journal
MENU ▼
Read by QxMD icon Read
search

Genome Medicine

journal
https://www.readbyqxmd.com/read/28081722/emerging-links-between-m-6-a-and-misregulated-mrna-methylation-in-cancer
#1
Samie R Jaffrey, Michael G Kharas
N (6)-methyladenosine (m(6)A) in mRNA has emerged as a crucial epitranscriptomic modification that controls cellular differentiation and pluripotency. Recent studies are pointing to a role for the RNA methylation program in cancer self-renewal and cell fate, making this a new and promising therapeutic avenue for investigation.
January 12, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28081715/erratum-to-mutational-landscape-of-mucinous-ovarian-carcinoma-and-its-neoplastic-precursors
#2
Georgina L Ryland, Sally M Hunter, Maria A Doyle, Franco Caramia, Jason Li, Simone M Rowley, Michael Christie, Prue E Allan, Andrew N Stephens, David D L Bowtell, Ian G Campbell, Kylie L Gorringe
No abstract text is available yet for this article.
January 12, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28081714/clingen-pathogenicity-calculator-a-configurable-system-for-assessing-pathogenicity-of-genetic-variants
#3
Ronak Y Patel, Neethu Shah, Andrew R Jackson, Rajarshi Ghosh, Piotr Pawliczek, Sameer Paithankar, Aaron Baker, Kevin Riehle, Hailin Chen, Sofia Milosavljevic, Chris Bizon, Shawn Rynearson, Tristan Nelson, Gail P Jarvik, Heidi L Rehm, Steven M Harrison, Danielle Azzariti, Bradford Powell, Larry Babb, Sharon E Plon, Aleksandar Milosavljevic
BACKGROUND: The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through practice guidelines, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have published standards and guidelines for the interpretation of sequence variants. However, manual application of the guidelines is tedious and prone to human error...
January 12, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28007021/implementation-of-next-generation-sequencing-into-pediatric-hematology-oncology-practice-moving-beyond-actionable-alterations
#4
Jennifer A Oberg, Julia L Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N Sireci, Susan J Hsiao, Andrew T Turk, Filemon S Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J Andrews, James H Garvin, Darrell J Yamashiro, Wendy K Chung, Stephen G Emerson, Peter L Nagy, Mahesh M Mansukhani, Andrew L Kung
BACKGROUND: Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. METHODS: The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure...
December 23, 2016: Genome Medicine
https://www.readbyqxmd.com/read/28007036/genomic-landscape-of-colorectal-cancer-in-japan-clinical-implications-of-comprehensive-genomic-sequencing-for-precision-medicine
#5
Masayuki Nagahashi, Toshifumi Wakai, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Ryoma Yagi, Nobuaki Sato, Yuko Kitagawa, Hiroyuki Uetake, Kazuhiro Yoshida, Eiji Oki, Shin-Ei Kudo, Hiroshi Izutsu, Keisuke Kodama, Mitsutaka Nakada, Julie Tse, Meaghan Russell, Joerg Heyer, Winslow Powers, Ruobai Sun, Jennifer E Ring, Kazuaki Takabe, Alexei Protopopov, Yiwei Ling, Shujiro Okuda, Stephen Lyle
BACKGROUND: Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been limited to Western populations. In order to understand possible ethnic and geographic differences and to explore the broader application of CGS to other populations, we sequenced a panel of 415 important cancer genes to characterize clinically actionable genomic driver events in 201 Japanese patients with colorectal cancer (CRC)...
December 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/28007024/icages-integrated-cancer-genome-score-for-comprehensively-prioritizing-driver-genes-in-personal-cancer-genomes
#6
Chengliang Dong, Yunfei Guo, Hui Yang, Zeyu He, Xiaoming Liu, Kai Wang
Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are underdeveloped. Here we developed iCAGES, a novel statistical framework that infers driver variants by integrating contributions from coding, non-coding, and structural variants, identifies driver genes by combining genomic information and prior biological knowledge, then generates prioritized drug treatment...
December 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/28003022/the-variability-and-reproducibility-of-whole-genome-sequencing-technology-for-detecting-resistance-to-anti-tuberculous-drugs
#7
Jody Phelan, Denise M O'Sullivan, Diana Machado, Jorge Ramos, Alexandra S Whale, Justin O'Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F Huggett, Taane G Clark
BACKGROUND: The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles. METHODS: We investigated two sequencing platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor) using a well characterised reference strain (H37Rv) and clinical isolates from patients with tuberculosis resistant to up to 13 drugs...
December 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27993174/reconciling-evidence-based-medicine-and-precision-medicine-in-the-era-of-big-data-challenges-and-opportunities
#8
Jacques S Beckmann, Daniel Lew
This era of groundbreaking scientific developments in high-resolution, high-throughput technologies is allowing the cost-effective collection and analysis of huge, disparate datasets on individual health. Proper data mining and translation of the vast datasets into clinically actionable knowledge will require the application of clinical bioinformatics. These developments have triggered multiple national initiatives in precision medicine-a data-driven approach centering on the individual. However, clinical implementation of precision medicine poses numerous challenges...
December 19, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27964755/xgr-software-for-enhanced-interpretation-of-genomic-summary-data-illustrated-by-application-to-immunological-traits
#9
Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
BACKGROUND: Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem. RESULTS: We introduce eXploring Genomic Relations (XGR), an open source tool designed for enhanced interpretation of genomic summary data enabling downstream knowledge discovery...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27964749/truncating-de-novo-mutations-in-the-kr%C3%A3-ppel-type-zinc-finger-gene-znf148-in-patients-with-corpus-callosum-defects-developmental-delay-short-stature-and-dysmorphisms
#10
Servi J C Stevens, Anthonie J van Essen, Conny M A van Ravenswaaij, Abdallah F Elias, Jaclyn A Haven, Stefan H Lelieveld, Rolph Pfundt, Willy M Nillesen, Helger G Yntema, Kees van Roozendaal, Alexander P Stegmann, Christian Gilissen, Han G Brunner
BACKGROUND: Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptional co-activators or -repressors via interaction with chromatin remodeling proteins and other transcription factors. Only few ZNF genes are currently linked to human disorders and identification of ZNF gene-associated human diseases may help understand their function...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27964748/non-coding-single-nucleotide-variants-affecting-estrogen-receptor-binding-and-activity
#11
Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V Lee
BACKGROUND: Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic changes in different breast cancer models. We investigated whether single nucleotide variants (SNVs) in ER binding sites (regSNVs) contribute to ER action through changes in the ER cistrome, thereby affecting disease progression. Here we developed a computational pipeline to identify SNVs in ER binding sites using chromatin immunoprecipitation sequencing (ChIP-seq) data from ER+ breast cancer models...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27964746/alternate-locus-aware-variant-calling-in-whole-genome-sequencing
#12
Marten Jäger, Max Schubach, Tomasz Zemojtel, Knut Reinert, Deanna M Church, Peter N Robinson
BACKGROUND: The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. The new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS). METHODS: We developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27923400/allele-specific-expression-in-the-human-heart-and-its-application-to-postoperative-atrial-fibrillation-and-myocardial-ischemia
#13
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27887656/looking-beyond-the-cancer-cell-for-effective-drug-combinations
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
journal
journal
42021
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"