Articles

Correction to: Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities

Authors: Tesfaye B. Mersha and Tilahun Abebe

Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, ...

Authors: Liron Ganel, Lei Chen, Ryan Christ, Jagadish Vangipurapu, Erica Young, Indraniel Das, Krishna Kanchi, David Larson, Allison Regier, Haley Abel, Chul Joo Kang, Alexandra Scott, Aki Havulinna, Charleston W. K. Chiang, Susan Service, Nelson Freimer…

Predicting anticancer hyperfoods with graph convolutional networks

Recent efforts in the field of nutritional science have allowed the discovery of disease-beating molecules within foods based on the commonality of bioactive food molecules to FDA-approved drugs. The pioneerin...

Authors: Guadalupe Gonzalez, Shunwang Gong, Ivan Laponogov, Michael Bronstein and Kirill Veselkov

Genome-based therapeutic interventions for β-type hemoglobinopathies

For decades, various strategies have been proposed to solve the enigma of hemoglobinopathies, especially severe cases. However, most of them seem to be lagging in terms of effectiveness and safety. So far, the...

Authors: Kariofyllis Karamperis, Maria T. Tsoumpeli, Fotios Kounelis, Maria Koromina, Christina Mitropoulou, Catia Moutinho and George P. Patrinos

Correction to: An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses

Authors: Anastasios A. Tsonis, Geli Wang, Lvyi Zhang, Wenxu Lu, Aristotle Kayafas and Katia Del Rio-Tsonis

Epigenetics and microRNAs in UGT1As

UDP-glucuronosyltransferases (UGTs) are the main phase II drug-metabolizing enzymes mediating the most extensive glucuronidation-binding reaction in the human body. The UGT1A family is involved in more than ha...

Authors: Cui-Lan Meng, Wei Zhao and Dan-Ni Zhong

Initial study on TMPRSS2 p.Val160Met genetic variant in COVID-19 patients

Coronavirus disease 2019 (COVID-19) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 widely varies from asymptomatic infection to severe pneumonia and...

Authors: Laksmi Wulandari, Berliana Hamidah, Cennikon Pakpahan, Nevy Shinta Damayanti, Neneng Dewi Kurniati, Christophorus Oetama Adiatmaja, Monica Rizky Wigianita, Soedarsono, Dominicus Husada, Damayanti Tinduh, Cita Rosita Sigit Prakoeswa, Anang Endaryanto, Ni Nyoman Tri Puspaningsih, Yasuko Mori, Maria Inge Lusida, Kazufumi Shimizu…

Whole genome sequencing reveals a frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease

Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a hi...

Authors: Víctor Raggio, Nicolas Dell’Oca, Camila Simoes, Alejandra Tapié, Conrado Medici, Gonzalo Costa, Soledad Rodriguez, Gonzalo Greif, Estefania Garrone, María Laura Rovella, Virgina Gonzalez, Margarita Halty, Gabriel González, Jong-Yeon Shin, Sang-Yoon Shin, Changhoon Kim…

COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy

COVID-19 has engulfed the world and it will accompany us all for some time to come. Here, we review the current state at the milestone of 1 year into the pandemic, as declared by the WHO (World Health Organiza...

Authors: Giuseppe Novelli, Michela Biancolella, Ruty Mehrian-Shai, Vito Luigi Colona, Anderson F. Brito, Nathan D. Grubaugh, Vasilis Vasiliou, Lucio Luzzatto and Juergen K. V. Reichardt

An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses

Mathematical approaches have been for decades used to probe the structure of nucleotide sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is ap...

Authors: Anastasios A. Tsonis, Geli Wang, Lvyi Zhang, Wenxu Lu, Aristotle Kayafas and Katia Del Rio-Tsonis

The transcriptome profile of human trisomy 21 blood cells

Trisomy 21 (T21) is a genetic alteration characterised by the presence of an extra full or partial human chromosome 21 (Hsa21) leading to Down syndrome (DS), the most common form of intellectual disability (ID...

Authors: Francesca Antonaros, Rossella Zenatelli, Giulia Guerri, Matteo Bertelli, Chiara Locatelli, Beatrice Vione, Francesca Catapano, Alice Gori, Lorenza Vitale, Maria Chiara Pelleri, Giuseppe Ramacieri, Guido Cocchi, Pierluigi Strippoli, Maria Caracausi and Allison Piovesan

Cathelicidin antimicrobial peptide (CAMP) gene promoter methylation induces chondrocyte apoptosis

The occurrence of osteoarthritis is related to genetic and environmental factors. Among them, the change of chondrocyte gene expression pattern regulated by epigenetic modification is an important participant....

Authors: Guoliang Wang, Yanlin Li, Guang Yang, Tengyun Yang, Lu He and Yang Wang

An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients

Psoriasis is an immune-mediated, inflammatory disorder of the skin with chronic inflammation and hyper-proliferation of the epidermis. Since psoriasis has genetic components and the diseased tissue of psoriasi...

Authors: Suyan Tian and Chi Wang

Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis

Currently, Chlamydia trachomatis–specific host defense mechanisms in humans remain poorly defined. To study the characteristics of host cells infected early with Chlamydia trachomatis, we used bioinformatics meth...

Authors: Guo-Dong Zhu, Xun-Jie Cao, Ya-Ping Li, Jia-Xin Li, Zi-Jian Leng, Li-Min Xie and Xu-Guang Guo

Targeted exome sequencing identifies mutational landscape in a cohort of 1500 Chinese patients with non-small cell lung carcinoma (NSCLC)

Non-small cell lung carcinoma (NSCLC) is one of the most common human cancers, comprising approximately 80–85% of all lung carcinomas. An estimated incidence of NSCLC is approximately 2 million new cases per y...

Authors: Ya-jun Zhou, Wei Zheng, Qing-hua Zeng, Yang Ye, Ce Wang, Cheng Fang, Chao-jun Liu, Li Niu and Li-ming Wu

How to design a national genomic project—a systematic review of active projects

An increasing number of countries are investing efforts to exploit the human genome, in order to improve genetic diagnostics and to pave the way for the integration of precision medicine into health systems. T...

Authors: Anja Kovanda, Ana Nyasha Zimani and Borut Peterlin

Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability

Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insig...

Authors: Xi Long and Hong Xue

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people’s health and social order. To better explore the infection mechanism and treatment, the three-dimens...

Authors: Ke-Ying Fang, Wen-Chao Cao, Tian-Ao Xie, Jie Lv, Jia-Xin Chen, Xun-Jie Cao, Zhong-Wei Li, Shu-Ting Deng and Xu-Guang Guo

Genetic and molecular biology of autism spectrum disorder among Middle East population: a review

Autism spectrum disorder (ASD) is a neurodevelopmental disease, characterized by impaired social communication, executive dysfunction, and abnormal perceptual processing. It is more frequent among males. All o...

Authors: Zahra Rahmani, Mohammad Reza Fayyazi Bordbar, Mohsen Dibaj, Maliheh Alimardani and Meysam Moghbeli

Ethical issues in genomics research on neurodevelopmental disorders: a critical interpretive review

Genomic research on neurodevelopmental disorders (NDDs), particularly involving minors, combines and amplifies existing research ethics issues for biomedical research. We performed a review of the literature o...

Authors: S. Mezinska, L. Gallagher, M. Verbrugge and E.M. Bunnik

C-X-C motif chemokine 16, modulated by microRNA-545, aggravates myocardial damage and affects the inflammatory responses in myocardial infarction

Myocardial infarction (MI), a common type of coronary heart disease, is the major cause of morbidity and mortality around the world. Chemokine-mediated inflammatory cell infiltration and local inflammatory dam...

Authors: Fang-Qian Liang, Jing-Yuan Gao and Ji-Wei Liu

cfDNA deconvolution via NIPT of a pregnant woman after bone marrow transplant and donor egg IVF

Cell-free DNA is known to be a mixture of DNA fragments originating from various tissue types and organs of the human body and can be utilized for several clinical applications and potentially more to be creat...

Authors: Jianjiang Zhu, Feng Hui, Xuequn Mao, Shaoqin Zhang, Hong Qi and Yang Du

Standardized nomenclature and open science in Human Genomics

Authors: Vasilis Vasiliou, Kirill Veselkov, Elspeth Bruford and Juergen K. V. Reichardt

The Human Genome Organisation (HUGO) and the 2020 COVID-19 pandemic

This letter is the Human Genome Organisation’s summary reaction to the 2020 COVID-19 pandemic. It identifies key areas for genomics research, and areas in which genomic scientists can contribute to a global re...

Authors: Benjamin Capps, Yann Joly, John Mulvihill and Won Bok Lee

Pathogenic convergence of CNVs in genes functionally associated to a severe neuromotor developmental delay syndrome

Complex developmental encephalopathy syndromes might be the consequence of unknown genetic alterations that are likely to contribute to the full neurological phenotype as a consequence of pathogenic gene combi...

Authors: Juan L. García-Hernández, Luis A. Corchete, Íñigo Marcos-Alcalde, Paulino Gómez-Puertas, Carmen Fons and Pedro A. Lazo

Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data

The severity of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly heterogeneous. Studies have reported that males and some ethnic groups a...

Authors: Jianchang Hu, Cai Li, Shiying Wang, Ting Li and Heping Zhang

Convergent lines of evidence support BIN1 as a risk gene of Alzheimer’s disease

Genome-wide association studies (GWAS) have identified several susceptibility loci of Alzheimer’s disease (AD), which were mainly located in noncoding regions of the genome. Meanwhile, the putative biological ...

Authors: Jin Zhu, Xia Liu, Hongtao Yin, Yan Gao and Hao Yu

ACE2 Nascence, trafficking, and SARS-CoV-2 pathogenesis: the saga continues

With the emergence of the novel coronavirus SARS-CoV-2 since December 2019, more than 65 million cases have been reported worldwide. This virus has shown high infectivity and severe symptoms in some cases, lea...

Authors: Sally Badawi and Bassam R. Ali

High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may ...

Authors: Weitong Cui, Huaru Xue, Lei Wei, Jinghua Jin, Xuewen Tian and Qinglu Wang

Genetic risk factors for autoimmune hepatitis: implications for phenotypic heterogeneity and biomarkers for drug response

Autoimmune hepatitis (AIH) is a rare chronic progressive liver disease with autoimmune features. It mainly affects middle-aged women. AIH is occasionally complicated with liver cirrhosis that worsens the progn...

Authors: Takashi Higuchi, Shomi Oka, Hiroshi Furukawa, Shigeto Tohma, Hiroshi Yatsuhashi and Kiyoshi Migita

Screening of disease-related biomarkers related to neuropathic pain (NP) after spinal cord injury (SCI)

Based on the molecular expression level, this paper compares lncRNA and mRNA expressions respectively in peripheral blood samples of the patients after SCI with NP and without NP, and screens disease-related b...

Authors: Jia Zhao, Li Yang, Limin Huang and Zinan Li

Correction to: Hyperinsulinism associated with GLUD1 mutation: allosteric regulation and functional characterization of p.G446V glutamate dehydrogenase

An amendment to this paper has been published and can be accessed via the original article.

Authors: Karolina Luczkowska, Caroline Stekelenburg, Frédérique Sloan-Béna, Emmanuelle Ranza, Giacomo Gastaldi, Valérie Schwitzgebel and Pierre Maechler

Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients

Functional disruptions by large germline genomic structural variants in susceptible genes are known risks for cancer. We used deletion structural variants (DSVs) generated from germline whole-genome sequencing...

Authors: Peng-Chan Lin, Hui-O Chen, Chih-Jung Lee, Yu-Min Yeh, Meng-Ru Shen and Jung-Hsien Chiang

Alu retrotransposons and COVID-19 susceptibility and morbidity

SARS-CoV-2 has spread rapidly across the world and is negatively impacting the global human population. COVID-19 patients display a wide variety of symptoms and clinical outcomes, including those attributed to...

Authors: Manci Li, Luca Schifanella and Peter A. Larsen

Network machine learning maps phytochemically rich “Hyperfoods” to fight COVID-19

In this paper, we introduce a network machine learning method to identify potential bioactive anti-COVID-19 molecules in foods based on their capacity to target the SARS-CoV-2-host gene-gene (protein-protein) ...

Authors: Ivan Laponogov, Guadalupe Gonzalez, Madelen Shepherd, Ahad Qureshi, Dennis Veselkov, Georgia Charkoftaki, Vasilis Vasiliou, Jozef Youssef, Reza Mirnezami, Michael Bronstein and Kirill Veselkov

COVID-19 update: the first 6 months of the pandemic

The COVID-19 pandemic is sweeping the world and will feature prominently in all our lives for months and most likely for years to come. We review here the current state 6 months into the declared pandemic. Spe...

Authors: Giuseppe Novelli, Michela Biancolella, Ruty Mehrian-Shai, Caroline Erickson, Krystal J. Godri Pollitt, Vasilis Vasiliou, Jessica Watt and Juergen K. V. Reichardt

A rational approach to COVID-19

It is crucial to use the wealth of information emerging from the ongoing SARS-CoV-2 pandemic and confront COVID-19 with a rational approach. There are proactive steps to prevent and fight COVID-19. Management ...

Authors: Ruty Mehrian-Shai

The haplotypes of various TNF related genes associated with scleritis in Chinese Han

Several studies have stated that TNF-α participates in the pathogenesis of scleritis, but also in several systemic autoimmune diseases and vasculitis, of which some are associated with scleritis. Earlier GWAS ...

Authors: Yingnan Gao, Liping Du, Fuzhen Li, Jiadong Ding, Geng Li, Qingfeng Cao, Na Li, Guannan Su, Aize Kijlstra and Peizeng Yang

KVarPredDB: a database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses

Germline variants of ten keratin genes (K1, K2, K5, K6A, K6B, K9, K10, K14, K16, and K17) have been reported for causing different types of genodermatoses with an autosomal dominant mode of inheritance. Among all...

Authors: Yuyi Ying, Lu Lu, Santasree Banerjee, Lizhen Xu, Qiang Zhao, Hao Wu, Ruiqi Li, Xiao Xu, Hua Yu, Dante Neculai, Yongmei Xi, Fan Yang, Jiale Qin and Chen Li

Pathogenic variants identified by whole-exome sequencing in 43 patients with epilepsy

Epilepsy is a group of neurological disorders characterized by recurrent epileptic seizures. Epilepsy is affected by many factors, approximately 20–30% of cases are caused by acquired conditions, but in the re...

Authors: Linlin Zhang, Jinshuang Gao, Hailiang Liu, Yuan Tian, Xiaoli Zhang, Wei Lei, Ying Li, Yaqing Guo, Haiyang Yu, Erfeng Yuan, Lisi Liang, Shihong Cui and Xiaoan Zhang

Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine appl...

Authors: Fatemeh Khodabandehloo, Sara Taleahmad, Reza Aflatoonian, Farzad Rajaei, Zahra Zandieh, Marjan Nassiri-Asl and Mohamadreza Baghaban Eslaminejad

Correction to: The social, economic, political, and genetic value of race and ethnicity in 2020

An amendment to this paper has been published and can be accessed via the original article.

Authors: Tesfaye B. Mersha and Andrew F. Beck

Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder

Mitochondrial folate enzyme ALDH1L2 (aldehyde dehydrogenase 1 family member L2) converts 10-formyltetrahydrofolate to tetrahydrofolate and CO₂ simultaneously producing NADPH. We have recently reported that the la...

Authors: Natalia I. Krupenko, Jaspreet Sharma, Peter Pediaditakis, Kristi L. Helke, Madeline S. Hall, Xiuxia Du, Susan Sumner and Sergey A. Krupenko

Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity

The emergence of the novel coronavirus in Wuhan, Hubei Province, China, in December 2019 marked the synchronization of the world to a peculiar clock that is counting infected cases and deaths instead of hours ...

Authors: Cleo Anastassopoulou, Zoi Gkizarioti, George P. Patrinos and Athanasios Tsakris

Mild dyserythropoiesis and β-like globin gene expression imbalance due to the loss of histone chaperone ASF1B

The expression of the human β-like globin genes follows a well-orchestrated developmental pattern, undergoing two essential switches, the first one during the first weeks of gestation (ε to γ), and the second ...

Authors: Petros Papadopoulos, Athanassia Kafasi, Iris M. De Cuyper, Vilma Barroca, Daniel Lewandowski, Zahra Kadri, Martijn Veldthuis, Jeffrey Berghuis, Nynke Gillemans, Celina María Benavente Cuesta, Frank G. Grosveld, Rob van Zwieten, Sjaak Philipsen, Muriel Vernet, Laura Gutiérrez and George P. Patrinos

A miR-182 variant and risk of hepatocellular carcinoma in a southern Chinese population

MicroRNAs (miRNAs) play important roles in the regulation of gene expression at the posttranscriptional level and are involved in human carcinogenesis. The aim of the current study was to investigate the assoc...

Authors: Moqin Qiu, Yingchun Liu, Qiuling Lin, Zihan Zhou, Yanji Jiang, Rongrui Huo, Xiumei Liang, Xiangyuan Yu, Ji Cao, Xianguo Zhou and Hongping Yu

The social, economic, political, and genetic value of race and ethnicity in 2020

Disparities across racial and ethnic groups are present for a range of health outcomes. In this opinion piece, we consider the origin of racial and ethnic groupings, a history that highlights the sociopolitica...

Authors: Tesfaye B. Mersha and Andrew F. Beck

Evaluation of a genetic risk score for severity of COVID-19 using human chromosomal-scale length variation

The course of COVID-19 varies from asymptomatic to severe in patients. The basis for this range in symptoms is unknown. One possibility is that genetic variation is partly responsible for the highly variable r...

Authors: Christopher Toh and James P. Brody

Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis

Precision medicine aims to empower clinicians to predict the most appropriate course of action for patients with complex diseases like cancer, diabetes, cardiomyopathy, and COVID-19. With a progressive interpr...

Authors: Zeeshan Ahmed

Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development

MicroRNAs are ~ 22-nucleotide-long biological modifiers that act as the post-transcriptional modulator of gene expression. Some of them are identified to be embedded within the introns of protein-coding genes,...

Authors: Abul Bashar Mir Md. Khademul Islam, Eusra Mohammad and Md. Abdullah-Al-Kamran Khan