Articles

Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study

Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no dire...

Authors: Kim Philipp Jablonski, Leopold Carron, Julien Mozziconacci, Thierry Forné, Marc-Thorsten Hütt and Annick Lesne

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders

Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin gene...

Authors: Minh Ho, Brian Thompson, Jeffrey Nicholas Fisk, Daniel W. Nebert, Elspeth A. Bruford, Vasilis Vasiliou and Christopher G. Bunick

Correction to: Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Authors: Shannon Bruse, Michael Moreau, Yana Bromberg, Jun-Ho Jang, Nan Wang, Hongseok Ha, Maria Picchi, Yong Lin, Raymond J. Langley, Clifford Qualls, Julia Klesney-Tait, Joseph Zabner, Shuguang Leng, Jenny Mao, Steven A. Belinsky, Jinchuan Xing…

Identification of a novel signature based on unfolded protein response-related gene for predicting prognosis in bladder cancer

The unfolded protein response (UPR) served as a vital role in the progression of tumors, but the molecule mechanisms of UPR in bladder cancer (BLCA) have been not fully investigated.

Authors: Ke Zhu, Liu Xiaoqiang, Wen Deng, Gongxian Wang and Bin Fu

Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset

Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have...

Authors: Daniel D. Domogala, Tomasz Gambin, Roni Zemet, Chung Wah Wu, Katharina V. Schulze, Yaping Yang, Theresa A. Wilson, Ido Machol, Pengfei Liu and Paweł Stankiewicz

Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease

Genetic variation databases provide invaluable information on the presence and frequency of genetic variants in the ‘untargeted’ human population, aggregated with the primary goal to facilitate the interpretat...

Authors: Vladimir Avramović, Simona Denise Frederiksen, Marjana Brkić and Maja Tarailo-Graovac

Estimating prevalence of human traits among populations from polygenic risk scores

The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause disparities, from variation in environments to divergent population genetic s...

Authors: Britney E. Graham, Brian Plotkin, Louis Muglia, Jason H. Moore and Scott M. Williams

A regulatory miRNA–mRNA network is associated with transplantation response in acute kidney injury

Acute kidney injury (AKI) is a life-threatening complication characterized by rapid decline in renal function, which frequently occurs after transplantation surgery. However, the molecular mechanism underlying...

Authors: Duan Guo, Yu Fan, Ji-Rong Yue and Tao Lin

Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells

In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from...

Authors: Nasna Nassir, Asma Bankapur, Bisan Samara, Abdulrahman Ali, Awab Ahmed, Ibrahim M. Inuwa, Mehdi Zarrei, Seyed Ali Safizadeh Shabestari, Ammar AlBanna, Jennifer L. Howe, Bakhrom K. Berdiev, Stephen W. Scherer, Marc Woodbury-Smith and Mohammed Uddin

RNA-seq driven expression and enrichment analysis to investigate CVD genes with associated phenotypes among high-risk heart failure patients

Heart failure (HF) is one of the most common complications of cardiovascular diseases (CVDs) and among the leading causes of death in the US. Many other CVDs can lead to increased mortality as well. Investigat...

Authors: Zeeshan Ahmed, Saman Zeeshan and Bruce T. Liang

A robust and stable gene selection algorithm based on graph theory and machine learning

Nowadays we are observing an explosion of gene expression data with phenotypes. It enables us to accurately identify genes responsible for certain medical condition as well as classify them for drug target. Li...

Authors: Subrata Saha, Ahmed Soliman and Sanguthevar Rajasekaran

Breast cancer in West Africa: molecular analysis of BRCA genes in early-onset breast cancer patients in Burkina Faso

Breast cancer (BC) is the most commonly diagnosed cancer and the second leading cause of cancer-related deaths among women in Africa after cervical cancer. Even if the epidemiological data are now aligned with...

Authors: Michela Biancolella, Nabonswindé Lamoussa Marie Ouédraogo, Nayi Zongo, Théodora Mahoukèdè Zohoncon, Barbara Testa, Barbara Rizzacasa, Andrea Latini, Chiara Conte, Tégwindé Rebeca Compaore, Charlemagne Marie Rayang-Newendé Ouedraogo, Si Simon Traore, Jacques Simpore and Giuseppe Novelli

Genetic polymorphisms of Vascular Endothelial Growth Factor (VEGF) associated with endometriosis in Nigerian women

To determine if genetic polymorphism of VEGF is associated with the development of endometriosis in Nigerian women.

Authors: Ochuwa Adiketu Babah, Oyesola Oyewole Ojewunmi, Akinniyi Adediran Osuntoki, Melissa A. Simon and Bosede Bukola Afolabi

Phenotypic intrafamilial variability including H syndrome and Rosai–Dorfman disease associated with the same c.1088G > A mutation in the SLC29A3 gene

Mutations in the SLC29A3 gene, which encodes the nucleoside transporter hENT3, have been implicated in syndromic forms of histiocytosis including H syndrome, pigmented hypertrichosis with insulin-dependent diabet...

Authors: Hamza Chouk, Mohamed Ben Rejeb, Lobna Boussofara, Haїfa Elmabrouk, Najet Ghariani, Badreddine Sriha, Ali Saad, Dorra H’Mida and Mohamed Denguezli

Development of the pharmacogenomics and genomics literacy framework for pharmacists

Pharmacists play a unique role in integrating genomic medicine and pharmacogenomics into the clinical practice and to translate pharmacogenomics from bench to bedside. However, the literature suggests that the...

Authors: Azhar T. Rahma, Iffat Elbarazi, Bassam R. Ali, George P. Patrinos, Luai A. Ahmed, Mahanna Elsheik and Fatma Al-Maskari

Seven novel glucose-6-phosphate dehydrogenase (G6PD) deficiency variants identified in the Qatari population

Glucose-6-phosphate dehydrogenase deficiency (G6PDD) is the most common red cell enzymopathy in the world. In Qatar, the incidence of G6PDD is estimated at around 5%; however, no study has investigated the gen...

Authors: Shaza Malik, Roan Zaied, Najeeb Syed, Puthen Jithesh and Mashael Al-Shafai

Protective chromosome 1q32 haplotypes mitigate risk for age-related macular degeneration associated with the CFH-CFHR5 and ARMS2/HTRA1 loci

Single-variant associations with age-related macular degeneration (AMD), one of the most prevalent causes of irreversible vision loss worldwide, have been studied extensively. However, because of a lack of ref...

Authors: Chris M. Pappas, Moussa A. Zouache, Stacie Matthews, Caitlin D. Faust, Jill L. Hageman, Brandi L. Williams, Burt T. Richards and Gregory S. Hageman

Correction to: Update on human genetic susceptibility to COVID-19: susceptibility to virus and response

Authors: Vito Luigi Colona, Vasilis Vasiliou, Jessica Watt, Giuseppe Novelli and Juergen K. V. Reichardt

Evaluation of low-pass genome sequencing in polygenic risk score calculation for Parkinson’s disease

Low-pass sequencing (LPS) has been extensively investigated for applicability to various genetic studies due to its advantages over genotype array data including cost-effectiveness. Predicting the risk of comp...

Authors: Sungjae Kim, Jong-Yeon Shin, Nak-Jung Kwon, Chang-Uk Kim, Changhoon Kim, Chong Sik Lee and Jeong-Sun Seo

Update on human genetic susceptibility to COVID-19: susceptibility to virus and response

Authors: Vito Luigi Colona, Vasilis Vasiliou, Jessica Watt, Giuseppe Novelli and Juergen K. V. Reichardt

Correction to: The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau

Authors: Hadi Charati, Min-Sheng Peng, Wei Chen, Xing-Yan Yang, Roghayeh Jabbari Ori, Mohsen Aghajanpour-Mir, Ali Esmailizadeh and Ya-Ping Zhang

Abnormal expression profile of plasma-derived exosomal microRNAs in patients with treatment-resistant depression

Whether microRNAs (miRNAs) from plasma exosomes might be dysregulated in patients with depression, especially treatment-resistant depression (TRD), remains unclear, based on study of which novel biomarkers and...

Authors: Lian-Di Li, Muhammad Naveed, Zi-Wei Du, Huachen Ding, Kai Gu, Lu-Lu Wei, Ya-Ping Zhou, Fan Meng, Chun Wang, Feng Han, Qi-Gang Zhou and Jing Zhang

Perception of personalized medicine, pharmacogenomics, and genetic testing among undergraduates in Hong Kong

The global development and advancement of genomic medicine in the recent decade has accelerated the implementation of personalized medicine (PM) and pharmacogenomics (PGx) into clinical practice, while catalyz...

Authors: Nicholas Yan Chai Cheung, Jasmine Lee Fong Fung, Yvette Nga Chung Ng, Wilfred Hing Sang Wong, Claudia Ching Yan Chung, Christopher Chun Yu Mak and Brian Hon Yin Chung

Identification of subgroups along the glycolysis-cholesterol synthesis axis and the development of an associated prognostic risk model

Skin cutaneous melanoma (SKCM) is one of the most highly prevalent and complicated malignancies. Glycolysis and cholesterogenesis pathways both play important roles in cancer metabolic adaptations. The main ai...

Authors: Enchong Zhang, Yijing Chen, Shurui Bao, Xueying Hou, Jing Hu, Oscar Yong Nan Mu, Yongsheng Song and Liping Shan

Established and candidate transthyretin amyloidosis variants identified in the Saudi population by data mining

Familial transthyretin (TTR) amyloidosis (ATTR) is an autosomal dominant disease with significant phenotypic heterogeneity. Its prevalence in Saudi Arabia has not previously been investigated. An existing exom...

Authors: Mohamed Abouelhoda, Dania Mohty, Islam Alayary, Brian F. Meyer, Stefan T. Arold, Bahaa M. Fadel and Dorota Monies

A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants

The field of pharmacogenomics focuses on the way a person’s genome affects his or her response to a certain dose of a specified medication. The main aim is to utilize this information to guide and personalize ...

Authors: Maria-Theodora Pandi, Maria Koromina, Iordanis Tsafaridis, Sotirios Patsilinakos, Evangelos Christoforou, Peter J. van der Spek and George P. Patrinos

LncRNA-TUG1 promotes the progression of infantile hemangioma by regulating miR-137/IGFBP5 axis

Previous studies indicated that lncRNA taurine upregulated gene 1 (TUG1) played essential roles in human cancers. This study aimed to investigate its function in infantile hemangioma (IH).

Authors: Lili Zhou, Xiao Jia and Xiangzheng Yang

The limits of clinical findings in similar phenotypes, from Carpenter to ATRX syndrome using a whole exome sequencing approach: a case review

The diagnostic process for uncommon disorders with similar manifestations is complicated and requires newer technology, like gene sequencing for a correct diagnosis.

Authors: Samantha S. Sáenz, Benjamin Arias, Kazuyoshi Hosomichi and Vanessa I. Romero

A comprehensive analysis of copy number variation in a Turkish dementia cohort

Copy number variants (CNVs) include deletions or multiplications spanning genomic regions. These regions vary in size and may span genes known to play a role in human diseases. As examples, duplications and tr...

Authors: Nadia Dehghani, Gamze Guven, Celia Kun-Rodrigues, Catarina Gouveia, Kalina Foster, Hasmet Hanagasi, Ebba Lohmann, Bedia Samanci, Hakan Gurvit, Basar Bilgic, Jose Bras and Rita Guerreiro

Altered splicing associated with the pathology of inflammatory bowel disease

Aberrant splicing of individual genes is a well-known mechanism promoting pathology for a wide range of conditions, but disease is less commonly attributed to global disruption of exon usage. To explore the po...

Authors: Kiera Berger, Hari Somineni, Jarod Prince, Subra Kugathasan and Greg Gibson

Implementation and implications for polygenic risk scores in healthcare

Increasing amounts of genetic data have led to the development of polygenic risk scores (PRSs) for a variety of diseases. These scores, built from the summary statistics of genome-wide association studies (GWA...

Authors: John L. Slunecka, Matthijs D. van der Zee, Jeffrey J. Beck, Brandon N. Johnson, Casey T. Finnicum, René Pool, Jouke-Jan Hottenga, Eco J. C. de Geus and Erik A. Ehli

ACER3-related leukoencephalopathy: expanding the clinical and imaging findings spectrum due to novel variants

Leukodystrophies are the main subgroup of inherited CNS white matter disorders which cause significant mortality and morbidity in early years of life. Diagnosis is mostly based on clinical context and neuroima...

Authors: Ali Zare Dehnavi, Erfan Heidari, Maryam Rasulinezhad, Morteza Heidari, Mahmoud Reza Ashrafi, Mohammad Mahdi Hosseini, Fatemeh Sadeghzadeh, Mohammad-Sadegh Fallah, Noushin Rostampour, Amir Bahraini, Masoud Garshasbi and Ali Reza Tavasoli

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo n...

Authors: Evin M. Padhi, Tristan J. Hayeck, Zhang Cheng, Sumantra Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Benech, Kevin Uguen, Séverine Audebert-Bellanger, Cédric Le Marechal, Claude Férec, Stephanie Efthymiou, Fatima Rahman…

High-throughput screening of circRNAs reveals novel mechanisms of tuberous sclerosis complex-related renal angiomyolipoma

Tuberous sclerosis complex (TSC) is a rare autosomal dominant disease characterized by lesions throughout the body. Our previous study showed the abnormal up-regulation of miRNAs plays an important part in the...

Authors: Yang Zhao, Hao Guo, Wenda Wang, Guoyang Zheng, Zhan Wang, Xu Wang and Yushi Zhang

TMEM263: a novel candidate gene implicated in human autosomal recessive severe lethal skeletal dysplasia

Skeletal dysplasia is a common, clinically and genetically heterogeneous disorder in the human population. An increasing number of different genes are being identified causing this disorder. We used whole exom...

Authors: Mahsa Sadat Asl Mohajeri, Atieh Eslahi, Zeinab Khazaii, Mohammad Reza Moradi, Reza Pazhoomand, Shima Farrokhi, Masoumeh Heidari Feizabadi, Farzaneh Alizadeh and Majid Mojarrad

Performances of NIPT for copy number variations at different sequencing depths using the semiconductor sequencing platform

To evaluate the performance of noninvasive prenatal testing (NIPT) and NIPT-PLUS for the detection of genome-wide microdeletion and microduplication syndromes (MMSs) at different sequencing depths. The NIPT se...

Authors: Jiexia Yang, Jing Wu, Haishan Peng, Yaping Hou, Fangfang Guo, Dongmei Wang, Haoxin Ouyang, Yixia Wang and Aihua Yin

Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome

Trisomy 18 syndrome (Edwards syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18. Aneuploidy is the leading cause of early pregnancy loss, intellectual disability, and multip...

Authors: Xiaofen Qiu, Haiyan Yu, Hongwei Wu, Zhiyang Hu, Jun Zhou, Hua Lin, Wen Xue, Wanxia Cai, Jiejing Chen, Qiang Yan, Weier Dai, Ming Yang, Donge Tang and Yong Dai

Identification of hub genes associated with prognosis, diagnosis, immune infiltration and therapeutic drug in liver cancer by integrated analysis

Liver cancer is one of the most common cancers and causes of cancer death worldwide. The objective was to elucidate novel hub genes which were benefit for diagnosis, prognosis, and targeted therapy in liver cance...

Authors: Xinyi Lei, Miao Zhang, Bingsheng Guan, Qiang Chen, Zhiyong Dong and Cunchuan Wang

HCP5, as the sponge of miR-1291, facilitates AML cell proliferation and restrains apoptosis via increasing PIK3R5 expression

Acute myeloid leukemia (AML) is recognized as a hematological neoplasm with heterogenetic cytology and short-term outcome. HCP5 has been proven to be related with the pathogenesis of AML. However, the underlyi...

Authors: Yan Liu, Xue-Bing Jing, Zhen-Cheng Wang and Qing-Kun Han

Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis

Genetic disposition is considered critical for identifying subjects at high risk for disease development. Investigating disease-causing and high and low expressed genes can support finding the root causes of u...

Authors: Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan and XinQi Dong

Regulatory VCAN polymorphism is associated with shoulder pain and disability in breast cancer survivors

Shoulder morbidity following breast cancer treatment is multifactorial. Despite several treatment- and patient-related factors being implicated, unexplained inter-individual variability exists in the developme...

Authors: Trevor S. Mafu, Alison V. September and Delva Shamley

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