Articles

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…

Evaluating the transcriptional fidelity of cancer models

Cancer researchers use cell lines, patient-derived xenografts, engineered mice, and tumoroids as models to investigate tumor biology and to identify therapies. The generalizability and power of a model derive ...

Authors: Da Peng, Rachel Gleyzer, Wen-Hsin Tai, Pavithra Kumar, Qin Bian, Bradley Isaacs, Edroaldo Lummertz da Rocha, Stephanie Cai, Kathleen DiNapoli, Franklin W. Huang and Patrick Cahan

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

Application of a framework to guide genetic testing communication across clinical indications

Genetic information is increasingly relevant across healthcare. Traditional genetic counseling (GC) may limit access to genetic information and may be more information and support than some individuals need. W...

Authors: Miranda L. G. Hallquist, Eric P. Tricou, Kelly E. Ormond, Juliann M. Savatt, Curtis R. Coughlin II, W. Andrew Faucett, Laura Hercher, Howard P. Levy, Julianne M. O’Daniel, Holly L. Peay, Melissa Stosic, Maureen Smith, Wendy R. Uhlmann, Hannah Wand, Karen E. Wain and Adam H. Buchanan

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer

Identification of germline variation and somatic mutations is a major issue in human genetics. However, due to the limitations of DNA sequencing technologies and computational algorithms, our understanding of ...

Authors: Akihiro Fujimoto, Jing Hao Wong, Yukiko Yoshii, Shintaro Akiyama, Azusa Tanaka, Hitomi Yagi, Daichi Shigemizu, Hidewaki Nakagawa, Masashi Mizokami and Mihoko Shimada

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WG...

Authors: Xiaotong Li, Sushant Kumar, Arif Harmanci, Shantao Li, Robert R. Kitchen, Yan Zhang, Vikram B. Wali, Sangeetha M. Reddy, Wendy A. Woodward, James M. Reuben, Joel Rozowsky, Christos Hatzis, Naoto T. Ueno, Savitri Krishnamurthy, Lajos Pusztai and Mark Gerstein

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na_V1.1 sodiu...

Authors: Jessica L. Haigh, Anna Adhikari, Nycole A. Copping, Tyler Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J. Kreun, Jasmine Carter…

Finding associations in a heterogeneous setting: statistical test for aberration enrichment

Most two-group statistical tests find broad patterns such as overall shifts in mean, median, or variance. These tests may not have enough power to detect effects in a small subset of samples, e.g., a drug that...

Authors: Aziz M. Mezlini, Sudeshna Das and Anna Goldenberg

The impact of genomics on precision public health: beyond the pandemic

Authors: Muin J. Khoury and Kathryn E. Holt

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

The large airway epithelial barrier provides one of the first lines of defense against respiratory viruses, including SARS-CoV-2 that causes COVID-19. Substantial inter-individual variability in individual dis...

Authors: Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jenna Nguyen, Elizabeth Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Z. Barjaktarevic, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David J. Couper…

Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation

Preclinical studies and early clinical trials have shown that targeting cancer neoantigens is a promising approach towards the development of personalized cancer immunotherapies. DNA vaccines can be rapidly an...

Authors: Lijin Li, Xiuli Zhang, Xiaoli Wang, Samuel W. Kim, John M. Herndon, Michelle K. Becker-Hapak, Beatriz M. Carreno, Nancy B. Myers, Mark A. Sturmoski, Michael D. McLellan, Christopher A. Miller, Tanner M. Johanns, Benjamin R. Tan, Gavin P. Dunn, Timothy P. Fleming, Ted H. Hansen…

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation

Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other inflammatory diseases with establis...

Authors: Fan Zhang, Joseph R. Mears, Lorien Shakib, Jessica I. Beynor, Sara Shanaj, Ilya Korsunsky, Aparna Nathan, Laura T. Donlin and Soumya Raychaudhuri

Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders

With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype–ph...

Authors: Madelyn A. Gillentine, Tianyun Wang, Kendra Hoekzema, Jill Rosenfeld, Pengfei Liu, Hui Guo, Chang N. Kim, Bert B. A. De Vries, Lisenka E. L. M. Vissers, Magnus Nordenskjold, Malin Kvarnung, Anna Lindstrand, Ann Nordgren, Jozef Gecz, Maria Iascone, Anna Cereda…

Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies

The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Vir...

Authors: Billy T. Lau, Dmitri Pavlichin, Anna C. Hooker, Alison Almeda, Giwon Shin, Jiamin Chen, Malaya K. Sahoo, Chun Hong Huang, Benjamin A. Pinsky, Ho Joon Lee and Hanlee P. Ji

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone a...

Authors: Leonor Sánchez-Busó, Corin A. Yeats, Benjamin Taylor, Richard J. Goater, Anthony Underwood, Khalil Abudahab, Silvia Argimón, Kevin C. Ma, Tatum D. Mortimer, Daniel Golparian, Michelle J. Cole, Yonatan H. Grad, Irene Martin, Brian H. Raphael, William M. Shafer, Katy Town…

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer

Currently, over half of breast cancer cases are unrelated to known risk factors, highlighting the importance of discovering other cancer-promoting factors. Since crosstalk between gut microbes and host immunit...

Authors: Alice Tzeng, Naseer Sangwan, Margaret Jia, Chin-Chih Liu, Karen S. Keslar, Erinn Downs-Kelly, Robert L. Fairchild, Zahraa Al-Hilli, Stephen R. Grobmyer and Charis Eng

Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases

Knowledge of the molecular etiology of neurodegenerative brain diseases (NBD) has substantially increased over the past three decades. Early genetic studies of NBD families identified rare and highly penetrant...

Authors: Federica Perrone, Rita Cacace, Julie van der Zee and Christine Van Broeckhoven

PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling

Aberrant changes in epigenetic mechanisms such as histone modifications play an important role in cancer progression. PRMT1 which triggers asymmetric dimethylation of histone H4 on arginine 3 (H4R3me2a) is upr...

Authors: Bing Yao, Tao Gui, Xiangwei Zeng, Yexuan Deng, Zhi Wang, Ying Wang, Dongjun Yang, Qixiang Li, Peipei Xu, Ruifeng Hu, Xinyu Li, Bing Chen, Jin Wang, Ke Zen, Haitao Li, Melissa J. Davis…

In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers

Mutations in the DMD gene encoding dystrophin—a critical structural element in muscle cells—cause Duchenne muscular dystrophy (DMD), which is the most common fatal genetic disease. Clustered regularly interspaced...

Authors: Menglong Chen, Hui Shi, Shixue Gou, Xiaomin Wang, Lei Li, Qin Jin, Han Wu, Huili Zhang, Yaqin Li, Liang Wang, Huan Li, Jinfu Lin, Wenjing Guo, Zhiwu Jiang, Xiaoyu Yang, Anding Xu…

Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes

ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane-anchored protein involved in diverse processes including mitochondrial dynamics, mitochondrial DNA organizati...

Authors: Zheng Yie Yap, Yo Han Park, Saskia B. Wortmann, Adam C. Gunning, Shlomit Ezer, Sukyeong Lee, Lita Duraine, Ekkehard Wilichowski, Kate Wilson, Johannes A. Mayr, Matias Wagner, Hong Li, Usha Kini, Emily Davis Black, Kristin G. Monaghan, James R. Lupski…

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home

Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical ri...

Authors: Quinten R. Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N. Bloem, Karuna E. W. Vendrik, Monique A. A. Caljouw, Ingrid M. J. G. Sanders, Sofie M. van Dorp, Man C. Wong, Romy D. Zwittink and Ed J. Kuijper

Persistent variations of blood DNA methylation associated with treatment exposures and risk for cardiometabolic outcomes in long-term survivors of childhood cancer in the St. Jude Lifetime Cohort

It is well-established that cancer treatment substantially increases the risk of long-term adverse health outcomes among childhood cancer survivors. However, there is limited research on the underlying mechani...

Authors: Nan Song, Chia-Wei Hsu, Haitao Pan, Yinan Zheng, Lifang Hou, Jin-ah Sim, Zhenghong Li, Heather Mulder, John Easton, Emily Walker, Geoffrey Neale, Carmen L. Wilson, Kirsten K. Ness, Kevin R. Krull, Deo Kumar Srivastava, Yutaka Yasui…

The global dissemination of hospital clones of Enterococcus faecium

The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains...

Authors: Sebastiaan J. van Hal, Rob J. L. Willems, Theodore Gouliouris, Susan A. Ballard, Teresa M. Coque, Anette M. Hammerum, Kristin Hegstad, Hendrik T. Westh, Benjamin P. Howden, Surbhi Malhotra-Kumar, Guido Werner, Katsunori Yanagihara, Ashlee M. Earl, Katherine E. Raven, Jukka Corander and Rory Bowden

Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae

Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalo...

Authors: Koji Yahara, Kevin C. Ma, Tatum D. Mortimer, Ken Shimuta, Shu-ichi Nakayama, Aki Hirabayashi, Masato Suzuki, Michio Jinnai, Hitomi Ohya, Toshiro Kuroki, Yuko Watanabe, Mitsuru Yasuda, Takashi Deguchi, Vegard Eldholm, Odile B. Harrison, Martin C. J. Maiden…

Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making

Newborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of ...

Authors: Daniela M. DeCristo, Laura V. Milko, Julianne M. O’Daniel, Ann Katherine M. Foreman, Lonna F. Mollison, Bradford C. Powell, Cynthia M. Powell and Jonathan S. Berg

Development of double-positive thymocytes at single-cell resolution

T cells generated from thymopoiesis are essential for the immune system, and recent single-cell studies have contributed to our understanding of the development of thymocytes at the genetic and epigenetic leve...

Authors: Young Li, Kun Li, Lianbang Zhu, Bin Li, Dandan Zong, Pengfei Cai, Chen Jiang, Pengcheng Du, Jun Lin and Kun Qu

Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study

Childhood obesity is reported to be associated with the risk of many diseases in adulthood. However, observational studies cannot fully account for confounding factors. We aimed to systematically assess the ca...

Authors: Shan-Shan Dong, Kun Zhang, Yan Guo, Jing-Miao Ding, Yu Rong, Jun-Cheng Feng, Shi Yao, Ruo-Han Hao, Feng Jiang, Jia-Bin Chen, Hao Wu, Xiao-Feng Chen and Tie-Lin Yang

Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation

Neuroinflammation and immune responses occurring minutes to hours after stroke are associated with brain injury after acute ischemic stroke (AIS). PPARγ coactivator-1α (PGC-1α), as a master coregulator of gene...

Authors: Bin Han, Wei Jiang, Pan Cui, Kai Zheng, Chun Dang, Junjie Wang, He Li, Lin Chen, Rongxin Zhang, Qing Mei Wang, Zhenyu Ju and Junwei Hao

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

DNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and p...

Authors: Thomas J. Nicholas, Michael J. Cormier, Xiaomeng Huang, Yi Qiao, Gabor T. Marth and Aaron R. Quinlan

CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genot...

Authors: Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. van Bergen and Ewa Szczurek

Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients

We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since m...

Authors: Henrik Stranneheim, Kristina Lagerstedt-Robinson, Måns Magnusson, Malin Kvarnung, Daniel Nilsson, Nicole Lesko, Martin Engvall, Britt-Marie Anderlid, Henrik Arnell, Carolina Backman Johansson, Michela Barbaro, Erik Björck, Helene Bruhn, Jesper Eisfeldt, Christoph Freyer, Giedre Grigelioniene…

Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated t...

Authors: Céline Callens, Keltouma Driouch, Anaïs Boulai, Zakia Tariq, Aurélie Comte, Frédérique Berger, Lisa Belin, Ivan Bièche, Vincent Servois, Patricia Legoix, Virginie Bernard, Sylvain Baulande, Walid Chemlali, François-Clément Bidard, Virginie Fourchotte, Anne Vincent- Salomon…

SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of ad...

Authors: Abdulaziz Almuqrin, Andrew D. Davidson, Maia Kavanagh Williamson, Philip A. Lewis, Kate J. Heesom, Susan Morris, Sarah C. Gilbert and David A. Matthews

Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer

Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning met...

Authors: Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck, Júlia Perera-Bel, Philip Stegmaier, Florian Auer, Frank Kramer, Andreas Leha and Tim Beißbarth

Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation

Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly n...

Authors: Shuquan Rao, Yao Yao and Daniel E. Bauer

Genetic disruption of serine biosynthesis is a key driver of macular telangiectasia type 2 aetiology and progression

Macular telangiectasia type 2 (MacTel) is a rare, heritable and largely untreatable retinal disorder, often comorbid with diabetes. Genetic risk loci subtend retinal vascular calibre and glycine/serine/threoni...

Authors: Roberto Bonelli, Brendan R. E. Ansell, Luca Lotta, Thomas Scerri, Traci E. Clemons, Irene Leung, Tunde Peto, Alan C. Bird, Ferenc B. Sallo, Claudia Langenberg and Melanie Bahlo

Genetic susceptibility, elevated blood pressure, and risk of atrial fibrillation: a Mendelian randomization study

Whether elevated blood pressure (BP) is a modifiable risk factor for atrial fibrillation (AF) is not established. We tested (1) whether the association between BP and risk of AF is causal, (2) whether it varie...

Authors: Milad Nazarzadeh, Ana-Catarina Pinho-Gomes, Zeinab Bidel, Dexter Canoy, Abbas Dehghan, Karl Smith Byrne, Derrick A. Bennett, George Davey Smith and Kazem Rahimi

Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India

Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up env...

Authors: Camila Alvarez-Silva, Alireza Kashani, Tue Haldor Hansen, Nishal Kumar Pinna, Ranjit Mohan Anjana, Anirban Dutta, Shruti Saxena, Julie Støy, Ulla Kampmann, Trine Nielsen, Torben Jørgensen, Visvanathan Gnanaprakash, Rameshkumar Gnanavadivel, Aswath Sukumaran, Coimbatore Subramanian Shanthi Rani, Kristine Færch…

Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark

Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of “prediabetic” (PD) subj...

Authors: Nishal Kumar Pinna, Ranjit Mohan Anjana, Shruti Saxena, Anirban Dutta, Visvanathan Gnanaprakash, Gnanavadivel Rameshkumar, Sukumaran Aswath, Srividhya Raghavan, Coimbatore Subramanian Shanthi Rani, Venkatesan Radha, Muthuswamy Balasubramanyam, Archana Pant, Trine Nielsen, Torben Jørgensen, Kristine Færch, Alireza Kashani…

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis

Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis i...

Authors: Damian R. Plichta, Juhi Somani, Matthieu Pichaud, Zachary S. Wallace, Ana D. Fernandes, Cory A. Perugino, Harri Lähdesmäki, John H. Stone, Hera Vlamakis, Daniel C. Chung, Dinesh Khanna, Shiv Pillai and Ramnik J. Xavier

Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been i...

Authors: William L. Macken, Annie Godwin, Gabrielle Wheway, Karen Stals, Liliya Nazlamova, Sian Ellard, Ahmed Alfares, Taghrid Aloraini, Lamia AlSubaie, Majid Alfadhel, Sulaiman Alajaji, Htoo A. Wai, Jay Self, Andrew G. L. Douglas, Alexander P. Kao, Matthew Guille…

Clinical-grade whole-genome sequencing and 3′ transcriptome analysis of colorectal cancer patients

Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Color...

Authors: Agata Stodolna, Miao He, Mahesh Vasipalli, Zoya Kingsbury, Jennifer Becq, Joanne D. Stockton, Mark P. Dilworth, Jonathan James, Toju Sillo, Daniel Blakeway, Stephen T. Ward, Tariq Ismail, Mark T. Ross and Andrew D. Beggs

ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data

Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false pos...

Authors: Andre E. Minoche, Ben Lundie, Greg B. Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger and Mark J. Cowley