Articles

NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer

The accurate screening of tumor genomic landscapes for somatic mutations using high-throughput sequencing involves a crucial step in precise clinical diagnosis and targeted therapy. However, the complex inhere...

Authors: Irantzu Anzar, Angelina Sverchkova, Richard Stratford and Trevor Clancy

Identification of potential biomarkers for diagnosis of pancreatic and biliary tract cancers by sequencing of serum microRNAs

Pancreatic and biliary tract cancer (PC and BTC, respectively) are difficult to diagnose because of their clinical characteristics; however, recent studies suggest that serum microRNAs (miRNAs) might be the ke...

Authors: Kwondo Kim, DongAhn Yoo, Hee Seung Lee, Kyong Joo Lee, Soo Been Park, Chanyang Kim, Jung Hyun Jo, Dawoon E. Jung and Si Young Song

Alternative cleavage and polyadenylation of genes associated with protein turnover and mitochondrial function are deregulated in Parkinson’s, Alzheimer’s and ALS disease

Transcriptome wide changes have been assessed extensively during the progression of neurodegenerative diseases. Alternative polyadenylation (APA) occurs in over 70% of human protein coding genes and it has rec...

Authors: Radhika Patel, Cillian Brophy, Mark Hickling, Jonathan Neve and André Furger

Systematic characterization of germline variants from the DiscovEHR study endometrial carcinoma population

Endometrial cancer (EMCA) is the fifth most common cancer among women in the world. Identification of potentially pathogenic germline variants from individuals with EMCA will help characterize genetic features...

Authors: Jason E. Miller, Raghu P. Metpally, Thomas N. Person, Sarathbabu Krishnamurthy, Venkata Ramesh Dasari, Manu Shivakumar, Daniel R. Lavage, Adam M. Cook, David J. Carey, Marylyn D. Ritchie, Dokyoon Kim and Radhika Gogoi

Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection

Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric ...

Authors: Mark H. Kaplan, Mark Kaminski, Judith M. Estes, Scott D. Gitlin, Joseph Zahn, James T. Elder, Trilokraj Tejasvi, Elizabeth Gensterblum, Amr H. Sawalha, Joseph Patrick McGowan, Michael H. Dosik, Haner Direskeneli, Guher Saruhan Direskeneli, Sally N. Adebamowo, Clement A. Adebamowo, Mohammad Sajadi…

LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients

To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients.

Authors: Xiongfa Liang, Yongchang Lai, Weizhou Wu, Dong Chen, Fangling Zhong, Jian Huang, Tao Zeng, Xiaolu Duan, Yapeng Huang, Shike Zhang, Shujue Li and Wenqi Wu

Sequencing and curation strategies for identifying candidate glioblastoma treatments

Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and ...

Authors: Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Esra Dikoglu, Sadia Rahman, Alice Fang, Vladimir Vacic, Ewa A. Bergmann…

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

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...

Authors: Pepita Barnard, Sarah Sharples, Brian J. Thomson and Jonathan M. Garibaldi

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

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.

Authors: Nina Hauptman, Daša Jevšinek Skok, Elena Spasovska, Emanuela Boštjančič and Damjan Glavač

Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth

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 syndro...

Authors: Silvana Pereyra, Claudio Sosa, Bernardo Bertoni and Rossana Sapiro

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

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 devel...

Authors: Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai

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

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 speci...

Authors: Justin Bo-Kai Hsu, Tzu-Hao Chang, Gilbert Aaron Lee, Tzong-Yi Lee and Cheng-Yu Chen

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

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 ...

Authors: Shuo Zhang, Dingding Zhao, Jun Zhang, Yan Mao, Lingyin Kong, Yueping Zhang, Bo Liang, Xiaoxi Sun and Congjian Xu

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

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 devel...

Authors: Wahab A. Khan, Ninette Cohen, Stuart A. Scott and Elaine M. Pereira

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

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 o...

Authors: Darya V. Telegina, Nataliya G. Kolosova and Oyuna S. Kozhevnikova

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

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 draina...

Authors: Olga V. Saik, Vadim V. Nimaev, Dilovarkhuja B. Usmonov, Pavel S. Demenkov, Timofey V. Ivanisenko, Inna N. Lavrik and Vladimir A. Ivanisenko

FTO haplotyping underlines high obesity risk for European populations

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 a...

Authors: Vladimir Babenko, Roman Babenko, Junaid Gamieldien and Arcady Markel

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

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.

Authors: Daria N. Kashirina, Andrew J. Percy, Liudmila Kh. Pastushkova, Christoph H. Borchers, Kirill S. Kireev, Vladimir A. Ivanisenko, Alexey S. Kononikhin, Eugene N. Nikolaev and Irina M. Larina

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

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 s...

Authors: Sergey V. Kulemzin, Daria A. Matvienko, Artur H. Sabirov, Arpine M. Sokratyan, Daria S. Chernikova, Tatyana N. Belovezhets, Anton N. Chikaev, Aleksandr V. Taranin and Andrey A. Gorchakov

Genotype-phenotype correlations in FSHD

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 ar...

Authors: Nikolay Zernov and Mikhail Skoblov

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

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 dri...

Authors: Peter Sparber, Alexandra Filatova, Mira Khantemirova and Mikhail Skoblov

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

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...

Authors: Larisa Litvinova, Pavel Zatolokin, Maria Vulf, Ilia Mazunin and Daria Skuratovskaia

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

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...

Authors: Daria Skuratovskaia, Pavel Zatolokin, Maria Vulf, Ilia Mazunin and Larisa Litvinova

Mutational load in carotid body tumor

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 ...

Authors: Anna V. Kudryavtseva, Elena N. Lukyanova, Dmitry V. Kalinin, Andrew R. Zaretsky, Anatoly V. Pokrovsky, Alexander L. Golovyuk, Maria S. Fedorova, Elena A. Pudova, Sergey L. Kharitonov, Vladislav S. Pavlov, Anastasiya A. Kobelyatskaya, Nataliya V. Melnikova, Alexey A. Dmitriev, Andrey P. Polyakov, Boris Y. Alekseev, Marina V. Kiseleva…

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

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 ...

Authors: Jun Lu, Wei Xu, Jie Qian, Shuyuan Wang, Bo Zhang, Lele Zhang, Rong Qiao, Minjuan Hu, Yiming Zhao, Xiaodong Zhao and Baohui Han

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

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 pol...

Authors: Alexander V. Lavrov, Ekaterina Yu. Chelysheva, Elmira P. Adilgereeva, Oleg A. Shukhov, Svetlana A. Smirnikhina, Konstantin S. Kochergin-Nikitsky, Valentina D. Yakushina, Grigory A. Tsaur, Sergey V. Mordanov, Anna G. Turkina and Sergey I. Kutsev

Medical genomics research at BGRS-2018

Authors: Ancha V. Baranova, Vadim V. Klimontov, Andrey Y. Letyagin and Yuriy L. Orlov

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

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 so...

Authors: Elena N. Voropaeva, Tatyana I. Pospelova, Mikhail I. Voevoda, Vladimir N. Maksimov, Yuriy L. Orlov and Olga B. Seregina

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

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 singl...

Authors: Tiago Fernando Chaves, Luan Freitas Oliveira, Maristela Ocampos, Ingrid Tremel Barbato, Gisele Rozone de Luca, Jorge Humbeto Barbato Filho, Louise Lapagesse de Camargo Pinto, Pricila Bernardi and Angelica Francesca Maris

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

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 th...

Authors: Elena Biagi, Daniele Zama, Simone Rampelli, Silvia Turroni, Patrizia Brigidi, Clarissa Consolandi, Marco Severgnini, Eleonora Picotti, Pietro Gasperini, Pietro Merli, Nunzia Decembrino, Marco Zecca, Simone Cesaro, Maura Faraci, Arcangelo Prete, Franco Locatelli…

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

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. Although di...

Authors: Marwan M. Refaat, Sylvana Hassanieh, Jad A. Ballout, Patrick Zakka, Mostafa Hotait, Athar Khalil, Fadi Bitar, Mariam Arabi, Samir Arnaout, Hadi Skouri, Antoine Abchee, Bernard Abi-Saleh, Maurice Khoury, Andreas Massouras and Georges Nemer

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

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 h...

Authors: Miguel Nava, Pranabananda Dutta, Nathan R. Zemke, Robin Farias-Eisner, Jaydutt V. Vadgama and Yanyuan Wu

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

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 chroni...

Authors: Felicity Newell, Kalpana Patel, Michael Gartside, Lutz Krause, Sandra Brosda, Lauren G. Aoude, Kelly A. Loffler, Vanessa F. Bonazzi, Ann-Marie Patch, Stephen H. Kazakoff, Oliver Holmes, Qinying Xu, Scott Wood, Conrad Leonard, Guy Lampe, Reginald V. Lord…

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

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 sem...

Authors: Marta Olszewska, Ewa Wiland, Nataliya Huleyuk, Monika Fraczek, Alina T. Midro, Danuta Zastavna and Maciej Kurpisz

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

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 di...

Authors: Mahmoud M. Mostafa, Christopher F. Rider, Suharsh Shah, Suzanne L. Traves, Paul M. K. Gordon, Anna Miller-Larsson, Richard Leigh and Robert Newton

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

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 underst...

Authors: Yixuan Wang, Xuanping Zhang, Shuai Ding, Yu Geng, Jianye Liu, Zhongmeng Zhao, Rong Zhang, Xiao Xiao and Jiayin Wang

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

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 li...

Authors: Xueyan Zhao, Xin Geng, Vinodh Srinivasasainagendra, Ninad Chaudhary, Suzanne Judd, Virginia Wadley, Orlando M. Gutiérrez, Henry Wang, Ethan M. Lange, Leslie A. Lange, Daniel Woo, Frederick W. Unverzagt, Monika Safford, Mary Cushman, Nita Limdi, Rakale Quarells…

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

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 n...

Authors: Fan Zhang, Linda Ding, Li Cui, Robert Barber and Bin Deng

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

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 ...

Authors: Mark Menor, Yong Zhu, Yu Wang, Jicai Zhang, Bin Jiang and Youping Deng

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

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 ...

Authors: Lijun Cheng, Pankita H. Pandya, Enze Liu, Pooja Chandra, Limei Wang, Mary E. Murray, Jacquelyn Carter, Michael Ferguson, Mohammad Reza Saadatzadeh, Khadijeh Bijangi-Visheshsaraei, Mark Marshall, Lang Li, Karen E. Pollok and Jamie L. Renbarger

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

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...

Authors: Alice Djotsa Nono, Ken Chen and Xiaoming Liu

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

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 exam...

Authors: William Z. D. Zeng, Benjamin S. Glicksberg, Yangyan Li and Bin Chen

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

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, ...

Authors: Degui Zhi, Zhongming Zhao, Fuhai Li, Zhijin Wu, Xiaoming Liu and Kai Wang

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

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-heterogene...

Authors: Yuchao Xia, Yun Liu, Minghua Deng and Ruibin Xi

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

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. How...

Authors: Yang Chen and Rong Xu

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

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 ...

Authors: Aimin Li, Guimin Qin, Akiko Suzuki, Mona Gajera, Junichi Iwata, Peilin Jia and Zhongming Zhao

Predict drug sensitivity of cancer cells with pathway activity inference

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,...

Authors: Xuewei Wang, Zhifu Sun, Michael T. Zimmermann, Andrej Bugrim and Jean-Pierre Kocher

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

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 fe...

Authors: Shicai Fan, Jianxiong Tang, Qi Tian and Chunguo Wu

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

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...

Authors: Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee and Kwangsik Nho

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

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 ...

Authors: Fang Shi, Yao Yao, Yannan Bin, Chun-Hou Zheng and Junfeng Xia