Articles

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage

Gene expression is highly variable across tissues of multi-cellular organisms, influencing the codon usage of the tissue-specific transcriptome. Cancer disrupts the gene expression pattern of healthy tissue re...

Authors: Douglas Meyer, Jacob Kames, Haim Bar, Anton A. Komar, Aikaterini Alexaki, Juan Ibla, Ryan C. Hunt, Luis V. Santana-Quintero, Anton Golikov, Michael DiCuccio and Chava Kimchi-Sarfaty

An implementation science approach to evaluating pathogen whole genome sequencing in public health

Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease ...

Authors: Angeline S. Ferdinand, Margaret Kelaher, Courtney R. Lane, Anders Gonçalves da Silva, Norelle L. Sherry, Susan A. Ballard, Patiyan Andersson, Tuyet Hoang, Justin T. Denholm, Marion Easton, Benjamin P. Howden and Deborah A. Williamson

We need to bring R0 < 1 to treat cancer too

If each cancer cell produces on average more than one cancer cell, we see a net growth of the tumors and metastases and vice versa. We review recent clinical results for microsatellite stable metastatic colore...

Authors: Devabhaktuni Srikrishna and Kris Sachsenmeier

Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed n...

Authors: Yanping Xu, Jianfeng Zhang, Meng Wang, Meng Liu, Guitian Liu, Hongping Qu, Jialin Liu, Zixin Deng, Jingyong Sun, Hong-Yu Ou and Jieming Qu

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We...

Authors: John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jette…

Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis

Multiple sclerosis (MS) is a major health problem, leading to a significant disability and patient suffering. Although chronic activation of the immune system is a hallmark of the disease, its pathogenesis is ...

Authors: Marti Bernardo-Faura, Melanie Rinas, Jakob Wirbel, Inna Pertsovskaya, Vicky Pliaka, Dimitris E. Messinis, Gemma Vila, Theodore Sakellaropoulos, Wolfgang Faigle, Pernilla Stridh, Janina R. Behrens, Tomas Olsson, Roland Martin, Friedemann Paul, Leonidas G. Alexopoulos, Pablo Villoslada…

Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models

The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Her...

Authors: Deepak Vangala, Swetlana Ladigan, Sven T. Liffers, Soha Noseir, Abdelouahid Maghnouj, Tina-Maria Götze, Berlinda Verdoodt, Susanne Klein-Scory, Laura Godfrey, Martina K. Zowada, Mario Huerta, Daniel L. Edelstein, Jaime Martinez de Villarreal, Miriam Marqués, Jörg Kumbrink, Andreas Jung…

An international policy on returning genomic research results

The Global Alliance for Genomics and Health has approved a policy for the return of clinically actionable genomic research results, the first such policy approved by an international body. The policy acknowled...

Authors: Anna C. F. Lewis, Bartha Maria Knoppers and Robert C. Green

Haplotype-resolved germline and somatic alterations in renal medullary carcinomas

Renal medullary carcinomas (RMCs) are rare kidney cancers that occur in adolescents and young adults of African ancestry. Although RMC is associated with the sickle cell trait and somatic loss of the tumor sup...

Authors: Kar-Tong Tan, Hyunji Kim, Jian Carrot-Zhang, Yuxiang Zhang, Won Jun Kim, Guillaume Kugener, Jeremiah A. Wala, Thomas P. Howard, Yueh-Yun Chi, Rameen Beroukhim, Heng Li, Gavin Ha, Seth L. Alper, Elizabeth J. Perlman, Elizabeth A. Mullen, William C. Hahn…

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. T...

Authors: Clément Meiller, François Montagne, Theo Z. Hirsch, Stefano Caruso, Julien de Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie-Christine Copin…

DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data

Multi-omics data are good resources for prognosis and survival prediction; however, these are difficult to integrate computationally. We introduce DeepProg, a novel ensemble framework of deep-learning and mach...

Authors: Olivier B. Poirion, Zheng Jing, Kumardeep Chaudhary, Sijia Huang and Lana X. Garmire

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification

High-grade serous tubo-ovarian cancer (HGSTOC) is characterised by extensive inter- and intratumour heterogeneity, resulting in persistent therapeutic resistance and poor disease outcome. Molecular subtype cla...

Authors: Siel Olbrecht, Pieter Busschaert, Junbin Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne-Sophie Van Rompuy, Diether Lambrechts and Ignace Vergote

A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank

Multimorbidities greatly increase the global health burdens, but the landscapes of their genetic risks have not been systematically investigated.

Authors: Guiying Dong, Jianfeng Feng, Fengzhu Sun, Jingqi Chen and Xing-Ming Zhao

Correction to: Family history assessment significantly enhances delivery of precision medicine in the genomics era

Authors: Yasmin Bylstra, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R. Ryanne Wu, Jing Xian Teo, Sonia Davila, Jyn Ling Kuan, Sock Hoai Chan, Nicolas Bertin, Cheng Xi Yang, Steve Rozen, Bin Tean Teh, Khung Keong Yeo, Stuart Alexander Cook, Saumya Shekhar Jamuar…

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches

Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida i...

Authors: Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica L. Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander and Micah T. McClain

Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer

Immune checkpoint inhibitors (ICIs) are monoclonal antibodies that block immune inhibitory pathways. Administration of ICIs augments T cell-mediated immune responses against tumor, resulting in improved overal...

Authors: Eiko Hayase and Robert R. Jenq

Correction to: Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

Authors: Na Zhu, Emilia M. Swietlik, Carrie L. Welch, Michael W. Pauciulo, Jacob J. Hagen, Xueya Zhou, Yicheng Guo, Johannes Karten, Divya Pandya, Tobias Tilly, Katie A. Lutz, Jennifer M. Martin, Carmen M. Treacy, Erika B. Rosenzweig, Usha Krishnan, Anna W. Coleman…

Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery

The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardi...

Authors: Rima M. Chakaroun, Lucas Massier, Anna Heintz-Buschart, Nedal Said, Joerg Fallmann, Alyce Crane, Tatjana Schütz, Arne Dietrich, Matthias Blüher, Michael Stumvoll, Niculina Musat and Peter Kovacs

Genetic correlation and causal relationships between cardio-metabolic traits and lung function impairment

Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability...

Authors: Matthias Wielscher, Andre F. S. Amaral, Diana van der Plaat, Louise V. Wain, Sylvain Sebert, David Mosen-Ansorena, Juha Auvinen, Karl-Heinz Herzig, Abbas Dehghan, Debbie L. Jarvis and Marjo-Riitta Jarvelin

Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma

Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality and morbidity. Existing treatment protocols are aggressive in nature resulting in signi...

Authors: Laura A. Genovesi, Amanda Millar, Elissa Tolson, Matthew Singleton, Emily Hassall, Marija Kojic, Caterina Brighi, Emily Girard, Clara Andradas, Mani Kuchibhotla, Dharmesh D. Bhuva, Raelene Endersby, Nicholas G. Gottardo, Anne Bernard, Christelle Adolphe, James M. Olson…

Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men

A higher intake of dietary fiber is associated with a decreased risk of chronic inflammatory diseases such as cardiovascular disease and inflammatory bowel disease. This may function in part due to abrogation ...

Authors: Wenjie Ma, Long H. Nguyen, Mingyang Song, Dong D. Wang, Eric A. Franzosa, Yin Cao, Amit Joshi, David A. Drew, Raaj Mehta, Kerry L. Ivey, Lisa L. Strate, Edward L. Giovannucci, Jacques Izard, Wendy Garrett, Eric B. Rimm, Curtis Huttenhower…

Landscape and selection of vaccine epitopes in SARS-CoV-2

Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4⁺ T cell, and CD8⁺ T cell stimulation. The rationale for this design was to drive bot...

Authors: Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric Routh, Julia Kodysh, Timothy O’Donnell, Carsten Haber…

Maintenance of the human memory T cell repertoire by subset and tissue site

Immune-mediated protection is mediated by T cells expressing pathogen-specific T cell antigen receptors (TCR) that are maintained at diverse sites of infection as tissue-resident memory T cells (TRM) or that d...

Authors: Michelle Miron, Wenzhao Meng, Aaron M. Rosenfeld, Shirit Dvorkin, Maya Meimei Li Poon, Nora Lam, Brahma V. Kumar, Yoram Louzoun, Eline T. Luning Prak and Donna L. Farber

Genetic subtypes, allelic effects, and convergent neurodevelopmental mechanisms

High-throughput sequencing of large affected cohorts have helped uncover a plethora of risk genes for complex neurodevelopmental disorders. However, untangling complex disease etiology also involves understand...

Authors: Maitreya Das and Santhosh Girirajan

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR...

Authors: Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S. Arcilla, Damian C. Melles, Menno D. de Jong, Constance Schultsz, Gautam Dantas and John Penders

Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

Metagenomic next-generation sequencing (mNGS) of body fluids is an emerging approach to identify occult pathogens in undiagnosed patients. We hypothesized that metagenomic testing can be simultaneously used to...

Authors: Wei Gu, Eric Talevich, Elaine Hsu, Zhongxia Qi, Anatoly Urisman, Scot Federman, Allan Gopez, Shaun Arevalo, Marc Gottschall, Linda Liao, Jack Tung, Lei Chen, Harumi Lim, Chandler Ho, Maya Kasowski, Jean Oak…

Advancing precision public health using human genomics: examples from the field and future research opportunities

Precision public health is a relatively new field that integrates components of precision medicine, such as human genomics research, with public health concepts to help improve population health. Despite inter...

Authors: Megan C. Roberts, Alison E. Fohner, Latrice Landry, Dana Lee Olstad, Amelia K. Smit, Erin Turbitt and Caitlin G. Allen

Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients

Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the f...

Authors: Dana W. Y. Tsui, Michael L. Cheng, Maha Shady, Julie L. Yang, Dennis Stephens, Helen Won, Preethi Srinivasan, Kety Huberman, Fanli Meng, Xiaohong Jing, Juber Patel, Maysun Hasan, Ian Johnson, Erika Gedvilaite, Brian Houck-Loomis, Nicholas D. Socci…

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks

Understanding cell-type-specific gene regulatory mechanisms from genetic variants to diseases remains challenging. To address this, we developed a computational pipeline, scGRNom (single-cell Gene Regulatory Netw...

Authors: Ting Jin, Peter Rehani, Mufang Ying, Jiawei Huang, Shuang Liu, Panagiotis Roussos and Daifeng Wang

Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses

The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this p...

Authors: Rosanne C. van Deuren, Peer Arts, Giulio Cavalli, Martin Jaeger, Marloes Steehouwer, Maartje van de Vorst, Christian Gilissen, Leo A. B. Joosten, Charles A. Dinarello, Musa M. Mhlanga, Vinod Kumar, Mihai G. Netea, Frank L. van de Veerdonk and Alexander Hoischen

Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood.

Authors: Sushant Patkar, Kerstin Heselmeyer-Haddad, Noam Auslander, Daniela Hirsch, Jordi Camps, Daniel Bronder, Markus Brown, Wei-Dong Chen, Rachel Lokanga, Darawalee Wangsa, Danny Wangsa, Yue Hu, Annette Lischka, Rüdiger Braun, Georg Emons, B. Michael Ghadimi…

Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries

Public trust is central to the collection of genomic and health data and the sustainability of genomic research. To merit trust, those involved in collecting and sharing data need to demonstrate they are trust...

Authors: Richard Milne, Katherine I. Morley, Mohamed A. Almarri, Shamim Anwer, Jerome Atutornu, Elena E. Baranova, Paul Bevan, Maria Cerezo, Yali Cong, Alessia Costa, Christine Critchley, Josepine Fernow, Peter Goodhand, Qurratulain Hasan, Aiko Hibino, Gry Houeland…

PhenCards: a data resource linking human phenotype information to biomedical knowledge

We present PhenCards (https://​phencards.​org), a database and web server intended as a one-stop shop for previously disconnected biomedical knowledge related to hum...

Authors: James M. Havrilla, Cong Liu, Xiangchen Dong, Chunhua Weng and Kai Wang

Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders

We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder.

Authors: Ilaria Mannucci, Nghi D. P. Dang, Hannes Huber, Jaclyn B. Murry, Jeff Abramson, Thorsten Althoff, Siddharth Banka, Gareth Baynam, David Bearden, Ana Beleza-Meireles, Paul J. Benke, Siren Berland, Tatjana Bierhals, Frederic Bilan, Laurence A. Bindoff, Geir Julius Braathen…

Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer

Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressur...

Authors: Zachary T. Weber, Katharine A. Collier, David Tallman, Juliet Forman, Sachet Shukla, Sarah Asad, Justin Rhoades, Samuel Freeman, Heather A. Parsons, Nicole O. Williams, Romualdo Barroso-Sousa, Elizabeth H. Stover, Haider Mahdi, Carrie Cibulskis, Niall J. Lennon, Gavin Ha…

Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker

Macrophages are the most common infiltrating immune cells in gliomas and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tum...

Authors: Andrew X. Chen, Robyn D. Gartrell, Junfei Zhao, Pavan S. Upadhyayula, Wenting Zhao, Jinzhou Yuan, Hanna E. Minns, Athanassios Dovas, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter Canoll, Peter A. Sims and Raul Rabadan

Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial

The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults wi...

Authors: François Bertucci, Anthony Gonçalves, Arnaud Guille, José Adelaïde, Séverine Garnier, Nadine Carbuccia, Emilien Billon, Pascal Finetti, Patrick Sfumato, Audrey Monneur, Christophe Pécheux, Martin Khran, Serge Brunelle, Lenaïg Mescam, Jeanne Thomassin-Piana, Flora Poizat…

Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with a...

Authors: Jose Espejo Valle-Inclan, Christina Stangl, Anouk C. de Jong, Lisanne F. van Dessel, Markus J. van Roosmalen, Jean C. A. Helmijr, Ivo Renkens, Roel Janssen, Sam de Blank, Chris J. de Witte, John W. M. Martens, Maurice P. H. M. Jansen, Martijn P. Lolkema and Wigard P. Kloosterman

Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer

Single liquid biopsy analytes (LBAs) have been utilized for therapy selection in metastatic breast cancer (MBC). We performed integrative statistical analyses to examine the clinical relevance of using multipl...

Authors: Corinna Keup, Vinay Suryaprakash, Siegfried Hauch, Markus Storbeck, Peter Hahn, Markus Sprenger-Haussels, Hans-Christian Kolberg, Mitra Tewes, Oliver Hoffmann, Rainer Kimmig and Sabine Kasimir-Bauer

Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating t...

Authors: Stephen D. Bentley and Stephanie W. Lo

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility

While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysi...

Authors: Liuyang Wang, Thomas J. Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R. Ko, Geoffrey S. Ginsburg, Mark R. DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser and Dennis C. Ko

Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq

Preclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations. The ideal platform would enable rap...

Authors: Wenting Zhao, Athanassios Dovas, Eleonora Francesca Spinazzi, Hanna Mendes Levitin, Matei Alexandru Banu, Pavan Upadhyayula, Tejaswi Sudhakar, Tamara Marie, Marc L. Otten, Michael B. Sisti, Jeffrey N. Bruce, Peter Canoll and Peter A. Sims

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are l...

Authors: Sunny Z. Wu, Daniel L. Roden, Ghamdan Al-Eryani, Nenad Bartonicek, Kate Harvey, Aurélie S. Cazet, Chia-Ling Chan, Simon Junankar, Mun N. Hui, Ewan A. Millar, Julia Beretov, Lisa Horvath, Anthony M. Joshua, Phillip Stricker, James S. Wilmott, Camelia Quek…

Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart ...

Authors: Na Zhu, Emilia M. Swietlik, Carrie L. Welch, Michael W. Pauciulo, Jacob J. Hagen, Xueya Zhou, Yicheng Guo, Johannes Karten, Divya Pandya, Tobias Tilly, Katie A. Lutz, Jennifer M. Martin, Carmen M. Treacy, Erika B. Rosenzweig, Usha Krishnan, Anna W. Coleman…

Translating the human microbiome: a path to improving health

Authors: Ramnik J. Xavier

Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period

Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captu...

Authors: Guilhem Royer, Mélanie Mercier Darty, Olivier Clermont, Bénédicte Condamine, Cédric Laouenan, Jean-Winoc Decousser, David Vallenet, Agnès Lefort, Victoire de Lastours and Erick Denamur

Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease

Alzheimer’s disease (AD) is an incurable neurodegenerative disease currently affecting 1.75% of the US population, with projected growth to 3.46% by 2050. Identifying common genetic variants driving difference...

Authors: Jake Gockley, Kelsey S. Montgomery, William L. Poehlman, Jesse C. Wiley, Yue Liu, Ekaterina Gerasimov, Anna K. Greenwood, Solveig K. Sieberts, Aliza P. Wingo, Thomas S. Wingo, Lara M. Mangravite and Benjamin A. Logsdon

Single-cell sequencing of the small and AT-skewed genome of malaria parasites

Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, wit...

Authors: Shiwei Liu, Adam C. Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell and Jennifer L. Güler

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. ...

Authors: Charles E. Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D. Szeto, Xiaoguang Xu, Daniel L. McCartney, Rong Jiang, Amit Patki, Holly J. Kramer, James M. Eales, Laura Raffield, Leslie Lange, Ethan Lange, Peter Durda, Yongmei Liu, Russ P. Tracy…

Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer

Abnormal DNA methylation is observed as an early event in breast carcinogenesis. However, how such alterations arise is still poorly understood. microRNAs (miRNAs) regulate gene expression at the post-transcri...

Authors: Miriam Ragle Aure, Thomas Fleischer, Sunniva Bjørklund, Jørgen Ankill, Jaime A. Castro-Mondragon, Anne-Lise Børresen-Dale, Jörg Tost, Kristine K. Sahlberg, Anthony Mathelier, Xavier Tekpli and Vessela N. Kristensen