Chemotherapy Choice Can Be Aided By Assessing TDP Profile

MedicalResearch.com Interview with:

Ed Liu, M.D President and CEO The Jackson Laboratory (JAX)

Dr. Ed Liu

Ed Liu, M.D
President and CEO
The Jackson Laboratory (JAX)

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: A few years ago we and others identified a complex genomic instability profile commonly found in the genomes of breast, ovarian and endometrial carcinomas, which is characterized by hundreds of isolated head-to-tail duplications of DNA segments, called tandem duplications. We refer to this configuration as the tandem duplicator phenotype, or TDP.

In this study, we perform a meta-analysis of over 2,700 cancer genomes from over 30 different tumor types and provide a detailed description of six different types of TDP, distinguished by the presence of tandem duplications of different sizes. Collectively, these profiles are found in ~50% of breast, ovarian and endometrial carcinomas as well as 10-30% of adrenocortical, esophageal, stomach and lung adeno-carcinomas. We show that distinct genetic abnormalities associate with the distinct TDPs, clearly suggesting that distinct molecular mechanisms are driving TDP formation. In particular, we provide strong evidence of a casual relationship between joint abrogation of the BRCA1 and TP53 tumor suppressor genes and the emergence of a short-span (~11 Kb) TDP profile. We also observe a significant association between hyper-activation of the CCNE1 pathway and TDP with medium-span (~230 Kb) tandem duplications, and between mutation of the CDK12 gene and medium- and large-span TDP (coexisting 230 Kb and 1.7 Kb tandem duplications).

Importantly, we find that different forms of TDP result in the perturbation of alternative sets of cancer genes, with short-span TDP profiles leading to the loss of tumor suppressor genes via double transections, and larger-span TDP profiles resulting in the duplication (i.e. copy number gain) of oncogenes and gene regulatory elements, such as super-enhancers and disease-associated SNPs.  Continue reading

Epigenetic DNA Variants Predictive of Coronary Artery Disease

MedicalResearch.com Interview with:

Stella Aslibekyan, PhD Associate Professor PhD Program Director Department of Epidemiology University of Alabama at Birmingham

Dr. Aslibekyan

Stella Aslibekyan, PhD
Associate Professor
PhD Program Director
Department of Epidemiology
University of Alabama at Birmingham

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: When the human genome was sequenced in 2003, there were somewhat unrestrained expectations of unraveling all etiologic mysteries and discovering breakthrough treatments. Needless to say, that did not happen, in part because individual genetic variants can only account for a small fraction of trait variability. Since then, epigenetics– the study of mitotically heritable changes in gene expression– has emerged as another promising avenue for understanding disease risk. The best studied epigenetic process in humans is DNA methylation, and earlier studies (including some from our group) have shown interesting associations between changes in methylation in specific genomic regions and cardiovascular disease traits, e.g. plasma cholesterol levels.

In this project, we have combined DNA methylation data on thousands of individuals from multiple international cohorts and interrogated epigenetic contributions to circulating tumor necrosis factor alpha (TNFa), a marker of systemic inflammation. We identified and replicated several epigenomic markers of TNFa, linked them to variation in gene expression, and showed that these methylation changes (which were located in interferon pathway genes) were predictive of coronary heart disease later in life. Interestingly, the variants we discovered were not sequence-dependent (in other words, they were not associated with any genetic mutations), highlighting the role of the environment.

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Mouse Model Shows Gene Therapy Can Reverse Blue Cone Vision Disorder

MedicalResearch.com Interview with:

Wen-Tao Deng,

Dr. Wen-Tao Deng

Wen-Tao Deng, Ph.D.
Department of Ophthalmology, College of Medicine|
University of Florida, Gainesville, FL

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: Blue cone monochromay (BCM) is a devastating vision disorder characterized by loss function of both L- and M-cones due to mutations in the L- and M-opin gene cluster on the X chromosome. BCM patients display severely reduced visual acuity, loss of color-vision, myopia, nystagmus, and minimally detectable cone-mediated electroretinogram. In our studies, we showed that an M-opsin knockout mouse model resembles human BCM, and expression of either human M- or L-opsin individually or combined through adeno-associated viral vector promotes regrowth of cone outer segments and rescues M-cone function in the treated M-opsin dorsal retin

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Reassessment of Tumor Sequencing For Patients with Potentially Inheritable Colon Cancer

MedicalResearch.com Interview with:

Heather Hampel, MS, LGC Associate Director, Division of Human Genetics Associate Director, Biospecimen Research Professor, Internal Medicine Licensed Genetic Counselor The Ohio State University Comprehensive Cancer Center Columbus, OH  43221

Heather Hampel

Heather Hampel, MS, LGC
Associate Director, Division of Human Genetics
Associate Director, Biospecimen Research
Professor, Internal Medicine
Licensed Genetic Counselor
The Ohio State University Comprehensive Cancer Center
Columbus, OH  4322

MedicalResearch.com:  What is the background for this study?  What are the main findings?

Response: The background is that we had recently shown that some colorectal cancer patients who underwent traditional screening for Lynch syndrome were eventually found to have double somatic (two acquired) mutations in the MMR genes and they did not have Lynch syndrome at all. This was discovered after their tumor had already had MSI and/or IHC screening test, followed by MLH1 methylation and/or BRAF testing, followed by germline DNA testing on a blood sample from the patient for MMR gene mutations, then finally by sequencing their tumor. This gave us the idea to reverse the sequence and start with tumor sequencing since it might streamline testing, save time, and prevent several other tests.

In addition, we knew that all stage IV colorectal cancer are already supposed to have tumor sequencing of the KRAS, NRAS, and BRAF genes and MSI testing for treatment purposes. Our hypothesis was that an upfront tumor sequencing test could replace all these separate tests with similar sensitivity and specificity.

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Two Genes Linked to Severe Nausea and Vomiting in Pregnancy

MedicalResearch.com Interview with:

Marlena Fejzo, PhD Aassociate researche David Geffen School of Medicine UCLA.

Dr. Fejzo

Marlena Fejzo, PhD
Aassociate researche
David Geffen School of Medicine
UCLA. 

MedicalResearch.com: What is the background for this study?

Response: Most women experience some nausea and vomiting of pregnancy, and the worst 2% are diagnosed with Hyperemesis Gravidarum which is associated with poor maternal and fetal outcomes. I had HG in 2 pregnancies. In my second pregnancy my HG was so severe that I could not move without vomiting and did not keep any food or water down for 10 weeks. I was put on a feeding tube, but ultimately lost the baby in the second trimester. I am a medical scientist by training so I looked into what was known about HG. At the time, very little was known, so I decided to study it. I partnered with the Hyperemesis Education and Research Foundation (HER) and we did a survey on family history of .Hyperemesis Gravidarum that provided evidence to support a role for genes. I collected saliva samples from HG patients and their unaffected acquaintances to do a DNA study. Then I partnered with the personal genetics company, 23andMe to do a genome scan and validation study, which identified 2 genes, GDF15 and IGFBP7, linked to HG.

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Genetic Variant of p53 Associated With Poor Breast Cancer Survival

MedicalResearch.com Interview with:
Maureen E. Murphy, Ph.D.
Program Leader and Professor
Molecular and Cellular Oncogenesis and
Subhasree Basu PhD
Postdoctoral researcher
The Wistar Institute
Philadelphia, PA 19104

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: Unlike most other genes that are intimately involved in the cause of cancer, the p53 gene displays considerable genetic variation; in other words, p53 is unusual among cancer genes in that the amino acids in p53 protein can frequently differ amongst different populations and ethnic groups. Additionally, unlike most other tumor suppressor genes, when p53 is mutated in a tumor, as it is in 50% of human cancers, that mutant protein now has a positive function in cancer progression, changing tumor metabolism and promoting tumor metastasis.

In this study, the authors analyze for the first time the impact of a common genetic variant in p53 (single nucleotide polymorphism, or SNP) in the ability of mutant p53 to promote tumor metabolism and metastasis, and they find significant differences.  Continue reading

BRCA1/BRCA2 Testing Varies Widely Worldwide

MedicalResearch.com Interview with:

Amanda Toland, PhD, Cancer biology and genetics researcher of The Ohio State University Comprehensive Cancer Center -- Arthur G. James Cancer Hospital and Richard J. Solove Research Institute 

Dr. Toland

Amanda Toland, PhD,
Cancer biology and genetics researcher of
The Ohio State University Comprehensive Cancer Center — Arthur G. James Cancer Hospital and Richard J. Solove Research Institute

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: The Breast Information Core (or BIC) is a database that catalogs BRCA1 and BRCA2 sequenced variants.  The BIC is hosted by the National Human Genome Research Institute at NIH and has a steering committee that oversees the BIC and has members from Europe, the middle East, Australia and the US.  In BIC SC discussions, we learned that there are differences in how BRCA1/2 clinical is testing between countries.

To characterize this variation, we performed an international survey of 86 genetic testing labs from around the world.

Our main findings are that there were many variations between testing laboratories.  These include: technologies differed for finding “large” genetic sequence variants, what parts of the genes were assessed, how genetic variants were classified as disease associated or not being associated with diseases, if genetic sequencing information was shared in public databases and testing volume.

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Genetic Pathways Determine Susceptibility to Dengue Shock Syndrome

MedicalResearch.com Interview with:

CDC/ Frederick Murphy

This transmission electron microscopic (TEM) image depicts a number of round, Dengue virus particles that were revealed in this tissue specimen. CDC image

Luisa Pereira PhD
Institute for Research and Innovation in Health
University of Porto 

MedicalResearch.com: What is the background for this study? What are the main findings?

Response: By using admixture mapping along the genome in Thai cohorts, we were able to identify new candidate genes conferring protection/susceptibility to dengue fever. A very interesting result was that the set of genes differed with the dengue phenotype: genes coding proteins that may link to the virus, conditioning its entrance in the host cells and mobility therein were associated with the less severe phenotype; genes related with blood vessels permeability were associated with the dengue shock syndrome.  Continue reading

How Much Genetic Information From Prenatal Testing Do Pregnant Women Want?

“Pregnancy 1” by operalynn is licensed under CC BY 2.0MedicalResearch.com Interview with:
Professor Jane Halliday, PhD
Group Leader, Public Health Genetics
Genetics
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Parkville, Victoria  AUS 

MedicalResearch.com: What is the background for this study?

Response: The aim of the study was to examine the choice that pregnant women make about the amount of genetic information they want from their pregnancy. Women who underwent prenatal testing via chorionic villus sampling (CVS) or amniocentesis were recruited from across seven sites in Victoria.

Provision of this choice is not routinely offered but we thought it was important to look at this issue carefully, in a real-time setting, because, over the last five years, advances in technology have transformed how genetic abnormalities can be detected during a pregnancy.  Rather than examining genetic material (chromosomes) down the microscope, it is now possible to use a technique called ‘microarray’ which can do the analysis with 100 times greater depth than can be achieved using a microscope. The plus side is that the microarray technique can detect a far greater number of potentially important genetic differences; but a down side is that it can also detect many changes for which the impact on the health of the baby is unknown or uncertain.

Examples of genetic differences that carry certainty are major chromosome abnormalities such as the trisomies e.g. Down Syndrome, and deletions associated with severe intellectual disability in 100% of cases, e.g. 1p.36 deletion. Uncertain findings are the various small deletions and duplications that are known to only have an adverse outcome in 10-20% of people with them.

All participants were provided with a decision aid which described in detail the choice available in regards to the genetic information. The options were ‘targeted’, where only the information that would affect health of the baby was provided, or ‘extended’, where all information, even the uncertain aspects, was provided. Participants were asked to read the decision aid, complete a ten minute survey along with indicating their choice of genetic information.

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Genetic Risk Score Predictive of Aggressive Prostate Cancer

MedicalResearch.com Interview with:
“DNA” by Caroline Davis2010 is licensed under CC BY 2.0Tyler Seibert, MD, PhD

Radiation Oncology
Center for Multimodal Imaging & Genetics
UC San Diego

MedicalResearch.com: What is the background for this study?

Response: Prostate cancer is an extremely common condition in men. Many die from it each year, and many others live with debilitating pain caused by prostate cancer. Screening for prostate cancer with prostate-specific antigen (PSA) testing can be effective, but there are concerns with the test.

  • First, screening everyone gives a large proportion of false-positive results, and those men end up undergoing unnecessary procedures such as prostate biopsy. S
  • econd, a significant portion of men who develop prostate cancer will develop a slow-growing form of the disease that is likely not life-threatening and may not require treatment.

    These concerns have led to a drop in prostate cancer screening. But avoiding screening leaves a large number of men vulnerable to diagnosis of an aggressive prostate cancer at a later stage, when it is more difficult—or impossible—to be cured. Doctors are left to guess which of their patients are at risk of aggressive disease and at which age they need to start screening those patients.

Our study sought to develop a tool to provide men and their doctors with objective, personalized information about each man’s risk of prostate cancer. Based on the man’s genetics, we wanted to predict the risk of aggressive prostate cancer and at what age in his life that risk becomes elevated.

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