{"id":28138,"date":"2022-06-15T15:00:19","date_gmt":"2022-06-15T15:00:19","guid":{"rendered":"https:\/\/news.cancerresearchuk.org\/?p=24351"},"modified":"2024-11-03T15:13:37","modified_gmt":"2024-11-03T15:13:37","slug":"picking-out-the-patterns-how-scientists-are-finding-cancers-signatures-in-tumour-dna","status":"publish","type":"post","link":"https:\/\/ogkologos.com\/en\/picking-out-the-patterns-how-scientists-are-finding-cancers-signatures-in-tumour-dna\/","title":{"rendered":"Picking out the patterns: How scientists are finding cancer\u2019s signatures in tumour DNA"},"content":{"rendered":"
\"A<\/div>\n

Cancers begin when changes in genes called <\/span>mutations<\/span><\/a> cause cells to start multiplying uncontrollably.<\/span> <\/span><\/p>\n

Mutations can be the result of damage to DNA caused by external agents, like <\/span>UV light<\/span><\/a> or chemicals in cigarettes, or caused by \u2018mistakes\u2019 when DNA is replicated in cells before they divide.<\/span> <\/span><\/p>\n

Cancer cells can have large numbers of these mutations in their DNA, and often cells within the same tumour are heterogenous, meaning that their DNA differs from cell to cell. <\/span> <\/span><\/p>\n

However, there are certain \u2018types\u2019 of DNA mistake that occur in most cancers. One of these mistakes is called aneuploidy or, more simply, chromosome copy number changes. <\/span> <\/span><\/p>\n

This means that a cell has too many, or too few, chromosomes, coiled structures of DNA that store our genetic code, compared to normal. To give an example, a human cancer cell may have 45 or 47 chromosomes as opposed to the normal 46. <\/span> <\/span><\/p>\n

Chromosome copy number changes can make the genetic code of cancer cells highly complex. Imagine trying to read a book that\u2019s missing entire chapters, or has chapters duplicated and inserted back in the wrong place.<\/span> <\/span><\/p>\n

It results in tumours growing and spreading more quickly, and can result in resistance to treatment, meaning that the prognosis for the patient is poorer. <\/span> <\/span><\/p>\n

Seeing the bigger picture<\/span><\/b> <\/span><\/h2>\n

Mutations have been studied in cancers for decades and we have been able to identify simple ones using a technique called DNA sequencing to see how the DNA differs from that of normal cells. However, the understanding of complex mutations, like aneuploidy, is still a gap in our knowledge. <\/span> <\/span><\/p>\n

\u201cTo stay one step ahead of cancer, we need to anticipate how it adapts and changes,\u201d says Dr Nischalan Pillay, Associate Professor in Sarcoma Genomics at University College London (UCL).<\/span> <\/span><\/p>\n

\u201cMutations are the key drivers of cancer, but a lot of our understanding is focused on changes to individual genes in cancer. We\u2019ve lacked the tools to better understand how vast swathes of genes can be copied, moved around or deleted without catastrophic consequences for the tumour, and how these could be used to classify cancer.\u201d<\/span> <\/span><\/p>\n

Now, an international team of researchers at UCL and the University of California, San Diego (UC San Diego), co-led by Pillay and with funding from <\/span>Cancer Grand Challenges<\/span><\/a>, are using artificial intelligence to find new ways to identify and classify these complicated genetic changes.<\/span> <\/span><\/p>\n

Finding the patterns<\/span><\/b> <\/span><\/h2>\n

Using machine learning techniques, the team developed an algorithm to investigate and categorise the size and scale of DNA changes across the genome, a cell\u2019s complete genetic code, when cancer starts and grows. <\/span> <\/span><\/p>\n

This algorithm might sound complex, but it\u2019s not too different from one you might be familiar with. The way it analyses data to find patterns is similar to how the streaming service Netflix uses data on your viewing habits to recommend other films and series to watch.<\/span> <\/span><\/p>\n

The scientists looked for common patterns in how the chromosomes are reorganised in the tumours of over 9,000 patients with 33 different types of cancer.<\/span> <\/span><\/p>\n

From this massive amount of data, they were able to identify 21 common faults to the structure and number of chromosomes in tumours and categorise them into different \u201cgenres\u201d called copy number signatures. <\/span> <\/span><\/p>\n

These copy number signatures have provided a \u2018blueprint\u2019 of features that are common between cancer types that provides new insight into the complex genomes of cancers. <\/span> <\/span><\/p>\n

Now that these signatures have been identified, there\u2019s the potential to use them as targets for new therapies.<\/span> <\/span><\/p>\n

\u201cCancer is a complex disease, but we\u2019ve demonstrated that there are remarkable similarities in the changes to chromosomes that happen when it starts and how it grows,\u201d says Dr Ludmil Alexandrov, Associate Professor at UC San Diego and co-lead author of the study.<\/span> <\/span><\/p>\n

\u201cJust as Netflix can predict which shows you\u2019ll choose to binge watch next, we believe that we will be able to predict how your cancer is likely to behave, based on the changes its genome has previously experienced.\u201d<\/span> <\/span><\/p>\n

The team then further investigated the copy number signatures that most strongly affected outcomes for cancer patients. <\/span> <\/span><\/p>\n

Of the 21 signatures they identified, they found that tumours associated with the worst survival outcomes were ones that had gone through a process called chromothripsis, where the DNA in a chromosome completely shatters and reforms incorrectly.<\/span> <\/span><\/p>\n

For example, they found that people with <\/span>glioblastoma<\/span><\/a>, an aggressive type of brain tumour, had worse survival outcomes if cells in their tumour had undergone chromothripsis.<\/span> <\/span><\/p>\n

What\u2019s next?<\/span><\/b> <\/span> <\/span><\/h2>\n

The team hopes that the algorithm can now be refined to enable doctors to find out how a cancer is likely to behave, based on the genetic traits it acquires when it starts and the changes it picks up as it grows. <\/span> <\/span><\/p>\n

And to accelerate progress, they\u2019ve shared the blueprint of signatures they\u2019ve found, and the tools they used to uncover them, freely with the global scientific community. <\/span> <\/span><\/p>\n

That way, other scientists can build their own <\/span>Netflix-style<\/span> libraries of chromosome changes, based on data obtained from analysing tumours in their own research.<\/span> <\/span><\/p>\n

\u201cWe want to get to the point where doctors can look at a patient\u2019s fully sequenced tumour and match the key features of the tumour against our blueprint for genomic faults,\u201d Alexandrov adds.<\/span> <\/span><\/p>\n

\u201cArmed with that information, we believe that doctors will be able to offer better and more personalised cancer treatment in the future.\u201d<\/span> <\/span><\/p>\n

Jacob<\/em><\/p>\n

More on this topic<\/h3>\n<\/p>\n

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

Cancers begin when changes in genes called mutations cause cells to start multiplying uncontrollably. Mutations can be the result of damage to DNA caused by external agents, like UV light or chemicals in cigarettes, or caused by \u2018mistakes\u2019 when DNA is replicated in cells before they divide. Cancer cells can have large numbers of these […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"footnotes":""},"categories":[5137],"tags":[],"class_list":["post-28138","post","type-post","status-publish","format-standard","hentry","category-world-news"],"_links":{"self":[{"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/posts\/28138","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/comments?post=28138"}],"version-history":[{"count":1,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/posts\/28138\/revisions"}],"predecessor-version":[{"id":43293,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/posts\/28138\/revisions\/43293"}],"wp:attachment":[{"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/media?parent=28138"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/categories?post=28138"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ogkologos.com\/en\/wp-json\/wp\/v2\/tags?post=28138"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}