Articles

Genomics of lipid-laden human hepatocyte cultures enables drug target screening for the treatment of non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is a major health burden in need for new medication. To identify potential drug targets a genomic study was performed in lipid-laden primary human hepatocyte (PHH) and...

Authors: Stephanie Breher-Esch, Nishika Sahini, Anna Trincone, Christin Wallstab and Jürgen Borlak

“Omics” data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy

Large-scale “omics” datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap.

Authors: Nzali V. Campbell, David A. Weitzenkamp, Ian L. Campbell, Ronald F. Schmidt, Chindo Hicks, Michael J. Morgan, David C. Irwin and John J. Tentler

Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine

Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is,...

Authors:

Identification of gene expression profiles in myocardial infarction: a systematic review and meta-analysis

Myocardial infarction (MI) is a multifactorial disease with complex pathogenesis, mainly the result of the interplay of genetic and environmental risk factors. The regulation of thrombosis, inflammation and ch...

Authors: Panagiota Kontou, Athanasia Pavlopoulou, Georgia Braliou, Spyridoula Bogiatzi, Niki Dimou, Sripal Bangalore and Pantelis Bagos

Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult ...

Authors: Tanjin T. Toma, Jeremy M. Dawson and Donald A. Adjeroh

Toward the precision breast cancer survival prediction utilizing combined whole genome-wide expression and somatic mutation analysis

Breast cancer is the most common type of invasive cancer in woman. It accounts for approximately 18% of all cancer deaths worldwide. It is well known that somatic mutation plays an essential role in cancer dev...

Authors: Yifan Zhang, William Yang, Dan Li, Jack Y Yang, Renchu Guan and Mary Qu Yang

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk

With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development...

Authors: Jingpu Zhang, shuai Zou and Lei Deng

Developing a healthcare dataset information resource (DIR) based on Semantic Web

The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the ...

Authors: Jingyi Shi, Mingna Zheng, Lixia Yao and Yaorong Ge

Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature

Non-small cell lung cancer (NSCLC) represents more than about 80% of the lung cancer. The early stages of NSCLC can be treated with complete resection with a good prognosis. However, most cases are detected at...

Authors: Dan Li, William Yang, Yifan Zhang, Jack Y Yang, Renchu Guan, Dong Xu and Mary Qu Yang

Distributed gene clinical decision support system based on cloud computing

The clinical decision support system can effectively break the limitations of doctors’ knowledge and reduce the possibility of misdiagnosis to enhance health care. The traditional genetic data storage and anal...

Authors: Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang and Xuehai Zhou

Discovery and disentanglement of aligned residue associations from aligned pattern clusters to reveal subgroup characteristics

A protein family has similar and diverse functions locally conserved. An aligned pattern cluster (APC) can reflect the conserved functionality. Discovering aligned residue associations (ARAs) in APCs can revea...

Authors: Pei-Yuan Zhou, Antonio Sze-To and Andrew K. C. Wong

Bi-stream CNN Down Syndrome screening model based on genotyping array

Human Down syndrome (DS) is usually caused by genomic micro-duplications and dosage imbalances of human chromosome 21. It is associated with many genomic and phenotype abnormalities. Even though human DS occur...

Authors: Bing Feng, William Hoskins, Yan Zhang, Zibo Meng, David C. Samuels, Jiandong Wang, Ruofan Xia, Chao Liu, Jijun Tang and Yan Guo

MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes

Miniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop...

Authors: Jialu Hu, Yan Zheng and Xuequn Shang

integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth

The integration of high-quality, genome-wide analyses offers a robust approach to elucidating genetic factors involved in complex human diseases. Even though several methods exist to integrate heterogeneous om...

Authors: Haley R. Eidem, Jacob L. Steenwyk, Jennifer H. Wisecaver, John A. Capra, Patrick Abbot and Antonis Rokas

Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

BAP1 is a histone deubiquitinase that acts as a tumor and metastasis suppressor associated with disease progression in human cancer. We have used the “Calling Card System” of transposase-directed transposon in...

Authors: Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra and Michael D. Onken

A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and ...

Authors: Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen and Shuang Wang

Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis

Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, includi...

Authors: Pengfei Xu, Jian Yang, Junhui Liu, Xue Yang, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu and Qianxue Chen

Nucleotide excision repair is a predictor of early relapse in pediatric acute lymphoblastic leukemia

Nucleotide Excision Repair (NER) is a major pathway of mammalian DNA repair that is associated with drug resistance and has not been well characterized in acute lymphoblastic leukemia (ALL). The objective of t...

Authors: Omar M. Ibrahim, Homood M. As Sobeai, Stephen G. Grant and Jean J. Latimer

Current landscape of personalized medicine adoption and implementation in Southeast Asia

The emergence of personalized medicine (PM) has raised some tensions in healthcare systems. PM is expensive and health budgets are constrained - efficient healthcare delivery is therefore critical. Notwithstan...

Authors: Huey Yi Chong, Pascale A. Allotey and Nathorn Chaiyakunapruk

Identifying the genetic causes for prenatally diagnosed structural congenital anomalies (SCAs) by whole-exome sequencing (WES)

Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal...

Authors: Gordon K C Leung, Christopher C Y Mak, Jasmine L F Fung, Wilfred H S Wong, Mandy H Y Tsang, Mullin H C Yu, Steven L C Pei, K S Yeung, Gary T K Mok, C P Lee, Amelia P W Hui, Mary H Y Tang, Kelvin Y K Chan, Anthony P Y Liu, Wanling Yang, P C Sham…

Role of PUF60 gene in Verheij syndrome: a case report of the first Chinese Han patient with a de novo pathogenic variant and review of the literature

Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical featu...

Authors: Qiong Xu, Chun-yang Li, Yi Wang, Hui-ping Li, Bing-bing Wu, Yong-hui Jiang and Xiu Xu

Clinical analysis of germline copy number variation in DMD using a non-conjugate hierarchical Bayesian model

Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe...

Authors: Velina Kozareva, Clayton Stroff, Maxwell Silver, Jonathan F. Freidin and Nigel F. Delaney

Strategies to minimize false positives and interpret novel microdeletions based on maternal copy-number variants in 87,000 noninvasive prenatal screens

Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. Hig...

Authors: Kristjan Eerik Kaseniit, Gregory J Hogan, Kevin M D’Auria, Carrie Haverty and Dale Muzzey

Mitochondrial DNA 7908–8816 region mutations in maternally inherited essential hypertensive subjects in China

Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. Th...

Authors: Ye Zhu, Xiang Gu and Chao Xu

Logistic regression over encrypted data from fully homomorphic encryption

One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patien...

Authors: Hao Chen, Ran Gilad-Bachrach, Kyoohyung Han, Zhicong Huang, Amir Jalali, Kim Laine and Kristin Lauter

Logistic regression model training based on the approximate homomorphic encryption

Security concerns have been raised since big data became a prominent tool in data analysis. For instance, many machine learning algorithms aim to generate prediction models using training data which contain se...

Authors: Andrey Kim, Yongsoo Song, Miran Kim, Keewoo Lee and Jung Hee Cheon

Privacy-preserving logistic regression training

Logistic regression is a popular technique used in machine learning to construct classification models. Since the construction of such models is based on computing with large datasets, it is an appealing idea ...

Authors: Charlotte Bonte and Frederik Vercauteren

Privacy-preserving record linkage in large databases using secure multiparty computation

Practical applications for data analysis may require combining multiple databases belonging to different owners, such as health centers. The analysis should be performed without violating privacy of neither th...

Authors: Peeter Laud and Alisa Pankova

Secure top most significant genome variants search: iDASH 2017 competition

One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most si...

Authors: Sergiu Carpov and Thibaud Tortech

iDASH secure genome analysis competition 2017

Authors: XiaoFeng Wang, Haixu Tang, Shuang Wang, Xiaoqian Jiang, Wenhao Wang, Diyue Bu, Lei Wang, Yicheng Jiang and Chenghong Wang

Genomics of drug sensitivity in bladder cancer: an integrated resource for pharmacogenomic analysis in bladder cancer

Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in ...

Authors: Adnan Ahmad Ansari, Inkeun Park, Inki Kim, Sojung Park, Sung-Min Ahn and Jae-lyun Lee

New insights into the phenotypic spectrum of 14q22q23 deletions: a case report and literature review

Mutations occurring in the orthodenticle homeobox 2 gene (OTX2) are responsible for a rare genetic syndrome, characterized mainly by microphthalmia/anophthalmia associated with extra-ocular defects such as brain ...

Authors: Anna Pichiecchio, Giovanni Vitale, Camilla Caporali, Cecilia Parazzini, Donatella Milani, Maria Paola Recalcati, Laura D’Amico, Sabrina Signorini, Umberto Balottin and Stefano Bastianello

Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) is an important step during breast carcinogenesis. Understanding its molecular changes may help to identify high-risk DCIS...

Authors: Silke Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm and Hans J. Neubauer

Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data

Large-scale collaborative precision medicine initiatives (e.g., The Cancer Genome Atlas (TCGA)) are yielding rich multi-omics data. Integrative analyses of the resulting multi-omics data, such as somatic mutat...

Authors: Yasser EL-Manzalawy, Tsung-Yu Hsieh, Manu Shivakumar, Dokyoon Kim and Vasant Honavar

Local genetic ancestry in CDKN2B-AS1 is associated with primary open-angle glaucoma in an African American cohort extracted from de-identified electronic health records

Glaucoma is a leading cause of blindness in developed countries. Primary open-angle glaucoma (POAG), the most prevalent clinical subtype of glaucoma in the United States, affects African Americans at a higher ...

Authors: Nicole A. Restrepo, Sarah M. Laper, Eric Farber-Eger and Dana C. Crawford

Frequency and phenotype consequence of APOC3 rare variants in patients with very low triglyceride levels

High levels of triglycerides (TG ≥200 mg/dL) are an emerging risk factor for cardiovascular disease. Conversely, very low levels of TG are associated with decreased risk for cardiovascular disease. Precision m...

Authors: Dana C. Crawford, Nicole A. Restrepo, Kirsten E. Diggins, Eric Farber-Eger and Quinn S. Wells

Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer

Integrative analysis on multi-omics data has gained much attention recently. To investigate the interactive effect of gene expression and DNA methylation on cancer, we propose a directed random walk-based appr...

Authors: So Yeon Kim, Tae Rim Kim, Hyun-Hwan Jeong and Kyung-Ah Sohn

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine

RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (...

Authors: Naresh Prodduturi, Aditya Bhagwate, Jean-Pierre A. Kocher and Zhifu Sun

Pathway networks generated from human disease phenome

Understanding the effect of human genetic variations on disease can provide insight into phenotype-genotype relationships, and has great potential for improving the effectiveness of personalized medicine. Whil...

Authors: Ann G. Cirincione, Kaylyn L. Clark and Maricel G. Kann

Rare variants in the splicing regulatory elements of EXOC3L4 are associated with brain glucose metabolism in Alzheimer’s disease

Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases that causes problems related to brain function. To some extent it is understood on a molecular level how AD arises, however there a...

Authors: Jason E. Miller, Manu K. Shivakumar, Younghee Lee, Seonggyun Han, Emrin Horgousluoglu, Shannon L. Risacher, Andrew J. Saykin, Kwangsik Nho and Dokyoon Kim

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

RNA-seq is a powerful and cost-effective technology for molecular diagnostics of cancer and other diseases, and it can reach its full potential when coupled with validated clinical-grade informatics tools. Des...

Authors: Readman Chiu, Ka Ming Nip, Justin Chu and Inanc Birol

Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

CRISPR/CAS9 (epi)genome editing revolutionized the field of gene and cell therapy. Our previous study demonstrated that a rapid and robust reactivation of the HIV latent reservoir by a catalytically-deficient ...

Authors: Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao-Feng Yang, Hong Wang, Layne T. Watson, Liqing Zhang and Wenhui Hu

Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common f...

Authors: Morag A. Lewis, Lisa S. Nolan, Barbara A. Cadge, Lois J. Matthews, Bradley A. Schulte, Judy R. Dubno, Karen P. Steel and Sally J. Dawson

Correction to: The Cancer Omics Atlas: an integrative resource for cancer omics annotations

Following publication of the original article [1], the authors reported an error in Fig. 1A.

Authors: Qingrong Sun, Mengyuan Li and Xiaosheng Wang

Circulating miRNome profiling in Moyamoya disease-discordant monozygotic twins and endothelial microRNA expression analysis using iPS cell line

Moyamoya disease (MMD) is characterized by progressive stenosis of intracranial arteries in the circle of Willis with unknown etiology even after the identification of a Moyamoya susceptible gene, RNF213. Rece...

Authors: Haruto Uchino, Masaki Ito, Ken Kazumata, Yuka Hama, Shuji Hamauchi, Shunsuke Terasaka, Hidenao Sasaki and Kiyohiro Houkin

Differentially expressed proteins in positive versus negative HNSCC lymph nodes

Lymph node metastasis is one of the most important prognostic factors in head and neck squamous cell carcinomas (HNSCCs) and critical for delineating their treatment. However, clinical and histological criteri...

Authors: Alessandra Vidotto, Giovana M. Polachini, Marina de Paula-Silva, Sonia M. Oliani, Tiago Henrique, Rossana V. M. López, Patrícia M. Cury, Fabio D. Nunes, José F. Góis-Filho, Marcos B. de Carvalho, Andréia M. Leopoldino and Eloiza H. Tajara

Multiple occurrence of psychomotor retardation and recurrent miscarriages in a family with a submicroscopic reciprocal translocation t(7;17)(p22;p13.2)

Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in ph...

Authors: Magdalena Pasińska, Ewelina Łazarczyk, Katarzyna Jułga, Magdalena Bartnik-Głaska, Beata Nowakowska and Olga Haus

Additional germline findings from a tumor profiling program

Matched tumor-normal sequencing, applied in precision cancer medicine, can identify unidentified germline Medically Actionable Variants (gMAVS) in cancer predisposition genes. We report patient preferences for...

Authors: Neda Stjepanovic, Tracy L. Stockley, Philippe L. Bedard, Jeanna M. McCuaig, Melyssa Aronson, Spring Holter, Kara Semotiuk, Natasha B. Leighl, Raymond Jang, Monika K. Krzyzanowska, Amit M. Oza, Abha Gupta, Christine Elser, Lailah Ahmed, Lisa Wang, Suzanne Kamel-Reid…

Association between genetic risk variants and glucose intolerance during pregnancy in north Indian women

Gestational diabetes (GDM) is a more common problem in India than in many other parts of the world but it is not known whether this is due to unique environmental factors or a unique genetic background. To add...

Authors: Geeti P. Arora, Peter Almgren, Charlotte Brøns, Richa G. Thaman, Allan A. Vaag, Leif Groop and Rashmi B. Prasad

The Cancer Omics Atlas: an integrative resource for cancer omics annotations

The Cancer Genome Atlas (TCGA) is an important data resource for cancer biologists and oncologists. However, a lack of bioinformatics expertise often hinders experimental cancer biologists and oncologists from...

Authors: Qingrong Sun, Mengyuan Li and Xiaosheng Wang