1,228 results match your criteria BMC Med Genomics[Journal]


Genome-wide identification of methylated CpG sites in nongenital cutaneous warts.

BMC Med Genomics 2020 Jul 8;13(1):100. Epub 2020 Jul 8.

Department of Internal Medicine, Jordan University of Science and Technology, Irbid, 22110, Jordan.

Background: Low-risk HPV infection has not been the subject of epigenetic investigation. The present study was carried out in order to investigate the methylation status of CpG sites in non-genital cutaneous warts.

Methods: Genomic DNA was extracted from 24 paired epidermal samples of warts and normal skin. Read More

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http://dx.doi.org/10.1186/s12920-020-00745-6DOI Listing

Mitochondrial GWAS and association of nuclear - mitochondrial epistasis with BMI in T1DM patients.

BMC Med Genomics 2020 Jul 7;13(1):97. Epub 2020 Jul 7.

Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland.

Background: BMI is a strong indicator of complications from type I diabetes, especially under intensive treatment.

Methods: We have genotyped 435 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays and performed mitoGWAS on BMI. Read More

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http://dx.doi.org/10.1186/s12920-020-00752-7DOI Listing

A rare Down syndrome foetus with de novo 21q;21q rearrangements causing false negative results in non-invasive prenatal testing: a case report.

BMC Med Genomics 2020 Jul 6;13(1):96. Epub 2020 Jul 6.

Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.

Background: Non-invasive prenatal testing (NIPT) has been established as a routine prenatal screening to assess the risk of common foetal aneuploidy disorder (trisomy 21, 18, and 13). NIPT has high sensitivity and high specificity, but false positive and false negative results still exist. False negative NIPT results involving Down syndrome are rare, but have a high clinical impact on families and society. Read More

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http://dx.doi.org/10.1186/s12920-020-00751-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7339513PMC

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples.

BMC Med Genomics 2020 Jul 6;13(1):94. Epub 2020 Jul 6.

Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, Ghent, Belgium.

Background: Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. Read More

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http://dx.doi.org/10.1186/s12920-020-00746-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336445PMC

Statistical driver genes as a means to uncover missing heritability for age-related macular degeneration.

BMC Med Genomics 2020 Jul 6;13(1):95. Epub 2020 Jul 6.

Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.

Background: Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h) exist; however, a substantial proportion of h is not attributable to known genomic loci. The International AMD Genomics Consortium (IAMDGC) gathered the largest dataset of advanced AMD (ADV) cases and controls available and identified 34 loci containing 52 independent risk variants defining known AMD h. Read More

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http://dx.doi.org/10.1186/s12920-020-00747-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336430PMC

Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression.

BMC Med Genomics 2020 Jul 3;13(1):92. Epub 2020 Jul 3.

Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.

Background: The role of histone modifications is poorly characterized in breast cancer, especially within the major subtypes. While epigenetic modifications may enhance the adaptability of a cell to both therapy and the surrounding environment, the mechanisms by which this is accomplished remains unclear. In this study we focus on the HER2 subtype and investigate two histone trimethylations that occur on the histone 3; the trimethylation located at lysine 4 (H3K4me3) found in active promoters and the trimethylation located at lysine 27 (H3K27me3) that correlates with gene repression. Read More

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http://dx.doi.org/10.1186/s12920-020-00749-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333309PMC

Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure.

BMC Med Genomics 2020 Jul 3;13(1):93. Epub 2020 Jul 3.

Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China.

Background: Left-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant modules, pivotal genes and candidate regulatory components governing the progression of left-sided HF by bioinformatical analysis. Read More

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http://dx.doi.org/10.1186/s12920-020-00750-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333416PMC

Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes.

BMC Med Genomics 2020 Jun 29;13(1):89. Epub 2020 Jun 29.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA.

Background: Genetic associations link hematopoietic traits and disease end-points, but most causal variants and genes underlying these relationships are unknown. Here, we used genetic colocalization to nominate loci and genes related to shared genetic signal for hematopoietic, cardiovascular, autoimmune, neuropsychiatric, and cancer phenotypes.

Methods: Our aim was to identify colocalization sites for human traits among established genome-wide significant loci. Read More

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http://dx.doi.org/10.1186/s12920-020-00742-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325014PMC

Long non-coding RNA profiling of pediatric Medulloblastoma.

BMC Med Genomics 2020 Jun 26;13(1):87. Epub 2020 Jun 26.

Department of Pediatrics, Hematology and Oncology Division, University of Nebraska Medical Center, Omaha, NE, 986395, USA.

Background: Medulloblastoma (MB) is one of the most common malignant cancers in children. MB is primarily classified into four subgroups based on molecular and clinical characteristics as (1) WNT (2) Sonic-hedgehog (SHH) (3) Group 3 (4) Group 4. Molecular characteristics used for MB classification are based on genomic and mRNAs profiles. Read More

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http://dx.doi.org/10.1186/s12920-020-00744-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318516PMC

Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.

BMC Med Genomics 2020 Jun 26;13(1):85. Epub 2020 Jun 26.

Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala, Sweden.

Background: Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea and the oesophagus, i.e. Read More

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http://dx.doi.org/10.1186/s12920-020-00737-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318369PMC

Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension.

BMC Med Genomics 2020 Jun 26;13(1):86. Epub 2020 Jun 26.

Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China.

Background: Pulmonary arterial hypertension (PAH) is a life-threatening condition. The aim of this study was to explore potential crucial genes and pathways associated with PAH based on integrative analyses of gene expression and to shed light on the identification of biomarker for PAH.

Methods: Gene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). Read More

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http://dx.doi.org/10.1186/s12920-020-00740-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318763PMC

Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer.

BMC Med Genomics 2020 Jun 22;13(1):84. Epub 2020 Jun 22.

Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.

Background: A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains unclear.

Methods: Based on the competitive endogenous RNA (ceRNA) theory, we constructed a lncRNA-miRNA-mRNA network in oral cancer with the human expression profiles GSE74530 from the Gene Expression Omnibus (GEO) database. Read More

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http://dx.doi.org/10.1186/s12920-020-00741-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310129PMC

Leukocyte telomere length in patients with transfusion-dependent thalassemia.

BMC Med Genomics 2020 Jun 1;13(1):73. Epub 2020 Jun 1.

Cardiac Electrophysiology Research and Training Center (CERT Center), Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.

Background: Thalassemia is a hereditary hemolytic anemia with a severity ranging from mild, non-transfusion dependent to severe chronic anemia requiring lifelong transfusion. Transfusional iron overload is a major complication in patients with transfusion-dependent thalassemia (TDT). Telomeres are sequences of nucleotides forming the end caps of chromosomes that act as a DNA repair system. Read More

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http://dx.doi.org/10.1186/s12920-020-00734-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268254PMC
June 2020
2.873 Impact Factor

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts.

BMC Med Genomics 2020 Jun 1;13(1):74. Epub 2020 Jun 1.

Program in Computational Biology and Bioinformatics, Yale University, Whitney Avenue, New Haven, 06520, CT, USA.

Background: As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storage and sharing is Ethereum smart contracts. Ethereum is a blockchain platform, and smart contracts are immutable pieces of code running on virtual machines in this platform that can be invoked by a user or another contract (in the blockchain network). Read More

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http://dx.doi.org/10.1186/s12920-020-00732-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268467PMC

MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.

BMC Med Genomics 2020 Jun 1;13(1):76. Epub 2020 Jun 1.

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden.

Background: The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into smaller areas within a tissue sample, e.g. Read More

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http://dx.doi.org/10.1186/s12920-020-00731-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268502PMC

Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining study.

BMC Med Genomics 2020 Jun 1;13(1):75. Epub 2020 Jun 1.

Faculty of Sciences, El Manar University, Tunis, Tunisia.

Background: Recurrent pregnancy loss (RPL) is a significant adverse pregnancy complication, with an incompletely understood pathology. While many entities were proposed to elucidate the pathogenic basis of RPL, only few were significant enough to warrant investigation in all affected couples.. Read More

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http://dx.doi.org/10.1186/s12920-020-00730-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268288PMC
June 2020
2.873 Impact Factor

Mitochondrial tRNA methylation in Alzheimer's disease and progressive supranuclear palsy.

BMC Med Genomics 2020 May 19;13(1):71. Epub 2020 May 19.

Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.

Background: Methylation of mitochondrial tRNAs (mt-tRNA) at the 9th position ("p9 site") is known to impact translational efficiency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation is challenging. Recent RNA sequence-based methods have been developed to reliably identify post-transcriptional methylation. Though p9 methylation has been studied in healthy human populations and in the context of cancer, it has not yet been analyzed in neurodegenerative disease, where mitochondrial dysfunction is a prominent and early hallmark of disease progression. Read More

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http://dx.doi.org/10.1186/s12920-020-0727-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236490PMC

The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing.

BMC Med Genomics 2020 May 19;13(1):70. Epub 2020 May 19.

Kaiumph Medical Diagnostics Co,Ltd, Beijing, 100102, China.

Background: Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for ID due to high detection rate of copy number variation (CNV).

Methods: To identify an appropriate clinical detection scheme for ID in Han Chinese patients, whole genome low-coverage sequencing was performed as the first-tier diagnostic test, and medical exome sequencing (MES) as the second-tier diagnostic test for patients with negative results of CNVs. Read More

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http://dx.doi.org/10.1186/s12920-020-0726-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236547PMC

ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer.

BMC Med Genomics 2020 May 14;13(1):69. Epub 2020 May 14.

Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.

Background: Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote extensive translocations and copy-number alterations in proximal contact regions through inappropriate DNA stitching. Although studies have proposed models to explain the initiation of chromothripsis, few discussed how TFs influence this process for tumor progression. Read More

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http://dx.doi.org/10.1186/s12920-020-0729-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222439PMC

Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families.

BMC Med Genomics 2020 May 13;13(1):68. Epub 2020 May 13.

Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.

Background: The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, parents could use this information to opt for fetal genotyping in subsequent pregnancies, which could inform decisions about elective termination of pregnancy. The use of NGS diagnostic sequencing in families has not been demonstrated to yield benefit in subsequent pregnancies to reduce recurrence. Read More

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http://dx.doi.org/10.1186/s12920-020-0714-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218834PMC
May 2020
2.873 Impact Factor

MyoMiner: explore gene co-expression in normal and pathological muscle.

BMC Med Genomics 2020 May 11;13(1):67. Epub 2020 May 11.

Sorbonne Université, Inserm, Institut de Myologie, U974, Center for Research in Myology, 47 Boulevard de l'hôpital, 75013, Paris, France.

Background: High-throughput transcriptomics measures mRNA levels for thousands of genes in a biological sample. Most gene expression studies aim to identify genes that are differentially expressed between different biological conditions, such as between healthy and diseased states. However, these data can also be used to identify genes that are co-expressed within a biological condition. Read More

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http://dx.doi.org/10.1186/s12920-020-0712-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216615PMC

Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1.

BMC Med Genomics 2020 May 7;13(1):66. Epub 2020 May 7.

Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.

Background: Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11. Read More

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http://dx.doi.org/10.1186/s12920-020-0728-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206777PMC

Modified entropy-based procedure detects gene-gene-interactions in unconventional genetic models.

BMC Med Genomics 2020 Apr 23;13(1):65. Epub 2020 Apr 23.

Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.

Background: Since it is assumed that genetic interactions play an important role in understanding the mechanisms of complex diseases, different statistical approaches have been suggested in recent years for this task. One interesting approach is the entropy-based IGENT method by Kwon et al. that promises an efficient detection of main effects and interaction effects simultaneously. Read More

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http://dx.doi.org/10.1186/s12920-020-0703-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7181579PMC

Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood.

BMC Med Genomics 2020 Apr 20;13(1):64. Epub 2020 Apr 20.

RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK.

Background: Circular RNAs are non-coding RNA molecules with gene regulatory potential that have been associated with several human diseases. They are stable and present in the circulation, making them excellent candidates for biomarkers of disease. Despite their promise as biomarkers or future therapeutic targets, information on their expression and functionality in human pancreatic islets is a relatively unexplored subject. Read More

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http://dx.doi.org/10.1186/s12920-020-0713-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171860PMC

A case report of familial 4q13.3 microdeletion in three individuals with syndromic intellectual disability.

BMC Med Genomics 2020 Apr 16;13(1):63. Epub 2020 Apr 16.

Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių st. 2, 08661, Vilnius, LT, Lithuania.

Background: Interstitial 4q deletions are rare chromosomal alterations. Most of the previously reported deletions involving the 4q13.3 region are large chromosomal alterations with a common loss of band 4q21 resulting in marked growth restriction, severe intellectual disability, and absent or severely delayed speech. Read More

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http://dx.doi.org/10.1186/s12920-020-0711-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160938PMC

Clinical, cytogenetic, and molecular findings in a patient with ring chromosome 4: case report and literature review.

BMC Med Genomics 2019 11 21;12(1):167. Epub 2019 Nov 21.

Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE. Av. Mariscal Sucre y Av. Mariana de Jesús, Sede Occidental, Bloque I, 2 floor, 170129, Quito, Ecuador.

Background: Since 1969, 49 cases have been presented on ring chromosome 4. All of these cases have been characterized for the loss of genetic material. The genes located in these chromosomal regions are related to the phenotype. Read More

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http://dx.doi.org/10.1186/s12920-019-0614-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087353PMC
November 2019

Prevalence of clinically actionable disease variants in exceptionally long-lived families.

BMC Med Genomics 2020 Apr 10;13(1):61. Epub 2020 Apr 10.

Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 609, 420 Delaware street, Minneapolis, MN, 55455, USA.

Background: Phenotypic expression of pathogenic variants in individuals with no family history of inherited disorders remains unclear.

Methods: We evaluated the prevalence of pathogenic variants in 25 genes associated with Mendelian-inherited disorders in 3015 participants from 485 families in the Long Life Family Study (LLFS). Boot-strapping and Fisher's exact test were used to determine whether allele frequencies in LLFS were significantly different from the allele frequencies reported in publicly available genomic databases. Read More

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http://dx.doi.org/10.1186/s12920-020-0710-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146901PMC

Absolute measurement of the tissue origins of cell-free DNA in the healthy state and following paracetamol overdose.

BMC Med Genomics 2020 Apr 6;13(1):60. Epub 2020 Apr 6.

Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.

Background: Despite the emergence of cell-free DNA (cfDNA) as a clinical biomarker in cancer, the tissue origins of cfDNA in healthy individuals have to date been inferred only by indirect and relative measurement methods, such as tissue-specific methylation and nucleosomal profiling.

Methods: We performed the first direct, absolute measurement of the tissue origins of cfDNA, using tissue-specific knockout mouse strains, in both healthy mice and following paracetamol (APAP) overdose. We then investigated the utility of total cfDNA and the percentage of liver-specific cfDNA as clinical biomarkers in patients presenting with APAP overdose. Read More

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http://dx.doi.org/10.1186/s12920-020-0705-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133021PMC

E. coli diversity: low in colorectal cancer.

BMC Med Genomics 2020 Apr 6;13(1):59. Epub 2020 Apr 6.

Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.

Background: Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. Read More

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http://dx.doi.org/10.1186/s12920-020-0704-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133007PMC
April 2020
2.873 Impact Factor

Comprehensive chromosomal aberrations in a case of a patient with TCF3-HLF-positive BCP-ALL.

BMC Med Genomics 2020 Apr 3;13(1):58. Epub 2020 Apr 3.

Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland.

Background: The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. Read More

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http://dx.doi.org/10.1186/s12920-020-0709-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118981PMC

Convolutional neural network models for cancer type prediction based on gene expression.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):44. Epub 2020 Apr 3.

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

Background: Precise prediction of cancer types is vital for cancer diagnosis and therapy. Through a predictive model, important cancer marker genes can be inferred. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that can potentially bias the identification of cancer markers. Read More

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http://dx.doi.org/10.1186/s12920-020-0677-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119277PMC

Comparative evaluation of network features for the prediction of breast cancer metastasis.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):40. Epub 2020 Apr 3.

Department of Computer Science, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA.

Background: Discovering a highly accurate and robust gene signature for the prediction of breast cancer metastasis from gene expression profiling of primary tumors is one of the most challenging tasks to reduce the number of deaths in women. Due to the limited success of gene-based features in achieving satisfactory prediction accuracy, many methodologies have been proposed in recent years to develop network-based features by integrating network information with gene expression. However, evaluation results are inconsistent to confirm the effectiveness of network-based features, because of many confounding factors involved in classification model learning process, such as data normalization, dimension reduction, and feature selection. Read More

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http://dx.doi.org/10.1186/s12920-020-0676-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119280PMC

Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer's disease.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):53. Epub 2020 Apr 3.

Department of BioHealth Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA.

Background: Alzheimer's disease (AD) is one of the leading causes of death in the US and there is no validated drugs to stop, slow or prevent AD. Despite tremendous effort on biomarker discovery, existing findings are mostly individual biomarkers and provide limited insights into the transcriptomic decoupling underlying AD. We propose to explore the gene co-expression patterns in multiple AD stages, including cognitively normal (CN), early mild cognitive impairment (EMCI), late MCI and AD. Read More

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http://dx.doi.org/10.1186/s12920-020-0689-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118822PMC

SCNrank: spectral clustering for network-based ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):50. Epub 2020 Apr 3.

Department of Biomedical informatics, College of medicine, the Ohio State University, Columbus, OH, 43210, USA.

Background: Pancreatic ductal adenocarcinoma (PDAC) is the most common pancreatic malignancy. Due to its wide heterogeneity, PDAC acts aggressively and responds poorly to most chemotherapies, causing an urgent need for the development of new therapeutic strategies. Cell lines have been used as the foundation for drug development and disease modeling. Read More

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http://dx.doi.org/10.1186/s12920-020-0681-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119297PMC

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):39. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

Background: Cleft lip with or without cleft palate (CL/P) is one of the most common congenital human birth defects. A combination of genetic and epidemiology studies has contributed to a better knowledge of CL/P-associated candidate genes and environmental risk factors. However, the etiology of CL/P remains not fully understood. Read More

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http://dx.doi.org/10.1186/s12920-020-0675-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118807PMC

Highly robust model of transcription regulator activity predicts breast cancer overall survival.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):49. Epub 2020 Apr 3.

Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

Background: While several multigene signatures are available for predicting breast cancer prognosis, particularly in early stage disease, effective molecular indicators are needed, especially for triple-negative carcinomas, to improve treatments and predict diagnostic outcomes. The objective of this study was to identify transcriptional regulatory networks to better understand mechanisms giving rise to breast cancer development and to incorporate this information into a model for predicting clinical outcomes.

Methods: Gene expression profiles from 1097 breast cancer patients were retrieved from The Cancer Genome Atlas (TCGA). Read More

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http://dx.doi.org/10.1186/s12920-020-0688-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118819PMC

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):47. Epub 2020 Apr 3.

Department of internal medicine, comprehensive cancer center, University of New Mexico, Albuquerque, NM, 87131, USA.

In this editorial, we briefly summarized the International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019) that was held on June 9-11, 2019 at Columbus, Ohio, USA. We further introduced the 19 research articles included in this supplement issue, covering four major areas, namely computational method development, genomics analysis, network-based analysis and biomarker prediction. The selected papers perform cutting edge computational research applied to a broad range of human diseases such as cancer, neural degenerative and chronic inflammatory disease. Read More

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http://dx.doi.org/10.1186/s12920-020-0678-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119270PMC

ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):52. Epub 2020 Apr 3.

Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China.

Background: Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Read More

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http://dx.doi.org/10.1186/s12920-020-0683-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118832PMC

Prediction of circRNA-disease associations based on inductive matrix completion.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):42. Epub 2020 Apr 3.

Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China.

Background: Currently, numerous studies indicate that circular RNA (circRNA) is associated with various human complex diseases. While identifying disease-related circRNAs in vivo is time- and labor-consuming, a feasible and effective computational method to predict circRNA-disease associations is worthy of more studies.

Results: Here, we present a new method called SIMCCDA (Speedup Inductive Matrix Completion for CircRNA-Disease Associations prediction) to predict circRNA-disease associations. Read More

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http://dx.doi.org/10.1186/s12920-020-0679-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118830PMC

A pan-cancer study of class-3 semaphorins as therapeutic targets in cancer.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):45. Epub 2020 Apr 3.

Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH, 43210, USA.

Background: Initially characterized as axon guidance factors, semaphorins also have been implicated to have critical roles in multiple physiological and developmental functions, including the regulation of immune responses, angiogenesis, organ formation, and the etiology of multiple forms of cancer. Moreover, their contribution in immunity and the regulation of tumour microenvironment is becoming increasingly recognized. Here, we provide a comprehensive analysis of class-3 semaphorins, the only secreted family of genes among veterbrate semaphorins, in terms of their expression profiles and their association with patient survival. Read More

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http://dx.doi.org/10.1186/s12920-020-0682-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118829PMC

Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):46. Epub 2020 Apr 3.

College of Public Health, Division of Biostatistics, The Ohio State University, 1841 Neil Ave., 208E Cunz Hall, Columbus, OH 43210, US.

Background: With the development of next generation sequencing (NGS) technology and genotype imputation methods, statistical methods have been proposed to test a set of genomic variants together to detect if any of them is associated with the phenotype or disease. In practice, within the set, there is an unknown proportion of variants truly causal or associated with the disease. There is a demand for statistical methods with high power in both dense and sparse scenarios, where the proportion of causal or associated variants is large or small respectively. Read More

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http://dx.doi.org/10.1186/s12920-020-0684-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118831PMC

Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):41. Epub 2020 Apr 3.

Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

Background: Recent advances in kernel-based Deep Learning models have introduced a new era in medical research. Originally designed for pattern recognition and image processing, Deep Learning models are now applied to survival prognosis of cancer patients. Specifically, Deep Learning versions of the Cox proportional hazards models are trained with transcriptomic data to predict survival outcomes in cancer patients. Read More

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http://dx.doi.org/10.1186/s12920-020-0686-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118823PMC

Somatic synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):43. Epub 2020 Apr 3.

Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China.

Background: Non-synonymous mutations altering tumor suppressor genes and oncogenes are widely studied. However, synonymous mutations, which do not alter the protein sequence, are rarely investigated in melanoma genome studies.

Methods: We explored the role of somatic synonymous mutations in melanoma samples from TCGA (The Cancer Genome Atlas). Read More

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http://dx.doi.org/10.1186/s12920-020-0685-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119296PMC

The landscape of alternative splicing in HIV-1 infected CD4 T-cells.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):38. Epub 2020 Apr 3.

Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA.

Background: Elucidating molecular mechanisms that are altered during HIV-1 infection may provide a better understanding of the HIV-1 life cycle and how it interacts with infected T-cells. One such mechanism is alternative splicing (AS), which has been studied for HIV-1 itself, but no systematic analysis has yet been performed on infected T-cells. We hypothesized that AS patterns in infected T-cells may illuminate the molecular mechanisms underlying HIV-1 infection and identify candidate molecular markers for specifically targeting infected T-cells. Read More

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http://dx.doi.org/10.1186/s12920-020-0680-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118826PMC

Dense module searching for gene networks associated with multiple sclerosis.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):48. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

Background: Multiple sclerosis (MS) is a complex disease in which the immune system attacks the central nervous system. The molecular mechanisms contributing to the etiology of MS remain poorly understood. Genome-wide association studies (GWAS) of MS have identified a small number of genetic loci significant at the genome level, but they are mainly non-coding variants. Read More

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http://dx.doi.org/10.1186/s12920-020-0674-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118851PMC

Pseudogene-gene functional networks are prognostic of patient survival in breast cancer.

BMC Med Genomics 2020 Apr 3;13(Suppl 5):51. Epub 2020 Apr 3.

Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.

Background: Given the vast range of molecular mechanisms giving rise to breast cancer, it is unlikely universal cures exist. However, by providing a more precise prognosis for breast cancer patients through integrative models, treatments can become more individualized, resulting in more successful outcomes. Specifically, we combine gene expression, pseudogene expression, miRNA expression, clinical factors, and pseudogene-gene functional networks to generate these models for breast cancer prognostics. Read More

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http://dx.doi.org/10.1186/s12920-020-0687-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118805PMC

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model.

BMC Med Genomics 2020 Mar 30;13(1):56. Epub 2020 Mar 30.

Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA.

Background: The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at identifying disease-associated miRNA-mRNA pairs. Hierarchical integrative models (HIM) offer the opportunity to uncover the relationships between disease and the levels of different molecules measured in multiple omic studies. Read More

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http://dx.doi.org/10.1186/s12920-020-0706-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106691PMC

Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma.

BMC Med Genomics 2020 Mar 30;13(1):57. Epub 2020 Mar 30.

Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.

Background: As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during the advanced stage of the disease and exhibits a low five-year survival rate. The importance of tumor microenvironment (TME) in tumor initiation and metastasis is widely recognized. In addition, accumulating evidence indicates that long non-coding RNA (lncRNA) is involved in crosstalk between TME and tumor cells. Read More

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http://dx.doi.org/10.1186/s12920-020-0707-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104528PMC

Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases.

BMC Med Genomics 2020 Mar 29;13(1):55. Epub 2020 Mar 29.

Genome Medical Science Project (Toyama), National Center for for Global Health and Medicine, Tokyo, Japan.

Background: Copy number variants (CNVs) have been reported to be associated with diseases, traits, and evolution. However, it is hard to determine which gene should have priority as a target for further functional experiments if a CNV is rare or a singleton. In this study, we attempted to overcome this issue by using two approaches: by assessing the influences of gene dosage sensitivity and gene expression sensitivity. Read More

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http://dx.doi.org/10.1186/s12920-020-0699-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104509PMC

Potential role of genomic imprinted genes and brain developmental related genes in autism.

BMC Med Genomics 2020 03 26;13(1):54. Epub 2020 Mar 26.

Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.

Background: Autism is a complex disease involving both environmental and genetic factors. Recent efforts have implicated the correlation of genomic imprinting and brain development in autism, however the pathogenesis of autism is not completely clear. Here, we used bioinformatic tools to provide a comprehensive analysis of the autism-related genes, genomic imprinted genes and the spatially and temporally differentially expressed genes of human brain, aiming to explore the relationship between autism, brain development and genomic imprinting. Read More

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http://dx.doi.org/10.1186/s12920-020-0693-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099798PMC