Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing

Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chroma...

Authors: Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau and Victor X. Jin

Sensitivity to sequencing depth in single-cell cancer genomics

Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with s...

Authors: João M. Alves and David Posada

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

The interplay of epigenetic processes and the intestinal microbiota may play an important role in intestinal development and homeostasis. Previous studies have established that the microbiota regulates a large...

Authors: Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Philipp Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Jörn Walter, Sven Künzel, John F. Baines, Stefan Schreiber…

New additions to the cancer precision medicine toolkit

New computational and database-driven tools are emerging to aid in the interpretation of cancer genomic data as its use becomes more common in clinical evidence-based cancer medicine. Two such open source tool...

Authors: Elaine R. Mardis

Integrated biology approach reveals molecular and pathological interactions among Alzheimer’s Aβ42, Tau, TREM2, and TYROBP in Drosophila models

Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network mo...

Authors: Michiko Sekiya, Minghui Wang, Naoki Fujisaki, Yasufumi Sakakibara, Xiuming Quan, Michelle E. Ehrlich, Philip L. De Jager, David A. Bennett, Eric E. Schadt, Sam Gandy, Kanae Ando, Bin Zhang and Koichi M. Iijima

Elevated polygenic burden for autism is associated with differential DNA methylation at birth

Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD invo...

Authors: Eilis Hannon, Diana Schendel, Christine Ladd-Acosta, Jakob Grove, Christine Søholm Hansen, Shan V. Andrews, David Michael Hougaard, Michaeline Bresnahan, Ole Mors, Mads Vilhelm Hollegaard, Marie Bækvad-Hansen, Mady Hornig, Preben Bo Mortensen, Anders D. Børglum, Thomas Werge, Marianne Giørtz Pedersen…

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Inte...

Authors: David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P. Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez and Nuria Lopez-Bigas

Local adaptation in European populations affected the genetics of psychiatric disorders and behavioral traits

Recent studies have used genome-wide data to investigate evolutionary mechanisms related to behavioral phenotypes, identifying widespread signals of positive selection. Here, we conducted a genome-wide investi...

Authors: Renato Polimanti, Manfred H. Kayser and Joel Gelernter

The emerging roles of exosomes in the modulation of immune responses in cancer

Exosomes are promising tools for improving cancer care, but conversely may also contribute to tumor progression. Here, we highlight recently discovered roles of exosomes in modulating immune responses in cance...

Authors: Paul Kurywchak, Jena Tavormina and Raghu Kalluri

Detection of Creutzfeldt-Jakob disease prions in skin: implications for healthcare

Evidence has recently been reported of prion seeding activity in skin tissue from patients with sporadic Creutzfeldt-Jakob disease (sCJD). This is relevant information for infection control measures during sur...

Authors: Akin Nihat and Simon Mead

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstr...

Authors: Amit A. Upadhyay, Robert C. Kauffman, Amber N. Wolabaugh, Alice Cho, Nirav B. Patel, Samantha M. Reiss, Colin Havenar-Daughton, Reem A. Dawoud, Gregory K. Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F. Eun-Hyung Lee, Jens Wrammert and Steven E. Bosinger

Advances in liquid biopsy approaches for early detection and monitoring of cancer

Progress in sensitive analytical approaches has opened new avenues for the detection of cells or products such as circulating cell-free DNA released by tumors. These ‘liquid biopsies’ are being explored in cli...

Authors: Anna Babayan and Klaus Pantel

From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards

A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hind...

Authors: Júlia Perera-Bel, Barbara Hutter, Christoph Heining, Annalen Bleckmann, Martina Fröhlich, Stefan Fröhling, Hanno Glimm, Benedikt Brors and Tim Beißbarth

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels

There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous ...

Authors: Timothy D. O’Brien, Peilin Jia, Neil E. Caporaso, Maria Teresa Landi and Zhongming Zhao

NSAID use and somatic exomic mutations in Barrett’s esophagus

Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett’s esophagus (...

Authors: Patricia C. Galipeau, Kenji M. Oman, Thomas G. Paulson, Carissa A. Sanchez, Qing Zhang, Jerry A. Marty, Jeffrey J. Delrow, Mary K. Kuhner, Thomas L. Vaughan, Brian J. Reid and Xiaohong Li

Characterization of cross-tissue genetic-epigenetic effects and their patterns in schizophrenia

One of the major challenges in current psychiatric epigenetic studies is the tissue specificity of epigenetic changes since access to brain samples is limited. Peripheral tissues have been studied as surrogate...

Authors: Dongdong Lin, Jiayu Chen, Nora Perrone-Bizzozero, Juan R. Bustillo, Yuhui Du, Vince D. Calhoun and Jingyu Liu

Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks

Genome-wide association studies of Alzheimer’s disease (AD) have identified a number of significant risk loci, the majority of which lie in non-coding regions of the genome. The lack of causal alleles and cons...

Authors: Katherine E. Tansey, Darren Cameron and Matthew J. Hill

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymor...

Authors: A. R. Last, H. Pickering, C. h. Roberts, F. Coll, J. Phelan, S. E. Burr, E. Cassama, M. Nabicassa, H. M. B. Seth-Smith, J. Hadfield, L. T. Cutcliffe, I. N. Clarke, D. C. W. Mabey, R. L. Bailey, T. G. Clark, N. R. Thomson…

Endophenotypes in psychiatric disease: prospects and challenges

Endophenotypes, quantitative neurobehavioral traits that index genetic susceptibility for a psychiatric disorder, have been examined in thousands of studies. Nevertheless, they have underexploited potential to...

Authors: William G. Iacono

The microbiome in precision medicine: the way forward

Novel associations between the human microbiome and health and disease are routinely emerging, and important host–microbiome interactions are targets for new diagnostics and therapeutics. Understanding how bro...

Authors: Joseph F. Petrosino

Calcitonin gene-related peptide (receptor) antibodies: an exciting avenue for migraine treatment

Specific prophylactic migraine treatments are urgently needed because of the unmet needs of many migraine patients. Antibodies targeting calcitonin gene-related peptide (CGRP) or its receptor have recently sho...

Authors: Antoinette MaassenVanDenBrink, Gisela M. Terwindt and Arn M. J. M. van den Maagdenberg

Synaptic dysfunction in complex psychiatric disorders: from genetics to mechanisms

Breakthroughs on many fronts have provided strong evidence to support synaptic dysfunction as a causal factor for neuropsychiatric diseases. Genetic studies have identified variants implicated in novel biologi...

Authors: Xinyuan Wang, Kimberly M. Christian, Hongjun Song and Guo-li Ming

Translating neurogenomics: deconvoluting complex brain disorders

Authors: Rabia Begum

Detection and analysis of methicillin-resistant human-adapted sequence type 398 allows insight into community-associated methicillin-resistant Staphylococcus aureus evolution

Severe infections with highly virulent community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are a global problem. However, the molecular events defining the evolution of CA-MRSA are still po...

Authors: Lei He, Hong-Xiang Zheng, Yanan Wang, Katherine Y. Le, Qian Liu, Jun Shang, Yingxin Dai, Hongwei Meng, Xing Wang, Tianming Li, Qianqian Gao, Juanxiu Qin, Huiying Lu, Michael Otto and Min Li

Host genetic variation and its microbiome interactions within the Human Microbiome Project

Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the comp...

Authors: Raivo Kolde, Eric A. Franzosa, Gholamali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J. Daly, Ramnik J. Xavier and Curtis Huttenhower