973 results match your criteria BMC Medical Genomics [Journal]


Non-familial cardiomyopathies in Lebanon: exome sequencing results for five idiopathic cases.

BMC Med Genomics 2019 Feb 14;12(1):33. Epub 2019 Feb 14.

Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine and Medical Center (AUBMC), Phase I, 8th floor, Room C-823, PO Box 11-0236, Riad El-Solh, Beirut, 1107 2020, Lebanon.

Background: Cardiomyopathies affect more than 0.5% of the general population. They are associated with high risk of sudden cardiac death, which can result from either heart failure or electrical abnormalities. Read More

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http://dx.doi.org/10.1186/s12920-019-0478-7DOI Listing
February 2019

Transcriptomic and ChIP-sequence interrogation of EGFR signaling in HER2+ breast cancer cells reveals a dynamic chromatin landscape and S100 genes as targets.

BMC Med Genomics 2019 Feb 8;12(1):32. Epub 2019 Feb 8.

Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, 1731 East 120th Street, Los Angeles, CA, 90059, USA.

Background: The Human Epidermal Growth Factor Receptor (EGFR/HER1) can be activated by several ligands including Transforming Growth Factor alpha (TGF-α) and Epidermal Growth Factor (EGF). Following ligand binding, EGFR heterodimerizes with other HER family members, such as HER2 (human epidermal growth factor receptor-2). Previously, we showed that the EGFR is upregulated in trastuzumab resistant HER2 positive (HER2+) breast cancer cells. Read More

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http://dx.doi.org/10.1186/s12920-019-0477-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368760PMC
February 2019
1 Read
2.873 Impact Factor

Complex structural rearrangements are present in high-grade dysplastic Barrett's oesophagus samples.

BMC Med Genomics 2019 Feb 4;12(1):31. Epub 2019 Feb 4.

Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, QLD, 4102, Australia.

Background: Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett's oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals. Read More

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http://dx.doi.org/10.1186/s12920-019-0476-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360790PMC
February 2019

Chromosome (re)positioning in spermatozoa of fathers and sons - carriers of reciprocal chromosome translocation (RCT).

BMC Med Genomics 2019 Feb 1;12(1):30. Epub 2019 Feb 1.

Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.

Background: Non-random chromosome positioning has been observed in the nuclei of several different tissue types, including human spermatozoa. The nuclear arrangement of chromosomes can be altered in men with decreased semen parameters or increased DNA fragmentation and in males with chromosomal numerical or structural aberrations. An aim of this study was to determine whether and how the positioning of nine chromosome centromeres was (re)arranged in the spermatozoa of fathers and sons - carriers of the same reciprocal chromosome translocation (RCT). Read More

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http://dx.doi.org/10.1186/s12920-018-0470-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359769PMC
February 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):20. Epub 2019 Jan 31.

Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

During June 10-12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics ranging from 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics to systems biology. While medical genomics has always been a main theme in ICIBM, this year we for the first time organized the BMC Medical Genomics Supplement for ICIBM. Read More

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http://dx.doi.org/10.1186/s12920-018-0448-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357345PMC
January 2019

Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):13. Epub 2019 Jan 31.

Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.

Background: At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer's disease (AD).

Methods: We developed a splicing decision model as a molecular mechanism to identify functional exon skipping events and genetic variation affecting alternative splicing on a genome-wide scale by integrating genomics, transcriptomics, and neuroimaging data in a systems biology approach. Read More

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http://dx.doi.org/10.1186/s12920-018-0453-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357347PMC
January 2019
1 Read
2.873 Impact Factor

Computational identification of deleterious synonymous variants in human genomes using a feature-based approach.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):12. Epub 2019 Jan 31.

Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, 111 Jiulong Avenue, Hefei, 230601, China.

Background: Although synonymous single nucleotide variants (sSNVs) do not alter the protein sequences, they have been shown to play an important role in human disease. Distinguishing pathogenic sSNVs from neutral ones is challenging because pathogenic sSNVs tend to have low prevalence. Although many methods have been developed for predicting the functional impact of single nucleotide variants, only a few have been specifically designed for identifying pathogenic sSNVs. Read More

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http://dx.doi.org/10.1186/s12920-018-0455-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357349PMC
January 2019

Selecting precise reference normal tissue samples for cancer research using a deep learning approach.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):21. Epub 2019 Jan 31.

Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.

Background: Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered. Read More

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http://dx.doi.org/10.1186/s12920-018-0463-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357350PMC
January 2019

Network-based identification of critical regulators as putative drivers of human cleft lip.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):16. Epub 2019 Jan 31.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.

Background: Cleft lip (CL) is one of the most common congenital birth defects with complex etiology. While genome-wide association studies (GWAS) have made significant advances in our understanding of mutations and their related genes with potential involvement in the etiology of CL, it remains unknown how these genes are functionally regulated and interact with each other in lip development. Currently, identifying the disease-causing genes in human CL is urgently needed. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0458-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357351PMC
January 2019
2 Reads

Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):22. Epub 2019 Jan 31.

Human Genetics Center, UTHealth School of Public Health, Houston, TX, USA.

Background: Identifying cancer driver genes (CDG) is a crucial step in cancer genomic toward the advancement of precision medicine. However, driver gene discovery is a very challenging task because we are not only dealing with huge amount of data; but we are also faced with the complexity of the disease including the heterogeneity of background somatic mutation rate in each cancer patient. It is generally accepted that CDG harbor variants conferring growth advantage in the malignant cell and they are positively selected, which are critical to cancer development; whereas, non-driver genes harbor random mutations with no functional consequence on cancer. Read More

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http://dx.doi.org/10.1186/s12920-018-0452-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357357PMC
January 2019
1 Read

A PheWAS study of a large observational epidemiological cohort of African Americans from the REGARDS study.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):26. Epub 2019 Jan 31.

School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

Background: Cardiovascular disease, diabetes, and kidney disease are among the leading causes of death and disability worldwide. However, knowledge of genetic determinants of those diseases in African Americans remains limited.

Results: In our study, associations between 4956 GWAS catalog reported SNPs and 67 traits were examined among 7726 African Americans from the REasons for Geographic and Racial Differences in Stroke (REGARDS) study, which is focused on identifying factors that increase stroke risk. Read More

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http://dx.doi.org/10.1186/s12920-018-0462-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357353PMC
January 2019

Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells.

BMC Med Genomics 2019 Jan 31;12(1):29. Epub 2019 Jan 31.

Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.

Background: Glucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease or exacerbations indicates a need to improve ICS actions.

Methods: Glucocorticoid-driven transcriptomes were compared using PrimeView microarrays between primary human bronchial epithelial (HBE) cells and the model cell lines, pulmonary type II A549 and bronchial epithelial BEAS-2B cells. Read More

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http://dx.doi.org/10.1186/s12920-018-0467-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357449PMC
January 2019

Context-sensitive network analysis identifies food metabolites associated with Alzheimer's disease: an exploratory study.

Authors:
Yang Chen Rong Xu

BMC Med Genomics 2019 Jan 31;12(Suppl 1):17. Epub 2019 Jan 31.

Department of Population and Quantitative Health Science, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.

Background: Diet plays an important role in Alzheimer's disease (AD) initiation, progression and outcomes. Previous studies have shown individual food-derived substances may have neuroprotective or neurotoxic effects. However, few works systematically investigate the role of food and food-derived metabolites on the development and progression of AD. Read More

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http://dx.doi.org/10.1186/s12920-018-0459-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357669PMC
January 2019

Identification of long non-coding RNA-related and -coexpressed mRNA biomarkers for hepatocellular carcinoma.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):25. Epub 2019 Jan 31.

Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA.

Background: While changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. Read More

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http://dx.doi.org/10.1186/s12920-019-0472-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357343PMC
January 2019

A robust fuzzy rule based integrative feature selection strategy for gene expression data in TCGA.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):14. Epub 2019 Jan 31.

Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, China.

Background: Lots of researches have been conducted in the selection of gene signatures that could distinguish the cancer patients from the normal. However, it is still an open question on how to extract the robust gene features.

Methods: In this work, a gene signature selection strategy for TCGA data was proposed by integrating the gene expression data, the methylation data and the prior knowledge about cancer biomarkers. Read More

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http://dx.doi.org/10.1186/s12920-018-0451-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357346PMC
January 2019

Detecting virus integration sites based on multiple related sequencing data by VirTect.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):19. Epub 2019 Jan 31.

School of Mathematical Sciences, Peking University, Beijing, 100871, China.

Background: Since tumor often has a high level of intra-tumor heterogeneity, multiple tumor samples from the same patient at different locations or different time points are often sequenced to study tumor intra-heterogeneity or tumor evolution. In virus-related tumors such as human papillomavirus- and Hepatitis B Virus-related tumors, virus genome integrations can be critical driving events. It is thus important to investigate the integration sites of the virus genomes. Read More

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http://dx.doi.org/10.1186/s12920-018-0461-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357354PMC
January 2019
1 Read

Integration of genomic copy number variations and chemotherapy-response biomarkers in pediatric sarcoma.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):23. Epub 2019 Jan 31.

Herman B Wells Center for Pediatric Research, Department of Pediatrics, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA.

Background: While most pediatric sarcomas respond to front-line therapy, some bone sarcomas do not show radiographic response like soft-tissue sarcomas (rhabdomyosarccomas) but do show 90% necrosis. Though, new therapies are urgently needed to improve survival and quality of life in pediatric patients with sarcomas. Complex chromosomal aberrations such as amplifications and deletions of DNA sequences are frequently observed in pediatric sarcomas. Read More

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http://dx.doi.org/10.1186/s12920-018-0456-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357363PMC
January 2019
2.873 Impact Factor

Predicting drug response of tumors from integrated genomic profiles by deep neural networks.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):18. Epub 2019 Jan 31.

Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.

Background: The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent study screened for the response of a thousand human cancer cell lines to a wide collection of anti-cancer drugs and illuminated the link between cellular genotypes and vulnerability. However, due to essential differences between cell lines and tumors, to date the translation into predicting drug response in tumors remains challenging. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0460-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357352PMC
January 2019
2 Reads

A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):27. Epub 2019 Jan 31.

Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710048, China.

Background: Haplotype phasing is an important step in many bioinformatics workflows. In cancer genomics, it is suggested that reconstructing the clonal haplotypes of a tumor sample could facilitate a comprehensive understanding of its clonal architecture and further provide valuable reference in clinical diagnosis and treatment. However, the sequencing data is an admixture of reads sampled from different clonal haplotypes, which complicates the computational problem by exponentially increasing the solution-space and leads the existing algorithms to an unacceptable time-/space- complexity. Read More

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http://dx.doi.org/10.1186/s12920-018-0457-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357344PMC
January 2019

Development of somatic mutation signatures for risk stratification and prognosis in lung and colorectal adenocarcinomas.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):24. Epub 2019 Jan 31.

Department of Complementary & Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.

Background: Prognostic signatures are vital to precision medicine. However, development of somatic mutation prognostic signatures for cancers remains a challenge. In this study we developed a novel method for discovering somatic mutation based prognostic signatures. Read More

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http://dx.doi.org/10.1186/s12920-018-0454-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357362PMC
January 2019

Predict drug sensitivity of cancer cells with pathway activity inference.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):15. Epub 2019 Jan 31.

Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

Background: Predicting cellular responses to drugs has been a major challenge for personalized drug therapy regimen. Recent pharmacogenomic studies measured the sensitivities of heterogeneous cell lines to numerous drugs, and provided valuable data resources to develop and validate computational approaches for the prediction of drug responses. Most of current approaches predict drug sensitivity by building prediction models with individual genes, which suffer from low reproducibility due to biologic variability and difficulty to interpret biological relevance of novel gene-drug associations. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0449-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357358PMC
January 2019
1 Read

Identification of sequence variants associated with severe microtia-astresia by targeted sequencing.

BMC Med Genomics 2019 Jan 28;12(1):28. Epub 2019 Jan 28.

Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China.

Background: Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients.

Methods: We designed a panel of 131 genes associated with external/middle or inner ear deformity. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-019-0475-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348636PMC
January 2019
5 Reads

The added value of WES reanalysis in the field of genetic diagnosis: lessons learned from 200 exomes in the Lebanese population.

BMC Med Genomics 2019 Jan 21;12(1):11. Epub 2019 Jan 21.

Unité de Génétique Médicale, Faculté de Médecine, Campus De l'innovation et du sport, Université Saint-Joseph, rue de Damas, Beirut, Lebanon.

Background: The past few decades have witnessed a tremendous development in the field of genetics. The implementation of next generation sequencing (NGS) technologies revolutionized the field of molecular biology and made the genetic information accessible at a large scale. However, connecting a rare genetic variation to a complex phenotype remains challenging. Read More

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http://dx.doi.org/10.1186/s12920-019-0474-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341681PMC
January 2019
2.873 Impact Factor

A novel gene selection algorithm for cancer classification using microarray datasets.

BMC Med Genomics 2019 Jan 15;12(1):10. Epub 2019 Jan 15.

School of Information Technology, Deakin University, Burwood, 3125, VIC, Australia.

Background: Microarray datasets are an important medical diagnostic tool as they represent the states of a cell at the molecular level. Available microarray datasets for classifying cancer types generally have a fairly small sample size compared to the large number of genes involved. This fact is known as a curse of dimensionality, which is a challenging problem. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0447-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334429PMC
January 2019
5 Reads

Matrix association region/scaffold attachment region: the crucial player in defining the positions of chromosome breaks mediated by bile acid-induced apoptosis in nasopharyngeal epithelial cells.

BMC Med Genomics 2019 Jan 15;12(1). Epub 2019 Jan 15.

Faculty of Medicine and Health Sciences, Department of Paraclinical Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia.

Background: It has been found that chronic rhinosinusitis (CRS) increases the risk of developing nasopharyngeal carcinoma (NPC). CRS can be caused by gastro-oesophageal reflux (GOR) that may reach nasopharynx. The major component of refluxate, bile acid (BA) has been found to be carcinogenic and genotoxic. Read More

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http://dx.doi.org/10.1186/s12920-018-0465-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334432PMC
January 2019
9 Reads

Regulatory network analysis reveals the oncogenesis roles of feed-forward loops and therapeutic target in T-cell acute lymphoblastic leukemia.

BMC Med Genomics 2019 Jan 15;12(1). Epub 2019 Jan 15.

Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, China.

Background: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Aberrant expressed genes contribute to the development and progression of T-ALL. However, the regulation underlying their aberrant expression remains elusive. Read More

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http://dx.doi.org/10.1186/s12920-018-0469-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332896PMC
January 2019
5 Reads

Familial Xp11.22 microdeletion including SHROOM4 and CLCN5 is associated with intellectual disability, short stature, microcephaly and Dent disease: a case report.

BMC Med Genomics 2019 Jan 10;12(1). Epub 2019 Jan 10.

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.

Background: Two interstitial microdeletions Xp11.22 including the CLCN5 and SHROOM4 genes were recently reported in a male individual affected with Dent disease, short stature, psychomotor delay and minor facial anomalies. Dent disease, characterized by a specific renal phenotype, is caused by truncating mutations of CLCN5 in the majority of affected cases. Read More

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http://dx.doi.org/10.1186/s12920-018-0471-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327553PMC
January 2019
4 Reads

Identification of biomarkers for amyotrophic lateral sclerosis by comprehensive analysis of exosomal mRNAs in human cerebrospinal fluid.

BMC Med Genomics 2019 Jan 10;12(1). Epub 2019 Jan 10.

Innovative Biology Laboratories, Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.

Background: Exosomes are a subset of extracellular vesicles 30-200 nm in diameter secreted from cells, which contain functional mRNAs and microRNAs. Cerebrospinal fluid (CSF) is the primary source for liquid biopsy to examine diseases in central nervous system. To date, there is no available method to analyze exosomal mRNAs comprehensively in human CSF. Read More

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http://dx.doi.org/10.1186/s12920-019-0473-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329125PMC
January 2019
4 Reads

Co-occurrence of genomic imbalances on Xp22.1 in the SHOX region and 15q25.2 in a girl with short stature, precocious puberty, urogenital malformations and bone anomalies.

BMC Med Genomics 2019 Jan 9;12(1). Epub 2019 Jan 9.

Laboratory of Human Genetics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy.

Background: Mutations of SHOX represent the most frequent monogenic cause of short stature and related syndromes. The genetic alterations include point mutations and deletions/duplications spanning both SHOX and its regulatory regions, although microrearrangements are confined to either the downstream or upstream enhancers in many patients. Mutations in the heterozygous state have been identified in up to 60-80% of Leri-Weill Dyschondrosteosis (LWD; MIM #127300) and approximately 4-5% of Idiopathic Short Stature (ISS; MIM#300582) patients. Read More

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http://dx.doi.org/10.1186/s12920-018-0445-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327496PMC
January 2019
7 Reads

Correction to: Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

BMC Med Genomics 2019 Jan 9;12(1). Epub 2019 Jan 9.

Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.

ᅟ. Read More

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http://dx.doi.org/10.1186/s12920-018-0464-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325761PMC
January 2019
3 Reads

Association between changes in gene signatures expression and disease activity among patients with systemic lupus erythematosus.

BMC Med Genomics 2019 Jan 9;12(1). Epub 2019 Jan 9.

University of Maryland School of Medicine, Baltimore, MD, USA.

Background: We assessed the stability of BAFF, interferon, plasma cell and LDG neutrophil gene expression signatures over time, and whether changes in expression coincided with changes in SLE disease activity.

Methods: Two hundred forty-three patients with SLE were evaluated for disease activity, serological parameters and peripheral blood gene signatures in clinic visits (2 or more per patient) that occurred between 2009 and 2012. Levels of the BAFF gene transcript, plasma cell signature, Interferon (IFN) signature and the low density granulocytes (LDG)-associated neutrophil gene signature were assessed in PAX-gene-preserved peripheral blood by global microarray. Read More

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http://dx.doi.org/10.1186/s12920-018-0468-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327466PMC
January 2019
1 Read

Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1.

BMC Med Genomics 2019 Jan 9;12(1). Epub 2019 Jan 9.

Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea.

Background: In the absence of antiretroviral treatments (ARTs), a small group of individuals infected with HIV, including long-term non-progressors (LTNPs) who maintain high levels of CD4+ T cells for more than 7-10 years in the absence of ART and in particular a subgroup of LTNPs, elite controllers (ECs), who have low levels of viremia, remain clinically and/or immunologically stable for years. However, the mechanism of stable disease progression in LTNPs and ECs needs to be elucidated to help those infected with HIV-1 remain healthy. In this study, to identify the characteristics of gene expression profiles and biomarkers in LTNPs, we performed a meta-analysis using multiple gene expression profiles among LTNPs, individuals infected with HIV-1 without ART, individuals infected with HIV-1 with ART, and healthy controls. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0443-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325803PMC
January 2019
6 Reads

Comparison of DNA methylation profiles associated with spontaneous preterm birth in placenta and cord blood.

BMC Med Genomics 2019 Jan 3;12(1). Epub 2019 Jan 3.

Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China.

Background: The etiology and mechanism of spontaneous preterm birth (sPTB) are still unclear. Accumulating evidence has documented that various environmental exposure scenarios may cause maternal and fetal epigenetic changes, which initiates the focus on whether epigenetics can contribute to the occurrence of sPTB. Therefore, we conducted the current study to examine and compare the DNA methylation changes associated with sPTB in placenta and cord blood. Read More

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http://dx.doi.org/10.1186/s12920-018-0466-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318854PMC
January 2019
1 Read

Discovering functional impacts of miRNAs in cancers using a causal deep learning model.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):116. Epub 2018 Dec 31.

Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, 5607 Baum Blvd, Pittsburgh, PA, USA.

Background: Micro-RNAs (miRNAs) play a significant role in regulating gene expression under physiological and pathological conditions such as cancers. However, it remains a challenging problem to discover the target messenger RNAs (mRNAs) of a miRNA in a data driven fashion. On one hand, sequence-based methods for predicting miRNA targets tend to make too many false positive calls. Read More

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http://dx.doi.org/10.1186/s12920-018-0432-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311958PMC
December 2018
1 Read

Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer's disease patients.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):115. Epub 2018 Dec 31.

Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN, 46202, USA.

Background: Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies have systematically identified GCNs in multiple brain transcriptomic data of Alzheimer's disease (AD) patients and looked for their specific functions.

Methods: In this study, we first mined GCN modules from AD and normal brain samples in multiple datasets respectively; then identified gene modules that are specific to AD or normal samples; lastly, condition-specific modules with similar functional enrichments were merged and enriched differentially expressed upstream transcription factors were further examined for the AD/normal-specific modules. Read More

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http://dx.doi.org/10.1186/s12920-018-0431-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311927PMC
December 2018
2 Reads

An isomiR expression panel based novel breast cancer classification approach using improved mutual information.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):118. Epub 2018 Dec 31.

Advanced Analytics Institute, Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.

Background: Gene expression-based profiling has been used to identify biomarkers for different breast cancer subtypes. However, this technique has many limitations. IsomiRs are isoforms of miRNAs that have critical roles in many biological processes and have been successfully used to distinguish various cancer types. Read More

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http://dx.doi.org/10.1186/s12920-018-0434-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311920PMC
December 2018
1 Read

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):117. Epub 2018 Dec 31.

Department of Computer Science and Technology, Tongji University, Shanghai, China.

Background: Human cancers are complex ecosystems composed of cells with distinct molecular signatures. Such intratumoral heterogeneity poses a major challenge to cancer diagnosis and treatment. Recent advancements of single-cell techniques such as scRNA-seq have brought unprecedented insights into cellular heterogeneity. Read More

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http://dx.doi.org/10.1186/s12920-018-0433-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311928PMC
December 2018
1 Read

CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):120. Epub 2018 Dec 31.

CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China.

Background: Long noncoding RNAs (lncRNAs) are widely involved in the initiation and development of cancer. Although some computational methods have been proposed to identify cancer-related lncRNAs, there is still a demanding to improve the prediction accuracy and efficiency. In addition, the quick-update data of cancer, as well as the discovery of new mechanism, also underlay the possibility of improvement of cancer-related lncRNA prediction algorithm. Read More

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http://dx.doi.org/10.1186/s12920-018-0436-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311943PMC
December 2018
3 Reads

CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):114. Epub 2018 Dec 31.

CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, People's Republic of China.

Background: Recent studies demonstrated that long non-coding RNAs (lncRNAs) could be intricately implicated in cancer-related molecular networks, and related to cancer occurrence, development and prognosis. However, clinicopathological and molecular features for these cancer-related lncRNAs, which are very important in bridging lncRNA basic research with clinical research, fail to well settle to integration.

Results: After manually reviewing more than 2500 published literature, we collected the cancer-related lncRNAs with the experimental proof of functions. Read More

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http://dx.doi.org/10.1186/s12920-018-0430-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311896PMC
December 2018
2 Reads

Novel link prediction for large-scale miRNA-lncRNA interaction network in a bipartite graph.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):113. Epub 2018 Dec 31.

School of Medicine, Shenzhen University, Shenzhen, 518060, China.

Background: Current knowledge and data on miRNA-lncRNA interactions is still limited and little effort has been made to predict target lncRNAs of miRNAs. Accumulating evidences suggest that the interaction patterns between lncRNAs and miRNAs are closely related to relative expression level, forming a titration mechanism. It could provide an effective approach for characteristic feature extraction. Read More

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http://dx.doi.org/10.1186/s12920-018-0429-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311942PMC
December 2018
1 Read

Improvement of cancer subtype prediction by incorporating transcriptome expression data and heterogeneous biological networks.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):119. Epub 2018 Dec 31.

School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, 710072, China.

Background: Identification of cancer subtypes is of great importance to facilitate cancer diagnosis and therapy. A number of methods have been proposed to integrate multi-sources data to identify cancer subtypes in recent years. However, few of them consider the regulatory associations between genome features and the contribution weights of different data-views in data integration. Read More

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http://dx.doi.org/10.1186/s12920-018-0435-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311915PMC
December 2018
2 Reads
2.873 Impact Factor

Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities.

BMC Med Genomics 2018 Dec 31;11(Suppl 6):112. Epub 2018 Dec 31.

Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, 85721, USA.

Background: Forty-two percent of patients experience disease comorbidity, contributing substantially to mortality rates and increased healthcare costs. Yet, the possibility of underlying shared mechanisms for diseases remains not well established, and few studies have confirmed their molecular predictions with clinical datasets.

Methods: In this work, we integrated genome-wide association study (GWAS) associating diseases and single nucleotide polymorphisms (SNPs) with transcript regulatory activity from expression quantitative trait loci (eQTL). Read More

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http://dx.doi.org/10.1186/s12920-018-0428-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311938PMC
December 2018
1 Read

Analytical validation of a prognostic prostate cancer gene expression assay using formalin fixed paraffin embedded tissue.

BMC Med Genomics 2018 Dec 27;11(1):125. Epub 2018 Dec 27.

Almac Diagnostics Ltd., Craigavon, Northern Ireland, UK.

Background: There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. Read More

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http://dx.doi.org/10.1186/s12920-018-0442-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307209PMC
December 2018
1 Read

Cri-du-chat syndrome mimics Silver-Russell syndrome depending on the size of the deletion: a case report.

BMC Med Genomics 2018 Dec 27;11(1):124. Epub 2018 Dec 27.

Rare Diseases Research Group. Molecular (Epi)Genetics Laboratory, BioAraba Health Research Institute, OSI Araba University Hospital, Vitoria-Gasteiz, Araba, Spain.

Background: Silver-Russell Syndrome (SRS) is a rare growth-related genetic disorder mainly characterized by prenatal and postnatal growth failure. Although molecular causes are not clear in all cases, the most common mechanisms involved in SRS are loss of methylation on chromosome 11p15 (≈50%) and maternal uniparental disomy for chromosome 7 (upd(7)mat) (≈10%).

Case Presentation: We present a girl with clinical suspicion of SRS (intrauterine and postnatal growth retardation, prominent forehead, triangular face, mild psychomotor delay, transient neonatal hypoglycemia, mild hypotonia and single umbilical artery). Read More

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http://dx.doi.org/10.1186/s12920-018-0441-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307281PMC
December 2018
2 Reads

Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability.

BMC Med Genomics 2018 Dec 19;11(1):123. Epub 2018 Dec 19.

Department of Human Genetics and Center for Human Genetics, Laboratory for Cytogenetics and Genome Research, University Hospitals Leuven, KU Leuven, O&N I Herestraat 49 - box 606, 3000, Leuven, Belgium.

Background: The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read massive parallel sequencing approaches do not allow the detection of larger tandem repeat expansions, we hypothesized that such expansions could be a hidden cause of X-linked intellectual disability.

Methods: We selectively captured over 1800 tandem repeats on the X chromosome and characterized them by long read single molecule sequencing in 3 families with idiopathic X-linked intellectual disability. Read More

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http://dx.doi.org/10.1186/s12920-018-0446-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299999PMC
December 2018
2 Reads

A novel PAX5 rearrangement in TCF3-PBX1 acute lymphoblastic leukemia: a case report.

BMC Med Genomics 2018 Dec 18;11(1):122. Epub 2018 Dec 18.

Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.

Background: Chromosome translocations are a hallmark of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Additional genomic aberrations are also crucial in both BCP-ALL leukemogenesis and treatment management. Herein, we report the phenotypic and molecular cytogenetic characterization of an extremely rare case of BCP-ALL harboring two concomitant leukemia-associated chromosome translocations: t(1;19)(q23;q13. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0444-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299517PMC
December 2018
6 Reads

Genetic investigation into an increased susceptibility to biliary atresia in an extended New Zealand Māori family.

BMC Med Genomics 2018 Dec 18;11(1):121. Epub 2018 Dec 18.

Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand.

Background: Biliary atresia (BA), a fibrosing disorder of the developing biliary tract leading to liver failure in infancy, has an elevated incidence in indigenous New Zealand (NZ) Māori. We investigated a high rate of BA in a group of children (n = 12) belonging to a single Māori iwi (or 'tribe', related through a remote ancestor).

Methods: Population and geographical data was used to estimate the rate of BA in Māori sub-groups, and a pedigree linking most of the affected children was constructed from oral and documented history. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0440-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299523PMC
December 2018
5 Reads

Genomics of lipid-laden human hepatocyte cultures enables drug target screening for the treatment of non-alcoholic fatty liver disease.

BMC Med Genomics 2018 Dec 14;11(1):111. Epub 2018 Dec 14.

Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.

Background: Non-alcoholic fatty liver disease (NAFLD) is a major health burden in need for new medication. To identify potential drug targets a genomic study was performed in lipid-laden primary human hepatocyte (PHH) and human hepatoma cell cultures.

Methods: PHH, HuH7 and HepG2 hepatoma cell cultures were treated with lipids and/or TNFα. Read More

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http://dx.doi.org/10.1186/s12920-018-0438-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295111PMC
December 2018
4 Reads

"Omics" data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy.

BMC Med Genomics 2018 Dec 12;11(1):110. Epub 2018 Dec 12.

Colorado Clinical and Translational Sciences Institute, Mail Stop B141, 12401 E. 17th Ave, Aurora, CO, 80045, USA.

Background: Large-scale "omics" datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap.

Methods: We coupled RNA sequence (RNA-Seq) variant detection and transcriptome profiling with pathway analysis to model drug refractory dilated cardiomyopathy (drDCM) using the BaseSpace sequencing hub and Ingenuity Pathway Analysis. Read More

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http://dx.doi.org/10.1186/s12920-018-0439-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292014PMC
December 2018
1 Read

Identification of gene expression profiles in myocardial infarction: a systematic review and meta-analysis.

BMC Med Genomics 2018 Nov 27;11(1):109. Epub 2018 Nov 27.

Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131, Lamia, Greece.

Background: Myocardial infarction (MI) is a multifactorial disease with complex pathogenesis, mainly the result of the interplay of genetic and environmental risk factors. The regulation of thrombosis, inflammation and cholesterol and lipid metabolism are the main factors that have been proposed thus far to be involved in the pathogenesis of MI. Traditional risk-estimation tools depend largely on conventional risk factors but there is a need for identification of novel biochemical and genetic markers. Read More

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http://dx.doi.org/10.1186/s12920-018-0427-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260684PMC
November 2018
1 Read