<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mak, Angel C Y</style></author><author><style face="normal" font="default" size="100%">Sajuthi, Satria</style></author><author><style face="normal" font="default" size="100%">Joo, Jaehyun</style></author><author><style face="normal" font="default" size="100%">Xiao, Shujie</style></author><author><style face="normal" font="default" size="100%">Sleiman, Patrick M</style></author><author><style face="normal" font="default" size="100%">White, Marquitta J</style></author><author><style face="normal" font="default" size="100%">Lee, Eunice Y</style></author><author><style face="normal" font="default" size="100%">Saef, Benjamin</style></author><author><style face="normal" font="default" size="100%">Hu, Donglei</style></author><author><style face="normal" font="default" size="100%">Gui, Hongsheng</style></author><author><style face="normal" font="default" size="100%">Keys, Kevin L</style></author><author><style face="normal" font="default" size="100%">Lurmann, Fred</style></author><author><style face="normal" font="default" size="100%">Jain, Deepti</style></author><author><style face="normal" font="default" size="100%">Abecasis, Gonçalo</style></author><author><style face="normal" font="default" size="100%">Kang, Hyun Min</style></author><author><style face="normal" font="default" size="100%">Nickerson, Deborah A</style></author><author><style face="normal" font="default" size="100%">Germer, Soren</style></author><author><style face="normal" font="default" size="100%">Zody, Michael C</style></author><author><style face="normal" font="default" size="100%">Winterkorn, Lara</style></author><author><style face="normal" font="default" size="100%">Reeves, Catherine</style></author><author><style face="normal" font="default" size="100%">Huntsman, Scott</style></author><author><style face="normal" font="default" size="100%">Eng, Celeste</style></author><author><style face="normal" font="default" size="100%">Salazar, Sandra</style></author><author><style face="normal" font="default" size="100%">Oh, Sam S</style></author><author><style face="normal" font="default" size="100%">Gilliland, Frank D</style></author><author><style face="normal" font="default" size="100%">Chen, Zhanghua</style></author><author><style face="normal" font="default" size="100%">Kumar, Rajesh</style></author><author><style face="normal" font="default" size="100%">Martínez, Fernando D</style></author><author><style face="normal" font="default" size="100%">Wu, Ann Chen</style></author><author><style face="normal" font="default" size="100%">Ziv, Elad</style></author><author><style face="normal" font="default" size="100%">Hakonarson, Hakon</style></author><author><style face="normal" font="default" size="100%">Himes, Blanca E</style></author><author><style face="normal" font="default" size="100%">Williams, L Keoki</style></author><author><style face="normal" font="default" size="100%">Seibold, Max A</style></author><author><style face="normal" font="default" size="100%">Burchard, Esteban G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand  and Gene-By-Air-Pollution Interaction.</style></title><secondary-title><style face="normal" font="default" size="100%">Genetics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genetics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 07</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">215</style></volume><pages><style face="normal" font="default" size="100%">869-886</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV on chromosome 12 in 867 African American children with asthma ( = 1.26 × 10, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with  (KIT ligand, also known as ), and their minor alleles were associated with increased expression of the  gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure ( = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV, possibly mediated through , in African American children with asthma. This is the first study that has identified a genetic association between lung function and , which has established a role in orchestrating allergic inflammation in asthma.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32327564?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sajuthi, Satria P</style></author><author><style face="normal" font="default" size="100%">DeFord, Peter</style></author><author><style face="normal" font="default" size="100%">Li, Yingchun</style></author><author><style face="normal" font="default" size="100%">Jackson, Nathan D</style></author><author><style face="normal" font="default" size="100%">Montgomery, Michael T</style></author><author><style face="normal" font="default" size="100%">Everman, Jamie L</style></author><author><style face="normal" font="default" size="100%">Rios, Cydney L</style></author><author><style face="normal" font="default" size="100%">Pruesse, Elmar</style></author><author><style face="normal" font="default" size="100%">Nolin, James D</style></author><author><style face="normal" font="default" size="100%">Plender, Elizabeth G</style></author><author><style face="normal" font="default" size="100%">Wechsler, Michael E</style></author><author><style face="normal" font="default" size="100%">Mak, Angel C Y</style></author><author><style face="normal" font="default" size="100%">Eng, Celeste</style></author><author><style face="normal" font="default" size="100%">Salazar, Sandra</style></author><author><style face="normal" font="default" size="100%">Medina, Vivian</style></author><author><style face="normal" font="default" size="100%">Wohlford, Eric M</style></author><author><style face="normal" font="default" size="100%">Huntsman, Scott</style></author><author><style face="normal" font="default" size="100%">Nickerson, Deborah A</style></author><author><style face="normal" font="default" size="100%">Germer, Soren</style></author><author><style face="normal" font="default" size="100%">Zody, Michael C</style></author><author><style face="normal" font="default" size="100%">Abecasis, Gonçalo</style></author><author><style face="normal" font="default" size="100%">Kang, Hyun Min</style></author><author><style face="normal" font="default" size="100%">Rice, Kenneth M</style></author><author><style face="normal" font="default" size="100%">Kumar, Rajesh</style></author><author><style face="normal" font="default" size="100%">Oh, Sam</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Santana, Jose</style></author><author><style face="normal" font="default" size="100%">Burchard, Esteban G</style></author><author><style face="normal" font="default" size="100%">Seibold, Max A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Angiotensin-Converting Enzyme 2</style></keyword><keyword><style  face="normal" font="default" size="100%">Betacoronavirus</style></keyword><keyword><style  face="normal" font="default" size="100%">Child</style></keyword><keyword><style  face="normal" font="default" size="100%">Coronavirus Infections</style></keyword><keyword><style  face="normal" font="default" size="100%">COVID-19</style></keyword><keyword><style  face="normal" font="default" size="100%">Epithelial Cells</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Host-Pathogen Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Inflammation</style></keyword><keyword><style  face="normal" font="default" size="100%">Interferons</style></keyword><keyword><style  face="normal" font="default" size="100%">Interleukin-13</style></keyword><keyword><style  face="normal" font="default" size="100%">Middle Aged</style></keyword><keyword><style  face="normal" font="default" size="100%">Nasal Mucosa</style></keyword><keyword><style  face="normal" font="default" size="100%">Pandemics</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptidyl-Dipeptidase A</style></keyword><keyword><style  face="normal" font="default" size="100%">Pneumonia, Viral</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2</style></keyword><keyword><style  face="normal" font="default" size="100%">Serine Endopeptidases</style></keyword><keyword><style  face="normal" font="default" size="100%">Virus Internalization</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 10 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">5139</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, an emerging virus that utilizes host proteins ACE2 and TMPRSS2 as entry factors. Understanding the factors affecting the pattern and levels of expression of these genes is important for deeper understanding of SARS-CoV-2 tropism and pathogenesis. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci for both ACE2 and TMPRSS2, that vary in frequency across world populations. We find TMPRSS2 is part of a mucus secretory network, highly upregulated by type 2 (T2) inflammation through the action of interleukin-13, and that the interferon response to respiratory viruses highly upregulates ACE2 expression. IL-13 and virus infection mediated effects on ACE2 expression were also observed at the protein level in the airway epithelium. Finally, we define airway responses to common coronavirus infections in children, finding that these infections generate host responses similar to other viral species, including upregulation of IL6 and ACE2. Our results reveal possible mechanisms influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33046696?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sajuthi, Satria P</style></author><author><style face="normal" font="default" size="100%">DeFord, Peter</style></author><author><style face="normal" font="default" size="100%">Jackson, Nathan D</style></author><author><style face="normal" font="default" size="100%">Montgomery, Michael T</style></author><author><style face="normal" font="default" size="100%">Everman, Jamie L</style></author><author><style face="normal" font="default" size="100%">Rios, Cydney L</style></author><author><style face="normal" font="default" size="100%">Pruesse, Elmar</style></author><author><style face="normal" font="default" size="100%">Nolin, James D</style></author><author><style face="normal" font="default" size="100%">Plender, Elizabeth G</style></author><author><style face="normal" font="default" size="100%">Wechsler, Michael E</style></author><author><style face="normal" font="default" size="100%">Mak, Angel Cy</style></author><author><style face="normal" font="default" size="100%">Eng, Celeste</style></author><author><style face="normal" font="default" size="100%">Salazar, Sandra</style></author><author><style face="normal" font="default" size="100%">Medina, Vivian</style></author><author><style face="normal" font="default" size="100%">Wohlford, Eric M</style></author><author><style face="normal" font="default" size="100%">Huntsman, Scott</style></author><author><style face="normal" font="default" size="100%">Nickerson, Deborah A</style></author><author><style face="normal" font="default" size="100%">Germer, Soren</style></author><author><style face="normal" font="default" size="100%">Zody, Michael C</style></author><author><style face="normal" font="default" size="100%">Abecasis, Gonçalo</style></author><author><style face="normal" font="default" size="100%">Kang, Hyun Min</style></author><author><style face="normal" font="default" size="100%">Rice, Kenneth M</style></author><author><style face="normal" font="default" size="100%">Kumar, Rajesh</style></author><author><style face="normal" font="default" size="100%">Oh, Sam</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Santana, Jose</style></author><author><style face="normal" font="default" size="100%">Burchard, Esteban G</style></author><author><style face="normal" font="default" size="100%">Seibold, Max A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium.</style></title><secondary-title><style face="normal" font="default" size="100%">bioRxiv</style></secondary-title><alt-title><style face="normal" font="default" size="100%">bioRxiv</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Apr 10</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Coronavirus disease 2019 (COVID-19) outcomes vary from asymptomatic infection to death. This disparity may reflect different airway levels of the SARS-CoV-2 receptor, ACE2, and the spike protein activator, TMPRSS2. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci (eQTL) for both  and , that vary in frequency across world populations. Importantly, we find  is part of a mucus secretory network, highly upregulated by T2 inflammation through the action of interleukin-13, and that interferon response to respiratory viruses highly upregulates  expression. Finally, we define airway responses to coronavirus infections in children, finding that these infections upregulate  while also stimulating a more pronounced cytotoxic immune response relative to other respiratory viruses. Our results reveal mechanisms likely influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32511326?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Regier, Allison A</style></author><author><style face="normal" font="default" size="100%">Farjoun, Yossi</style></author><author><style face="normal" font="default" size="100%">Larson, David E</style></author><author><style face="normal" font="default" size="100%">Krasheninina, Olga</style></author><author><style face="normal" font="default" size="100%">Kang, Hyun Min</style></author><author><style face="normal" font="default" size="100%">Howrigan, Daniel P</style></author><author><style face="normal" font="default" size="100%">Chen, Bo-Juen</style></author><author><style face="normal" font="default" size="100%">Kher, Manisha</style></author><author><style face="normal" font="default" size="100%">Banks, Eric</style></author><author><style face="normal" font="default" size="100%">Ames, Darren C</style></author><author><style face="normal" font="default" size="100%">English, Adam C</style></author><author><style face="normal" font="default" size="100%">Li, Heng</style></author><author><style face="normal" font="default" size="100%">Xing, Jinchuan</style></author><author><style face="normal" font="default" size="100%">Zhang, Yeting</style></author><author><style face="normal" font="default" size="100%">Matise, Tara</style></author><author><style face="normal" font="default" size="100%">Abecasis, Goncalo R</style></author><author><style face="normal" font="default" size="100%">Salerno, Will</style></author><author><style face="normal" font="default" size="100%">Zody, Michael C</style></author><author><style face="normal" font="default" size="100%">Neale, Benjamin M</style></author><author><style face="normal" font="default" size="100%">Hall, Ira M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Genome, Human</style></keyword><keyword><style  face="normal" font="default" size="100%">Human Genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Whole Genome Sequencing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 10 02</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">4038</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power. A central challenge for joint analysis is that different WGS data processing pipelines cause substantial differences in variant calling in combined datasets, necessitating computationally expensive reprocessing. This approach is no longer tenable given the scale of current studies and data volumes. Here, we define WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results and produce significantly less variability than sequencing replicates. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for community-wide human genetics studies.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/30279509?dopt=Abstract</style></custom1></record></records></xml>