{"id":4064,"date":"2015-09-16T19:23:47","date_gmt":"2015-09-16T19:23:47","guid":{"rendered":"https:\/\/www.tmc.edu\/news\/the-genomics-revolution\/"},"modified":"2019-08-16T15:00:21","modified_gmt":"2019-08-16T15:00:21","slug":"the-genomics-revolution","status":"publish","type":"post","link":"https:\/\/www.tmc.edu\/news\/2015\/09\/the-genomics-revolution\/","title":{"rendered":"The Genomics Revolution"},"content":{"rendered":"
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First, there was Mendel and his peas. In the century-and-a-half that followed, matched pairs of chromosomes were identified, As\u00a0and Ts and Gs and Cs were coupled off, X-ray crystallography techniques exposed the double helix structure of DNA, and the code of life was cracked wide open.<\/p>\n

It was, of course, the Human Genome Project\u2014the international, multi-billion dollar endeavor in which thousands of researchers spent over a decade identifying and mapping the complete set of nucleic acid sequences encoded within the DNA of humans\u2014that ultimately catalyzed all of these scientific breakthroughs into something that could be translated into the world of health care. Today, just 12 years after its completion, some of the great minds of genomics research are bringing that science into clinics throughout the Texas Medical Center.<\/p>\n

\u201cBack in the 1980s, we knew that there\u00a0were genetic causes for important human conditions, and we recognized the potential\u00a0for understanding genetics and genes to really revolutionize the way we tackled therapy\u00a0and diagnostics and prognostics, but we
\ndidn\u2019t have the genome, and the technology\u00a0to get it wasn\u2019t there yet,\u201d explained Richard Gibbs, Ph.D., director of the Human Genome Sequencing Center at Baylor College of Medicine. \u201cNevertheless, the visionary quest was launched to sequence the human genome so that we would have this foundation to do\u00a0all of it\u2014whatever \u2018it\u2019 turned out to be. It was\u00a0a big breakthrough upon completion, and the question immediately became, \u2018How do we push the genome into medicine?\u2019 because impacting health is really what it\u2019s all about.\u201d<\/p>\n

The first genome cost around $3 billion, but by 2009, advances had reduced the cost\u00a0of mapping an individual\u2019s genome to less\u00a0than $50,000. Researchers then turned to straightforward problems\u2014diagnoses that, based on family history or other hereditary indicators, pointed towards a single genetic cause. Pediatric diseases quickly emerged as one of the most promising fields for genetic application because many of the disorders are inherited and triggered by the mutation of a single gene. The idea was to map the genome of the patient, and often his or her parents as well, to pinpoint what specific gene was missing or modified and how its expression was inherited.<\/p>\n<\/div>\n

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\u201cBaylor already had such a strong history\u00a0of studying single-gene diseases, and we were determined to move this forward, so we worked on refining the tests,\u201d said Gibbs. \u201cWe were able to simplify the analyses and developed some clever techniques in the lab that pulled out\u00a0the genes, which are only one percent of DNA anyway, with special hybridization tools.\u201d<\/p>\n

Known as whole exome sequencing,\u00a0the abbreviated assay dropped the price to $2,000 per genome. Now, Baylor routinely evaluates children with uninterpreted disorders, often providing answers where before, there were none. For individuals like Kristin Phillips, this kind of information is invaluable.<\/p>\n<\/div>\n

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Kristin\u2019s son, Jacob, was born in May 2009, seemingly healthy as could be. For the first year of his life, he was a cheerful and active baby, reaching all of his developmental milestones effortlessly until he came down with a common virus at 13 months old, during which time he spiked a 105-degree fever and suffered a small seizure.<\/p>\n

\u201cAfter Jacob got sick, he wasn\u2019t the same,\u201d said Phillips. \u201cHe was suddenly very colicky and fussy, and his motor skills began deteriorating drastically\u2014within two months, he was falling over on his face and could not longer bear weight on his legs.\u201d<\/p>\n

Phillips and her husband rushed their son to Texas Children\u2019s Hospital, where they ran exhaustive state-of-the-art testing: CTs, MRIs, lumbar punctures and repeated lab workups that perpetually came back negative. For over three years they tried to identify the cause of\u00a0his developmental regression, while Jacob\u2019s condition worsened. Despite brief misdiagnoses, visits with specialists from coast to coast and multiple lifestyle changes, nobody could explain what had happened. Then, in 2013, a genetic counselor at Baylor called to tell Phillips about the breakthroughs in whole exome sequencing. Jacob, she said, was a perfect candidate.<\/p>\n

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By August of that year, the Phillips family finally had a clear diagnosis: Jacob was suffering from an extremely rare genetic disorder\u00a0called infantile neuroaxonal dystrophy, a neurodegenerative disease caused by a mutation in the PLA2G6 gene. Through impaired function of necessary enzymes, the mutation causes progressive neurodegeneration, explaining Jacob\u2019s lapsed motor skills and reduced mobility. The condition is so rare that in 2013, Jacob was only the 10th child in the U.S. to have been diagnosed with the disease. His case is also unique\u2014as a rule, both parents must be carriers for the mutation to be passed on to the child, but in Jacob\u2019s case, only his mother tested positive for the recessive mutation. Geneticists believe the gene somehow mutated independently\u00a0or was double-copied from her chromosome. Unfortunately, there is no known cure for the disorder, which, like other neurodegenerative diseases such as Parkinson\u2019s or Alzheimer\u2019s, continues to advance as time passes.<\/p>\n

Jacob is now six years old and in hospice care\u2014he is 95 percent blind, nonverbal and has lost all motor skills. Still, his parents remain hopeful. Since his diagnosis in 2013, they\u00a0have raised enough funds to fully support two different research projects for the disease, one of which is exclusively focused on gene therapy, a promising new technique that harnesses genes to treat genetic disorders. While there\u00a0is no guarantee that either will produce a\u00a0treatment or cure, the value of the diagnosis itself cannot be underestimated.<\/p>\n

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\u201cBefore the diagnosis, we thought it was everything under the sun,\u201d said Phillips. \u201cFor so long we believed his condition had been directly caused by the virus, and although we suspect that may have been an environmental trigger for the disorder, at least now we know what we\u2019re working with. We know what to expect and how to manage his pain, and we\u2019re able to move forward as far as the research goes. Without the diagnosis, there would have been no hope, no\u00a0chance for his survival. At least now, through our research, there\u2019s that possibility.\u201d<\/p>\n

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\u201cIf you are a parent or a family in that situation, the impact of a diagnosis is huge,\u201d said Gibbs. \u201cWhen you are able to resolve this down to a genetic cause, you provide prediction, you provide a peer group, and you accentuate the pathway to therapeutics, which is the most active area of research right now. You can\u2019t underestimate the value of diagnostics and prognostics. We\u2019ve got to understand all the basic nuts and bolts before we can fix what\u2019s broken.\u201d<\/p>\n

Nowhere is the value of collecting and understanding data\u2014the basics of how the genes actually function\u2014potentially more significant than in the field of cancer research. At its core, genetic diagnostics winnows down to basic discovery and understanding. A child who has a single gene defect indicates the function of that gene\u2014if there is a mutation in the gene, the protein the gene codes for is altered or missing, and those effects tell scientists what\u00a0the protein normally does. That\u2019s genomics 101, and in cancer cells the same comparison can be made between cancer tissue and non-cancerous normal tissue.<\/p>\n

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By contrasting an individual\u2019s cancer cells with one of his or her normal cells, the changes that resulted in the malignancy become apparent. The simplicity of it is as elegant as the biology itself, but, as with most science, it also has the potential to be misleading\u2014especially when you move towards developing therapeutics\u00a0to confront the mutations.<\/p>\n

Designing cancer treatments based on\u00a0genomic evaluations is exceedingly difficult for many reasons, perhaps most of all the inherent heterogeneity of the disease, which in the simplest terms describes the complexity of the composition of cancerous tissue.<\/p>\n

\u201cThere is a lot of intricacy in cancer cells\u00a0and the process of malignancy,\u201d explained Andrew Futreal, Ph.D., Chair Ad Interim in
\nthe department of genomic medicine at The University of Texas MD Anderson Cancer Center. Notably, MD Anderson was recently named one of two new Genome Characterization Centers funded through the National Cancer Institute. \u201cThe biggest challenge in finding clinically useful information via genomic\u00a0data is comprehending heterogeneity.\u00a0Not only are tumors heterogeneous from\u00a0one patient to another, but there is also intra-tumor heterogeneity, wherein the\u00a0same tumor accumulates different kinds\u00a0of mutations over time.\u201d<\/p>\n

Futreal, who is known in the world of cancer research for identifying the BRCA1 and BRCA2 breast\/ovarian cancer susceptibility genes, is working to mine the research by integrating datasets from patient populations and then running analyses across time to identify genomic determinants of different variables, including response, resistance, toxicity and survival. Working closely with MD Anderson\u2019s Molecular Diagnostics Laboratory and the Institute for Personalized Cancer Therapy,\u00a0the hope is to move his findings into the\u00a0clinic to advance general therapeutics and precision oncology therapies, an approach that emphasizes the uniqueness of an individual\u2019s disease based on his or her genome and is considered by many to be the holy grail\u00a0of clinical genomics.<\/p>\n<\/div>\n

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The key is acquiring plenty of data, which, surprisingly, may not be the easy part of\u00a0the equation.<\/p>\n

\u201cClinical records are famously difficult to\u00a0get into research databases. Some of this is\u00a0for good reason, because people don\u2019t want
\ntheir health records shared indiscriminately,\u201d said Gibbs. \u201cBut even if you have a situation where everyone is on board for sharing, we still run into challenges because there is so much variation in the way clinical data is collected and measured. Everyone wants to see clinical records become more harmonized and standardized,\u00a0but of course the priority is physician care,
\nso a scientist\u2019s version of how data should be aggregated isn\u2019t going to come before that.\u201d<\/p>\n

Nevertheless, the move toward collecting and analyzing troves of genetic data for patient care purposes is becoming more and more prevalent in programs throughout the Texas Medical Center. At Texas Children\u2019s Hospital,\u00a0a research study called BASIC3 (Baylor Advancing Sequencing in Childhood Cancer Care) is investigating the utility of tumor and germline (familial) whole exome sequencing for children with newly diagnosed solid tumors. As the only pediatric cancer project funded by the National Human Genome Research Institute\u2019s Clinical Sequencing Exploratory Research program, the study is unique in that it is not only examining the results of the clinical testing, but also analyzing the process of gathering and\u00a0disseminating genomic data to patients and their primary oncologists.<\/p>\n

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\u201cOne of our primary goals for the study\u00a0was to set up the logistics and infrastructure\u00a0to perform clinical sequencing\u2014to take it\u00a0from a research tool to something that we can actually do for our patients,\u201d said Will Parsons, M.D., co-director of the Cancer Genetics and Genomics Program at Texas Children\u2019s Cancer and Hematology Centers and co-principal investigator of the BASIC3 study. \u201cThis includes everything from how we\u2019re going to obtain informed consent from families and explain the risks and benefits of genomic testing, to how to explain the test results to oncologists, patients and families, to how to write genomic test reports\u2014all the practical steps, from start\u00a0to finish, of performing sequencing as a\u00a0clinical test.\u201d<\/p>\n

In addition to also looking at the utility of these tests in the clinical setting and how the information can be applied to both diagnostics and therapeutics for patients and their families, the study has engaged a team of ethicists and social scientists to work with the oncologists, parents and patients to evaluate their experience and preferences for the testing process.<\/p>\n

\u201cBoth the oncologists and families are providing feedback regarding important issues related to genomic testing, such as how we\u2019re explaining the results to them, what kind of things they want to learn and whether or not they are bothered by any of the other types of results one can get when doing this scale of testing,\u201d said Parsons. \u201cBoth groups are longitudinally surveyed and interviewed so that we can gain a better understanding\u00a0of how we can best interact with our patients and their families and provide the most useful information possible.\u201d<\/p>\n

Ultimately, studies like these allow institutions to begin initiating prospective clinical trials using these genomic tests, a necessary next step towards evaluating the\u00a0impact of personalized medicine approaches and developing therapeutics.<\/p>\n

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Unlike single-gene pediatric disorders\u00a0and cancer, however, the argument for genetic testing for adult familial diseases (think cardiovascular, neurodegenerative or metabolic) has yet to catch on in the clinical world. The fact that these diseases run in families indicates that there is a clear genetic component, but because the majority of these conditions are caused by something more complex than a single-gene mutation, the challenge is determining all\u00a0the genetic risk factors and other causative elements that contribute to these \u201ctraits,\u201d or\u00a0put more appropriately, predispositions for developing the conditions.<\/p>\n

\u201cWe\u2019re kind of at a threshold moment right now,\u201d said Gibbs. \u201cIf you look at the value of\u00a0a genomic test for a particular class of adult disorders at this time, one could argue that its value and immediate clinical impact is minimal. But, if you sequence the whole person and the whole family and you add up the value you\u2019d get for examining any potential adult conditions, plus the value you\u2019d get for prediction of any possible childhood problems, then in aggregate you could easily justify the test.\u201d<\/p>\n

The problem, explained Gibbs, is that the structure of medical care is currently centered on acute treatment rather than evaluation of whole family health as a predictor for disease. Nevertheless, he believes the universal benefit of genetic data will become apparent soon enough.<\/p>\n

\u201cThrough this data, we\u2019re understanding targets better, we\u2019re understanding genetic processes, genetic chemistry and the biology better, and we\u2019re understanding what to\u00a0look for and what to test for when you screen drug compounds,\u201d said Gibbs. \u201cWe have this global mission and vision that ultimately, every person who has any health issue should have a genome sequence as part of their\u00a0work-up, just as they would have an X-ray or metabolite test.\u201d<\/p>\n<\/div>\n

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As with any goal of such mammoth proportions, it will take teamwork to get there. To help facilitate the collaboration required, member institutions of the Texas Medical Center, including Baylor, are coming together to set up a TMC Genomics Institute with the objective of being the world\u2019s most innovative genomics center for discovery and disease intervention.<\/p>\n

\u201cWe really want to see more integration of different programs in the medical center in general, and genomics is the perfect vehicle for it,\u201d said Gibbs. \u201cThat\u2019s the reality. In the past, we\u2019ve centralized the genomics activity and\u00a0it\u2019s been very expensive and has been mainly discovery-based, so it hasn\u2019t lent itself for such integration. But as we move towards these clinical arenas, there\u2019s more opportunity for collaboration and to synergize our expertise, whether it\u2019s in the lab or the clinic.\u201d<\/p>\n

The possibilities for clinical genomics to transform the world in which we live are as vast as the potential combinations of base pairs in human DNA. And although the focus now is on treating cancer, creating therapies for incurable diseases, developing lifesaving drugs to combat deadly viruses, and helping families understand hereditary risks of reproduction, no one can really predict how it will all come together.<\/p>\n

\u201cWe are all inclined to be conservative in\u00a0our future projections and we invariably just make fairly modest, linear projections,\u201d said Gibbs. \u201cWhen the computer was first introduced, most people just thought about the ability\u00a0to type more documents, not all of the other really innovative developments like Internet commerce and video gaming, or the fact that we now carry all of this around in our pockets. It\u2019s the same with genetics\u2014we don\u2019t know where\u00a0it will take us, but we have every reason to be extremely optimistic about it.\u201d<\/p>\n

\"sept_center\"<\/a>(Click image to enlarge)<\/em><\/p>\n<\/div>\n

Baylor Miraca Genetics Laboratories<\/h2>\n
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In the fall of 2014, Baylor College of Medicine and Miraca Holdings, Inc., a Japan-based international health care company focused on clinical diagnostics and laboratory tests, announced a joint venture in which the two institutions would share ownership and governance of their clinical genetics diagnostic laboratories. The Texas Medical Center-based venture, named Baylor Miraca Genetics Laboratories, allowed Baylor\u00a0to continue to independently drive its genetic diagnostic research agenda while expanding their laboratory diagnostic skills into a larger commercial enterprise. Hoping to play a major role in Houston\u2019s budding biotech industry, the marriage of Baylor\u2019s academic expertise and Miraca\u2019s international business acumen has already proven successful:\u00a0in May, the organizations announced the launch of an enhanced clinical exome sequencing test, providing physicians the option to speed up the delivery of final results to two-to-three weeks from three months. Baylor College of Medicine pioneered the research and development of the original whole exome sequencing test, initially launching it for clinical use in 2011.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

First, there was Mendel and his peas. In the century-and-a-half that followed, matched pairs of chromosomes were identified, As\u00a0and Ts and Gs and Cs were coupled off, X-ray crystallography techniques exposed the double helix structure of DNA, and the code of life was cracked wide open. It was, of course, the Human Genome Project\u2014the international, […]<\/p>\n","protected":false},"author":14,"featured_media":4070,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[805,776,44,41,46],"yoast_head":"\nThe Genomics Revolution - TMC News<\/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.tmc.edu\/news\/2015\/09\/the-genomics-revolution\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Genomics Revolution - TMC News\" \/>\n<meta property=\"og:description\" content=\"First, there was Mendel and his peas. 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