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BMC Medical Genomics

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https://www.readbyqxmd.com/read/30200994/tap-a-targeted-clinical-genomics-pipeline-for-detecting-transcript-variants-using-rna-seq-data
#1
Readman Chiu, Ka Ming Nip, Justin Chu, Inanc Birol
BACKGROUND: RNA-seq is a powerful and cost-effective technology for molecular diagnostics of cancer and other diseases, and it can reach its full potential when coupled with validated clinical-grade informatics tools. Despite recent advances in long-read sequencing, transcriptome assembly of short reads remains a useful and cost-effective methodology for unveiling transcript-level rearrangements and novel isoforms. One of the major concerns for adopting the proven de novo assembly approach for RNA-seq data in clinical settings has been the analysis turnaround time...
September 10, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30200981/comprehensive-off-target-analysis-of-dcas9-sam-mediated-hiv-reactivation-via-long-noncoding-rna-and-mrna-profiling
#2
Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao-Feng Yang, Hong Wang, Layne T Watson, Liqing Zhang, Wenhui Hu
BACKGROUND: CRISPR/CAS9 (epi)genome editing revolutionized the field of gene and cell therapy. Our previous study demonstrated that a rapid and robust reactivation of the HIV latent reservoir by a catalytically-deficient Cas9 (dCas9)-synergistic activation mediator (SAM) via HIV long terminal repeat (LTR)-specific MS2-mediated single guide RNAs (msgRNAs) directly induces cellular suicide without additional immunotherapy. However, potential off-target effect remains a concern for any clinical application of Cas9 genome editing and dCas9 epigenome editing...
September 10, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30180840/whole-exome-sequencing-in-adult-onset-hearing-loss-reveals-a-high-load-of-predicted-pathogenic-variants-in-known-deafness-associated-genes-and-identifies-new-candidate-genes
#3
Morag A Lewis, Lisa S Nolan, Barbara A Cadge, Lois J Matthews, Bradley A Schulte, Judy R Dubno, Karen P Steel, Sally J Dawson
BACKGROUND: Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studies of adult hearing status, it remains unclear whether the genetic architecture of this common sensory loss consists of multiple rare variants each with large effect size or many common susceptibility variants each with small to medium effects...
September 4, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30165852/correction-to-the-cancer-omics-atlas-an-integrative-resource-for-cancer-omics-annotations
#4
Qingrong Sun, Mengyuan Li, Xiaosheng Wang
Following publication of the original article [1], the authors reported an error in Fig. 1A.
August 30, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30157864/differentially-expressed-proteins-in-positive-versus-negative-hnscc-lymph-nodes
#5
Alessandra Vidotto, Giovana M Polachini, Marina de Paula-Silva, Sonia M Oliani, Tiago Henrique, Rossana V M López, Patrícia M Cury, Fabio D Nunes, José F Góis-Filho, Marcos B de Carvalho, Andréia M Leopoldino, Eloiza H Tajara
BACKGROUND: Lymph node metastasis is one of the most important prognostic factors in head and neck squamous cell carcinomas (HNSCCs) and critical for delineating their treatment. However, clinical and histological criteria for the diagnosis of nodal status remain limited. In the present study, we aimed to characterize the proteomic profile of lymph node metastasis from HNSCC patients. METHODS: In the present study, we used one- and two-dimensional electrophoresis and mass spectrometry analysis to characterize the proteomic profile of lymph node metastasis from HNSCC...
August 29, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30157848/circulating-mirnome-profiling-in-moyamoya-disease-discordant-monozygotic-twins-and-endothelial-microrna-expression-analysis-using-ips-cell-line
#6
Haruto Uchino, Masaki Ito, Ken Kazumata, Yuka Hama, Shuji Hamauchi, Shunsuke Terasaka, Hidenao Sasaki, Kiyohiro Houkin
BACKGROUND: Moyamoya disease (MMD) is characterized by progressive stenosis of intracranial arteries in the circle of Willis with unknown etiology even after the identification of a Moyamoya susceptible gene, RNF213. Recently, differences in epigenetic regulations have been investigated by a case-control study in MMD. Here, we employed a disease discordant monozygotic twin-based study design to unmask potential confounders. METHODS: Circulating genome-wide microRNA (miRNome) profiling was performed in MMD-discordant monozygotic twins, non-twin-MMD patients, and non-MMD healthy volunteers by microarray followed by qPCRvalidation, using blood samples...
August 29, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30126420/multiple-occurrence-of-psychomotor-retardation-and-recurrent-miscarriages-in-a-family-with-a-submicroscopic-reciprocal-translocation-t-7-17-p22-p13-2
#7
Magdalena Pasińska, Ewelina Łazarczyk, Katarzyna Jułga, Magdalena Bartnik-Głaska, Beata Nowakowska, Olga Haus
BACKGROUND: Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in phenotype, except when the translocation results in gene interruption. However, these people are at risk of production of unbalanced gametes during meiosis, as a result of various forms of chromosome segregation. This may cause infertility, non-implantation of the embryo, shorter embryo or foetus survival, as well as congenital defects and developmental disorders in children after birth...
August 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30092803/additional-germline-findings-from-a-tumor-profiling-program
#8
Neda Stjepanovic, Tracy L Stockley, Philippe L Bedard, Jeanna M McCuaig, Melyssa Aronson, Spring Holter, Kara Semotiuk, Natasha B Leighl, Raymond Jang, Monika K Krzyzanowska, Amit M Oza, Abha Gupta, Christine Elser, Lailah Ahmed, Lisa Wang, Suzanne Kamel-Reid, Lillian L Siu, Raymond H Kim
BACKGROUND: Matched tumor-normal sequencing, applied in precision cancer medicine, can identify unidentified germline Medically Actionable Variants (gMAVS) in cancer predisposition genes. We report patient preferences for the return of additional germline results, and describe various gMAV scenarios delivered through a clinical genetics service. METHODS: Tumor profiling was offered to 1960 advanced cancer patients, of which 1556 underwent tumor-normal sequencing with multigene hotspot panels containing 20 cancer predisposition genes...
August 9, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30089500/the-cancer-omics-atlas-an-integrative-resource-for-cancer-omics-annotations
#9
Qingrong Sun, Mengyuan Li, Xiaosheng Wang
BACKGROUND: The Cancer Genome Atlas (TCGA) is an important data resource for cancer biologists and oncologists. However, a lack of bioinformatics expertise often hinders experimental cancer biologists and oncologists from exploring the TCGA resource. Although a number of tools have been developed for facilitating cancer researchers to utilize the TCGA data, these existing tools cannot fully satisfy the large community of experimental cancer biologists and oncologists without bioinformatics expertise...
August 8, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30089489/association-between-genetic-risk-variants-and-glucose-intolerance-during-pregnancy-in-north-indian-women
#10
Geeti P Arora, Peter Almgren, Charlotte Brøns, Richa G Thaman, Allan A Vaag, Leif Groop, Rashmi B Prasad
BACKGROUND: Gestational diabetes (GDM) is a more common problem in India than in many other parts of the world but it is not known whether this is due to unique environmental factors or a unique genetic background. To address this question we examined whether the same genetic variants associated with GDM and Type 2 Diabetes (T2D) in Caucasians also were associated with GDM in North Indian women. METHODS: Five thousand one hundred pregnant women of gestational age 24-28 weeks from Punjab were studied by a 75 g oral glucose tolerance test (OGTT)...
August 8, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30086735/transcriptomic-signatures-reveal-immune-dysregulation-in-human-diabetic-and-idiopathic-gastroparesis
#11
Madhusudan Grover, Simon J Gibbons, Asha A Nair, Cheryl E Bernard, Adeel S Zubair, Seth T Eisenman, Laura A Wilson, Laura Miriel, Pankaj J Pasricha, Henry P Parkman, Irene Sarosiek, Richard W McCallum, Kenneth L Koch, Thomas L Abell, William J Snape, Braden Kuo, Robert J Shulman, Travis J McKenzie, Todd A Kellogg, Michael L Kendrick, James Tonascia, Frank A Hamilton, Gianrico Farrugia
BACKGROUND: Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear. METHODS: Diabetic gastroparetics, diabetic non-gastroparetic controls, idiopathic gastroparetics and non-diabetic non-gastroparetic controls underwent full-thickness gastric body biopsies. Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®...
August 7, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30037347/longitudinal-expression-profiling-of-cd4-and-cd8-cells-in-patients-with-active-to-quiescent-giant-cell-arteritis
#12
Elisabeth De Smit, Samuel W Lukowski, Lisa Anderson, Anne Senabouth, Kaisar Dauyey, Sharon Song, Bruce Wyse, Lawrie Wheeler, Christine Y Chen, Khoa Cao, Amy Wong Ten Yuen, Neil Shuey, Linda Clarke, Isabel Lopez Sanchez, Sandy S C Hung, Alice Pébay, David A Mackey, Matthew A Brown, Alex W Hewitt, Joseph E Powell
BACKGROUND: Giant cell arteritis (GCA) is the most common form of vasculitis affecting elderly people. It is one of the few true ophthalmic emergencies but symptoms and signs are variable thereby making it a challenging disease to diagnose. A temporal artery biopsy is the gold standard to confirm GCA, but there are currently no specific biochemical markers to aid diagnosis. We aimed to identify a less invasive method to confirm the diagnosis of GCA, as well as to ascertain clinically relevant predictive biomarkers by studying the transcriptome of purified peripheral CD4+ and CD8+ T lymphocytes in patients with GCA...
July 23, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30012129/concurrent-somatic-kras-mutation-and-germline-10q22-3-q23-2-deletion-in-a-patient-with-juvenile-myelomonocytic-leukemia-developmental-delay-and-multiple-malformations-a-case-report
#13
Ruen Yao, Tingting Yu, Yufei Xu, Guoqiang Li, Lei Yin, Yunfang Zhou, Jian Wang, Zhilong Yan
BACKGROUND: The proto-oncogene KRAS performs an essential function in normal tissue signaling, and the mutation of KRAS gene is a key step in the development of many cancers. Somatic KRAS mutations are often detected in patients with solid and non-solid tumors, whereas germline KRAS mutations are implicated in patients with the Noonan syndrome, cardio-facio-cutaneous (CFC) syndrome and Costello syndrome. The deletion of chromosome 10q22.3-q23.2 is a rare cytogenetic abnormality, which often leads to distinct facial appearance and delays in speech and global development...
July 16, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29996846/identification-of-differential-gene-expression-profile-from-peripheral-blood-cells-of-military-pilots-with-hypertension-by-rna-sequencing-analysis
#14
Xing-Cheng Zhao, Shao-Hua Yang, Yi-Quan Yan, Xin Zhang, Lin Zhang, Bo Jiao, Shuai Jiang, Zhi-Bin Yu
BACKGROUND: Elevated blood pressure is an important risk factor for cardiovascular disease and is also an important factor in global mortality. Military pilots are at high risk of cardiovascular disease because they undergo persistent noise, high mental tension, high altitude hypoxia, high acceleration and high calorie diet. Hypertension is the leading cause of cardiovascular disease in military pilots. In this study, we want to identify key genes from peripheral blood cells of military pilots with hypertension...
July 11, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29986705/comprehensive-genomic-diagnosis-of-non-syndromic-and-syndromic-hereditary-hearing-loss-in-spanish-patients
#15
Rubén Cabanillas, Marta Diñeiro, Guadalupe A Cifuentes, David Castillo, Patricia C Pruneda, Rebeca Álvarez, Noelia Sánchez-Durán, Raquel Capín, Ana Plasencia, Mónica Viejo-Díaz, Noelia García-González, Inés Hernando, José L Llorente, Alfredo Repáraz-Andrade, Cristina Torreira-Banzas, Jordi Rosell, Nancy Govea, Justo Ramón Gómez-Martínez, Faustino Núñez-Batalla, José A Garrote, Ángel Mazón-Gutiérrez, María Costales, María Isidoro-García, Belén García-Berrocal, Gonzalo R Ordóñez, Juan Cadiñanos
BACKGROUND: Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation. METHODS: We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL...
July 9, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29980210/phenotype-driven-gene-prioritization-for-rare-diseases-using-graph-convolution-on-heterogeneous-networks
#16
Aditya Rao, Saipradeep Vg, Thomas Joseph, Sujatha Kotte, Naveen Sivadasan, Rajgopal Srinivasan
BACKGROUND: One of the major goals of genomic medicine is the identification of causal genomic variants in a patient and their relation to the observed clinical phenotypes. Prioritizing the genomic variants by considering only the genotype information usually identifies a few hundred potential variants. Narrowing it down further to find the causal disease genes and relating them to the observed clinical phenotypes remains a significant challenge, especially for rare diseases. METHODS: We propose a phenotype-driven gene prioritization approach using heterogeneous networks in the context of rare diseases...
July 6, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29940959/association-of-nos1-gene-polymorphisms-with-cerebral-palsy-in-a-han-chinese-population-a-case-control-study
#17
Ting Yu, Lei Xia, Dan Bi, Yangong Wang, Qing Shang, Dengna Zhu, Juan Song, Yong Wang, Xiaoyang Wang, Changlian Zhu, Qinghe Xing
BACKGROUND: Cerebral palsy (CP) is the leading cause of motor disability in children; however, its pathogenesis is unknown in most cases. Growing evidence suggests that Nitric oxide synthase 1 (NOS1) is involved in neural development and neurologic diseases. The purpose of this study was to determine whether genetic variants of NOS1 contribute to CP susceptibility in a Han Chinese population. METHODS: A case-control study involving 652 CP patients and 636 healthy controls was conducted...
June 25, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29925376/blood-pressure-signature-genes-and-blood-pressure-response-to-thiazide-diuretics-results-from-the-pear-and-pear-2-studies
#18
Ana Caroline C Sá, Amy Webb, Yan Gong, Caitrin W McDonough, Mohamed H Shahin, Somnath Datta, Taimour Y Langaee, Stephen T Turner, Amber L Beitelshees, Arlene B Chapman, Eric Boerwinkle, John G Gums, Steven E Scherer, Rhonda M Cooper-DeHoff, Wolfgang Sadee, Julie A Johnson
BACKGROUND: Recently, 34 genes had been associated with differential expression relative to blood pressure (BP)/ hypertension (HTN). We hypothesize that some of the genes associated with BP/HTN are also associated with BP response to antihypertensive treatment with thiazide diuretics. METHODS: We assessed these 34 genes for association with differential expression to BP response to thiazide diuretics with RNA sequencing in whole blood samples from 150 hypertensive participants from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) and PEAR-2 studies...
June 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29925367/genetic-interaction-effects-reveal-lipid-metabolic-and-inflammatory-pathways-underlying-common-metabolic-disease-risks
#19
Hyung Jun Woo, Jaques Reifman
BACKGROUND: Common metabolic diseases, including type 2 diabetes, coronary artery disease, and hypertension, arise from disruptions of the body's metabolic homeostasis, with relatively strong contributions from genetic risk factors and substantial comorbidity with obesity. Although genome-wide association studies have revealed many genomic loci robustly associated with these diseases, biological interpretation of such association is challenging because of the difficulty in mapping single-nucleotide polymorphisms (SNPs) onto the underlying causal genes and pathways...
June 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29898714/calculating-the-statistical-significance-of-rare-variants-causal-for-mendelian-and-complex-disorders
#20
Aliz R Rao, Stanley F Nelson
BACKGROUND: With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question. METHODS: We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample...
June 13, 2018: BMC Medical Genomics
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