Identifying statistically significant combinatorial markers for survival analysis

Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between...

Authors: Raissa T. Relator, Aika Terada and Jun Sese

Mut2Vec: distributed representation of cancerous mutations

Embedding techniques for converting high-dimensional sparse data into low-dimensional distributed representations have been gaining popularity in various fields of research. In deep learning models, embedding ...

Authors: Sunkyu Kim, Heewon Lee, Keonwoo Kim and Jaewoo Kang

Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions

Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimension...

Authors: Hye-Young Jung, Sangseob Leem and Taesung Park

Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely u...

Authors: Je-Keun Rhee and Tae-Min Kim

WISARD: workbench for integrated superfast association studies for related datasets

A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies—from heritability estima...

Authors: Sungyoung Lee, Sungkyoung Choi, Dandi Qiao, Michael Cho, Edwin K. Silverman, Taesung Park and Sungho Won

EAGLE: Explicit Alternative Genome Likelihood Evaluator

Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning...

Authors: Tony Kuo, Martin C. Frith, Jun Sese and Paul Horton

Exact association test for small size sequencing data

Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e...

Authors: Joowon Lee, Seungyeoun Lee, Jin-Young Jang and Taesung Park

LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data

Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to ...

Authors: Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh and Jie Zheng

An integrated clinical and genomic information system for cancer precision medicine

Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex natu...

Authors: Yeongjun Jang, Taekjin Choi, Jongho Kim, Jisub Park, Jihae Seo, Sangok Kim, Yeajee Kwon, Seungjae Lee and Sanghyuk Lee

IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics

With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we...

Authors: Jennifer D. Hintzsche, Minjae Yoo, Jihye Kim, Carol M. Amato, William A. Robinson and Aik Choon Tan

CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data

The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TC...

Authors: Seonggyun Han, Dongwook Kim, Youngjun Kim, Kanghoon Choi, Jason E. Miller, Dokyoon Kim and Younghee Lee

A meta-analysis of public microarray data identifies biological regulatory networks in Parkinson’s disease

Parkinson’s disease (PD) is a long-term degenerative disease that is caused by environmental and genetic factors. The networks of genes and their regulators that control the progression and development of PD r...

Authors: Lining Su, Chunjie Wang, Chenqing Zheng, Huiping Wei and Xiaoqing Song

Genetic analysis of Wnt/PCP genes in neural tube defects

Mouse homozygous mutants in Wnt/planar cell polarity (PCP) pathway genes have been shown to cause neural tube defects (NTDs) through the disruption of normal morphogenetic processes critical to neural tube clo...

Authors: Zhongzhong Chen, Yunping Lei, Xuanye Cao, Yufang Zheng, Fang Wang, Yihua Bao, Rui Peng, Richard H. Finnell, Ting Zhang and Hongyan Wang

Patient with multiple acyl-CoA dehydrogenase deficiency disease and ETFDH mutations benefits from riboflavin therapy: a case report

Lipid storage myopathy (LSM) is a diverse group of lipid metabolic disorders with great variations in the clinical phenotype and age of onset. Classical multiple acyl-CoA dehydrogenase deficiency (MADD) is kno...

Authors: Liuh Ling Goh, Yingshan Lee, Ee Shien Tan, James Soon Chuan Lim, Chia Wei Lim and Rinkoo Dalan

Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics

The use of next-generation sequencing approaches in clinical diagnostics has led to a tremendous increase in data and a vast number of variants of uncertain significance that require interpretation. Therefore,...

Authors: Corinna Ernst, Eric Hahnen, Christoph Engel, Michael Nothnagel, Jonas Weber, Rita K. Schmutzler and Jan Hauke

HLA and proteasome expression body map

The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA gen...

Authors: Sebastian Boegel, Martin Löwer, Thomas Bukur, Patrick Sorn, John C. Castle and Ugur Sahin

Integrated analysis of DNA-methylation and gene expression using high-dimensional penalized regression: a cohort study on bone mineral density in postmenopausal women

Using high-dimensional penalized regression we studied genome-wide DNA-methylation in bone biopsies of 80 postmenopausal women in relation to their bone mineral density (BMD). The women showed BMD varying from...

Authors: Tonje G. Lien, Ørnulf Borgan, Sjur Reppe, Kaare Gautvik and Ingrid Kristine Glad

Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To fi...

Authors: Alain Calender, Pierre Antoine Rollat Farnier, Adrien Buisson, Stéphane Pinson, Abderrazzaq Bentaher, Serge Lebecque, Harriet Corvol, Rola Abou Taam, Véronique Houdouin, Claire Bardel, Pascal Roy, Gilles Devouassoux, Vincent Cottin, Pascal Seve, Jean-François Bernaudin, Clarice X. Lim…

A combined linkage, microarray and exome analysis suggests MAP3K11 as a candidate gene for left ventricular hypertrophy

Electrocardiographic measures of left ventricular hypertrophy (LVH) are used as predictors of cardiovascular risk. We combined linkage and association analyses to discover novel rare genetic variants involved ...

Authors: Claudia Tamar Silva, Irina V. Zorkoltseva, Maartje N. Niemeijer, Marten E. van den Berg, Najaf Amin, Ayşe Demirkan, Elisa van Leeuwen, Adriana I. Iglesias, Laura B. Piñeros-Hernández, Carlos M. Restrepo, Jan A. Kors, Anatoly V. Kirichenko, Rob Willemsen, Ben A. Oostra, Bruno H. Stricker, André G. Uitterlinden…

Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations

Asthma exacerbations are an important cause of morbidity in asthma. Respiratory infections are often involved in asthma exacerbations in both children and adults. Some individuals with asthma have increased su...

Authors: Jose L. Gomez, Maria P. Diaz, Gustavo Nino and Clemente J. Britto

Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that vi...

Authors: Na Zhang, Yun-Juan Bao, Amy Hin-Yan Tong, Scott Zuyderduyn, Gary D. Bader, J. S. Malik Peiris, Si Lok and Suki Man-Yan Lee

Cumulative prognostic power of laminin genes in colorectal cancer

Laminins are a major family of extracellular matrix proteins and the main component of basement membranes. Laminins are involved in many if not all stages of cancer progression, and expression of laminin genes...

Authors: Vladimir V. Galatenko, Diana V. Maltseva, Alexey V. Galatenko, Sergey Rodin and Alexander G. Tonevitsky

Circadian succession of molecular processes in living tissues

Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression a...

Authors: Abeer Fadda, Mohammed El Anbari and Andrey Ptitsyn

Medical genomics at Belyaev Conference – 2017

Authors: Yuriy L. Orlov, Julio R. Fernandez-Masso, Ming Chen and Ancha V. Baranova

Primary microcephaly case from the Karachay-Cherkess Republic poses an additional support for microcephaly and Seckel syndrome spectrum disorders

Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagno...

Authors: Andrey V. Marakhonov, Fedor A. Konovalov, Amin Kh. Makaov, Tatyana A. Vasilyeva, Vitaly V. Kadyshev, Varvara A. Galkina, Elena L. Dadali, Sergey I. Kutsev and Rena A. Zinchenko