Articles

Constructing cancer patient-specific and group-specific gene networks with multi-omics data

Cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. The same treatment for patients of the same cancer type often results in different outcomes in terms of effica...

Authors: Wook Lee, De-Shuang Huang and Kyungsook Han

A machine learning framework for genotyping the structural variations with copy number variant

Genotyping of structural variation is an important computational problem in next generation sequence data analysis. However, in cancer genomes, the copy number variant(CNV) often coexists with other types of s...

Authors: Tian Zheng, Xiaoyan Zhu, Xuanping Zhang, Zhongmeng Zhao, Xin Yi, Jiayin Wang and Hongle Li

A novel neoantigen discovery approach based on chromatin high order conformation

High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify ...

Authors: Yi Shi, Mingxuan Zhang, Luming Meng, Xianbin Su, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lintai Da, Tom Weidong Cai, Guang He and Ze-Guang Han

Association of blood pressure with cognitive function at midlife: a Mendelian randomization study

Whether high blood pressure has a causal effect on cognitive function as early as middle age is unclear. We investigated whether high blood pressure (BP) causally impairs cognitive function at midlife using Me...

Authors: Daokun Sun, Emy A. Thomas, Lenore J. Launer, Stephen Sidney, Kristine Yaffe and Myriam Fornage

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture...

Authors: Thomas W. Winkler, Felix Grassmann, Caroline Brandl, Christina Kiel, Felix Günther, Tobias Strunz, Lorraine Weidner, Martina E. Zimmermann, Christina A. Korb, Alicia Poplawski, Alexander K. Schuster, Martina Müller-Nurasyid, Annette Peters, Franziska G. Rauscher, Tobias Elze, Katrin Horn…

Unraveling the molecular heterogeneity in type 2 diabetes: a potential subtype discovery followed by metabolic modeling

Type 2 diabetes mellitus (T2DM) is a complex multifactorial disease with a high prevalence worldwide. Insulin resistance and impaired insulin secretion are the two major abnormalities in the pathogenesis of T2...

Authors: Maryam Khoshnejat, Kaveh Kavousi, Ali Mohammad Banaei-Moghaddam and Ali Akbar Moosavi-Movahedi

HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma

DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC).

Authors: Hui He, Di Chen, Shimeng Cui, Gang Wu, Hailong Piao, Xun Wang, Peng Ye and Shi Jin

Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives

In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes. Typically, hapl...

Authors: Qing Li, Yan Mao, Shaoying Li, Hongzi Du, Wenzhi He, Jianchun He, Lingyin Kong, Jun Zhang, Bo Liang and Jianqiao Liu

Breast and prostate cancers harbor common somatic copy number alterations that consistently differ by race and are associated with survival

Pan-cancer studies of somatic copy number alterations (SCNAs) have demonstrated common SCNA patterns across cancer types, but despite demonstrable differences in aggressiveness of some cancers by race, pan-can...

Authors: Yalei Chen, Sudha M. Sadasivan, Ruicong She, Indrani Datta, Kanika Taneja, Dhananjay Chitale, Nilesh Gupta, Melissa B. Davis, Lisa A. Newman, Craig G. Rogers, Pamela L. Paris, Jia Li, Benjamin A. Rybicki and Albert M. Levin

Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes

Parkinson’s Disease (PD) and Hutchinson-Gilford Progeria Syndrome (HGPS) are two heterogeneous disorders, which both display molecular and clinical alterations associated with the aging process. However, simil...

Authors: Diana M. Hendrickx and Enrico Glaab

Clinical, genomics and networking analyses of a high-altitude native American Ecuadorian patient with congenital insensitivity to pain with anhidrosis: a case report

Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder characterized by insensitivity to pain, inability to sweat and intellectual disability. CIPA is caused ...

Authors: Andrés López-Cortés, Ana Karina Zambrano, Patricia Guevara-Ramírez, Byron Albuja Echeverría, Santiago Guerrero, Eliana Cabascango, Andy Pérez-Villa, Isaac Armendáriz-Castillo, Jennyfer M. García-Cárdenas, Verónica Yumiceba, Gabriela Pérez-M, Paola E. Leone and César Paz-y-Miño

Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development

Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the ...

Authors: Rong Wei, Ziyue Wang, Yaping Zhang, Bin Wang, Ningning Shen, Li E, Xin Li, Lifang Shang, Yangwei Shang, Wenpeng Yan, Xiaoqin Zhang, Wenxia Ma and Chen Wang

Fusion transcript detection using spatial transcriptomics

Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high sp...

Authors: Stefanie Friedrich and Erik L. L. Sonnhammer

A novel use for Levey-Jennings charts in prenatal molecular diagnosis

The goal of this study was to determine whether Levey-Jennings charts, which are widely used in clinical laboratories, can be used to create standardized internal quality controls (IQCs) for prenatal molecular...

Authors: Binghuan Weng, Ya-li Xu, Jun Ying, Hao-kun Yang, Lan Su, Yan-mei Yang and Min Chen

Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma

Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exa...

Authors: Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani and Mohammad Amin Kerachian

Analysis of exosomal circRNAs upon irradiation in pancreatic cancer cell repopulation

Pancreatic cancer is one of the most malignant tumors. However, radiotherapy can lead to tumor recurrence, which is caused by the residual surviving cells repopulation stimulated by some molecular released fro...

Authors: Yi-yun Chen, Ming-jie Jiang and Ling Tian

Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics

We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workf...

Authors: Marie Engvall, Nicola Cahill, Britt-Inger Jonsson, Martin Höglund, Helene Hallböök and Lucia Cavelier

Characterization of genetic and phenotypic heterogeneity of obstructive sleep apnea using electronic health records

Obstructive sleep apnea (OSA) is defined by frequent episodes of reduced or complete cessation of airflow during sleep and is linked to negative health outcomes. Understanding the genetic factors influencing e...

Authors: Olivia J. Veatch, Christopher R. Bauer, Brendan T. Keenan, Navya S. Josyula, Diego R. Mazzotti, Kanika Bagai, Beth A. Malow, Janet D. Robishaw, Allan I. Pack and Sarah A. Pendergrass

Decentralized genomics audit logging via permissioned blockchain ledgering

One of the tasks in the iDASH Secure Genome Analysis Competition in 2018 was to develop blockchain-based immutable logging and querying for a cross-site genomic dataset access audit trail. The specific challen...

Authors: Nicholas D. Pattengale and Corey M. Hudson

Semi-Parallel logistic regression for GWAS on encrypted data

The sharing of biomedical data is crucial to enable scientific discoveries across institutions and improve health care. For example, genome-wide association studies (GWAS) based on a large number of samples ca...

Authors: Miran Kim, Yongsoo Song, Baiyu Li and Daniele Micciancio

iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching

Authors: Tsung-Ting Kuo, Xiaoqian Jiang, Haixu Tang, XiaoFeng Wang, Tyler Bath, Diyue Bu, Lei Wang, Arif Harmanci, Shaojie Zhang, Degui Zhi, Heidi J. Sofia and Lucila Ohno-Machado

Efficient logging and querying for blockchain-based cross-site genomic dataset access audit

Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module...

Authors: Shuaicheng Ma, Yang Cao and Li Xiong

Achieving GWAS with homomorphic encryption

One way of investigating how genes affect human traits would be with a genome-wide association study (GWAS). Genetic markers, known as single-nucleotide polymorphism (SNP), are used in GWAS. This raises privac...

Authors: Jun Jie Sim, Fook Mun Chan, Shibin Chen, Benjamin Hong Meng Tan and Khin Mi Mi Aung

Privacy-preserving semi-parallel logistic regression training with fully homomorphic encryption

Privacy-preserving computations on genomic data, and more generally on medical data, is a critical path technology for innovative, life-saving research to positively and equally impact the global population. I...

Authors: Sergiu Carpov, Nicolas Gama, Mariya Georgieva and Juan Ramon Troncoso-Pastoriza

Optimized homomorphic encryption solution for secure genome-wide association studies

Genome-Wide Association Studies (GWAS) refer to observational studies of a genome-wide set of genetic variants across many individuals to see if any genetic variants are associated with a certain trait. A typi...

Authors: Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, Kurt Rohloff and Vinod Vaikuntanathan

Leveraging blockchain for immutable logging and querying across multiple sites

Blockchain has emerged as a decentralized and distributed framework that enables tamper-resilience and, thus, practical immutability for stored data. This immutability property is important in scenarios where ...

Authors: Mustafa Safa Ozdayi, Murat Kantarcioglu and Bradley Malin

Using blockchain to log genome dataset access: efficient storage and query

Genomic variants are considered sensitive information, revealing potentially private facts about individuals. Therefore, it is important to control access to such data. A key aspect of controlled access is sec...

Authors: Gamze Gürsoy, Robert Bjornson, Molly E. Green and Mark Gerstein

Privacy-preserving approximate GWAS computation based on homomorphic encryption

One of three tasks in a secure genome analysis competition called iDASH 2018 was to develop a solution for privacy-preserving GWAS computation based on homomorphic encryption. The scenario is that a data holde...

Authors: Duhyeong Kim, Yongha Son, Dongwoo Kim, Andrey Kim, Seungwan Hong and Jung Hee Cheon

Privately computing set-maximal matches in genomic data

Finding long matches in deoxyribonucleic acid (DNA) sequences in large aligned genetic sequences is a problem of great interest. A paradigmatic application is the identification of distant relatives via large ...

Authors: Katerina Sotiraki, Esha Ghosh and Hao Chen

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis

Atrial fibrillation (AF) is at least partially heritable, affecting 2–3% of the population in Europe and the USA. However, a substantial proportion of heritability is still lacking. In the present study, we ai...

Authors: Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye and Guowei Li

What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations

Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Fi...

Authors: Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar, Azza Althagafi, Ahmed Alahmad, Mamoon Rashid, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Faroug Ababneh, Mohammed Albalwi, Raniah Alotaibi, Mashael Almutairi, Nouf Altharawi, Alhanouf Alsamer…

Next-generation sequencing analysis of endometrial screening liquid-based cytology specimens: a comparative study to tissue specimens

Liquid-based cytology (LBC) is now a widely used method for cytologic screening and cancer diagnosis. Since the cells are fixed with alcohol-based fixatives, and the specimens are stored in a liquid condition,...

Authors: Toshiaki Akahane, Ikumi Kitazono, Shintaro Yanazume, Masaki Kamio, Shinichi Togami, Ippei Sakamoto, Sachio Nohara, Seiya Yokoyama, Hiroaki Kobayashi, Tsubasa Hiraki, Shinsuke Suzuki, Shinichi Ueno and Akihide Tanimoto

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

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.

Authors: Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan and Firas A. Al-Qarqaz

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

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

Authors: Agnieszka H. Ludwig-Słomczyńska, Michał T. Seweryn, Przemysław Kapusta, Ewelina Pitera, Samuel K. Handelman, Urszula Mantaj, Katarzyna Cyganek, Paweł Gutaj, Łucja Dobrucka, Ewa Wender-Ożegowska, Maciej T. Małecki and Paweł P. Wołkow

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

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 sp...

Authors: Hui-Hui Xu, Mei-Zhen Dai, Kai Wang, Yang Zhang, Fei-Yan Pan and Wei-Wu Shi

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

Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h²) exist; however, a substantial proportion of h² is not attr...

Authors: Andrea R. Waksmunski, Michelle Grunin, Tyler G. Kinzy, Robert P. Igo Jr, Jonathan L. Haines and Jessica N. Cooke Bailey

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

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...

Authors: Louise de Schaetzen van Brienen, Maarten Larmuseau, Kim Van der Eecken, Frederic De Ryck, Pauline Robbe, Anna Schuh, Jan Fostier, Piet Ost and Kathleen Marchal

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

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...

Authors: Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jingtian Peng, Ran Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei and Tong Wen

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

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 s...

Authors: Damien Kaukonen, Riina Kaukonen, Lélia Polit, Bryan T. Hennessy, Riikka Lund and Stephen F. Madden

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

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 g...

Authors: Christopher S. Thom and Benjamin F. Voight

Long non-coding RNA profiling of pediatric Medulloblastoma

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) ...

Authors: Varun Kesherwani, Mamta Shukla, Don W. Coulter, J. Graham Sharp, Shantaram S. Joshi and Nagendra K. Chaturvedi

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

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 expres...

Authors: Jing Luo, Haiyan Li, Zhenwei Liu, Chenlu Li, Ruochen Wang, Jinxia Fang, Saisai Lu, Jing Guo, Xiaochun Zhu and Xiaobing Wang

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

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 an...

Authors: Joakim Klar, Helene Engstrand-Lilja, Khurram Maqbool, Jonas Mattisson, Lars Feuk and Niklas Dahl

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

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 ...

Authors: Junhao Yin, Xiaoli Zeng, Zexin Ai, Miao Yu, Yang’ou Wu and Shengjiao Li

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

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 sma...

Authors: Stefanie Friedrich, Remus Barbulescu, Thomas Helleday and Erik L. L. Sonnhammer

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

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 w...

Authors: Wael Bahia, Ismael Soltani, Anouar Abidi, Anis Haddad, Salima Ferchichi, Samia Menif and Wassim Y. Almawi

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

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 storag...

Authors: Gamze Gürsoy, Charlotte M. Brannon and Mark Gerstein

Leukocyte telomere length in patients with transfusion-dependent thalassemia

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 complic...

Authors: Nithita Nanthatanti, Adisak Tantiworawit, Pokpong Piriyakhuntorn, Thanawat Rattanathammethee, Sasinee Hantrakool, Chatree Chai-Adisaksopha, Ekarat Rattarittamrong, Lalita Norasetthada, Wirote Tuntiwechapikul, Kanda Fanhchaksai, Pimlak Charoenkwan, Sirinart Kumfu and Nipon Chattipakorn

Mitochondrial tRNA methylation in Alzheimer’s disease and progressive supranuclear palsy

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 ...

Authors: Talisa K. Silzer, Gita A. Pathak and Nicole R. Phillips

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

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...

Authors: Jun Wang, Yan Wang, Liwen Wang, Wang Yang Chen and Min Sheng