{"id":6260,"date":"2015-10-26T13:24:10","date_gmt":"2015-10-26T17:24:10","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=6260"},"modified":"2015-10-26T13:24:10","modified_gmt":"2015-10-26T17:24:10","slug":"ctcs-cfdna-and-germline-all-working-in-harmony","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/ctcs-cfdna-and-germline-all-working-in-harmony\/","title":{"rendered":"CTCs, cfDNA, and Germline All Working in Harmony"},"content":{"rendered":"

Life is all about scarcity of time and resources, and when you need to get the most out of your archived samples, it seems that life imitates art in the lab. We\u2019ve been seeing a trend in researchers turning to NGS to get the most out of their samples.\u00a0 Let’s take a look at how these three different templates work in concert.<\/p>\n

NGS analysis of cfDNA<\/em><\/h3>\n

Cell-free DNA<\/a> is readily available in whole blood. However, the majority of fragmented DNA from plasma derives from normal cells. Our target for research analysis is circulating tumor DNA (ctDNA). It represents a tiny fraction of cfDNA, and provides molecular information about the tumor cell profile primarily in the form of point mutations and copy number variations.<\/p>\n

Research with ctDNA depends on managing the signal-to-noise ratio\u2014finding mutations at low frequency increases the risk of false positives. It\u2019s a bit like tuning an orchestra before a performance. There\u2019s lots of noise but very little that sounds like music.<\/p>\n

Hang on to that orchestra concept for a minute.<\/p>\n

Isolating and enriching CTCs<\/em><\/h3>\n

Circulating tumor cells are rare\u2014occurring at about 1 in every 109<\/sup> cells. CTCs may be mobilized by shearing events, mesenchymal transition, or programmed release of metastatic stem cells, and provide access to understanding the heterogeneity of tumor cells. They contain useful biomarkers that reflect the tissue of origin, such as proteins, RNA and DNA templates.<\/p>\n

CTCs can be selected and enriched. The challenge here is to isolate CTCs without missing cells or damaging those collected. Cell surface markers are commonly used to identify cells for isolation\u2014choosing the right antibody or cell surface binding is critical to achieving a high CTC recovery rate.<\/p>\n

And, there is a clear need to manage the number of background cells selected. CTC purity\u2014the ratio of CTCs to captured white blood cells in the isolated cell population\u2014drives the accuracy of downstream NGS analysis and is a limiting factor for some commercial technologies. Here too, think of an orchestra; too much brass and you lose the melody.<\/p>\n

Using germline DNA to identify somatic mutations<\/em><\/h3>\n

NGS analysis from both ctDNA and CTCs increases sensitivity. Yet, the rarity of ctDNA and DNA from CTCs in blood and the heterogenous nature of tumor DNA necessitate case control sequencing. By sequencing normal healthy cells from the same sample, you\u2019re able to distinguish noise caused by any sequencing test, as well as changes that are not specific to the tumor DNA.<\/p>\n

\"LB1\"<\/p>\n

 <\/p>\n

Figure 1. Identifying mutations in germline DNA, ctcDNA and cfDNA using the LiquidBiopsy\u2122 workflow including Ion Torrent technology<\/strong>. Representative data shows single nucleotide polymorphisms (SNPs) across all three templates, along with a point mutation at varying frequency in the ctcDNA and cfDNA.<\/p>\n

\"LB2\"<\/p>\n

 <\/p>\n

Figure 2. Subtracting germline SNPs using the LiquidBiopsy\u2122 workflow.<\/strong> Removing the Mendelian SNPs using Ion Reporter\u2122 Software results in a clear view of somatic mutations.<\/p>\n

 <\/p>\n

Tune your liquid biopsy research<\/em><\/h3>\n

Fine tuning your liquid biopsy research results doesn\u2019t have to be complex. Like orchestra sections, let the templates work together and you\u2019ll be humming along in no time.<\/p>\n

Find out more about the LiquidBiopsy\u2122 workflow at thermofisher.com\/liquidbiopsy<\/a><\/u>.<\/p>\n

 <\/p>\n

Upcoming liquid biopsy platform events\/conferences in 2016<\/em><\/h3>\n

March Events:<\/h4>\n

Molecular Medicine Triconference<\/a>
\nSan Francisco, CA, USA 6th\u201311th March 2016
\nVenue: Moscone North Convention Center
\nSpeaker: Michael J. Donovan, MD, PhD, Wed Mar 9, \u201cAnalyzing Liquid Biopsy Samples with Next-generation Sequencing in Clinical Research\u201d<\/p>\n

3rd Austrian Biomarker Symposium 2016 Early Diagnostics<\/a>.
\n<\/span>Vienna, Austria 10th\u201311th March 2016
\n<\/span>March 10th, 10.30 AM – Session 1: Personalized Medicine and Early Diagnosis
\n<\/span>Dr. Luca Quagliata<\/a>‘s talk is titled, \u201cLiquid Biopsy a new tool in the era of personalized medicine.\u201d<\/span><\/p>\n

I<\/span><\/a>nternational Symposium Minimal Residual Cancer<\/a>.
\n<\/span>Hamburg, Germany 19th\u201321st March 2016<\/span>
\n<\/span>March 21st: Session \u201cCompanies with novel technologies\u201d
\n<\/span>Professor Jos\u00e9 Luis Costa<\/a> will present his Liquid Biopsy research on lung samples<\/span><\/p>\n

Arab Lab
\n<\/a>Dubai, UAE 20th\u201323rd March 2016
\nVenue: Dubai World Trade Center<\/p>\n

April Events:<\/h4>\n

Biopsia liquida: la firma dei tumori nei fluidi biologici
\n<\/a>Milan, Italy 6th April\u00a02016
\nVenue : Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Aula A,<\/p>\n

Exosomes and Liquid Biopsies Asia<\/a>
\nTaipei, Taiwan 7th\u20138th April 2016
\nSpeaker: Xingwang Fang, Senior Staff Scientist, Thermo Fisher Scientific, Talk title TBD<\/p>\n

American Association for Cancer Research Annual Meeting<\/a>
\nNew Orleans, LA, USA 16th\u201320th April 2016
\nVenue: Ernest N. Morial Convention Center<\/p>\n

Liquid Biopsy – A revolution in Cancer treatment
\n<\/a>IPG, Gosselies, Belgium,\u00a0<\/span>27 April 2016<\/span><\/p>\n

Liquid Biopsy: Tracking Cancer<\/a>
\nRome, Italy 29th\u201330th April 2016
\nVenue:\u00a0Aula A Patologia Generale- Policlinico Umberto I, Viale Regina Elena, 324<\/p>\n

May\u2013Dec Events:<\/h4>\n

The European Human Genetics Conference 2016<\/a>
\nBarcelona, Spain 21st\u201324th May 2016<\/p>\n

European Association for Cancer Research
\n<\/a>Manchester, UK 9th\u201312th July 2016<\/p>\n

World CDx<\/a>
\n<\/strong>Boston, MA, USA 27th\u201329th September 2016
\nSpeaker TBD.<\/p>\n

Association for Molecular Pathology (AMP) Annual Meeting
\n<\/a>Charlotte, NC, USA 10th\u201312th November 2016
\nVenue: Charlotte Convention Center<\/p>\n

 <\/p>\n

 <\/p>\n

For Research Use Only. Not for use in diagnostic procedures.<\/strong><\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

Life is all about scarcity of time and resources, and when you need to get the most out of your archived samples, it seems that life imitates art in the lab. We\u2019ve been seeing a trend in researchers turning to NGS to get the most out of their samples.\u00a0 Let’s take a look at how<\/p>\n","protected":false},"author":107,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[54],"tags":[17,11,55],"division":[],"class_list":{"0":"post-6260","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-cancer-research","7":"tag-applied-biosystems","8":"tag-ion-torrent","9":"tag-peripheral-monitoring","10":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nCTCs, cfDNA, and Germline All Working in Harmony - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/ctcs-cfdna-and-germline-all-working-in-harmony\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"CTCs, cfDNA, and Germline All Working in Harmony\" \/>\n<meta property=\"og:description\" content=\"Life is all about scarcity of time and resources, and when you need to get the most out of your archived samples, it seems that life imitates art in the lab. 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