{"id":2892,"date":"2018-09-16T19:54:27","date_gmt":"2018-09-16T23:54:27","guid":{"rendered":"https:\/\/www.med.unc.edu\/bigs2?page_id=2892&preview_id=2892"},"modified":"2019-10-08T17:29:24","modified_gmt":"2019-10-08T21:29:24","slug":"genomic-analysis","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/","title":{"rendered":"Genomic Analysis"},"content":{"rendered":"
\n
\n
\n
\n
\n

Title:\u00a0<\/strong>Tumor Heterogeneity: Clonal Structure Idetification<\/b><\/h4>\n

 <\/p>\n

Introduction<\/h4>\n

Tumor at diagnosis consists of genotypically distinct cell populations referred to as (sub)clones which is often of crucial interest in cancer study.\u00a0This is not only because the clonal structure itself provides an important clue for clinical treatment to the cancer but also subsequent analysis heavily\u00a0depends on the identified structure.<\/p>\n

Recently, PyClone was developped to efficiently identify the subclonal structure in DNA-seq. PyClone employs Bayesian hierarchical model based on\u00a0the so called cellular prevalence that measures proportions of cells harbouring a mutation. The structure is then identified by clustering the estimated\u00a0cellular prevalence under assumption of a perfect and persistent phylogeny of the clonal populations. The subclonal structure identification via PyClone\u00a0consists of two stages: i) estimating cellular prevalences and ii) clustering based on the estimated cellular prevalences.<\/p>\n


\n<\/p>\n

Questions<\/h4>\n

Using low read depth whole genome sequencing data to identify clone and subclones in a tumor sample.<\/p>\n

Methods<\/h4>\n

a) We designed a pairwise difference penalized method, called CliP (Clonal structure identification through penalized pairwise difference), to try to address the problem<\/p>\n

b) A non-concave penalty frame work was implemented to search for the most suitable solution<\/p>\n

Findings<\/h4>\n

We have applied our method to the ICGC whole genome sequencing samples from different organ sites, obtained satisfactory results.
\n<\/p>\n

References<\/h4>\n

Fan, J. and Li, R. (2001). Variable selection via nonconcave penalized likelihood and its oracle properties, Journal of the American statistical Association 96(456): 1348-1360.<\/p>\n

Ke, T., Fan, J. and Wu, Y. (2014). Homogeneity pursuit, Journal of the American Statistical Association .<\/p>\n

Roth, A., Khattra, J., Yap, D., Wan, A., Laks, E., Biele, J., Ha, G., Aparicio, S., Bouchard-Cote, A. and Shah, S. P. (2014). Pyclone: statistical inference of clonal population structure in cancer, Nature methods .<\/p>\n

Tibshirani, R., Saunders, M., Rosset, S., Zhu, J. and Knight, K. (2005). Sparsity and smoothness via the fused lasso, Journal of the Royal Statistical Society: Series B (Statistical Methodology) 67(1): 91-108.<\/p>\n<\/div>\n<\/div>\n<\/div>\n

\n

<\/p>\n

 <\/p>\n<\/div>\n<\/div>\n

\n

 <\/p>\n<\/div>\n<\/div>\n

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

Title:\u00a0Tumor Heterogeneity: Clonal Structure Idetification   Introduction Tumor at diagnosis consists of genotypically distinct cell populations referred to as (sub)clones which is often of crucial interest in cancer study.\u00a0This is not only because the clonal structure itself provides an important clue for clinical treatment to the cancer but also subsequent analysis heavily\u00a0depends on the identified … Read more<\/a><\/p>\n","protected":false},"author":55348,"featured_media":0,"parent":2857,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2892","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"\nGenomic Analysis - BIG-S2<\/title>\n<meta name=\"robots\" content=\"noindex, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Genomic Analysis - BIG-S2\" \/>\n<meta property=\"og:description\" content=\"Title:\u00a0Tumor Heterogeneity: Clonal Structure Idetification   Introduction Tumor at diagnosis consists of genotypically distinct cell populations referred to as (sub)clones which is often of crucial interest in cancer study.\u00a0This is not only because the clonal structure itself provides an important clue for clinical treatment to the cancer but also subsequent analysis heavily\u00a0depends on the identified … Read more\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/\" \/>\n<meta property=\"og:site_name\" content=\"BIG-S2\" \/>\n<meta property=\"article:modified_time\" content=\"2019-10-08T21:29:24+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/\",\"url\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/\",\"name\":\"Genomic Analysis - BIG-S2\",\"isPartOf\":{\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg\",\"datePublished\":\"2018-09-16T23:54:27+00:00\",\"dateModified\":\"2019-10-08T21:29:24+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage\",\"url\":\"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg\",\"contentUrl\":\"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg\",\"width\":863,\"height\":604},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/www.med.unc.edu\/bigs2\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Projects\",\"item\":\"https:\/\/www.med.unc.edu\/bigs2\/projects\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Genomic Analysis\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.med.unc.edu\/bigs2\/#website\",\"url\":\"https:\/\/www.med.unc.edu\/bigs2\/\",\"name\":\"BIG-S2\",\"description\":\"Biostatistics and Imaging Genomics analysis lab - Statistics & Signal\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.med.unc.edu\/bigs2\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Genomic Analysis - BIG-S2","robots":{"index":"noindex","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"og_locale":"en_US","og_type":"article","og_title":"Genomic Analysis - BIG-S2","og_description":"Title:\u00a0Tumor Heterogeneity: Clonal Structure Idetification   Introduction Tumor at diagnosis consists of genotypically distinct cell populations referred to as (sub)clones which is often of crucial interest in cancer study.\u00a0This is not only because the clonal structure itself provides an important clue for clinical treatment to the cancer but also subsequent analysis heavily\u00a0depends on the identified … Read more","og_url":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/","og_site_name":"BIG-S2","article_modified_time":"2019-10-08T21:29:24+00:00","og_image":[{"url":"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg","type":"","width":"","height":""}],"twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/","url":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/","name":"Genomic Analysis - BIG-S2","isPartOf":{"@id":"https:\/\/www.med.unc.edu\/bigs2\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage"},"image":{"@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage"},"thumbnailUrl":"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg","datePublished":"2018-09-16T23:54:27+00:00","dateModified":"2019-10-08T21:29:24+00:00","breadcrumb":{"@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#primaryimage","url":"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg","contentUrl":"https:\/\/www.med.unc.edu\/bigs2\/wp-content\/uploads\/sites\/822\/2018\/09\/project_genomic_introduction1.jpg","width":863,"height":604},{"@type":"BreadcrumbList","@id":"https:\/\/www.med.unc.edu\/bigs2\/projects\/genomic-analysis\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.med.unc.edu\/bigs2\/"},{"@type":"ListItem","position":2,"name":"Projects","item":"https:\/\/www.med.unc.edu\/bigs2\/projects\/"},{"@type":"ListItem","position":3,"name":"Genomic Analysis"}]},{"@type":"WebSite","@id":"https:\/\/www.med.unc.edu\/bigs2\/#website","url":"https:\/\/www.med.unc.edu\/bigs2\/","name":"BIG-S2","description":"Biostatistics and Imaging Genomics analysis lab - Statistics & Signal","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.med.unc.edu\/bigs2\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"}]}},"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/pages\/2892","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/users\/55348"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/comments?post=2892"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/pages\/2892\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/pages\/2857"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/bigs2\/wp-json\/wp\/v2\/media?parent=2892"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}