Articles

Transcriptome profiling reveals significant changes in the gastric muscularis externa with obesity that partially overlap those that occur with idiopathic gastroparesis

Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the s...

Authors: B. Paul Herring, Meng Chen, Plamen Mihaylov, April M. Hoggatt, Anita Gupta, Attila Nakeeb, Jennifer N. Choi and John M. Wo

Retrovirus insertion site analysis of LGL leukemia patient genomes

Large granular lymphocyte (LGL) leukemia is an uncommon cancer characterized by sustained clonal proliferation of LGL cells. Antibodies reactive to retroviruses have been documented in the serum of patients wi...

Authors: Weiling Li, Lei Yang, Robert S. Harris, Lin Lin, Thomas L. Olson, Cait E. Hamele, David J. Feith, Thomas P. Loughran Jr and Mary Poss

A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

The availability and generation of large amounts of genomic data has led to the development of a new paradigm in cancer treatment emphasizing a precision approach at the molecular and genomic level. Statistica...

Authors: Joshua D. Mannheimer, Dawn L. Duval, Ashok Prasad and Daniel L. Gustafson

Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue

RNA-seq is poised to play a major role in the management of kidney transplant patients. Rigorous definition of housekeeping genes (HKG) is essential for further progress in this field. Using single genes or a ...

Authors: Zijie Wang, Zili Lyu, Ling Pan, Gang Zeng and Parmjeet Randhawa

Prenatal identification of partial 3q duplication syndrome

The 3q duplication syndrome is a result of duplication of a large fragment of the long arm of chromosome 3, mainly 3q21-qter, and in most cases it is diagnosed only after birth. The phenotypic consequences res...

Authors: Magdalena Pasińska, Rafał Adamczak, Anna Repczyńska, Ewelina Łazarczyk, Barbara Iskra, Agata Klaudia Runge and Olga Haus

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients....

Authors: Avantika Lal, Daniele Ramazzotti, Ziming Weng, Keli Liu, James M. Ford and Arend Sidow

Unbalanced segregation of a paternal t(9;11)(p24.3;p15.4) translocation causing familial Beckwith-Wiedemann syndrome: a case report

The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy...

Authors: Caroline Lekszas, Indrajit Nanda, Barbara Vona, Julia Böck, Farah Ashrafzadeh, Nahid Donyadideh, Farnoosh Ebrahimzadeh, Najmeh Ahangari, Reza Maroofian, Ehsan Ghayoor Karimiani and Thomas Haaf

Entropy of mitochondrial DNA circulating in blood is associated with hepatocellular carcinoma

Ultra-Deep Sequencing (UDS) enabled identification of specific changes in human genome occurring in malignant tumors, with current approaches calling for the detection of specific mutations associated with cer...

Authors: David S. Campo, Vishal Nayak, Ganesh Srinivasamoorthy and Yury Khudyakov

African KhoeSan ancestry linked to high-risk prostate cancer

Genetic diversity is greatest within Africa, in particular the KhoeSan click-speaking peoples of southern Africa. South African populations represent admixture fractions including differing degrees of African,...

Authors: Desiree C. Petersen, Weerachai Jaratlerdsiri, Abraham van Wyk, Eva K. F. Chan, Pedro Fernandez, Ruth J. Lyons, Shingai B. A. Mutambirw, Andre van der Merwe, Philip A. Venter, William Bates, M. S. Riana Bornman and Vanessa M. Hayes

Targeted next generation sequencing as a tool for precision medicine

Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential ...

Authors: Markus Gulilat, Tyler Lamb, Wendy A. Teft, Jian Wang, Jacqueline S. Dron, John F. Robinson, Rommel G. Tirona, Robert A. Hegele, Richard B. Kim and Ute I. Schwarz

Hepatic transcriptomic signatures of statin treatment are associated with impaired glucose homeostasis in severely obese patients

Clinical data identified an association between the use of HMG-CoA reductase inhibitors (statins) and incident diabetes in patients with underlying diabetes risk factors such as obesity, hypertension and dysli...

Authors: Daniel Margerie, Philippe Lefebvre, Violeta Raverdy, Uwe Schwahn, Hartmut Ruetten, Philip Larsen, Alain Duhamel, Julien Labreuche, Dorothée Thuillier, Bruno Derudas, Céline Gheeraert, Hélène Dehondt, Quentin Dhalluin, Jérémy Alexandre, Robert Caiazzo, Pamela Nesslany…

Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole c...

Authors: Yanding Zhao, Robert Carter, Sivaraman Natarajan, Frederick S. Varn, Duane A. Compton, Charles Gawad, Chao Cheng and Kristina M. Godek

Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

Presently, a 50-gene expression model (PAM50) serves as a breast cancer (BC) subtype classifier that is insufficient to distinguish, within each single PAM50-classified subtype, patient subpopulations having d...

Authors: J. Astor Ankney, Ling Xie, John A. Wrobel, Li Wang and Xian Chen

Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells

The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic in...

Authors: Atsushi Hattori, Kohji Okamura, Yumiko Terada, Rika Tanaka, Yuko Katoh-Fukui, Yoichi Matsubara, Keiko Matsubara, Masayo Kagami, Reiko Horikawa and Maki Fukami

Increased diagnostic yield by reanalysis of data from a hearing loss gene panel

Congenital hearing loss affects approximately 1–2 infants out of every 1000, with 50% of the cases resulting from genetic factors. Targeted gene panels have been widely used for genetic diagnosis of hearing lo...

Authors: Yu Sun, Jiale Xiang, Yidong Liu, Sen Chen, Jintao Yu, Jiguang Peng, Zijing Liu, Lisha Chen, Jun Sun, Yun Yang, Yaping Yang, Yulin Zhou and Zhiyu Peng

DNA methylation status of TBX20 in patients with tetralogy of Fallot

TBX20 plays an important role in heart development; however, its epigenetic regulation in the pathogenesis of tetralogy of Fallot (TOF) remains unclear.

Authors: Juan Gong, Wei Sheng, Duan Ma, Guoying Huang and Fang Liu

Comprehensive analysis of key genes and microRNAs in radioresistant nasopharyngeal carcinoma

Radioresistance is one of the main obstacle limiting the therapeutic efficacy and prognosis of patients, the molecular mechanisms of radioresistance is still unclear. The purpose of this study was to identify ...

Authors: Ya Guo, Yang Zhang, Shu Juan Zhang, Yi Nan Ma and Yun He

DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se

Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genom...

Authors: C. F. Nicoletti, M. A. S. Pinhel, A. Diaz-Lagares, F. F. Casanueva, A. Jácome, V. C. Pinhanelli, B. A. P. de Oliveira, A. B. Crujeiras and C. B. Nonino

Histamine H4 receptor gene polymorphisms: a potential contributor to Meniere disease

The immune system is likely involved in the pathophysiology of Meniere’s disease (MD). However, its role of patients with MD has not been well studied. Given that histamine H4 receptors are highly expressed in...

Authors: Danxia Qin, Han Zhang, Jiehua Wang and Zhuquan Hong

Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population

Tick-borne encephalitis (TBE) is a viral infectious disease caused by tick-borne encephalitis virus (TBEV). TBEV infection is responsible for a variety of clinical manifestations ranging from mild fever to sev...

Authors: Elena V. Ignatieva, Andrey A. Yurchenko, Mikhail I. Voevoda and Nikolay S. Yudin

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes hav...

Authors: Mona Gajera, Neha Desai, Akiko Suzuki, Aimin Li, Musi Zhang, Goo Jun, Peilin Jia, Zhongming Zhao and Junichi Iwata

Exploiting orthology and de novo transcriptome assembly to refine target sequence information

The ability to generate recombinant drug target proteins is important for drug discovery research as it facilitates the investigation of drug-target-interactions in vitro. To accomplish this, the target’s exac...

Authors: Julia F. Söllner, Germán Leparc, Matthias Zwick, Tanja Schönberger, Tobias Hildebrandt, Kay Nieselt and Eric Simon

Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report

Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF).

Authors: Angélica Martínez-Hernández, Julieta Larrosa, Francisco Barajas-Olmos, Humberto García-Ortíz, Elvia C. Mendoza-Caamal, Cecilia Contreras-Cubas, Elaheh Mirzaeicheshmeh, José Luis Lezana and Lorena Orozco

Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC

Chemoresistance is a primary clinical challenge for the management of small cell lung cancer. Additionally, transcriptional regulation by super enhancer (SE) has an important role in tumor evolution. The funct...

Authors: Jiarong Bao, Man Li, Shumei Liang, Yunchu Yang, Jingfang Wu, Qingqing Zou, Shun Fang, Size Chen and Linlang Guo

Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing

In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a maj...

Authors: Justin E. Ideozu, Vittobai Rangaraj, Hiam Abdala-Valencia, Xi Zhang, Manoj Kandpal, Marc A. Sala, Ramana V. Davuluri and Hara Levy

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

Following publication of the original article [1], the authors reported that Fig. 1 was not correctly processed during the production process. The correct Fig. 1 is given below.

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

Impact of cancer mutational signatures on transcription factor motifs in the human genome

Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large...

Authors: Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils and Carl Herrmann

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

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 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

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

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