{"id":1366247,"date":"2024-08-21T12:46:00","date_gmt":"2024-08-21T10:46:00","guid":{"rendered":"https:\/\/dnaera.com\/cs\/?p=1366247"},"modified":"2026-01-28T14:15:39","modified_gmt":"2026-01-28T13:15:39","slug":"celogenomove-sekvenovani-vs-genotypizace","status":"publish","type":"post","link":"https:\/\/dnaera.com\/cs\/blog\/celogenomove-sekvenovani-vs-genotypizace\/","title":{"rendered":"Celogenomov\u00e9 sekvenov\u00e1n\u00ed vs. genotypizace"},"content":{"rendered":"\n

Z\u00e1le\u017e\u00ed na kvalit\u011b, ne na kvantit\u011b dat<\/h2>\n\n\n\n

Deoxyribonukleov\u00e1 kyselina, ve zkratce DNA, je nositelkou genetick\u00e9 informace a nach\u00e1z\u00ed sa v j\u00e1d\u0159e t\u00e9m\u011b\u0159 ka\u017ed\u00e9 bu\u0148ky v na\u0161em t\u011ble. M\u016f\u017eeme si ji p\u0159edstavit jako \u201eknihu recept\u016f\u201c, ve ktor\u00e9 jednotliv\u00e9 recepty p\u0159edstavuj\u00ed geny. D\u00edky genomu si dok\u00e1\u017ee bu\u0148ka vyrobit v\u00fdsledn\u00e9 produkty, co\u017e jsou ve v\u011bt\u0161in\u011b p\u0159\u00edpad\u016f proteiny. Ty v na\u0161em organismu n\u00e1sledn\u011b zabezpe\u010duj\u00ed r\u016fzn\u00e9 \u00falohy, od stavebn\u00edch, regula\u010dn\u00edch, transportn\u00edch a mnoh\u00fdch dal\u0161\u00edch. Pokud se v t\u011bchto receptech (genech) vyskytne n\u011bjak\u00e1 chyba, v\u00fdsledn\u00fd produkt m\u016f\u017ee m\u00edt jin\u00e9 vlastnosti, p\u0159\u00edpadn\u011b se nemus\u00ed v\u016fbec tvo\u0159it. Tyto chyby ozna\u010dujeme jako \u201emutace\u201c a pr\u00e1v\u011b ty jsou ve velk\u00e9 m\u00ed\u0159e zodpov\u011bdn\u00e9 za r\u016fzn\u00e9 odli\u0161nosti v na\u0161em organismu.<\/p>\n\n\n\n

Co konkr\u00e9tn\u011b se p\u00ed\u0161e v t\u011bchto receptech se n\u00e1m poda\u0159ilo odhalit a\u017e za\u010d\u00e1tkem tohoto stolet\u00ed, kdy v\u011bdci p\u0159e\u010detli cel\u00fd lidsk\u00fd genom. Ten se skl\u00e1d\u00e1 z p\u0159ibli\u017en\u011b 3 miliard stavebn\u00edch blok\u016f, kter\u00e9 ozna\u010dujeme jako tzv. \u201enukleotidy\u201c. Cel\u00e1 sekvence DNA je poskl\u00e1d\u00e1na ze 4 z\u00e1kladn\u00edch nukleotid\u016f \u2013 adenin, guanin, cytosin a thymin. Z tohoto d\u016fvodu se p\u0159i sekvenci DNA setk\u00e1me s p\u00edsmenky A, G, C a T. Samotn\u00fd sled p\u00edsmen n\u00e1m v\u0161ak nic ne\u0159ekne. Dnes ji\u017e v\u00edme, \u017ee geny tvo\u0159\u00ed jen p\u0159ibli\u017en\u011b 2 % lidsk\u00e9ho genomu a m\u00e1me jich p\u0159ibli\u017en\u011b 20 000. Zbytek v\u00edce-m\u00e9n\u011b nezn\u00e1me, i kdy\u017e v\u00edme, \u017ee i v t\u00e9to \u010d\u00e1sti se nach\u00e1zej\u00ed d\u016fle\u017eit\u00e9 oblasti pro spr\u00e1vn\u00e9 fungov\u00e1n\u00ed na\u0161ich bun\u011bk.<\/p>\n\n\n\n

Jak moc se z pohledu genetiky navz\u00e1jem li\u0161\u00edme?<\/h3>\n\n\n\n

Na\u0161e DNA se mezi n\u00e1mi shoduje a\u017e do m\u00edry 99,9 %.<\/strong> Na prvn\u00ed pohled se m\u016f\u017ee zd\u00e1t, \u017ee se t\u00e9m\u011b\u0159 neli\u0161\u00edme. Pokud se v\u0161ak vr\u00e1t\u00edme k velikosti na\u0161eho genomu, zjist\u00edme, \u017ee se li\u0161\u00edme v p\u0159ibli\u017en\u011b 3 milionech nukleotid\u016f. A pr\u00e1v\u011b tyto m\u00edsta, na kter\u00fdch se v populaci nach\u00e1zej\u00ed r\u016fzn\u00e1 p\u00edsmena, jsou obrovsk\u00fdm z\u00e1jmem mnoh\u00fdch studi\u00ed. D\u00edky t\u011bmto studi\u00edm dnes dok\u00e1\u017eeme nap\u0159\u00edklad \u0159\u00edct, \u017ee pokud se u v\u00e1s vyskytuje na konkr\u00e9tn\u00edm m\u00edst\u011b v DNA n\u011bjak\u00e9 konkr\u00e9tn\u00ed p\u00edsmeno, potom m\u00e1te zv\u00fd\u0161enou genetickou predispozici k rozvoji n\u011bjak\u00e9ho onemocn\u011bn\u00ed, jako je nap\u0159\u00edklad melanom nebo infarkt myokardu.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

V sou\u010dasnosti jsou vyu\u017e\u00edv\u00e1ny hlavn\u011b dva zp\u016fsoby \u010dten\u00ed DNA \u2013 sekvenov\u00e1n\u00ed a genotypizace.<\/strong><\/p>\n\n\n\n

Sekvenov\u00e1n\u00ed<\/h2>\n\n\n\n

Jednou z technik vyu\u017e\u00edvan\u00fdch ke stanoven\u00ed sekvence DNA je tzv. sekvenov\u00e1n\u00ed, tedy ur\u010dov\u00e1n\u00ed po\u0159ad\u00ed nukleotid\u016f v genomu jednotlivce. V sou\u010dasnosti se vyu\u017e\u00edvaj\u00ed zejm\u00e9na dva p\u0159\u00edstupy, a to tzv. celoexomov\u00e9 a celogenomov\u00e9 sekvenov\u00e1n\u00ed.<\/p>\n\n\n\n

Celoexomov\u00e9 sekvenov\u00e1n\u00ed<\/h4>\n\n\n\n

Technologie celoexomov\u00e9ho sekvenov\u00e1n\u00ed je zam\u011b\u0159en\u00e1 jen na konkr\u00e9tn\u00ed m\u00edsta v genomu, kter\u00e9 poskytuj\u00ed informace na v\u00fdrobu protein\u016f. P\u0159edpokl\u00e1d\u00e1 se, \u017ee tyto \u010d\u00e1sti, naz\u00fdvan\u00e9 jako \u201eexony\u201c, tvo\u0159\u00ed p\u0159ibli\u017en\u011b 1 % genomu \u010dlov\u011bka. Spole\u010dn\u011b v\u0161echny exony v genomu jsou zn\u00e1my jako \u201eexom\u201c, a proto je jejich zp\u016fsob sekvenov\u00e1n\u00ed zn\u00e1m\u00fd jako celoexomov\u00e9 sekvenov\u00e1n\u00ed. Tento p\u0159\u00edstup umo\u017e\u0148uje identifikovat mutace v k\u00f3duj\u00edc\u00ed oblasti jak\u00e9hokoliv genu, a ne pouze v n\u011bkter\u00fdch vybran\u00fdch genech. A jeliko\u017e se v\u011bt\u0161ina zn\u00e1m\u00fdch mutac\u00ed zp\u016fsobuj\u00edc\u00edch onemocn\u011bn\u00ed vyskytuje pr\u00e1v\u011b v exonech, tento zp\u016fsob sekvenov\u00e1n\u00ed je efektivn\u00ed v identifikaci takov\u00fdchto potenci\u00e1ln\u00edch mutac\u00ed.<\/p>\n\n\n\n

Celogenomov\u00e9 sekvenov\u00e1n\u00ed<\/h4>\n\n\n\n

Je v\u0161ak zn\u00e1mo, \u017ee i mutace mimo oblasti exon\u016f mohou ovlivnit genovou aktivitu a produkci b\u00edlkovin, a t\u00edm p\u00e1dem mohou v\u00e9st k r\u016fzn\u00fdm onemocn\u011bn\u00edm. Pr\u00e1v\u011b proto je nejide\u00e1ln\u011bj\u0161\u00edm zp\u016fsobem celogenomov\u00e9ho sekvenov\u00e1n\u00ed, kter\u00e9 ur\u010duje po\u0159ad\u00ed t\u00e9m\u011b\u0159 v\u0161ech nukleotid\u016f v genomu jednotlivce.<\/p>\n\n\n\n

V sou\u010dasnosti je nejb\u011b\u017en\u011bji pou\u017e\u00edvanou metodou tzv. ILLUMINA sekvenov\u00e1n\u00ed, d\u00edky kter\u00e9mu vzniklo v\u00edce ne\u017e 90 % v\u0161ech sekvena\u010dn\u00edch dat na sv\u011bt\u011b. N\u00e1zev t\u00e9to metody odkazuje na americkou spole\u010dnost, kter\u00e1 se pod\u00edl\u00ed na v\u00fdvoji, v\u00fdrob\u011b a prodeji syst\u00e9m\u016f pro anal\u00fdzu genetick\u00fdch variac\u00ed a biologick\u00fdch funkc\u00ed, a kter\u00e1 tuto metodu komercionalizovala.Tato metoda je zalo\u017eena na detekov\u00e1n\u00ed jednotliv\u00fdch nukleotid\u016f (A, G, C a T) pot\u00e9, co se za\u010dlen\u00ed do rostouc\u00edho vl\u00e1kna DNA. Detekce nukleotid\u016f je zalo\u017eena na fluorescen\u010dn\u00edm sign\u00e1lu, to znamen\u00e1, \u017ee ka\u017ed\u00fd nukleotid je ozna\u010den n\u011bjakou fluorescen\u010dn\u00ed zna\u010dkou (m\u016f\u017eeme si ji p\u0159edstavit jako n\u011bjakou barevnou zna\u010dku) a po p\u0159id\u00e1n\u00ed se do \u0159et\u011bzce po\u010d\u00edta\u010d vyhodnot\u00ed dan\u00fd sign\u00e1l.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Sta\u010d\u00ed v\u0161ak p\u0159e\u010d\u00edst cel\u00fd genom jen jednou?<\/h2>\n\n\n\n

Moment\u00e1ln\u011b je\u0161t\u011b nejsme v bod\u011b, kdy by sta\u010dilo p\u0159e\u010d\u00edst cel\u00fd lidsk\u00fd genom jen jedenkr\u00e1t. V sou\u010dasnosti toti\u017e je\u0161t\u011b nejsou tak p\u0159esn\u00e9 sekvena\u010dn\u00ed metody, kter\u00e9 by dok\u00e1zaly jen b\u011bhem jednoho \u010dten\u00ed p\u0159e\u010d\u00edst bezchybn\u011b cel\u00fd genom. Pr\u00e1v\u011b z tohoto d\u016fvodu doporu\u010duje spole\u010dnost ILLUMINA minim\u00e1ln\u00ed pokryt\u00ed 30x. To znamen\u00e1, \u017ee v pr\u016fm\u011bru je ka\u017ed\u00fd nukleotid p\u0159e\u010dten nez\u00e1visle 30-kr\u00e1t.<\/p>\n\n\n\n

N\u011bkter\u00e9 spole\u010dnosti v\u0161ak dnes nab\u00edz\u00ed i celogenomov\u00e9 sekvenov\u00e1n\u00ed s mnohem men\u0161\u00edm pokryt\u00edm, v n\u011bkter\u00fdch p\u0159\u00edpadech dokonce s pokryt\u00edm jen 1x. P\u0159i sekvenov\u00e1n\u00ed s tak n\u00edzk\u00fdm pokryt\u00edm je v sou\u010dasnosti nere\u00e1ln\u00e9 p\u0159e\u010d\u00edst cel\u00fd genom. Jak je potom mo\u017en\u00e9 poskl\u00e1dat celou skl\u00e1da\u010dku, kdy\u017e z \u010dten\u00ed nejsou k dispozici n\u011bkter\u00e9 d\u00edlky? <\/p>\n\n\n\n

Tento proces je pom\u011brn\u011b slo\u017eit\u00fd, ale jednodu\u0161e se vyu\u017e\u00edv\u00e1 princip tzv. \u201eimputace\u201c. T\u00edmto zp\u016fsobem se statisticky dopln\u00ed nep\u0159e\u010dten\u00e1 m\u00edsta, a to na z\u00e1klad\u011b zn\u00e1m\u00fdch haplotyp\u016f v populaci. Vyu\u017e\u00edv\u00e1 se tu to, \u017ee jednotliv\u00e9 nukleotidy se ned\u011bd\u00ed samostatn\u011b, ale d\u011bd\u00ed se spole\u010dn\u011b ve skupin\u00e1ch, kter\u00e9 ozna\u010dujeme jako \u201ehaplotypy\u201c. Aby jsme v\u0161ak mohli pova\u017eovat sekvenov\u00e1n\u00ed s tak n\u00edzk\u00fdm pokryt\u00edm za relevantn\u00ed, je nutn\u00e9 m\u00edt velk\u00fd a popula\u010dn\u011b specifick\u00fd referen\u010dn\u00ed panel, na z\u00e1klad\u011b kter\u00e9ho bude mo\u017en\u00e9 doplnit chyb\u011bj\u00edc\u00ed d\u00edlky genomu jednotlivce s vysokou p\u0159esnost\u00ed. Av\u0161ak i p\u0159i spln\u011bn\u00ed t\u011bchto podm\u00ednek nen\u00ed tento p\u0159\u00edstup vhodn\u00fd pro anal\u00fdzu velmi vz\u00e1cn\u00fdch genetick\u00fdch variant.<\/p>\n\n\n\n

Sekvenov\u00e1n\u00ed specifick\u00fdch gen\u016f<\/h2>\n\n\n\n

V klinick\u00e9 praxi sa \u010dastokr\u00e1t nesekvenuje cel\u00fd genom, ani exom, ale sekvenuj\u00ed se jen konkr\u00e9tn\u00ed vybran\u00e9 \u00faseky \u2013 konkr\u00e9tn\u00ed geny. Toto diagnostick\u00e9 vy\u0161et\u0159en\u00ed je \u00fa\u010dinn\u00fdm n\u00e1strojem potvrzen\u00ed nebo vyvr\u00e1cen\u00ed n\u011bjak\u00e9 specifick\u00e9 patogenn\u00ed mutace vedouc\u00ed k n\u011bjak\u00e9mu z\u00e1va\u017en\u00e9mu onemocn\u011bn\u00ed, kter\u00e9 se ve v\u011bt\u0161\u00ed m\u00ed\u0159e vyskytuje v rodinn\u00e9 historii dan\u00e9ho pacienta. <\/p>\n\n\n\n

Genotypizace<\/h2>\n\n\n\n

P\u0159esto\u017ee n\u00e1m celogenomov\u00e9 sekvenov\u00e1n\u00ed poskytuje nejlep\u0161\u00ed obraz o na\u0161em genomu, st\u00e1le pat\u0159\u00ed mezi relativn\u011b drah\u00e9 metody. Pr\u00e1v\u011b proto se v sou\u010dasnosti v komer\u010dn\u00edch testech DNA vyu\u017e\u00edv\u00e1 zejm\u00e9n p\u0159\u00edstup tzv. genotypizace, a to z d\u016fvodu jej\u00ed efektivity v pom\u011bru cena\/v\u00fdkon. Jde o anal\u00fdzu konkr\u00e9tn\u00edch m\u00edst v DNA na \u010dipu. Na rozd\u00edl od celogenomov\u00e9ho sekvenov\u00e1n\u00ed sa tedy ne\u010dte cel\u00e1 DNA, ale jen konkr\u00e9tn\u00ed m\u00edsta, kter\u00e9 byly vybr\u00e1ny na z\u00e1klad\u011b toho, zda o nich n\u011bco v\u00edme a tedy zda je dok\u00e1\u017eeme s n\u011b\u010d\u00edm asociovat. Tyto m\u00edsta zahrnuj\u00ed nap\u0159\u00edklad mutace spojovan\u00e9 s r\u016fzn\u00fdmi onemocn\u011bn\u00edmi nebo s atletick\u00fdm potenci\u00e1lem. V\u00edce o tom, jak prob\u00edh\u00e1 genotypizace, si m\u016f\u017eete p\u0159e\u010d\u00edst v tomto blogu<\/a>.<\/p>\n\n\n\n

Kter\u00fd p\u0159\u00edstup je tedy v sou\u010dasnosti vhodn\u011bj\u0161\u00ed pro komer\u010dn\u00ed genetick\u00e9 testov\u00e1n\u00ed?<\/h2>\n\n\n\n

Jak bylo u\u017e zm\u00edn\u011bno v\u00fd\u0161e v textu, samotn\u00fd sled nukleotid\u016f v genomu n\u00e1m nic ne\u0159ekne, kl\u00ed\u010dov\u00e1 je asociace konkr\u00e9tn\u00edch zm\u011bn s konkr\u00e9tn\u00edmi znaky.

Celogenomov\u00e9 sekvenov\u00e1n\u00ed sice poskytuje nejucelen\u011bj\u0161\u00ed pohled na genom jednotlivce, av\u0161ak mus\u00ed b\u00fdt provedeno kvalitn\u011b, s dostate\u010dn\u011b velk\u00fdm pokryt\u00edm. To je v\u0161ak st\u00e1le pom\u011brn\u011b n\u00e1kladn\u00e9, a proto v kombinaci s t\u00edm, \u017ee v sou\u010dasnosti nezn\u00e1me funkci v\u011bt\u0161iny m\u00edst v genomu, nem\u016f\u017eeme dnes pova\u017eovat tento p\u0159\u00edstup za efektivn\u00ed pro komer\u010dn\u00ed genetick\u00e9 testov\u00e1n\u00ed.

P\u0159i genotypizaci se neanalyzuje cel\u00fd genom, sleduj\u00ed se jen vybran\u00e1 m\u00edsta se zn\u00e1mou funkc\u00ed. Tento efektivn\u00ed p\u0159\u00edstup umo\u017enil sn\u00ed\u017eit cenu za genetick\u00e9 testov\u00e1n\u00ed natolik, \u017ee se stal vhodn\u00fdm n\u00e1strojem pro komer\u010dn\u00ed vyu\u017eit\u00ed. Pr\u00e1v\u011b proto vyu\u017e\u00edv\u00e1me tento p\u0159\u00edstup v na\u0161ich testech DNA i my v DNA ERA.
<\/p>\n\n\n\n

Zdroje<\/strong>:<\/p>\n\n\n\n

    \n
  1. Li, Y., Willer, C., Sanna, S., & Abecasis, G. (2009). Genotype imputation. Annual review of genomics and human genetics, 10, 387-406.<\/li>\n\n\n\n
  2. Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., Schloss, J. A., & Waterston, R. H. (2017). DNA sequencing at 40: past, present and future. Nature, 550(7676), 345-353.<\/li>\n\n\n\n
  3. https:\/\/www.illumina.com\/science\/technology\/next-generation-sequencing\/plan-experiments\/coverage.html<\/li>\n<\/ol>\n\n\n\n

    <\/p>\n\n\n\n

    Zdroje fotografi\u00ed:<\/strong><\/p>\n\n\n\n

      \n
    1. https:\/\/www.freepik.com\/photos\/technology‘>Technology photo created by freepik – www.freepik.com<\/a><\/li>\n\n\n\n
    2. https:\/\/en.wikipedia.org\/wiki\/$1,000_genome#\/media\/File:Cost_per_Genome.png<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

      Z\u00e1le\u017e\u00ed na kvalit\u011b, ne na kvantit\u011b dat Deoxyribonukleov\u00e1 kyselina, ve zkratce DNA, je nositelkou genetick\u00e9 informace a nach\u00e1z\u00ed sa v j\u00e1d\u0159e t\u00e9m\u011b\u0159 ka\u017ed\u00e9 bu\u0148ky v na\u0161em t\u011ble. M\u016f\u017eeme si ji p\u0159edstavit jako \u201eknihu recept\u016f\u201c, ve ktor\u00e9 jednotliv\u00e9 recepty p\u0159edstavuj\u00ed geny. D\u00edky genomu si dok\u00e1\u017ee bu\u0148ka vyrobit v\u00fdsledn\u00e9 produkty, co\u017e jsou ve v\u011bt\u0161in\u011b p\u0159\u00edpad\u016f proteiny. Ty […]<\/p>\n","protected":false},"author":873,"featured_media":1383799,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"content-type":"","inline_featured_image":false,"footnotes":""},"categories":[33],"tags":[58,59],"place-taxonomy":[],"class_list":["post-1366247","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized-cs","tag-dna-analyza","tag-dna-test"],"acf":[],"views":2175,"_links":{"self":[{"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/posts\/1366247","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/users\/873"}],"replies":[{"embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/comments?post=1366247"}],"version-history":[{"count":4,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/posts\/1366247\/revisions"}],"predecessor-version":[{"id":1383804,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/posts\/1366247\/revisions\/1383804"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/media\/1383799"}],"wp:attachment":[{"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/media?parent=1366247"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/categories?post=1366247"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/tags?post=1366247"},{"taxonomy":"place-taxonomy","embeddable":true,"href":"https:\/\/dnaera.com\/cs\/wp-json\/wp\/v2\/place-taxonomy?post=1366247"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}