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Genome Medicine

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https://www.readbyqxmd.com/read/27887656/looking-beyond-the-cancer-cell-for-effective-drug-combinations
#1
Jonathan R Dry, Mi Yang, Julio Saez-Rodriguez
Combinations of therapies are being actively pursued to expand therapeutic options and deal with cancer's pervasive resistance to treatment. Research efforts to discover effective combination treatments have focused on drugs targeting intracellular processes of the cancer cells and in particular on small molecules that target aberrant kinases. Accordingly, most of the computational methods used to study, predict, and develop drug combinations concentrate on these modes of action and signaling processes within the cancer cell...
November 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27887638/mitochondrial-replacement-approaches-challenges-for-clinical-implementation
#2
Thomas Klopstock, Barbara Klopstock, Holger Prokisch
The advent of mitochondrial replacement techniques poses many scientific, regulatory, and ethical questions. Previous studies suggest good safety and efficacy profiles of these techniques, but challenges remain for clinical implementation and international consensus is needed on the regulation of these approaches.
November 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27884207/potential-contribution-of-the-uterine-microbiome-in-the-development-of-endometrial-cancer
#3
Marina R S Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J Distad, E Heidi Cheek, Gary L Keeney, Douglas J Creedon, Heidi Nelson, Andrea Mariani, Nicholas Chia
BACKGROUND: Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic expression is the microbiome. We set out to inquire about the composition of the uterine microbiome and its putative role in endometrial cancer. METHODS: We undertook a study of the microbiome in samples taken from different locations along the female reproductive tract in patients with endometrial cancer (n = 17), patients with endometrial hyperplasia (endometrial cancer precursor, n = 4), and patients afflicted with benign uterine conditions (n = 10)...
November 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27876088/erratum-to-illuminating-uveitis-metagenomic-deep-sequencing-identifies-common-and-rare-pathogens
#4
Thuy Doan, Michael R Wilson, Emily D Crawford, Eric D Chow, Lillian M Khan, Kristeene A Knopp, Brian D O'Donovan, Dongxiang Xia, Jill K Hacker, Jay M Stewart, John A Gonzales, Nisha R Acharya, Joseph L DeRisi
No abstract text is available yet for this article.
November 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27876072/high-specificity-bioinformatics-framework-for-epigenomic-profiling-of-discordant-twins-reveals-specific-and-shared-markers-for-acpa-and-acpa-positive-rheumatoid-arthritis
#5
David Gomez-Cabrero, Malin Almgren, Louise K Sjöholm, Aase H Hensvold, Mikael V Ringh, Rakel Tryggvadottir, Juha Kere, Annika Scheynius, Nathalie Acevedo, Lovisa Reinius, Margaret A Taub, Carolina Montano, Martin J Aryee, Jason I Feinberg, Andrew P Feinberg, Jesper Tegnér, Lars Klareskog, Anca I Catrina, Tomas J Ekström
BACKGROUND: Twin studies are powerful models to elucidate epigenetic modifications resulting from gene-environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpowered situation afflicted with false positives and hampered by low sensitivity. We investigated genome-wide DNA methylation data from two small sets of monozygotic twins representing different phases during the progression of rheumatoid arthritis (RA) to find novel genes for further research...
November 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27846907/copy-number-analysis-by-low-coverage-whole-genome-sequencing-using-ultra-low-input-dna-from-formalin-fixed-paraffin-embedded-tumor-tissue
#6
Tanjina Kader, David L Goode, Stephen Q Wong, Jacquie Connaughton, Simone M Rowley, Lisa Devereux, David Byrne, Stephen B Fox, Gisela Mir Arnau, Richard W Tothill, Ian G Campbell, Kylie L Gorringe
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays...
November 15, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27846896/genome-editing-progress-and-challenges-for-medical-applications
#7
Dana Carroll
The development of the CRISPR-Cas platform for genome editing has greatly simplified the process of making targeted genetic modifications. Applications of genome editing are expected to have a substantial impact on human therapies through the development of better animal models, new target discovery, and direct therapeutic intervention.
November 15, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27825374/low-heritability-in-pharmacokinetics-of-talinolol-a-pharmacogenetic-twin-study-on-the-heritability-of-the-pharmacokinetics-of-talinolol-a-putative-probe-drug-of-mdr1-and-other-membrane-transporters
#8
Johannes Matthaei, Mladen V Tzvetkov, Valerie Gal, Cordula Sachse-Seeboth, Daniel Sehrt, Jakob B Hjelmborg, Ute Hofmann, Matthias Schwab, Reinhold Kerb, Jürgen Brockmöller
BACKGROUND: Efflux transporters like MDR1 and MRP2 may modulate the pharmacokinetics of about 50 % of all drugs. It is currently unknown how much of the variation in the activities of important drug membrane transporters like MDR1 or MRP2 is determined by genetic or by environmental factors. In this study we assessed the heritability of the pharmacokinetics of talinolol as a putative probe drug for MDR1 and possibly other membrane transporters. METHODS: Talinolol pharmacokinetics were investigated in a repeated dose study in 42 monozygotic and 13 same-sex dizygotic twin pairs...
November 8, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27821178/erratum-to-making-sense-of-big-data-in-health-research-towards-an-eu-action-plan
#9
Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek, Norbert Graf, Vera Grimm, Henk-Jan Guchelaar, Yi-Ke Guo, Ivo Glynne Gut, Allan Hanbury, Shahid Hanif, Ralf-Dieter Hilgers, Ángel Honrado, D Rod Hose, Jeanine Houwing-Duistermaat, Tim Hubbard, Sophie Helen Janacek, Haralampos Karanikas, Tim Kievits, Manfred Kohler, Andreas Kremer, Jerry Lanfear, Thomas Lengauer, Edith Maes, Theo Meert, Werner Müller, Dörthe Nickel, Peter Oledzki, Bertrand Pedersen, Milan Petkovic, Konstantinos Pliakos, Magnus Rattray, Josep Redón I Màs, Reinhard Schneider, Thierry Sengstag, Xavier Serra-Picamal, Wouter Spek, Lea A I Vaas, Okker van Batenburg, Marc Vandelaer, Peter Varnai, Pablo Villoslada, Juan Antonio Vizcaíno, John Peter Mary Wubbe, Gianluigi Zanetti
No abstract text is available yet for this article.
November 7, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27814769/somatic-cancer-variant-curation-and-harmonization-through-consensus-minimum-variant-level-data
#10
Deborah I Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F Davis, Reece K Hart, Christine Micheel, Meredith Weaver, Eliezer M Van Allen, Donald W Parsons, Howard L McLeod, Michael S Watson, Sharon E Plon, Shashikant Kulkarni, Subha Madhavan
BACKGROUND: To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD). MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice...
November 4, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27799067/identification-of-a-rai1-associated-disease-network-through-integration-of-exome-sequencing-transcriptomics-and-3d-genomics
#11
Maria Nicla Loviglio, Christine R Beck, Janson J White, Marion Leleu, Tamar Harel, Nicolas Guex, Anne Niknejad, Weimin Bi, Edward S Chen, Isaac Crespo, Jiong Yan, Wu-Lin Charng, Shen Gu, Ping Fang, Zeynep Coban-Akdemir, Chad A Shaw, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Jacques Rougemont, Ioannis Xenarios, James R Lupski, Alexandre Reymond
BACKGROUND: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. METHODS: We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27799064/mipep-recessive-variants-cause-a-syndrome-of-left-ventricular-non-compaction-hypotonia-and-infantile-death
#12
Mohammad K Eldomery, Zeynep C Akdemir, F-Nora Vögtle, Wu-Lin Charng, Patrycja Mulica, Jill A Rosenfeld, Tomasz Gambin, Shen Gu, Lindsay C Burrage, Aisha Al Shamsi, Samantha Penney, Shalini N Jhangiani, Holly H Zimmerman, Donna M Muzny, Xia Wang, Jia Tang, Ravi Medikonda, Prasanna V Ramachandran, Lee-Jun Wong, Eric Boerwinkle, Richard A Gibbs, Christine M Eng, Seema R Lalani, Jozef Hertecant, Richard J Rodenburg, Omar A Abdul-Rahman, Yaping Yang, Fan Xia, Meng C Wang, James R Lupski, Chris Meisinger, V Reid Sutton
BACKGROUND: Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. METHODS: Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27799057/integrative-network-analysis-of-nineteen-brain-regions-identifies-molecular-signatures-and-networks-underlying-selective-regional-vulnerability-to-alzheimer-s-disease
#13
Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J Brennand, Gabriele C De Luca, John F Crary, Patrizia Casaccia, Joseph D Buxbaum, Michelle Ehrlich, Sam Gandy, Alison Goate, Pavel Katsel, Eric Schadt, Vahram Haroutunian, Bin Zhang
BACKGROUND: Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. However, despite extensive clinical and genomic studies, the molecular basis of AD development and progression remains elusive. METHODS: To elucidate molecular systems associated with AD, we developed a large scale gene expression dataset from 1053 postmortem brain samples across 19 cortical regions of 125 individuals with a severity spectrum of dementia and neuropathology of AD...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27799065/a-case-study-of-an-integrative-genomic-and-experimental-therapeutic-approach-for-rare-tumors-identification-of-vulnerabilities-in-a-pediatric-poorly-differentiated-carcinoma
#14
Filemon S Dela Cruz, Daniel Diolaiti, Andrew T Turk, Allison R Rainey, Alberto Ambesi-Impiombato, Stuart J Andrews, Mahesh M Mansukhani, Peter L Nagy, Mariano J Alvarez, Andrea Califano, Farhad Forouhar, Beata Modzelewski, Chelsey M Mitchell, Darrell J Yamashiro, Lianna J Marks, Julia L Glade Bender, Andrew L Kung
BACKGROUND: Precision medicine approaches are ideally suited for rare tumors where comprehensive characterization may have diagnostic, prognostic, and therapeutic value. We describe the clinical case and molecular characterization of an adolescent with metastatic poorly differentiated carcinoma (PDC). Given the rarity and poor prognosis associated with PDC in children, we utilized genomic analysis and preclinical models to validate oncogenic drivers and identify molecular vulnerabilities...
October 31, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27793177/approaches-to-modernize-the-combination-drug-development-paradigm
#15
REVIEW
Daphne Day, Lillian L Siu
Recent advances in genomic sequencing and omics-based capabilities are uncovering tremendous therapeutic opportunities and rapidly transforming the field of cancer medicine. Molecularly targeted agents aim to exploit key tumor-specific vulnerabilities such as oncogenic or non-oncogenic addiction and synthetic lethality. Additionally, immunotherapies targeting the host immune system are proving to be another promising and complementary approach. Owing to substantial tumor genomic and immunologic complexities, combination strategies are likely to be required to adequately disrupt intricate molecular interactions and provide meaningful long-term benefit to patients...
October 28, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27788678/application-of-rnai-induced-gene-expression-profiles-for-prognostic-prediction-in-breast-cancer
#16
Yue Wang, Kenneth M K Mark, Matthew H Ung, Arminja Kettenbach, Todd Miller, Wei Xu, Wenqing Cheng, Tian Xia, Chao Cheng
Homologous recombination (HR) is the primary pathway for repairing double-strand DNA breaks implicating in the development of cancer. RNAi-based knockdowns of BRCA1 and RAD51 in this pathway have been performed to investigate the resulting transcriptomic profiles. Here we propose a computational framework to utilize these profiles to calculate a score, named RNA-Interference derived Proliferation Score (RIPS), which reflects cell proliferation ability in individual breast tumors. RIPS is predictive of breast cancer classes, prognosis, genome instability, and neoadjuvant chemosensitivity...
October 27, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27784341/technological-considerations-for-genome-guided-diagnosis-and-management-of-cancer
#17
REVIEW
Niall J Lennon, Viktor A Adalsteinsson, Stacey B Gabriel
Technological, methodological, and analytical advances continue to improve the resolution of our view into the cancer genome, even as we discover ways to carry out analyses at greater distances from the primary tumor sites. These advances are finally making the integration of cancer genomic profiling into clinical practice feasible. Formalin fixation and paraffin embedding, which has long been the default pathological biopsy medium, is now being supplemented with liquid biopsy as a means to profile the cancer genomes of patients...
October 26, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27784327/integrating-cancer-genomic-data-into-electronic-health-records
#18
REVIEW
Jeremy L Warner, Sandeep K Jain, Mia A Levy
The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10-15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics...
October 26, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27782862/acquired-resistance-to-anti-pd1-therapy-checkmate-to-checkpoint-blockade
#19
Jake S O'Donnell, Mark J Smyth, Michele W L Teng
Anti-programmed cell death 1 (PD1) immunotherapies are among the most effective anti-cancer immunotherapies available; however, a large number of patients present with or develop resistance to them. Unfortunately, very little is known regarding the mechanisms of resistance to such therapies. A recent study sought to identify mutations associated with resistance to anti-PD1 therapy. Results from this study demonstrated that mutations which affected the sensitivity of tumor cells to T-cell-derived interferons, and mutations limiting tumor-cell antigen presentation, could cause acquired resistance...
October 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27782854/molecular-profiling-of-advanced-solid-tumors-and-patient-outcomes-with-genotype-matched-clinical-trials-the-princess-margaret-impact-compact-trial
#20
Tracy L Stockley, Amit M Oza, Hal K Berman, Natasha B Leighl, Jennifer J Knox, Frances A Shepherd, Eric X Chen, Monika K Krzyzanowska, Neesha Dhani, Anthony M Joshua, Ming-Sound Tsao, Stefano Serra, Blaise Clarke, Michael H Roehrl, Tong Zhang, Mahadeo A Sukhai, Nadia Califaretti, Mateya Trinkaus, Patricia Shaw, Theodorus van der Kwast, Lisa Wang, Carl Virtanen, Raymond H Kim, Albiruni R A Razak, Aaron R Hansen, Celeste Yu, Trevor J Pugh, Suzanne Kamel-Reid, Lillian L Siu, Philippe L Bedard
BACKGROUND: The clinical utility of molecular profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical "actionability" of somatic variants, enrollment in mutation-targeted or other clinical trials, and outcome of molecular profiling for advanced solid tumor patients at the Princess Margaret Cancer Centre (PM). METHODS: Patients with advanced solid tumors aged ≥18 years, good performance status, and archival tumor tissue available were prospectively consented...
October 25, 2016: Genome Medicine
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