Somatic mutation landscapes at single-molecule resolution
preprint
OA: closed
Abstract
Abstract Somatic mutations drive cancer development and may contribute to ageing and other diseases. Yet, the difficulty of detecting mutations present only in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. To overcome these limitations, we introduce nanorate sequencing (NanoSeq), a new duplex sequencing protocol with error rates <5 errors per billion base pairs in single DNA molecules from cell populations. The version of the protocol described here uses clean genome fragmentation with a restriction enzyme to prevent end-repair-associated errors and ddBTPs/dATPs during A-tailing to prevent nick extension. Both changes reduce the error rate of standard duplex sequencing protocols by preventing the fixation of DNA damage into both strands of DNA molecules during library preparation. We also use qPCR quantification of the library prior to amplification to optimise the complexity of the sequencing library given the desired sequencing coverage, maximising duplex coverage. The sample preparation protocol takes between 1 and 2 days, depending on the number of samples processed. The bioinformatic protocol is described in:https://github.com/cancerit/NanoSeqhttps://github.com/fa8sanger/NanoSeq_Paper_Code
Full text
5,583 characters
· extracted from
preprint-html
· click to expand
:root { --font-inter: 'Inter', sans-serif, Symbol; --font-monospace: monospace; --font-sans-serif: sans-serif; } html, body, div, span, h1, h2, h3, h4, h5, h6, p, ol, ul, li, table, caption, tbody, tfoot, thead, tr, th, td {margin: 0;padding: 0;border: 0;font-size: 100%;font: inherit;vertical-align: baseline;} html {font-size: 14px;line-height: 1.5;} body {font-size: 14px;line-height: 1.5;font-family: var(--font-Inter);} ol, ul {list-style: none;} blockquote, q {quotes: none;} blockquote:before, blockquote:after, q:before, q:after {content: '';content: none;} img {max-width: 100%;} table {border-collapse: collapse;border-spacing: 0;} b {font-weight: bold;} a {color: #2c71d6;text-decoration: none;} p {margin: 10px 0 10px 0;} .no-select {-o-user-select: none;-moz-user-select: none;-khtml-user-select: none;-webkit-user-select: none;user-select: none;} * {box-sizing: border-box;} @keyframes blink {0% {opacity: .1;}20% {opacity: 1;}100% {opacity: .1;}} .main-preloader{position:fixed;display: flex;top:0;bottom:0;left:0;right:0;align-items: center;justify-content: center;z-index:200000000;text-align:center;background:#F2F3F6;} .main-preloader.dark{background:#363636;} .main-preloader.hidden {display: none;} .main-preloader .mp-logo{height:100px;width:100px;} Somatic mutation landscapes at single-molecule resolution V.1 {"@context":"https://schema.org","@id":"https://www.protocols.io/#org","@type":"Organization","logo":{"@type":"ImageObject","height":"1550","url":"https://www.protocols.io/img/protocols-og.jpg","width":"1920"},"name":"protocols.io","url":"https://www.protocols.io/"} {"@context":"https://schema.org","@id":"https://www.protocols.io/#website","@type":"WebSite","name":"protocols.io","publisher":{"@id":"https://www.protocols.io/#org"},"url":"https://www.protocols.io/"} {"@context":"https://schema.org","@id":"https://www.protocols.io/view/somatic-mutation-landscapes-at-single-molecule-res-rm7vzkp98vx1/v1#webpage","@type":"WebPage","about":{"@id":"https://www.protocols.io/#org"},"description":"Somatic mutation landscapes at single-molecule resolution\n. Somatic mutations drive cancer development. Read full protocol, steps, and materials on protocols.io","isPartOf":{"@id":"https://www.protocols.io/#website"},"name":"Somatic mutation landscapes at single-molecule resolution\n V.1","url":"https://www.protocols.io/view/somatic-mutation-landscapes-at-single-molecule-res-rm7vzkp98vx1/v1"} {"@context":"https://schema.org","@id":"https://www.protocols.io/view/somatic-mutation-landscapes-at-single-molecule-res-d3va8n2e#article","@type":"Article","author":{"@type":"Person","affiliation":"Dev","name":"Protocols Importer"},"dateModified":"2021-04-28T17:04:17Z","datePublished":"2021-04-28T17:04:17Z","description":"Somatic mutation landscapes at single-molecule resolution\n. Somatic mutations drive cancer development. Read full protocol, steps, and materials on protocols.io","headline":"Somatic mutation landscapes at single-molecule resolution\n V.1","image":{"@type":"ImageObject","url":"https://files.protocols.io/webapp/images/q2ckeg/meta/protocolsio.png"},"mainEntityOfPage":{"@id":"https://www.protocols.io/view/somatic-mutation-landscapes-at-single-molecule-res-d3va8n2e#webpage"},"publisher":{"@id":"https://www.protocols.io/#org"}} var WebappBundlePath = "https:\/\/files.protocols.io\/webapp\/bundles\/production-12becbb\/"; var AMPLITUDE_API_KEY="c250ed1d862cb9c01587e1f779a32c9";var FFMPEG_HOST="https://ffmpeg.protocols.io";var FILES_CDN_URL="https://files.protocols.io";var FILES_S3_BUCKET="protocols-io-files";var FILES_S3_PREFIX="external";var GA_MEASUREMENT_ID="G-33ZGV5CT0B";var GOOGLE_CLIENT_ID="182746271041-rdtjk0b1h9706r0fgpq1o2h55lgbo8un.apps.googleusercontent.com";var HAS_SSR= false ;var HOST_ROLE= 1 ;var HOST_ROLES={"HOST_DEV":2,"HOST_LOCAL":3,"HOST_PROD":1};var IMAGE_BASE_PATH="https://files.protocols.io/webapp/images/q2ckeg/";var NATS_SERVER="wss://ws.protocols.io";var ORCID_CLIENT_ID="APP-7405TP4958GFSZXV";var ORCID_URL="https://orcid.org/oauth/authorize";var RECAPTCHA_SITE_ID="6LeMF6YUAAAAAOYzOqfc9Ml3PdTgIzO1oDdIwCYc";var SITE_URL="https://www.protocols.io";var SPRINGERNATURE_CLIENT_ID="protocolsio";var SPRINGERNATURE_REDIRECT="https://www.protocols.io/api/v1/auth/springernature/authcallback";var SPRINGERNATURE_URL="https://idp.springernature.com";var STRIPE_PUB_KEY="pk_live_51PfMxdRshFFmaQRVGeDsSX7NFFLMkMuqr17SxP6JcJuieglmQYHPgM7cz0XdO91IEVP9k4E4MC7PZB2ATyuuaOy800ivYpRURi";var UIPE="ccW9Kn73Dw3C4V1lovN9dnriPRBEq/u77eY3wEAkK0M=";var VPC_ALLOW_REGENTS_LINKING= false ;var VPC_DISABLED_INVITE_COLLEAGUES= false ;var VPC_DISABLED_PUBLISHING= false ;var VPC_DISABLED_SIGN_UP= false ;var VPC_DISABLED_WORKSPACE_CREATION= false ;var VPC_EXTERNAL_STORAGES= null ;var VPC_FORWARDED_VIEW_URL_PREFIX="";var VPC_MAIN_CLOUD_URL="https://www.protocols.io";var VPC_REQUIRE_SIGN_IN= false ;var VPC_USE_MAIN_GLOBAL_SEARCH= false ;var WEBAPP_VERSION="production-12becbb";var YJS_WEBSOCKET_URL="wss://www.protocols.io";var __stripeGlobal= null ;var cookie_session_guid="4FC6201C87CA11F199810A58A9FEAC02";var gosessid="4FC61D8987CA11F199810A58A9FEAC02";var is_premium= false ;var loadedAmplitude= false ;var loadedGA= false ;var logged_in= false ;var session_guid="";var show_loader= true ;var user_theme="default"; var is_grecaptcha_loaded = false; if (!Element.prototype.matches) Element.prototype.matches = Element.prototype.msMatchesSelector; if (!Element.prototype.closest) Element.prototype.closest = function (selector) {var el = this; while (el) {if (el.matches(selector)) return el; el = el.parentElement;}};
Text is read by the "Ask this paper" AI Q&A widget below. Extraction quality varies by source — PMC NXML preserves structure cleanly, OA-HTML may include some navigation residue, and OA-PDF can have broken hyphenation. The publisher copy (via DOI) is the canonical version.
My notes (saved in your browser only)
Ask this paper
Answers must be backed by verbatim quotes from this paper's full text. Hallucinated quotes are dropped automatically; if no verbatim passage answers the question, we say so. How this works
Citation neighborhood (no data yet)
We don't have any in-corpus citations linked to this paper yet. The paper's references may be in our DB but unresolved to ``paper_id`` (resolution happens at ingest when the cited DOI matches a row we already have). Run the cross-source citation reconcile pass to retry.
Source provenance
- europepmc
- last seen: 2026-05-19T01:45:01.086888+00:00