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Medical genomics

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https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#1
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28546713/current-concepts-of-epigenetics-in-testicular-cancer
#2
REVIEW
Alfredo Harb-De la Rosa, Meenakkshy Manoharan, Ahmed Saeed Goolam
Testicular germ cell tumors (GCTs) are characterized into seminomas (SGCTs) and non-seminomatous testicular germ cell tumors (NSGCTs). Serum tumor markers (STMs) play an important role in testicular cancer as they provide useful information for diagnosis, staging, and detection of recurrence. Nonetheless, additional tumor markers for early diagnosis and therapeutic options are required to enhance specificity of serological diagnosis of testes cancers. Epigenetics is defined as inherited changes in gene expression that are not encoded in the DNA structure...
June 2017: Indian Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28546526/molecular-signature-for-lymphatic-invasion-associated-with-survival-of-epithelial-ovarian-cancer
#3
E Sun Paik, Hyun Jin Choi, Tae-Joong Kim, Jeong-Won Lee, Byoung-Gie Kim, Duk-Soo Bae, Chel Hun Choi
Purpose: We aimed to develop molecular classifier that can predict lymphatic invasion and their clinical significance in epithelial ovarian cancer (EOC) patients. Materials and Methods: We analyzed gene expression (mRNA, methylated DNA) in data from The Cancer Genome Atlas. To identify molecular signatures for lymphatic invasion, we found differentially expressed genes. The performance of classifier was validated by receiver operating characteristics analysis, logistic regression, linear discriminant analysis (LDA), and support vector machine (SVM)...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28545823/novel-molecular-subgroups-for-clinical-classification-and-outcome-prediction-in-childhood-medulloblastoma-a-cohort-study
#4
Edward C Schwalbe, Janet C Lindsey, Sirintra Nakjang, Stephen Crosier, Amanda J Smith, Debbie Hicks, Gholamreza Rafiee, Rebecca M Hill, Alice Iliasova, Thomas Stone, Barry Pizer, Antony Michalski, Abhijit Joshi, Stephen B Wharton, Thomas S Jacques, Simon Bailey, Daniel Williamson, Steven C Clifford
BACKGROUND: International consensus recognises four medulloblastoma molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGrp3), and group 4 (MBGrp4), each defined by their characteristic genome-wide transcriptomic and DNA methylomic profiles. These subgroups have distinct clinicopathological and molecular features, and underpin current disease subclassification and initial subgroup-directed therapies that are underway in clinical trials. However, substantial biological heterogeneity and differences in survival are apparent within each subgroup, which remain to be resolved...
May 22, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28545270/-correlation-between-mutation-of-p53-gene-2-4-exons-from-peripheral-blood-and-hpv16-positive-cervical-cancer-susceptibility-and-clinical-significance
#5
C M Yin, Y F Yao, Z L Yan, H Y Yang
Objective: To detect mutations of p53 gene 2-4 exons from peripheral blood and to explore their relevance in HPV16-positive cervical cancer susceptibility and clinical significance. Methods: Collected firstly cases from the Third Affiliated Hospital of Kunming Medical University from October 2012 to April 2014, included 167 cases HPV16-postive cervical cancer and 160 cases HPV-negative healthy women. Genomic DNA from the host peripheral venous blood was taken, mutations of p53 gene 2-4 exons were analyzed with software DNAstar after PCR and bidirectional sequencing...
May 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28545070/pou4f3-mutation-screening-in-japanese-hearing-loss-patients-massively-parallel-dna-sequencing-based-analysis-identified-novel-variants-associated-with-autosomal-dominant-hearing-loss
#6
Tomohiro Kitano, Maiko Miyagawa, Shin-Ya Nishio, Hideaki Moteki, Kiyoshi Oda, Kenji Ohyama, Hiromitsu Miyazaki, Hiroshi Hidaka, Ken-Ichi Nakamura, Takaaki Murata, Rina Matsuoka, Yoko Ohta, Nobuhiro Nishiyama, Kozo Kumakawa, Sakiko Furutate, Satoshi Iwasaki, Takechiyo Yamada, Yumi Ohta, Natsumi Uehara, Yoshihiro Noguchi, Shin-Ichi Usami
A variant in a transcription factor gene, POU4F3, is responsible for autosomal dominant nonsyndromic hereditary hearing loss, DFNA15. To date, 14 variants, including a whole deletion of POU4F3, have been reported to cause HL in various ethnic groups. In the present study, genetic screening for POU4F3 variants was carried out for a large series of Japanese hearing loss (HL) patients to clarify the prevalence and clinical characteristics of DFNA15 in the Japanese population. Massively parallel DNA sequencing of 68 target candidate genes was utilized in 2,549 unrelated Japanese HL patients (probands) to identify genomic variations responsible for HL...
2017: PloS One
https://www.readbyqxmd.com/read/28542097/genome-wide-association-and-pathway-analysis-of-left-ventricular-function-after-anthracycline-exposure-in-adults
#7
Quinn S Wells, Olivia J Veatch, Joshua P Fessel, Aron Y Joon, Rebecca T Levinson, Jonathan D Mosley, Elizabeth P Held, Chase S Lindsay, Christian M Shaffer, Peter E Weeke, Andrew M Glazer, Kevin R Bersell, Sara L Van Driest, Jason H Karnes, Marcia A Blair, Lore W Lagrone, Yan R Su, Erica A Bowton, Ziding Feng, Bonnie Ky, Daniel J Lenihan, Michael J Fisch, Joshua C Denny, Dan M Roden
BACKGROUND: Anthracyclines are important chemotherapeutic agents, but their use is limited by cardiotoxicity. Candidate gene and genome-wide studies have identified putative risk loci for overt cardiotoxicity and heart failure, but there has been no comprehensive assessment of genomic variation influencing the intermediate phenotype of anthracycline-related changes in left ventricular (LV) function. The purpose of this study was to identify genetic factors influencing changes in LV function after anthracycline chemotherapy...
May 24, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28540771/identifying-therapeutic-targets-for-alzheimer-s-disease-with-big-data
#8
Nilüfer Ertekin-Taner
Nilüfer Ertekin-Taner is a Professor of Neuroscience and Neurology at the Mayo Clinic, Jacksonville, FL, USA. A neurogeneticist and board-certified behavioral neurologist, she received her medical degree from Hacettepe University Medical School in Ankara, Turkey and her doctorate degree in Molecular Neuroscience from Mayo Graduate School. She completed her residency training in the Department of Neurology at Mayo Clinic in Rochester (MN, USA) and fellowship in Behavioral Neurology at Mayo Clinic in Jacksonville...
April 2017: Neurodegenerative Disease Management
https://www.readbyqxmd.com/read/28539731/improved-annotations-of-23-differentially-expressed-hypothetical-proteins-in-methicillin-resistant-s-aureus
#9
Jessica Marklevitz, Laura K Harris
Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. These strains are appearing in the community with increasing frequency. New diagnostic and therapeutic options are needed to combat this deadly infection. Interestingly, around 50% of the proteins in S. aureus are annotated as hypothetical. Methods to select hypothetical proteins related to antibiotic resistance have been inadequate...
2017: Bioinformation
https://www.readbyqxmd.com/read/28539122/an-inference-method-from-multi-layered-structure-of-biomedical-data
#10
Myungjun Kim, Yonghyun Nam, Hyunjung Shin
BACKGROUND: Biological system is a multi-layered structure of omics with genome, epigenome, transcriptome, metabolome, proteome, etc., and can be further stretched to clinical/medical layers such as diseasome, drugs, and symptoms. One advantage of omics is that we can figure out an unknown component or its trait by inferring from known omics components. The component can be inferred by the ones in the same level of omics or the ones in different levels. METHODS: To implement the inference process, an algorithm that can be applied to the multi-layered complex system is required...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28536537/-gestaltomics-systems-biology-schemes-for-the-study-of-neuropsychiatric-diseases
#11
REVIEW
Nora A Gutierrez Najera, Osbaldo Resendis-Antonio, Humberto Nicolini
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the "psychiatric phenotype" is to provide an improved vision of the shape of the phenotype as it is visualized by "Gestalt" psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28534435/genome-editing-technologies-and-patent-landscape-overview
#12
Fairouz Benahmed-Miniuk, Mat Kresz, Jitendra K Kanaujiya, Christopher D Southgate
Unlike with zinc finger nuclease and transcriptional activator-like effector nuclease DNA modification technologies that rely on lead proteins, developed through expensive and time-consuming processes, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system has rapidly emerged as the most promising gene-editing technology to date for the modification of any selected DNA sequence. CRISPR is receiving tremendous fanfare due, in part, to its potential to provide a means to fundamentally alter medical genetics and especially cancer medicine...
May 23, 2017: Pharmaceutical Patent Analyst
https://www.readbyqxmd.com/read/28534357/comparative-study-of-receptor-discordance-between-primary-and-corresponding-metastatic-lesions-in-breast-cancer
#13
Gokmen U Erdem, Kadri Altundag, Nuriye Y Ozdemir, Suleyman Sahin, Nebi S Demirci, Fatih Karatas, Yakup Bozkaya, Aydin Aytekin, Vildan Tasdemir, Alma C Aslan, Ali R Sever, Nurullah Zengin
PURPOSE: It is well-known that tumor phenotype may change during the progression of breast cancer (BC). The purpose in this study was to compare the discordance in estrogen receptor (ER), progesterone receptor (PgR) and human epidermal growth factor receptor 2 (HER2) between primary and recurrent/metastatic lesions (RML) and also to evaluate the prognostic significance of change in tumor phenotype on survival in patients with metastatic BC. METHODS: The medical records of 6638 patients with BC from two breast centers treated between 1992 and 2015 were retrospectively analyzed...
March 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28533660/genes-emotions-and-gut-microbiota-the-next-frontier-for-the-gastroenterologist
#14
REVIEW
Arturo Panduro, Ingrid Rivera-Iñiguez, Maricruz Sepulveda-Villegas, Sonia Roman
Most medical specialties including the field of gastroenterology are mainly aimed at treating diseases rather than preventing them. Genomic medicine studies the health/disease process based on the interaction of the human genes with the environment. The gastrointestinal (GI) system is an ideal model to analyze the interaction between our genes, emotions and the gut microbiota. Based on the current knowledge, this mini-review aims to provide an integrated synopsis of this interaction to achieve a better understanding of the GI disorders related to bad eating habits and stress-related disease...
May 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28532983/towards-the-goal-of-achieving-a-normal-duration-and-quality-of-life-after-fontan-operation-creation-of-the-international-fontan-interest-group-i-fig-an-international-collaborative-initiative-dedicated-to-improving-outcomes
#15
Yves d'Udekem, Jack Rychik
A growing population of patients are now surviving the Fontan procedure and face an uncertain future and a clear burden of disease. The best medical therapy and follow-up modalities for these patients have not yet been identified, indications for transplantation are unclear and we have not been successful in mechanically supporting their circulation. There has only been a limited number of trials to address these issues. An international group has now been created to launch the large scale multi-centric research needed to provide the best future to this growing population: the International Fontan Interest Group (I-FIG)...
May 11, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28532976/microbiological-problems-and-biofilms-associated-with-mycobacterium-chimaera-in-heater-cooler-units-used-for-cardiopulmonary-bypass
#16
REVIEW
J Walker, G Moore, S Collins, S Parks, M I Garvey, T Lamagni, G Smith, L Dawkin, S Goldenberg, M Chand
The role of heater-cooler units (HCUs) in the transmission of Mycobacterium chimaera during open heart surgery has been recognized since 2013. Subsequent investigations uncovered a remarkable global outbreak reflecting the wide distribution of implicated devices. HCUs are an essential component of cardiopulmonary bypass operations and their withdrawal would severely affect capacity for life-saving cardiac surgery. However, studies have demonstrated that many HCUs are contaminated with a wide range of micro-organisms, including M...
April 26, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28531898/plasma-et-1-concentrations-are-elevated-in-patients-with-hypertension-meta-analysis-of-clinical-studies
#17
Mei Xu, Yong-Ping Lu, Ahmed Abdallah Hasan, Berthold Hocher
BACKGROUND/AIMS: A recent study revealed that global overexpression of ET-1 causes a slight reduction in systemic blood pressure. Moreover, heterozygous ET-1 knockout mice are hypertensive. The role of ET-1 in human hypertension was so far not addressed by a strict meta-analysis of published human clinical studies. METHODS: We included studies published between January 1, 1990 and February 28, 2017. We included case control studies analyzing untreated essential hypertension or hypertensive patients where antihypertensive medication was discontinued for at least two weeks...
May 26, 2017: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/28530328/-the-israeli-rat-genome-center
#18
REVIEW
Yoram Yagil, Chana Yagil
The Israeli Rat Genome Center, which is located at the Barzilai Medical Center Campus of the Faculty of Health Sciences of the Ben-Gurion University of the Negev in Ashkelon, was established to provide a repository of unique genetic strains of rats that were created in Israel and that simulate complex diseases. The Center incorporates models of: salt-sensitive hypertension (SBN/y and SBH/y rats), type 2 diabetes (CDr and CDs rats), combined hypertension and diabetes (CRDH) and additional genetic strains (transgenics, consomics, congenics)...
August 2016: Harefuah
https://www.readbyqxmd.com/read/28529696/in-silico-gene-expression-profiling-in-cannabis-sativa
#19
Luca Massimino
The cannabis plant and its active ingredients (i.e., cannabinoids and terpenoids) have been socially stigmatized for half a century. Luckily, with more than 430,000 published scientific papers and about 600 ongoing and completed clinical trials, nowadays cannabis is employed for the treatment of many different medical conditions. Nevertheless, even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills...
2017: F1000Research
https://www.readbyqxmd.com/read/28527892/outbreak-of-zika-virus-infection-in-singapore-an-epidemiological-entomological-virological-and-clinical-analysis
#20
(no author information available yet)
BACKGROUND: An outbreak of Zika virus infection was detected in Singapore in August, 2016. We report the first comprehensive analysis of a national response to an outbreak of Zika virus infection in Asia. METHODS: In the first phase of the outbreak, patients with suspected Zika virus infection were isolated in two national referral hospitals until their serum tested negative for the virus. Enhanced vector control and community engagement measures were deployed in disease clusters, including stepped-up mosquito larvicide and adulticide use, community participation in source reduction (destruction of mosquito breeding sites), and work with the local media to promote awareness of the outbreak...
May 17, 2017: Lancet Infectious Diseases
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