u011f\u0131ml\u0131 olmama<\/li>\n\n\n\n<li>Dezavantajlar\u0131: k\u0131sa dizileme okumalar\u0131 (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22829749\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Biomed Biotechnol 2012;2012:251364\u00a0<\/a>)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Sentez yoluyla dizileme (SBS)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Klinik uygulamalarda kullan\u0131lan en yayg\u0131n y\u00f6ntemlerden biri (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28782984\/\" target=\"_blank\" rel=\"noreferrer noopener\">Arch Pathol Lab Med 2017;141:1544<\/a>\u00a0)<\/li>\n\n\n\n<li>Dizileme mekanizmas\u0131\n<ul class=\"wp-block-list\">\n<li>Her d\u00f6ng\u00fcde, farkl\u0131 ayr\u0131labilir floresan boyalar ve \u00e7\u0131kar\u0131labilir bir blokaj grubu i\u00e7eren ak\u0131\u015f h\u00fccresine t\u00fcm 4 deoksin\u00fckleotid trifosfat (dNTP) eklenir<\/li>\n\n\n\n<li>DNA polimeraz\u0131 taraf\u0131ndan floresanla i\u015faretlenmi\u015f dNTP&#8217;nin dahil edilmesi, her d\u00f6ng\u00fcde polimerizasyonu sonland\u0131r\u0131r ve floresan sinyali, b\u00fcy\u00fcyen DNA ipli\u011fine \u00f6zg\u00fcl n\u00fckleotidi belirler<\/li>\n\n\n\n<li>Floresan boya ve bloke edici grup enzimatik olarak par\u00e7alan\u0131r, b\u00f6ylece bir sonraki d\u00f6ng\u00fc s\u0131ras\u0131nda yeni bir n\u00fckleotid eklenebilir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnek: Illumina dizilemesi (MiSeq, HiSeq, NextSeq ve NovaSeq platformlar\u0131)<\/li>\n\n\n\n<li>Avantajlar\u0131: y\u00fcksek do\u011fruluk (baz baz diziler), en b\u00fcy\u00fck \u00e7\u0131kt\u0131, en ucuz, tek n\u00fckleotid ekleme platformlar\u0131na (Ion Torrent, pirosekanslama) g\u00f6re homopolimer hatalar\u0131na daha az duyarl\u0131<\/li>\n\n\n\n<li>Dezavantajlar\u0131: d\u00f6ng\u00fcsel yap\u0131s\u0131 uzun dizileme s\u00fcrelerine, k\u0131sa okuma birle\u015ftirmeye yol a\u00e7ar (\u00a0<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/B9780128008867000030?via%3Dihub\" target=\"_blank\" rel=\"noreferrer noopener\">Coleman: Diagnostic Molecular Pathology, 2016<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22829749\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Biomed Biotechnol 2012;2012:251364<\/a>\u00a0)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>\u0130yon yar\u0131 iletken dizilemesi<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Klinik uygulamalarda kullan\u0131lan en yayg\u0131n y\u00f6ntemlerden biri (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28782984\/\" target=\"_blank\" rel=\"noreferrer noopener\">Arch Pathol Lab Med 2017;141:1544<\/a>\u00a0)<\/li>\n\n\n\n<li>Dizileme mekanizmas\u0131: \u0130yon Torrent dizilemesi (yar\u0131 iletken dizilemesi)\n<ul class=\"wp-block-list\">\n<li>DNA par\u00e7alar\u0131 boncuklar \u00fczerinde zenginle\u015ftirilir ve daha sonra bir mikro kuyu plakas\u0131na dizilir, b\u00f6ylece yaln\u0131zca bir boncuk bir kuyuyu kaplar<\/li>\n\n\n\n<li>De\u011fi\u015ftirilmemi\u015f tek n\u00fckleotidler mikrokuyu \u00e7ipe ard\u0131\u015f\u0131k olarak eklenir (tek n\u00fckleotid eklenmesiyle dizileme)<\/li>\n\n\n\n<li>DNA polimeraz\u0131 taraf\u0131ndan bir n\u00fckleotidin dahil edilmesi, tamamlay\u0131c\u0131 bir n\u00fckleotidin her eklendi\u011finde pH&#8217;daki de\u011fi\u015fikliklere duyarl\u0131 bir iyon sens\u00f6r\u00fc taraf\u0131ndan tespit edilen bir protonun sal\u0131nmas\u0131na neden olur<\/li>\n\n\n\n<li>S\u0131ra, her ard\u0131\u015f\u0131k n\u00fckleotid maruziyeti s\u0131ras\u0131nda elektrik sinyali yo\u011funlu\u011funun de\u011ferlendirilmesiyle belirlenir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnek: Ion Torrent (Thermo Fisher)<\/li>\n\n\n\n<li>Avantajlar\u0131: h\u0131zl\u0131 dizileme (kamera veya floresansa ba\u011f\u0131ml\u0131 olmama), d\u00fc\u015f\u00fck maliyet, daha k\u00fc\u00e7\u00fck cihaz boyutu<\/li>\n\n\n\n<li>Bak\u0131m noktas\u0131 testleri ve gen panelleri i\u00e7in kullan\u0131\u015fl\u0131d\u0131r<\/li>\n\n\n\n<li>Dezavantajlar\u0131: artan homopolimer hatas\u0131yla daha az do\u011fruluk (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333\u00a0<\/a>)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Tek molek\u00fcl ger\u00e7ek zamanl\u0131 (SMRT) dizileme<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Di\u011fer sistemlerle kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131nda, eklenen her dNTP i\u00e7in hedef b\u00f6lgenin klonal amplifikasyonuna veya kimyasal d\u00f6ng\u00fcye g\u00fcvenilmez<\/li>\n\n\n\n<li>Dizileme mekanizmas\u0131\n<ul class=\"wp-block-list\">\n<li>Her biri tek bir immobilize polimeraz ve hedef molek\u00fcl\u00fcn bir kopyas\u0131n\u0131 i\u00e7eren binlerce mikro kuyuya sahip \u00f6zel ak\u0131\u015f h\u00fccresi, genellikle birden fazla kez dizilenebilen dairesel bir \u015fablon<\/li>\n\n\n\n<li>Mikrokuyular, floresanla i\u015faretlenmi\u015f n\u00fckleotidlerin fazlas\u0131yla doldurulur<\/li>\n\n\n\n<li>Boya, DNA polimeraz\u0131 taraf\u0131ndan dahil edilme s\u0131ras\u0131nda par\u00e7alan\u0131r, bu da boyan\u0131n sens\u00f6rden uzakla\u015fmas\u0131na ve DNA polimeraz\u0131n\u0131n aktif b\u00f6lgesinin bir sonraki dNTP i\u00e7in kullan\u0131labilir hale gelmesine olanak tan\u0131r<\/li>\n\n\n\n<li>Mikrokuyudaki \u0131\u015f\u0131k dedekt\u00f6r\u00fc, n\u00fckleotidler dahil edildik\u00e7e sinyali ger\u00e7ek zamanl\u0131 olarak alg\u0131lar<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\u00d6rnek: Pacific Biosciences<\/li>\n\n\n\n<li>Avantajlar\u0131: en h\u0131zl\u0131 y\u00f6ntem, daha uzun hedefleri s\u0131ralayabilir, PCR&#8217;ye atfedilen \u00f6nyarg\u0131y\u0131 ve hatay\u0131 azalt\u0131r, yeni genom birle\u015ftirme uygulamalar\u0131 i\u00e7in idealdir, ger\u00e7ek zamanl\u0131 veri \u00fcretimi<\/li>\n\n\n\n<li>Dezavantajlar\u0131: daha d\u00fc\u015f\u00fck do\u011fruluk ve verim (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22829749\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Biomed Biotechnol 2012;2012:251364<\/a>\u00a0)\n<ul class=\"wp-block-list\">\n<li>Platform performans\u0131ndaki iyile\u015ftirmeler, artan verim (PacBio Sequence II platformunda ak\u0131\u015f h\u00fccresi ba\u015f\u0131na 160 Gb&#8217;ye kadar) dahil olmak \u00fczere, artan okuma derinli\u011fine (genomik kapsam\u0131n 40 kat\u0131na kadar) olanak tan\u0131m\u0131\u015f ve sonu\u00e7 olarak okumalar aras\u0131ndaki fikir birli\u011fi do\u011frulu\u011funu %99,9&#8217;a kadar art\u0131rm\u0131\u015ft\u0131r (<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">\u00a0Nat Rev Genet 2020;21:597<\/a>\u00a0)<\/li>\n\n\n\n<li>Y\u00fcksek do\u011fruluklu okumalar (PacBio platformlar\u0131 taraf\u0131ndan \u00fcretilenler gibi) daha fazla zaman ve kaynak (hesaplamal\u0131 i\u015flem g\u00fcc\u00fc dahil) gerektirir ve her \u015fablon molek\u00fcl\u00fc ve dizileme h\u00fccresi ba\u015f\u0131na birden fazla okuma \u00fcretilmesi nedeniyle genomik birle\u015ftirme ba\u015f\u0131na daha y\u00fcksek bir maliyetle sonu\u00e7lan\u0131r, ancak \u00fcretilen okumalar hem uzundur (&gt; 10 Kb) hem de do\u011frudur (&gt; %99) (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2020;21:597<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Nanog\u00f6zenek<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Di\u011fer sistemlerle kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131nda bu sistem n\u00fckleotidlerin dahil edilmesini izlemez veya ikincil bir sinyal (floresans, pH, vb.) kullanmaz.<\/li>\n\n\n\n<li>Dizileme mekanizmas\u0131\n<ul class=\"wp-block-list\">\n<li>\u0130yonik ak\u0131m nano g\u00f6zenek proteinlerinden ge\u00e7irilir<\/li>\n\n\n\n<li>Hedef DNA daha sonra bir nano g\u00f6zenekten ge\u00e7irilir ve her baz ak\u0131m\u0131 de\u011fi\u015ftirir<\/li>\n\n\n\n<li>DNA molek\u00fcl\u00fc nano g\u00f6zeneklerden ge\u00e7erken dizileme ger\u00e7ek zamanl\u0131 olarak ger\u00e7ekle\u015fir<\/li>\n\n\n\n<li>Sa\u00e7 tokas\u0131 k\u00fct\u00fcphane yap\u0131s\u0131 ileri ve geri ipliklerin dizilenmesine olanak tan\u0131r (\u00f6rne\u011fin, Oxford Nanopore Technologies)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Avantajlar\u0131: \u00e7ok uzun molek\u00fclleri s\u0131ralayabilir (standart uzunluk: 10 Kb ila 100 Kb; ultra uzun okumalar: &gt; 100 Kb), daha d\u00fc\u015f\u00fck maliyet, k\u00fc\u00e7\u00fck ve ta\u015f\u0131nabilir, ger\u00e7ek zamanl\u0131 veri \u00fcretimi; de novo montaj, yap\u0131sal varyantlar (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2020;21:597\u00a0<\/a>)\n<ul class=\"wp-block-list\">\n<li>Platform ba\u015f\u0131na ak\u0131\u015f h\u00fccrelerinin artmas\u0131yla (\u00f6rne\u011fin, ayn\u0131 anda 48 ak\u0131\u015f h\u00fccresi \u00e7al\u0131\u015ft\u0131rabilen Oxford Nanopore Technologies&#8217; PromethION), verim potansiyel olarak baz\u0131 k\u0131sa okuma tabanl\u0131 platformlar\u0131n (\u00f6rne\u011fin, Illumina NovaSeq) verimini a\u015fabilir (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2020;21:597\u00a0<\/a>)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Dezavantajlar\u0131: nispeten y\u00fcksek hata oran\u0131 (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27184599\/\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Rev Genet 2016;17:333<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22829749\/\" target=\"_blank\" rel=\"noreferrer noopener\">J Biomed Biotechnol 2012;2012:251364<\/a>\u00a0)\n<ul class=\"wp-block-list\">\n<li>Temel \u00e7a\u011fr\u0131lar\u0131n do\u011frulu\u011fu b\u00fcy\u00fck \u00f6l\u00e7\u00fcde kullan\u0131lan algoritmalara ba\u011fl\u0131d\u0131r; algoritmalardaki iyile\u015ftirmeler standart okumalar\u0131n (10 &#8211; 100 Kb) ortalama do\u011frulu\u011funu %87 &#8211; %98&#8217;e \u00e7\u0131karm\u0131\u015ft\u0131r, fikir birli\u011fi okuma do\u011frulu\u011fu ise %97 &#8211; %98 civar\u0131ndad\u0131r (<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32504078\/\" target=\"_blank\" rel=\"noreferrer noopener\">\u00a0Nat Rev Genet 2020;21:597<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>Bilgisayar Bilimi<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Genel bak\u0131\u015f:<\/strong> Ham dizileme verileri ayr\u0131 dizilere (okumalar) \u00e7evrilir, her okuma genomdaki hedeflenen b\u00f6lgesine e\u015flenir ve bu hizalama daha sonra \u00f6rnek DNA ile standartla\u015ft\u0131r\u0131lm\u0131\u015f referans aras\u0131ndaki farkl\u0131l\u0131klar\u0131 belirler.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Baz \u00e7a\u011fr\u0131s\u0131 ve demultipleksleme: <\/strong>Ham formatl\u0131 veriler (floresan yo\u011funlu\u011fu, elektriksel uyar\u0131, vb.) hedef DNA dizisindeki her bir pozisyona atanan bir n\u00fckleotid dizisine d\u00f6n\u00fc\u015ft\u00fcr\u00fcl\u00fcr (\u00f6rne\u011fin, ikili baz \u00e7a\u011fr\u0131s\u0131 (BCL) format\u0131)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Sinyalin arka plan g\u00fcr\u00fclt\u00fcs\u00fcne g\u00f6re yo\u011funlu\u011fu, temel \u00e7a\u011fr\u0131 algoritmas\u0131n\u0131n her n\u00fckleotid ile ili\u015fkili bir g\u00fcven puan\u0131 olu\u015fturmas\u0131na olanak tan\u0131r<\/li>\n\n\n\n<li>Okunan veriler, okuma tan\u0131mlay\u0131c\u0131s\u0131, n\u00fckleotid dizisi ve g\u00fcven puanlar\u0131 i\u00e7eren BCL&#8217;den FASTQ format\u0131na d\u00f6n\u00fc\u015ft\u00fcr\u00fclerek demultiplekslenir\n<ul class=\"wp-block-list\">\n<li>FASTQ format\u0131:\n<ul class=\"wp-block-list\">\n<li>Sat\u0131r 1: @Sequence tan\u0131mlay\u0131c\u0131 (ve iste\u011fe ba\u011fl\u0131 a\u00e7\u0131klama)<\/li>\n\n\n\n<li>Sat\u0131r 2: Ham dizi \u015fu \u015fekilde okunur: \u201cACTGACTG\u201d<\/li>\n\n\n\n<li>Sat\u0131r 3: Bo\u015fluk: &#8216;+&#8217;<\/li>\n\n\n\n<li>Sat\u0131r 4: Sat\u0131r 2&#8217;nin Phred kalite puan\u0131 (olas\u0131l\u0131k taban\u0131 s\u0131ralay\u0131c\u0131 taraf\u0131ndan yanl\u0131\u015f bir \u015fekilde \u00e7a\u011fr\u0131lm\u0131\u015ft\u0131r): &#8216;!AA&gt;**!C<\/li>\n\n\n\n<li>S = -log(10)P<\/li>\n\n\n\n<li>Q = Phred kalite puan\u0131<\/li>\n\n\n\n<li>P = Yanl\u0131\u015f bir baz \u00e7a\u011fr\u0131s\u0131n\u0131n olas\u0131l\u0131\u011f\u0131 (tepe \u015fekli ve bazlardaki \u00f6rt\u00fc\u015fme ile hesaplan\u0131r)<\/li>\n\n\n\n<li>\u00d6rnek yaz\u0131l\u0131m: CASAVA (Illumina)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>S\u0131ra hizalamas\u0131:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>T\u00fcm bireysel okumalar\u0131n genom \u00fczerindeki konumlara e\u015flenmesi<\/li>\n\n\n\n<li>Okunan verilere ve bir referans dizisine (bireysel okumalar\u0131n kar\u015f\u0131la\u015ft\u0131r\u0131ld\u0131\u011f\u0131 ve hizaland\u0131\u011f\u0131 bir standart) ihtiya\u00e7 duyar\n<ul class=\"wp-block-list\">\n<li>Biyolojik fakt\u00f6rler (iyi huylu varyantlar ve mutasyonlar) ve teknik fakt\u00f6rler (dizilemedeki hatalar veya yanl\u0131\u015f baz \u00e7a\u011fr\u0131lar\u0131) kusurlu hizalamaya katk\u0131da bulunur<\/li>\n\n\n\n<li>Hatal\u0131 hizalama i\u00e7in cezalar \u00fcretilir; belirli bir ceza e\u015fi\u011finde, bir okuman\u0131n hizalanamayaca\u011f\u0131 d\u00fc\u015f\u00fcn\u00fcl\u00fcr<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Kapsam (derinlik): Bir n\u00fckleotidin dizilendi\u011fi zaman say\u0131s\u0131 veya tek bir baz \u00fczerinde hizalanan okumalar\u0131n say\u0131s\u0131\n<ul class=\"wp-block-list\">\n<li>Art\u0131r\u0131lm\u0131\u015f kapsama, o konumdaki temel \u00e7a\u011fr\u0131y\u0131 do\u011frular ve temel \u00e7a\u011fr\u0131n\u0131n orijinal hedef dizisini do\u011fru bir \u015fekilde temsil etti\u011fine dair g\u00fcveni art\u0131r\u0131r<\/li>\n\n\n\n<li>Saf veya germ hatt\u0131 \u00f6rne\u011finde ad\u0131 ge\u00e7en bazdan emin olmak i\u00e7in yirmi kat kapsama (hedef b\u00f6lge \u00fczerinde 20 okuma, genellikle 20x olarak belirtilir) gereklidir<\/li>\n\n\n\n<li>T\u00fcm\u00f6r \u00f6rnekleri gibi kar\u0131\u015f\u0131k \u00f6rneklerdeki varyantlar\u0131 belirlemek i\u00e7in be\u015f y\u00fcz ila bin kat (500 &#8211; 1.000x) kapsamaya ihtiya\u00e7 vard\u0131r<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Hizalama bi\u00e7imleri: dizi hizalamas\u0131\/haritas\u0131 (SAM) ve ikili BAM bi\u00e7imi, hizalama verilerini referans dizi konumuna g\u00f6re dizinleyerek depolar<\/li>\n\n\n\n<li>\u00d6rnek yaz\u0131l\u0131mlar: BWA, Bowtie 2, MAQ, Stampy, Novoalign<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Varyant \u00e7a\u011fr\u0131:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Referans genoma hizaland\u0131ktan sonra, tek n\u00fckleotid polimorfizmleri (SNP&#8217;ler), tek n\u00fckleotid varyantlar\u0131 (SNV&#8217;ler) ve ekleme\/silmeler (indeller) tan\u0131mlanabilir<\/li>\n\n\n\n<li>Kapsam derinli\u011fini, de\u011fi\u015fken frekans\u0131 ve hizalama puan\u0131n\u0131 dikkate al\u0131r<\/li>\n\n\n\n<li>Dosya bi\u00e7imi: varyant \u00e7a\u011fr\u0131 bi\u00e7imi (VCF), mutasyon a\u00e7\u0131klama bi\u00e7imi (MAF)<\/li>\n\n\n\n<li>\u00d6rnek yaz\u0131l\u0131mlar: SAM ara\u00e7lar\u0131 Mpileup, GATK<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Verilerin g\u00f6rselle\u015ftirilmesi:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\u00d6rnek yaz\u0131l\u0131m: entegre genomik g\u00f6r\u00fcnt\u00fcleyici (IGV),\u00a0<a href=\"https:\/\/genome.ucsc.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">UCSC genom taray\u0131c\u0131s\u0131<\/a>\u00a0,\u00a0<a href=\"https:\/\/www.ensembl.org\/index.html\" target=\"_blank\" rel=\"noreferrer noopener\">ENSEMBL genom taray\u0131c\u0131s\u0131<\/a><\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Referans:<\/strong>\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28782984\/\" target=\"_blank\" rel=\"noreferrer noopener\">Arch Pathol Lab Med 2017;141:1544<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31977297\/\" target=\"_blank\" rel=\"noreferrer noopener\">Annu Rev Pathol 2020;15:97<\/a><\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><br \/>NGS uygulamalar\u0131<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>DNA dizilimi<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Veri analizi: Nokta mutasyonlar\u0131n\u0131, eklemeleri\/silmeleri (indeller), kopya say\u0131s\u0131 varyantlar\u0131n\u0131 (CNV&#8217;ler), yap\u0131sal varyantlar\u0131; t\u00fcm\u00f6r mutasyon y\u00fck\u00fcn\u00fc (TMB), mutasyon imzas\u0131n\u0131 belirler<\/li>\n\n\n\n<li>T\u00fcm genom dizilimi\n<ul class=\"wp-block-list\">\n<li>Genomun hem kodlayan hem de kodlamayan b\u00f6lgelerini s\u0131ralar<\/li>\n\n\n\n<li>Avantajlar\u0131: K\u00fct\u00fcphane haz\u0131rlama zenginle\u015ftirme veya amplifikasyon gerektirmez (y\u00fcksek \u00f6zg\u00fcll\u00fck)<\/li>\n\n\n\n<li>Dezavantajlar\u0131: y\u00fcksek maliyet, daha az derinlikte kapsam, karma\u015f\u0131k veri analizi ve yorumlama<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>T\u00fcm ekzom dizilimi\n<ul class=\"wp-block-list\">\n<li>Genomun yaln\u0131zca protein kodlama alan\u0131n\u0131n dizilenmesi (~%1 &#8211; 2)<\/li>\n\n\n\n<li>Mutasyon tespiti i\u00e7in yeterli \u00f6zg\u00fcll\u00fck ve duyarl\u0131l\u0131k i\u00e7in n\u00fckleotid ba\u015f\u0131na &gt; 20x kapsamaya ihtiya\u00e7 vard\u0131r<\/li>\n\n\n\n<li>Avantajlar\u0131: Klinik kullan\u0131m i\u00e7in daha uygun fiyatl\u0131d\u0131r<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Hedeflenen dizileme\n<ul class=\"wp-block-list\">\n<li>Genomun belirli b\u00f6lgelerini dizilemek i\u00e7in spesifik primerlerle zenginle\u015ftirmeyi kullan\u0131r<\/li>\n\n\n\n<li>Avantajlar\u0131: Her dizileme reaksiyonunda daha fazla say\u0131da bireysel numunenin \u00e7al\u0131\u015ft\u0131r\u0131lmas\u0131na olanak tan\u0131r, ilgi duyulan b\u00f6lgelerin kapsanma derinli\u011fini art\u0131r\u0131r ve maliyeti azalt\u0131r<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Gen panelleri\n<ul class=\"wp-block-list\">\n<li>Genomik t\u0131p\n<ul class=\"wp-block-list\">\n<li>Kal\u0131tsal sendromlar (\u00f6rne\u011fin Lynch sendromu, kal\u0131tsal meme\/yumurtal\u0131k kanseri sendromu) veya mitokondriyal hastal\u0131klar<\/li>\n\n\n\n<li>Germ hatt\u0131 varyantlar\u0131n\u0131 tespit etmek i\u00e7in 80x derinlik yeterlidir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Somatik mutasyonlar\n<ul class=\"wp-block-list\">\n<li>Kat\u0131 t\u00fcm\u00f6r ve hematolenfoid neoplazm panelleri<\/li>\n\n\n\n<li>&gt;Somatik mutasyonlar i\u00e7in 500x kapsamaya ihtiya\u00e7 var<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>RNA dizilemesi (RNA seq)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Ters transkriptaz PCR&#8217;yi (RT PCR) kullan\u0131r<\/li>\n\n\n\n<li>Veri analizi: farkl\u0131 ifade, gen f\u00fczyonlar\u0131, alternatif ekleme ve RNA d\u00fczenleme<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Di\u011fer<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Metilasyon dizilemesi (metil seq): DNA metilasyon modellerini analiz etmek i\u00e7in bis\u00fclfitle i\u015flenmi\u015f DNA&#8217;y\u0131 kullan\u0131r\n<ul class=\"wp-block-list\">\n<li>Ebeveyn bask\u0131s\u0131 gibi epigenetik de\u011fi\u015fiklikleri analiz etmek i\u00e7in yararl\u0131d\u0131r<\/li>\n\n\n\n<li>Metilasyon profili, MSS t\u00fcm\u00f6r s\u0131n\u0131fland\u0131rmas\u0131 i\u00e7in de giderek daha \u00f6nemli hale geliyor (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34185076\/\" target=\"_blank\" rel=\"noreferrer noopener\">Neuro Oncol 2021;23:1231<\/a>\u00a0)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Kromatin imm\u00fcno\u00e7\u00f6kt\u00fcrme (ChIP seq): Kromatin imm\u00fcno\u00e7\u00f6kt\u00fcrme kullan\u0131larak DNA protein etkile\u015fimlerinin analizi (\u00a0<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/B9780128008867000030?via%3Dihub\" target=\"_blank\" rel=\"noreferrer noopener\">Coleman: Diagnostic Molecular Pathology, 2016<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23887774\/\" target=\"_blank\" rel=\"noreferrer noopener\">Genet Med 2013;15:733<\/a>\u00a0)<\/li>\n\n\n\n<li>Dizileme ile transpozaza eri\u015filebilir kromatin i\u00e7in deney (ATAC seq)<\/li>\n\n\n\n<li>Kes ve ka\u00e7<\/li>\n<\/ul>\n\n\n\n<blockquote class=\"wp-block-quote is-layout-flow wp-block-quote-is-layout-flow\">\n<h5 class=\"wp-block-heading\"><br \/>Klinik uygulamalar<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/><strong>Onkoloji testleri<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><br \/>Genellikle hematolojik veya solid malignitelere \u00f6zg\u00fc somatik varyantlar\u0131 veya dizi varyantlar\u0131n\u0131 tan\u0131mlamak i\u00e7in belirli gen panellerini kullan\u0131r.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Tan\u0131ya yard\u0131mc\u0131 olur<\/li>\n\n\n\n<li>Prognostik bilgi sunar<\/li>\n\n\n\n<li>Etkili tedavi se\u00e7enekleri (hedefli tedaviler)<\/li>\n\n\n\n<li>BRAF\u00a0V600E mutasyonu BRAF inhibit\u00f6r\u00fc (\u00f6rne\u011fin vemurafenib) ile tedavi edilir<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Ticari testler (\u00f6rne\u011fin FoundationOne) y\u00fczlerce genomik b\u00f6lgenin test edilmesine olanak tan\u0131r<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Dola\u015f\u0131mdaki t\u00fcm\u00f6r DNA&#8217;s\u0131n\u0131 kullanarak kanser taramas\u0131 (<a href=\"https:\/\/emea.illumina.com\/company\/news-center\/press-releases\/2016\/2127903.html\" target=\"_blank\" rel=\"noreferrer noopener\">\u00a0Illumina: Illumina, Kan Bazl\u0131 Tarama Yoluyla Erken Kanser Tespiti Sa\u011flamak \u0130\u00e7in Yeni Bir \u015eirket Kuruyor [Eri\u015fim Tarihi 3 Mart 2023]\u00a0<\/a>)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Germ hatt\u0131 testi<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Germ hatt\u0131 DNA varyantlar\u0131n\u0131 tan\u0131mlamak i\u00e7in WES, WGS veya hedeflenen germ hatt\u0131 panelleri kullan\u0131l\u0131r.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Kal\u0131tsal hastal\u0131klar\u0131 te\u015fhis edin<\/li>\n\n\n\n<li>Muhtemelen genetik k\u00f6kenli olan fenotipleri a\u00e7\u0131klay\u0131n<\/li>\n\n\n\n<li>Kanser yatk\u0131nl\u0131\u011f\u0131n\u0131 (\u00a0BRCA1\u00a0\/\u00a0BRCA2\u00a0veya\u00a0TP53\u00a0mutasyonlar\u0131 vb.) belirlemek<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Ticari testler SNP tespiti ve analizine olanak sa\u011flar (\u00f6rne\u011fin, 23andme, Ancestry, Gene Dx, Ambry geneti\u011fi, vb.)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Mikrobiyoloji<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">WGS ve metagenomik dizileme y\u00f6ntemleri \u015fu ama\u00e7lar i\u00e7in kullan\u0131l\u0131r:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Patojenlerin ve terap\u00f6tik diren\u00e7 mekanizmalar\u0131n\u0131n tan\u0131mlanmas\u0131<\/li>\n\n\n\n<li>Sa\u011fl\u0131k kurulu\u015flar\u0131n\u0131n i\u00e7inde ve d\u0131\u015f\u0131nda antimikrobiyal direncin izlenmesi<\/li>\n\n\n\n<li>Patojenlerin ve patojenik su\u015flar\u0131n genotiplendirilmesi yoluyla hastal\u0131k salg\u0131nlar\u0131n\u0131n epidemiyolojik izlenmesi (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29074157\/\" target=\"_blank\" rel=\"noreferrer noopener\">Clin Microbiol Infect 2018;24:335<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36140733\/\" target=\"_blank\" rel=\"noreferrer noopener\">Genes (Basel) 2022;13:1566<\/a>\u00a0)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Farmakogenomik<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Genomik varyasyonlar\u0131 ila\u00e7 tepkisindeki veya ila\u00e7-ila\u00e7 etkile\u015fimlerindeki fenotipik farkl\u0131l\u0131klara ba\u011flay\u0131n (\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29844222\/\" target=\"_blank\" rel=\"noreferrer noopener\">Cold Spring Harb Perspect Med 2019;9:a033027<\/a>\u00a0)<\/p>\n\n\n\n<h5 class=\"wp-block-heading\">Ortaya \u00e7\u0131kan tan\u0131lamalar<\/h5>\n\n\n\n<p class=\"wp-block-paragraph\">Tek h\u00fccreli transkriptomik, uzaysal transkriptomik, tek h\u00fccreli ATAC dizisi<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Optik genom haritalama (OGM)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\u0130lk olarak 1990 y\u0131l\u0131nda tan\u0131t\u0131lan genom g\u00f6r\u00fcnt\u00fcleme tekniklerine dayanmaktad\u0131r<\/li>\n\n\n\n<li>Uzun, do\u011frusalla\u015ft\u0131r\u0131lm\u0131\u015f DNA molek\u00fclleri (tek zincirli par\u00e7a uzunluklar\u0131 0,15 &#8211; 2,5 Mb aras\u0131nda de\u011fi\u015fen y\u00fcksek molek\u00fcler a\u011f\u0131rl\u0131kl\u0131 DNA&#8217;dan t\u00fcretilmi\u015ftir) dizi motifine \u00f6zg\u00fc floresan i\u015faretleyicilerle (genellikle 100 kb ba\u015f\u0131na yakla\u015f\u0131k 15 etiket) etiketlenir, nano g\u00f6zenek kanallar\u0131ndan ge\u00e7irilir ve y\u00fcksek verimli g\u00f6r\u00fcnt\u00fcleme yoluyla analiz edilir.<\/li>\n\n\n\n<li>Floresan etiketlerinin tespit edilen deseni daha sonra bir referans genom haritas\u0131yla kar\u015f\u0131la\u015ft\u0131r\u0131lan yeni bir genom olu\u015fturmak i\u00e7in kullan\u0131l\u0131r<\/li>\n\n\n\n<li>Referans genom haritalar\u0131na g\u00f6re etiket desenlerindeki varyasyonlar, eklemeler, silmeler, ters \u00e7evirmeler, yer de\u011fi\u015ftirmeler ve kromozomal aneuploidi dahil olmak \u00fczere yap\u0131sal varyasyonlar\u0131 tespit etmek i\u00e7in kullan\u0131l\u0131r<\/li>\n\n\n\n<li>Faydalar\n<ul class=\"wp-block-list\">\n<li>NGS ve kar\u015f\u0131la\u015ft\u0131rmal\u0131 genomik hibridizasyon dizileri (aCGH) genetik varyantlar\u0131 dizi d\u00fczeyinde ve kopya say\u0131s\u0131 varyasyonuna g\u00f6re tespit edebilirken, OGM dengeli yap\u0131sal varyantlar\u0131 (\u00f6rne\u011fin ters \u00e7evirmeler ve dengeli translokasyonlar) ve karma\u015f\u0131k yap\u0131sal yeniden d\u00fczenlemeleri daha iyi tespit edebilir ve varyant k\u0131r\u0131lma noktalar\u0131n\u0131n y\u00fcksek \u00e7\u00f6z\u00fcn\u00fcrl\u00fc\u011f\u00fcne sahip olabilir.<\/li>\n\n\n\n<li>Tarihsel olarak dizilenmesi zor olan kromozomlar\u0131n tekrarlayan b\u00f6lgeleri daha kolay haritalanabilir\n<ul class=\"wp-block-list\">\n<li>Bir\u00e7ok genetik olay benzersiz olmayan\/tekrarlayan dizilerde meydana geldi\u011finden, OGM, bu alanlardaki yap\u0131sal d\u00fczenlemeleri \u015fu anda NGS ve aCGH ile yap\u0131labilenden daha etkili bir \u015fekilde tespit etme potansiyeline sahiptir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>500 bp kadar k\u00fc\u00e7\u00fck eklemeler ve \u00e7\u0131karmalar tespit edilebilir<\/li>\n\n\n\n<li>OGM verilerinin olu\u015fturulmas\u0131, geleneksel h\u00fccre k\u00fclt\u00fcr\u00fc ve karyotiplemeye k\u0131yasla daha k\u0131sa bir geri d\u00f6n\u00fc\u015f s\u00fcresine sahip olabilir ve bu da yap\u0131sal varyantlar\u0131n potansiyel olarak daha h\u0131zl\u0131 tan\u0131mlanmas\u0131na olanak tan\u0131r<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>S\u0131n\u0131rlamalar\n<ul class=\"wp-block-list\">\n<li>Yap\u0131sal ve genetik varyantlar tespit edilebilecek veya \u00e7\u00f6z\u00fclebilecek kadar b\u00fcy\u00fck olmal\u0131d\u0131r<\/li>\n\n\n\n<li>Kromozomlar\u0131n baz\u0131 b\u00f6lgeleri iyi haritalanmaz (\u00f6rne\u011fin, baz\u0131 \u00e7al\u0131\u015fmalar X kromozomunun subtelomerik b\u00f6lgesinin zay\u0131f \u00e7\u00f6z\u00fcn\u00fcrl\u00fc\u011f\u00fcn\u00fc ve sonras\u0131nda belirli yap\u0131sal yeniden d\u00fczenlemeleri tespit edememeyi bildirmektedir)<\/li>\n\n\n\n<li>OGM analizleri, numune ba\u015f\u0131na birden fazla yap\u0131sal varyant\u0131 belirleyebilir ve bazen onlarca ila y\u00fczlerce (veya daha fazla) potansiyel varyant\u0131n belirlenmesiyle sonu\u00e7lanabilir.\n<ul class=\"wp-block-list\">\n<li>Teknolojinin ara\u015ft\u0131rma ve potansiyel olarak klinik ortamlardaki g\u00f6receli yenili\u011fi g\u00f6z \u00f6n\u00fcne al\u0131nd\u0131\u011f\u0131nda, mevcut veri filtreleme ayarlar\u0131 ve stratejileri s\u0131n\u0131rl\u0131d\u0131r<\/li>\n\n\n\n<li>Heterozigotlu\u011fun kopya say\u0131s\u0131 n\u00f6tr kayb\u0131 i\u00e7in analitik algoritmalar eksiktir<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Mevcut referans haritalar\u0131 nispeten k\u00fc\u00e7\u00fck bir kohorttan t\u00fcretilmi\u015ftir<\/li>\n\n\n\n<li>Mevcut \u00f6l\u00e7eklendirme yetenekleri klinik uygulamalar a\u00e7\u0131s\u0131ndan s\u0131n\u0131rl\u0131d\u0131r.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Genel olarak, OGM, \u00f6l\u00e7ek b\u00fcy\u00fctme yeteneklerindeki geli\u015fmeler ve analitik algoritmalar\u0131n iyile\u015ftirilmesi beklenerek, tan\u0131 testlerine (ister birincil tan\u0131 testi ister di\u011fer geleneksel \u00e7al\u0131\u015fmalardan elde edilen sonu\u00e7lar\u0131n do\u011frulanmas\u0131 i\u00e7in olsun) yararl\u0131 bir katk\u0131 sa\u011flamay\u0131 vaat ediyor (<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34237281\/\" target=\"_blank\" rel=\"noreferrer noopener\">\u00a0Am J Hum Genet 2021;108:1423<\/a>\u00a0,\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34946907\/\" target=\"_blank\" rel=\"noreferrer noopener\">Genes (Basel) 2021;12:1958<\/a>\u00a0).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">&nbsp;<\/p>\n<\/blockquote>\n","protected":false},"excerpt":{"rendered":"<p>Next-generation sequencing (NGS) is a high-throughput technique that allows millions of nucleic acids to be sequenced simultaneously in parallel.<\/p>","protected":false},"author":1,"featured_media":2998,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11],"tags":[],"class_list":["post-2996","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-blog"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Yeni Nesil Dizileme (NGS) - Marmara Patoloji<\/title>\n<meta name=\"description\" content=\"Yeni nesil dizileme (NGS), 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