996 results match your criteria BMC Medical Genomics [Journal]


Young adults' attitudes to sharing whole-genome sequencing information: a university-based survey.

BMC Med Genomics 2019 Apr 16;12(1):55. Epub 2019 Apr 16.

Department of Computer Science, Jubilee Campus, University of Nottingham, Wollaton Road, NG8 1BB, Nottingham, England.

Background: Genomic services are increasingly accessible to young adults starting their independent lives with responsibility for their self-care, yet their attitudes to sharing genomic information remain under-researched. This study explored attitudes of university-based 18-25 year-olds towards sharing personal whole-genome sequencing (WGS) information with relatives.

Methods: We surveyed 112 young adults. Read More

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http://dx.doi.org/10.1186/s12920-019-0499-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469029PMC
April 2019
1 Read

Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer.

BMC Med Genomics 2019 Apr 15;12(1):54. Epub 2019 Apr 15.

Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia.

Background: Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide and in need of novel potential diagnostic biomarkers for early discovery.

Methods: We conducted a two-step study. We first employed bioinformatics on data from The Cancer Genome Atlas to obtain potential biomarkers and then experimentally validated some of them on our clinical samples. Read More

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http://dx.doi.org/10.1186/s12920-019-0501-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466812PMC

Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth.

BMC Med Genomics 2019 Apr 1;12(1):53. Epub 2019 Apr 1.

Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Av. General Flores 2125, C.P, 11800, Montevideo, Uruguay.

Background: Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proven challenging because of the multiple causes of PTB and the numerous maternal and fetal gestational tissues that must interact to facilitate parturition. The transcriptome of the chorioamnion membranes at the site of rupture in PTB and term fetuses may reflect the molecular pathways of preterm labor. Read More

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http://dx.doi.org/10.1186/s12920-019-0498-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444860PMC
April 2019
1 Read

Identification of potential biomarkers related to glioma survival by gene expression profile analysis.

BMC Med Genomics 2019 Mar 20;11(Suppl 7):34. Epub 2019 Mar 20.

Research Center of Translational Imaging, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.

Background: Recent studies have proposed several gene signatures as biomarkers for different grades of gliomas from various perspectives. However, most of these genes can only be used appropriately for patients with specific grades of gliomas.

Methods: In this study, we aimed to identify survival-relevant genes shared between glioblastoma multiforme (GBM) and lower-grade glioma (LGG), which could be used as potential biomarkers to classify patients into different risk groups. Read More

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http://dx.doi.org/10.1186/s12920-019-0479-6DOI Listing

Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma.

BMC Med Genomics 2019 Mar 20;11(Suppl 7):127. Epub 2019 Mar 20.

Department of Computational Biology and Medical Science, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan.

Background: Eukaryotes compact chromosomes densely and non-randomly, forming three-dimensional structures. Alterations of the chromatin structures are often associated with diseases. In particular, aggressive cancer development from the disruption of the humoral immune system presents abnormal gene regulation which is accompanied by chromatin reorganizations. Read More

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http://dx.doi.org/10.1186/s12920-018-0437-8DOI Listing
March 2019
1 Read
2.873 Impact Factor

BasePhasing: a highly efficient approach for preimplantation genetic haplotyping in clinical application of balanced translocation carriers.

BMC Med Genomics 2019 Mar 18;12(1):52. Epub 2019 Mar 18.

Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China.

Background: Preimplantation genetic testing (PGT) has already been applied in chromosomally balanced translocation carriers to improve the clinical outcome of assisted reproduction. However, traditional methods could not further distinguish embryos carrying a translocation from those with a normal karyotype prior to implantation.

Methods: To solve this problem, we developed a method named "Chromosomal Phasing on Base level" (BasePhasing), which based on Infinium Asian Screening Array-24 v1. Read More

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http://dx.doi.org/10.1186/s12920-019-0495-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423798PMC
March 2019
2 Reads

Familial inheritance of the 3q29 microdeletion syndrome: case report and review.

BMC Med Genomics 2019 Mar 18;12(1):51. Epub 2019 Mar 18.

Department of Pediatrics, Division of Clinical Genetics, New York-Presbyterian Morgan Stanley Children's Hospital, Columbia University Medical Center, New York, NY, 10032, USA.

Background: The chromosome 3q29 microdeletion syndrome is characterized by a clinical phenotype that includes behavioral features consistent with autism and attention deficit hyperactivity disorder, mild to moderate developmental delay, language-based learning disabilities, and/or dysmorphic features. In addition, recent data suggest that adults with chromosome 3q29 microdeletions have a significantly increased risk for psychosis and neuropsychiatric phenotypes.

Case Presentation: We report a 3-year-old male with global developmental delay, anemia, and mild dysmorphic facial features. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-019-0497-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421695PMC
March 2019
6 Reads

Mutational load in carotid body tumor.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):39. Epub 2019 Mar 13.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Carotid body tumor (CBT) is a rare neoplasm arising from paraganglion located near the bifurcation of the carotid artery. There is great intra-tumor heterogeneity, and CBT development could be associated with both germline and somatic allelic variants. Studies on the molecular genetics of CBT are limited, and the molecular mechanisms of its pathogenesis are not fully understood. Read More

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http://dx.doi.org/10.1186/s12920-019-0483-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416835PMC
March 2019
3 Reads

Exome, transcriptome and miRNA analysis don't reveal any molecular markers of TKI efficacy in primary CML patients.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):37. Epub 2019 Mar 13.

Laboratory of Mutagenesis, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russian Federation, 115522.

Background: Approximately 5-20% of chronic myeloid leukemia (CML) patients demonstrate primary resistance or intolerance to imatinib. None of the existing predictive scores gives a good prognosis of TKI efficacy. Gene polymorphisms, expression and microRNAs are known to be involved in the pathogenesis of TKI resistance in CML. Read More

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http://dx.doi.org/10.1186/s12920-019-0481-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416830PMC
March 2019
4 Reads

Design and analysis of stably integrated reporters for inducible transgene expression in human T cells and CAR NK-cell lines.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):44. Epub 2019 Mar 13.

Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.

Background: Cytotoxic activity of T- and NK-cells can be efficiently retargeted against cancer cells using chimeric antigen receptors (CARs) and rTCRs. In the context of solid cancers, use of armored CAR T- and NK cells secreting additional anti-cancer molecules such as cytokines, chemokines, antibodies, BiTEs, inverted cytokine receptors, and checkpoint inhibitors, appears particularly promising, as this may help overcome immunosuppressive tumor microenvironment, attract bystander immune cells, and boost CAR T/NK-cell persistence. Placing the expression of such molecules under the transcriptional control downstream of CAR-mediated T/NK-cell activation offers the advantage of targeted delivery, high local concentration, and reduced toxicity. Read More

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http://dx.doi.org/10.1186/s12920-019-0489-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417161PMC

The relationship between the mtDNA copy number in insulin-dependent tissues and markers of endothelial dysfunction and inflammation in obese patients.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):41. Epub 2019 Mar 13.

Immanuel Kant Baltic Federal University, Russian Federation, Kaliningrad, Gaidara 6 st, Russia.

Background: Mitochondria play a central role in the regulation of energy metabolism, and the biogenesis of mitochondria is enhanced by the action of nitric oxide (NO), which is the key signaling molecule in the regulation of vascular homeostasis. A disturbance in the regulation of energy metabolism can be a key reason for the formation of insulin resistance and type 2 diabetes mellitus. Moreover, mitochondrial dysfunction leads to oxidative stress, which increases the production of proinflammatory cytokines. Read More

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-019-0486-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416834PMC
March 2019
12 Reads

Medical genomics research at BGRS-2018.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):36. Epub 2019 Mar 13.

Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.

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http://dx.doi.org/10.1186/s12920-019-0480-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416836PMC

The molecular mechanisms driving physiological changes after long duration space flights revealed by quantitative analysis of human blood proteins.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):45. Epub 2019 Mar 13.

Institute for Biomedical Problems - Russian Federation State Scientific Research Center of RAS, Moscow, Russia.

Background: The conditions of space flight have a significant effect on the physiological processes in the human body, yet the molecular mechanisms driving physiological changes remain unknown.

Methods: Blood samples of 18 Russian cosmonauts who had conducted long-duration missions to the International Space Station were collected 30 days before launch and on the first and seventh days after landing.

Results: A panel of 125 proteins in the blood plasma was quantitated by a well-established and highly regarded targeted mass spectrometry approach. Read More

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http://dx.doi.org/10.1186/s12920-019-0490-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416832PMC
March 2019
1 Read

Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):47. Epub 2019 Mar 13.

Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.

Background: Currently, more than 150 million people worldwide suffer from lymphedema. It is a chronic progressive disease characterized by high-protein edema of various parts of the body due to defects in lymphatic drainage. Molecular-genetic mechanisms of the disease are still poorly understood. Read More

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http://dx.doi.org/10.1186/s12920-019-0492-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417156PMC
March 2019
1 Read

Interrelation of chemerin and TNF-α with mtDNA copy number in adipose tissues and blood cells in obese patients with and without type 2 diabetes.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):40. Epub 2019 Mar 13.

Immanuel Kant Baltic Federal University, Russian Federation, Kaliningrad, Gaidara 6 st, Russia.

Background: Inflammatory response plays a key role in the development of insulin resistance (IR) in obesity. Oxidative stress triggers the replication of the mitochondrial genome and division of the organelle. The purpose of this study was to identify the relationship of chemerin and TNF-α with mitochondrial DNA (mtDNA) copy number in subcutaneous adipose tissue (SAT) and visceral adipose tissue (mesentery of the small intestine (Mes), greater omentum (GO) and blood mononuclear cells (MNCs)) in patients with obesity with/without type 2 diabetes mellitus (T2DM). Read More

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http://dx.doi.org/10.1186/s12920-019-0485-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416837PMC
March 2019
1 Read

The role of long non-coding RNAs in the pathogenesis of hereditary diseases.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):42. Epub 2019 Mar 13.

Research Center for Medical Genetics, Moscow, Russia.

Background: Thousands of long non-coding RNA (lncRNA) genes are annotated in the human genome. Recent studies showed the key role of lncRNAs in a variety of fundamental cellular processes. Dysregulation of lncRNAs can drive tumorigenesis and they are now considered to be a promising therapeutic target in cancer. Read More

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http://dx.doi.org/10.1186/s12920-019-0487-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416829PMC

Immunohistochemical localization of NGF, BDNF, and their receptors in a normal and AMD-like rat retina.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):48. Epub 2019 Mar 13.

Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia.

Background: Age-related macular degeneration (AMD) is a major cause of blindness in developed countries, and the molecular pathogenesis of AMD is poorly understood. A large body of evidence has corroborated the key role of neurotrophins in development, proliferation, differentiation, and survival of retinal cells. Neurotrophin deprivation has been proposed to contribute to retinal-cell death associated with neurodegenerative diseases. Read More

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http://dx.doi.org/10.1186/s12920-019-0493-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417162PMC
March 2019
6 Reads

FTO haplotyping underlines high obesity risk for European populations.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):46. Epub 2019 Mar 13.

Federal Research Center Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Ave, Novosibirsk, Russian Federation, 630090.

Background: Fat mass and obesity-associated (FTO) gene has been under close investigation since the discovery of its high impact on the obesity status in 2007 by a range of publications. Recent report on its implication in adipocytes underscored its molecular and functional mechanics in pathology. Still, the population specific features of the locus structure have not been approached in detail. Read More

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http://dx.doi.org/10.1186/s12920-019-0491-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417164PMC
March 2019
1 Read

Genotype-phenotype correlations in FSHD.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):43. Epub 2019 Mar 13.

Research Center for Medical Genetics, Moscow, Russia.

Background: Facial-scapular-humeral myodystrophy Landouzy-Dejerine (FSHD) is an autosomal dominant disease, the basis of its pathogenesis is ectopic expression of the transcription factor DUX4 in skeletal muscle. There are two types of the disease: FSHD1 (MIM:158900) and FSHD2 (MIM: 158901), which have different genetic causes but are phenotypically indistinguishable. In FSHD1, partial deletion of the D4Z4 repeats on the 4th chromosome affects the expression of DUX4, whereas FSHD2 is caused by the mutations in the protein regulating the methylation status of chromatin - SMCHD1. Read More

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http://dx.doi.org/10.1186/s12920-019-0488-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416831PMC

Clinical aspects of TP53 gene inactivation in diffuse large B-cell lymphoma.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):35. Epub 2019 Mar 13.

Novosibirsk State Medical University, Novosibirsk, Russia.

Background: The knowledge about specific mechanisms generating TP53 dysfunction in diffuse large B-cell lymphoma is limited. The aim of the current study was to comprehensively explore TP53 gene variability resulting from somatic mutations, promoter methylation, and allelic imbalance in tumorous tissue of diffuse large B-cell lymphoma (DLBCL).

Methods: DNA samples from 74 patients with DLBCL were used. Read More

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http://dx.doi.org/10.1186/s12920-019-0484-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416833PMC
March 2019
1 Read

Transcriptome profiling analysis reveals that CXCL2 is involved in anlotinib resistance in human lung cancer cells.

BMC Med Genomics 2019 Mar 13;12(Suppl 2):38. Epub 2019 Mar 13.

Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 Huaihai West Rd, Shanghai, 200030, China.

Background: Anlotinib has been demonstrated its anti-tumor efficacy on non-small cell lung cancer (NSCLC) in clinical trials at 3rd line. However, anlotinib resistance occurs during its administration, and the underlying mechanism is still unclear.

Methods: Anlotinib resistant lung cancer cell line NCI-H1975 was established in vitro. Read More

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http://dx.doi.org/10.1186/s12920-019-0482-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416828PMC
March 2019
4 Reads

Long contiguous stretches of homozygosity detected by chromosomal microarrays (CMA) in patients with neurodevelopmental disorders in the South of Brazil.

BMC Med Genomics 2019 Mar 12;12(1):50. Epub 2019 Mar 12.

Biologist, PhD in Molecular Biology and Genetics, University Professor in the Department of Cell Biology, Embryology and Genetics, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.

Background: Currently, chromosomal microarrays (CMA) are recommended as first-tier test in the investigation of developmental disorders to examine copy number variations. The modern platforms also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH) also named runs of homozygosity (ROH). LCHS are chromosomal segments resulting from complete or segmental chromosomal homozygosity, which may be indicative of uniparental disomy (UPD), consanguinity, as well as replicative DNA repair events, however also are common findings in normal populations. Read More

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http://dx.doi.org/10.1186/s12920-019-0496-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417136PMC
March 2019
1 Read

Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders.

BMC Med Genomics 2019 Mar 7;12(1):49. Epub 2019 Mar 7.

Pediatric Oncology and Hematology Unit "Lalla Seràgnoli", Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Via Massarenti 9, 40138, Bologna, Italy.

Background: The onset of acute Graft-versus-Host Disease (aGvHD) has been correlated with the gut microbiota (GM) composition, but experimental observations are still few, mainly involving cohorts of adult patients. In the current scenario where fecal microbiota transplantation has been used as a pioneer therapeutic approach to treat steroid-refractory aGvHD, there is an urgent need to expand existing observational studies of the GM dynamics in Hematopoietic Stem Cell Transplantation (HSCT). Aim of the present study is to explore the GM trajectory in 36 pediatric HSCT recipients in relation to aGvHD onset. Read More

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http://dx.doi.org/10.1186/s12920-019-0494-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404274PMC

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375196PMC
February 2019
6 Reads

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
5 Reads
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
6 Reads

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
2 Reads

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
5 Reads
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
1 Read

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
7 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
3 Reads

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
1 Read

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
2.873 Impact Factor

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
1 Read

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
2 Reads

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 Reads
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
37 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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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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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
2 Reads

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
1 Read

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
8 Reads

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
7 Reads
2.873 Impact Factor

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
1 Read
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
8 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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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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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
15 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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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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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
13 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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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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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
8 Reads