Jekyll2018-03-09T17:21:40+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/BIMM-194 W18Winter 2018 BIMM-194 course at the University of Califorina San Diego (UCSD) that introduces students to the growing role of genomics in healthcare, for patient diagnoses, treatment and disease prevention.
CRISPR might not work in people2018-01-22T17:30:37+00:002018-01-22T17:30:37+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/22/CRISPR-might-not-work-in-people<p>There is enormous interest and excitement surrounding the <strong>CRISPR-Cas9</strong> genome editing tool and its potential for enabling a new era of precision gene therapy. A new report examining human blood samples has turned up a surprise: most people could be immune to arguably the biggest advance in genetic engineering of recent times.</p>
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<p><img src="https://cdn.raynaudsnews.com/wp-content/uploads/2017/03/shutterstock_527608225-1000x480.jpg" alt="blood-surprise" /></p>
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<p>With the first clinical trials, outside China, scheduled to begin later this year (<a href="http://ir.crisprtx.com/phoenix.zhtml?c=254376&p=irol-newsArticle&ID=2321577">for patients with beta globin mutants linked to beta thalassemia and sickle cell disease</a>) a sobering new report has emerged that may may put the breaks on further clinical use. Results for <a href="https://www.biorxiv.org/content/early/2018/01/05/243345">Charlesworth et al.</a> suggest that the majority of humans may have preexisting immune responses to one of the major components of the system - Cas9.</p>
<p>CRISPR relies on the Cas9 nucleases found originally in the bacteria <em>Staphylococcus aureus</em> and <em>Streptococcus pyogenes</em>. These these two bacterial species cause regular human infections. Now it turns out that the majority of humans may have preexisting antibodies to the CRISPR Cas9 homologs from these common bacteria.</p>
<p>The <a href="https://www.biorxiv.org/content/early/2018/01/05/243345">Charlesworth et al.</a> study, as <a href="https://www.technologyreview.com/the-download/609904/uh-oh-crispr-might-not-work-in-people/">MIT Technology Review</a> summarized, examined the blood of 12 adults and 22 newborns for antibodies to Cas9 proteins from Staphylococcus aureus and Streptococcus pyogenes. They found antibodies for S. pyogenes in 65 percent of donors and antibodies for S. aureus in 75 percent—and nearly half of the donors had CD4+ T-cells that specifically targeted Cas9 homologs from S. aureus.</p>
<p>The immunity could not only limit the effectiveness of CRISPR, but also “create safety concerns”.</p>
<p>Read more: <a href="https://www.biorxiv.org/content/early/2018/01/05/243345"><strong>Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans</strong></a></p>There is enormous interest and excitement surrounding the CRISPR-Cas9 genome editing tool and its potential for enabling a new era of precision gene therapy. A new report examining human blood samples has turned up a surprise: most people could be immune to arguably the biggest advance in genetic engineering of recent times.DNA Snakes and Ladders2018-01-11T22:17:31+00:002018-01-11T22:17:31+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/2018/01/11/dna-snakes-and-ladders<p>Today, it is well-known that DNA is the molecule containing our genetic code. Whether on crime programmes, talk shows, or the daily news, DNA will be mentioned without need for an explanation. But what is DNA and how long have we known about it? And who really deserves the credit for our current knowledge?</p>
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<p><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/e/e2/Eukaryote_DNA-en.svg/320px-Eukaryote_DNA-en.svg.png" alt="DNA" /></p>
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<p>To begin to study Genomics, we must look at the history of how we came to learn about and understand DNA.</p>
<p>It all started way back in the late 19th century, when a German biochemist discovered that the nucleic acids, DNA and RNA, consisted of long chains of subunits known as nucleotides. Each nucleotide is made up of a base, a sugar and a phosphate. DNA has deoxyribose as its sugar and the bases can be adenine (A), guanine (G), cytosine (C), or thymine (T).</p>
<p>However, it wasn’t until 1943 that an unassuming American scientist, Oswald Avery, proved that DNA carried genetic information. He was pooh-poohed at first – most people thought that it was proteins that carried genetic information, and that DNA was just a boring collection of bases.</p>
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<p><a href="https://en.wikipedia.org/wiki/Oswald_Avery" class="img-responsive"><img src="/bimm194_W18/class-material/pic_avery.jpg" alt="Oswald_Avery" /></a><br />
Black and white photograph of Oswald T Avery © Rockefeller Archive Center, Click for link to <a href="https://en.wikipedia.org/wiki/Oswald_Avery">wikipedia article</a>.</p>
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<p>However, soon, despite the fact that much of the world was still at war, his discovery was accepted and the scientific spotlight turned to DNA.</p>
<p>Still, DNA’s exact structure remained a mystery.</p>
<p>During the war, an Austrian biochemist named Erwin Chargaff fled the Nazis to America. Chargaff read Avery’s work and immediately focused the work of his laboratory toward the study of DNA. In 1950, Chargaff discovered that the bases A and T and C and G always occurred in a 1:1 ratio, suggesting that they were paired in some way. But this finding remained largely unknown.</p>
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<p>The race to detemine the structure of DNA had many ups and downs much like the ancient Indian game known as <a href="https://en.wikipedia.org/wiki/Snakes_and_Ladders">Snakes and Ladders</a>.</p>
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<p>By the early 1950s, the race was on to determine the structure of DNA. The American team was led by Linus Pauling at Caltech, and was widely tipped to be the favourite to find the structure first. In the meantime, two British teams, one based at King’s College London, and another, at Cambridge, worked hard to find the answer.</p>
<p>The Cambridge team was led by two young scientists, American research fellow, James Watson and graduate student Francis Crick. They tried to pinpoint the structure by making physical models to narrow down the possibilities.</p>
<p>On the King’s team were Maurice Wilkins and Rosalind Franklin, two scientists who had a notoriously difficult relationship. The King’s team were taking a more experimental approach than the Cambridge scientists, looking at X-Ray diffraction images of DNA obtained by Franklin. X-ray diffraction was a tool that allowed scientists to determine the structure of crystalline molecules by the way they scattered X-Ray beams. Franklin was a world expert in crystallography and pioneered the use of this technique to look at complex crystallised solids. She determined that there were two forms of DNA; the crystalline form and the ‘wet’ form, dissolved in water.</p>
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<p><a href="http://www.bbc.co.uk/science/0/22270604" class="img-responsive"><img src="/bimm194_W18/class-material/pic_dna_folks.jpg" alt="DNA_People" /></a><br />
Black and white portraits of Francis Crick, James Watson, Rosalind Franklin, Maurice Wilkins and Linus Pauling. Click for link to <a href="http://www.bbc.co.uk/science/0/22270604">BBC article</a> from which this image appeared.</p>
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<p>In 1951, Watson took a day trip to London to attend a lecture of Franklin’s, in which she presented her initial findings on her photographs of DNA.</p>
<p>He raced back to Cambridge and relayed what he remembered of the lecture to Crick. The pair then used this information to build a new model of DNA; a triple helix, with the bases on the outside of the molecule. Excited, they invited Franklin and Wilkins to their laboratory to test the structure against Franklin’s pictures.</p>
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<p><a href="http://www.bbc.co.uk/science/0/22270604" class="img-responsive"><img src="/bimm194_W18/class-material/pic_dna_diffraction.jpg" alt="DNA_People" /></a>
Photograph 51: X-ray diffraction image of the Double Helix Photograph 51: X-ray diffraction image of the double helix © Kings College London. Click for link to <a href="http://www.bbc.co.uk/science/0/22270604">BBC article</a> from which this image appeared.</p>
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<p>It was wrong. Embarrassing and wrong. Their head of lab told the humiliated pair to stop DNA research. Was DNA as a helix dead?</p>
<p>Maybe not. Over in California, Pauling was building his own models. He asked to see Franklin’s pictures but Wilkins, keen not to hand them over to a competitor in the race, told him they were not ready to share. Nonetheless, in early 1953, Pauling announced that he had discovered the structure of DNA.</p>
<p>Watson panicked. Pauling was his closest rival. Had he got there first?</p>
<p>He studied Pauling’s structure. It was also a triple helix. Watson knew this was wrong and breathed a sigh of relief. But they still couldn’t relax. Pauling would find out his mistake soon enough. Watson and Crick would still have to hurry if they wanted to beat him.</p>
<p>Back in London, Franklin continued to study her X-Ray diffraction pictures. By January 1953, her preliminary findings were that DNA in its wet form did show the characteristics of a helix. However, in her typically cautious style, she was not ready to share these findings. She wanted to confirm them first. Before she could, and apparently without her knowledge or consent, Wilkins, growing frustrated and impatient, showed her results to Watson.</p>
<p>From there, Watson and Crick took a big conceptual step. They suggested that the DNA molecule was made up of two chains of nucleotides, each in a helix, as Franklin found, but with one chain that went up and another that went down. This is what we now call the double helix. They used Chargaff’s finding about the 1:1 base ratios to add to the model, determining that matching base pairs A and T and C and G interlocked in the centre of the double helix, keeping a constant distance between the chains.</p>
<p>They went on to show that each strand of DNA was a template for the other, so that DNA can replicate without changing its structure. This explained one of life’s great mysteries: how genetic information can be inherited. The double helix structure of DNA fit the experimental data perfectly and the scientific community accepted it almost immediately. It was probably the most important biological work of the last century and it forms the basis for the evolving field of genetics and genomics.</p>
<p>In 1962, Watson and Crick won the Nobel Prize for physiology/medicine, sharing it with Wilkins. By then, Franklin had sadly died of ovarian cancer, possibly as a result of her work with X-Rays. Now, few people know her name. She, along with others such as Chargaff and Avery who contributed much to the discovery of the double helix, died without recognition.</p>
<p>Perhaps the race to solve the atomic structure of DNA was akin to Snakes and Ladders in more ways than one.</p>Today, it is well-known that DNA is the molecule containing our genetic code. Whether on crime programmes, talk shows, or the daily news, DNA will be mentioned without need for an explanation. But what is DNA and how long have we known about it? And who really deserves the credit for our current knowledge?Editing the Embryo2018-01-11T05:46:28+00:002018-01-11T05:46:28+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/10/editing_the_embryo<p>Just imagine if you could correct a genetic disease right there in the embryo, before the condition even developed. It may sound like science fiction, but this tantalizing idea edged closer to potential reality over the past few months following ground-breaking work on human embryo genome editing.</p>
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<p><img src="http://www.sciencemag.org/sites/default/files/styles/article_main_large/public/images/crispr-editorial.jpg?itok=5KVWZszv" alt="CRISPR" /></p>
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<p>In August 2017, a collaboration from USA and Korea reported the successful modification of human embryos to remove a genetic mutation causing an inherited heart condition, hypertrophic cardiomyopathy (HCM).</p>
<p>The team used the <strong>CRISPR-Cas9</strong> gene-editing tool to fix a genetic mutation carried by the sperm, using healthy DNA from the mother’s egg as the template.</p>
<p>The work was reported in the journal <a href="https://www.nature.com/articles/nature23305">Nature</a> and covered by <a href="https://www.theguardian.com/science/2017/aug/02/deadly-gene-mutations-removed-from-human-embryos-in-landmark-study">The Guardian</a> newspaper. For the full story on this breakthrough and discussion of the ethical issues surrounding it, enjoy Hannah Devlin’s excellent <a href="https://www.theguardian.com/science/audio/2017/aug/10/editing-the-embryo-removing-harmful-gene-mutations-science-weekly-podcast">podcast</a>.</p>
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<p>In fact, embryo editing has hardly been out of the news recently. For example, A team in China has successfully used a modified gene-editing tool to <a href="https://www.theguardian.com/science/2017/sep/28/chemical-surgery-used-to-mend-harmful-mutations-in-human-embryos-base-editing">correct a point mutation causing β-thalassaemia</a> in human embryos:</p>
<p>Meanwhile, researchers based at the Francis Crick Institute in London are <a href="https://www.theguardian.com/science/2017/sep/20/dna-editing-in-human-embryos-reveals-role-of-fertility-master-gene">using gene editing in human embryos to investigate genes that are critical in the first hours of life</a>, in order to better understand miscarriage and improve the success rates of fertility treatment:</p>
<p>Legislation around human embryo research currently prevents any modified embryos being allowed to develop into babies and we are a long way from even the suggestion that gene editing would be safe to do in this context. However, if in future the safety concerns are addressed, a bioethical debate of huge proportions looms.</p>
<p>Whilst some might be comfortable with the safe eradication of serious and life-limiting genetic conditions from human embryos, many would be justifiably concerned about the potential of this technology to create ‘<strong>designer babies</strong>’.</p>
<h4 id="where-do-you-stand">Where do you stand?</h4>Just imagine if you could correct a genetic disease right there in the embryo, before the condition even developed. It may sound like science fiction, but this tantalizing idea edged closer to potential reality over the past few months following ground-breaking work on human embryo genome editing.DIY Crispr: biohacking your own genome2018-01-09T06:37:29+00:002018-01-09T06:37:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/08/diy_crispr<p>With do-it-yourself Crispr kits now available online. Is it really possible to edit your own DNA, is it safe and how should it be regulated?</p>
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<p><img src="https://i.kinja-img.com/gawker-media/image/upload/s--vNwh21yP--/c_scale,f_auto,fl_progressive,q_80,w_800/sndrvqswohivf3tsbdqx.jpg" alt="Josiah Zayner" /></p>
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<p>In October, biohacker <a href="https://en.wikipedia.org/wiki/Josiah_Zayner">Josiah Zayner</a> gave a <a href="http://www.ifyoudontknownowyaknow.com/2017/10/the-first-human-to-attempt-crispr-gene.html">lecture in San Francisco</a> in which he claimed to be the first person known to have edited his own DNA using <strong>CRISPR</strong> technology. He insists it’s something anyone can do using one of his company’s gene engineering kits. But does this do-it-yourself approach have any evidence to back it up? Is it safe? And, ultimately, does this kind of self-experimentation drive science forward or expose the public to unacceptable risks?</p>
<h4 id="where-do-you-stand">Where do you stand?</h4>With do-it-yourself Crispr kits now available online. Is it really possible to edit your own DNA, is it safe and how should it be regulated?Direct-to-consumer testing2018-01-09T06:37:29+00:002018-01-09T06:37:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/08/Direct-to-consumer-testing<p><img src="http://www.genesinlife.org/sites/default/files/images/GA5-1-5.jpg" alt="DNA_test" /></p>
<p>Direct-to-consumer (DTC) testing came under fire recently with the publication of a <a href="https://www.futuremedicine.com/doi/full/10.2217/pme-2017-0001">paper in the journal, Future Medicine</a>, highlighting the lack of support around the genetic testing process offered by DTC companies, and calling for them to make pre- and post-test counseling available to their consumers.</p>
<p>The findings were reported in <a href="https://www.theguardian.com/science/2017/aug/26/alzheimers-disease-shock-for-genetic-ancestry-hunters">The Guardian</a>, where the potential for serious incidental findings to emerge from DTC testing, was highlighted using the example of individuals embarking on DTC for “a bit of fun” to explore their ethnic roots but then stumbling across information about their risks of developing Alzheimer’s disease. Have you been tempted to undergo DTC genetic testing? Were you aware that in doing so you might reveal that you had an 80% risk of developing Alzheimer’s disease by the age of 80? Still tempted?</p>
<h4 id="where-do-you-stand-on-direct-to-consumer-testing--is-it-for-you-should-it-come-with-a-health-warnings">Where do you stand on direct-to-consumer testing – is it for you? Should it come with a health warnings?</h4>Who has the right to know your genetic test results?2018-01-08T06:37:29+00:002018-01-08T06:37:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/07/who-has-the-right-to-know-your-genetic-test-results<p>If a relative receives a genetic test result that has potential implications for you but chooses not to share it, do the doctors have a duty to disclose the information anyway? As things stand, absolutely not.</p>
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<p><img src="https://d1jn4vzj53eli5.cloudfront.net/db/14309288358218.jpg" alt="DNA_test" /></p>
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<p>This principle came under fire earlier this year when a woman, known only as ABC, <a href="https://www.aol.co.uk/news/2017/05/16/woman-wins-court-fight-over-huntingtons-disease-claims/">won her appeal in the high court for the right to sue three NHS Trusts for damages</a>, for not disclosing her father’s genetic condition, which had implications for her and her unborn child.</p>
<p>In 2007, ABC’s father killed his wife (ABC’s mother) and was convicted of manslaughter on grounds of diminished responsibility. Following the incident, doctors noticed he had signs of Huntington’s disease, a devastating genetic condition causing late-onset progressive cognitive and motor decline and behavioral changes, for which there is no cure. Genetic testing in 2009 confirmed the diagnosis.</p>
<p>His doctors requested his consent to disclose this result to his daughter, who was now six weeks pregnant and was at 50% risk of inheriting the condition. He refused. ABC’s baby was born in 2010, and subsequently one of her father’s doctors accidentally disclosed his diagnosis of Huntington’s disease to her. ABC was then tested and told she had inherited the Huntington’s disease gene expansion.</p>
<p>ABC is now suing the UK hospital trusts involved for damages as she feels that, in light of her pregnancy, she should have been informed of her father’s diagnosis. She claims she would have been tested herself as soon as she found out and, as a single mother, if the diagnosis had been confirmed she would have terminated the pregnancy rather than risk her child becoming an orphan or inheriting the condition.</p>
<p>The case was initially rejected, but on appeal to the high court it is now being allowed to go to trial.</p>
<h4 id="would-you-like-to-be-a-juror-in-this-one-where-do-you-stand">Would you like to be a juror in this one? Where do you stand?</h4>If a relative receives a genetic test result that has potential implications for you but chooses not to share it, do the doctors have a duty to disclose the information anyway? As things stand, absolutely not.Older fathers pass on more mutations2018-01-07T06:37:29+00:002018-01-07T06:37:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/06/older-fathers-pass-on-more-mutations<p>It has long been recognized that certain genetically influenced conditions presenting in childhood such as intellectual disability and autism are more common in children from older fathers. A possible explanation for this phenomenon was described recently in a study suggesting that fathers accumulate and pass on mutations at a faster rate with increasing age than mothers.</p>
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<p><img src="http://journey.thesanctuarycentre.org/wp-content/uploads/2011/06/sanctuary_fathers.jpg" alt="DNA_test" /></p>
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<p>In a research study from Iceland, <a href="www.nature.com/nature/journal/v549/n7673/full/nature24018.html">published in Nature</a>, researchers sequenced the genomes of 14,000 Icelanders and their parents, isolating de novo mutations and determining the parent of origin.</p>
<p>They found that whilst the number of de novo mutations inherited from mothers increased by 0.37 per year of age, the number inherited from fathers increased by 1.51 per year of age.</p>
<p><a href="https://www.theguardian.com/science/2017/sep/20/fathers-pass-on-four-times-as-many-new-genetic-mutations-as-mothers-study">An article in The Guardian</a> reporting the study commented that these figures mean that ‘a child born to 30-year-old parents would, on average, inherit 11 new mutations from the mother, but 45 from the father’. And this discrepancy would only further increase with increasing age.</p>
<p>The authors hypothesize that one explanation for this could be that whilst women are born with their eggs already in situ, men continue to make sperm throughout their lives, during which time more mutations can accumulate.</p>It has long been recognized that certain genetically influenced conditions presenting in childhood such as intellectual disability and autism are more common in children from older fathers. A possible explanation for this phenomenon was described recently in a study suggesting that fathers accumulate and pass on mutations at a faster rate with increasing age than mothers.Calling cancer’s bluff with neoantigen vaccines2018-01-07T06:27:29+00:002018-01-07T06:27:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/06/calling-cancers-bluff-with-neoantigen-vaccines<p>State-of-the art tumour-genome sequencing and analysis is enabling researchers to provide uniquely personalized immunotherapy. This can be combined with another form of immunotherapy — checkpoint inhibition, which stops tumours from suppressing immune-system activity — to make personalized cancer vaccination feasible.</p>
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<p><img src="http://www.sanfordhealth.org/~/media/sanford-health/pageimages/cancer-immunotherapy-graphic-800x512.jpg?la=en" alt="cancer-immunotherapy" /></p>
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<p>Cancer is famous for its ability to deceive, appearing to the immune system as normal tissue while wreaking destruction on the body. But what if cancer cells had ‘tells’ — subtle but unmistakable characteristics that revealed their true nature?</p>
<p>A growing number of scientists say that neoantigens, which are peptides (fragments of proteins) found only on the surface of cancer cells, could be those tells. They are working to develop vaccines that use neoantigens to help a patients own immune systems fight tumours.</p>
<p>DNA sequencing is at the heart of this approach, which requires identifying mutations unique to cancer cells (i.e. mutations in the cancer that are not present in the same patients healthy cells). With RNA sequencing used to determine whether these mutant proteins are expressed in the tumor. This information is then used together patients immune system HLA information (also from sequencing) to develop vaccines personally optimized for that patient.</p>
<p>Read more about the recent exciting advances in this field in this <a href="https://www.nature.com/articles/d41586-017-08706-3">Nature Outlook article from late Dec 2017</a></p>State-of-the art tumour-genome sequencing and analysis is enabling researchers to provide uniquely personalized immunotherapy. This can be combined with another form of immunotherapy — checkpoint inhibition, which stops tumours from suppressing immune-system activity — to make personalized cancer vaccination feasible.The increasing cost of cancer therapies2018-01-07T05:27:29+00:002018-01-07T05:27:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/06/the-cost-of-cancer-therapies<p>Every cancer patient, and indeed every cancer, is different. It is becoming more and more apparent that just because two tumours arise from the same tissue or organ, it does not mean that they are the same or should be treated with the same drugs. It is therefore crucial that the molecular signatures of cancer are investigated and used to their full potential, to enable effective medical treatment. However, all the required genomic and molecular tests cost money, and the targeted treatments themselves can be very expensive. Who pays for these life-extending treatments?</p>
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<p><img src="https://ac-cdn.azureedge.net/infusionnewssiteimages/agingcare/52f4277e-5698-43f4-ac48-f50a2f80d84f.jpg" alt="cancer-costs" /></p>
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<p>For example, as we have already discussed, in breast cancer there are Estrogen Receptor positive and negative tumours, and HER2 positive and negative tumours. The presence or absence of these proteins will define the patient’s treatment. Similarly, not every patient with lung cancer is the same: some will have tumours with an EGFR mutation that makes them likely to respond to tyrosine kinase inhibitors; other patients will not present with this mutation so will be treated differently. Not all AML patients respond similarly to standard treatments. It is therefore crucial that the molecular signatures of cancer are used to their full potential, to enable a stratified medical approach.</p>
<p>However, all these genomic and molecular tests cost money, and the targeted treatments themselves can be very expensive. So, despite the fact that diagnostic tests and targeted therapies exist, it might be that they are not available to everyone as a result of the financial cost. You might expect that a cancer patient should be entitled to the best treatment options regardless of where they live, but unfortunately this is not always the case. Sometimes the novel therapies are too expensive and local healthcare systems are unable to cover the cost of treatments.</p>
<p>The following articles, which you may wish to read, illustrate these financial problems:</p>
<p><a href="http://www.bbc.com/news/health-34153136">Cancer drugs fund cuts 23 treatments</a>.</p>
<p><a href="http://www.bbc.co.uk/news/health-34831197">Breast cancer drug Kadcyla ‘too expensive’ for UK NHS</a></p>
<p><a href="https://money.usnews.com/money/personal-finance/articles/2014/02/10/how-to-pay-for-cancer-treatment-when-youre-broke">How to Pay for Cancer Treatment When You’re Broke in the US</a></p>Every cancer patient, and indeed every cancer, is different. It is becoming more and more apparent that just because two tumours arise from the same tissue or organ, it does not mean that they are the same or should be treated with the same drugs. It is therefore crucial that the molecular signatures of cancer are investigated and used to their full potential, to enable effective medical treatment. However, all the required genomic and molecular tests cost money, and the targeted treatments themselves can be very expensive. Who pays for these life-extending treatments?Can genomics help detect early cancer and monitor treatment effectiveness?2018-01-07T04:27:29+00:002018-01-07T04:27:29+00:00http://bioboot.github.io/bimm194_W18/bimm194_W18/jekyll/update/2018/01/06/Can-genomics-help-detect-early-cancer<p>Many cancers, such as ovarian cancer and some kidney cancers, are typically only detected when they are relatively far advanced, because they may not be associated with noticeable symptoms in the earlier stages. One remarkable discovery in the past few years has been the finding that the DNA of solid tumor cells often can be found in the blood and detected using sequencing and other approaches.</p>
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<p><img src="https://images.agoramedia.com/everydayhealth/gcms/10-Things-Doctor-Wont-Tell-About-Blood-Tests-722x406.jpg" alt="blood-test" /></p>
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<p>The discovery of this circulating tumor DNA (ctDNA, that presumably occurs through the death of cancer cells whose contents are then released into the bloodstream) is important because it offers the possibility that a blood test with subsequent genomic sequencing or probe based approaches might be used for detection of “silent” early cancers.</p>
<p>Indeed, in a recent study designed to detect regions from 139 genes that frequently carry somatic mutations in non-small-cell lung carcinoma (NSCLC), ctDNA was detected in approximately 50% of patients with early (Stage I) NSCLC and in all of the patients with more advanced (Stage II–IV) NSCLC. This type of ctDNA assay is theoretically adaptable to many types of cancer, and it is likely that screening for ctDNA will become a standard component of cancer early detection in the future.</p>
<p><a href="http://www.bbc.com/news/health-42736764">Cancer blood test ‘enormously exciting’</a>.</p>
<p><a href="http://www.bbc.com/news/health-39658680">‘Exciting’ blood test spots cancer a year early</a>.</p>
<p><a href="http://www.bbc.com/news/health-39103629">Blood tests spot ovarian cancer early</a>.</p>
<p><a href="http://www.bbc.com/news/health-40302692">Prostate cancer blood test ‘helps target treatment’</a>.</p>Many cancers, such as ovarian cancer and some kidney cancers, are typically only detected when they are relatively far advanced, because they may not be associated with noticeable symptoms in the earlier stages. One remarkable discovery in the past few years has been the finding that the DNA of solid tumor cells often can be found in the blood and detected using sequencing and other approaches.