<?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%">Garg, Shilpa</style></author><author><style face="normal" font="default" size="100%">Fungtammasan, Arkarachai</style></author><author><style face="normal" font="default" size="100%">Carroll, Andrew</style></author><author><style face="normal" font="default" size="100%">Chou, Mike</style></author><author><style face="normal" font="default" size="100%">Schmitt, Anthony</style></author><author><style face="normal" font="default" size="100%">Zhou, Xiang</style></author><author><style face="normal" font="default" size="100%">Mac, Stephen</style></author><author><style face="normal" font="default" size="100%">Peluso, Paul</style></author><author><style face="normal" font="default" size="100%">Hatas, Emily</style></author><author><style face="normal" font="default" size="100%">Ghurye, Jay</style></author><author><style face="normal" font="default" size="100%">Maguire, Jared</style></author><author><style face="normal" font="default" size="100%">Mahmoud, Medhat</style></author><author><style face="normal" font="default" size="100%">Cheng, Haoyu</style></author><author><style face="normal" font="default" size="100%">Heller, David</style></author><author><style face="normal" font="default" size="100%">Zook, Justin M</style></author><author><style face="normal" font="default" size="100%">Moemke, Tobias</style></author><author><style face="normal" font="default" size="100%">Marschall, Tobias</style></author><author><style face="normal" font="default" size="100%">Sedlazeck, Fritz J</style></author><author><style face="normal" font="default" size="100%">Aach, John</style></author><author><style face="normal" font="default" size="100%">Chin, Chen-Shan</style></author><author><style face="normal" font="default" size="100%">Church, George M</style></author><author><style face="normal" font="default" size="100%">Li, Heng</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Chromosome-scale, haplotype-resolved assembly of human genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosomes, Human</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Human</style></keyword><keyword><style  face="normal" font="default" size="100%">Haplotypes</style></keyword><keyword><style  face="normal" font="default" size="100%">Heterozygote</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 03</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">309-312</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98-99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.&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/33288905?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%">Patel, Aniruddh P</style></author><author><style face="normal" font="default" size="100%">Wang, Minxian</style></author><author><style face="normal" font="default" size="100%">Fahed, Akl C</style></author><author><style face="normal" font="default" size="100%">Mason-Suares, Heather</style></author><author><style face="normal" font="default" size="100%">Brockman, Deanna</style></author><author><style face="normal" font="default" size="100%">Pelletier, Renee</style></author><author><style face="normal" font="default" size="100%">Amr, Sami</style></author><author><style face="normal" font="default" size="100%">Machini, Kalotina</style></author><author><style face="normal" font="default" size="100%">Hawley, Megan</style></author><author><style face="normal" font="default" size="100%">Witkowski, Leora</style></author><author><style face="normal" font="default" size="100%">Koch, Christopher</style></author><author><style face="normal" font="default" size="100%">Philippakis, Anthony</style></author><author><style face="normal" font="default" size="100%">Cassa, Christopher A</style></author><author><style face="normal" font="default" size="100%">Ellinor, Patrick T</style></author><author><style face="normal" font="default" size="100%">Kathiresan, Sekar</style></author><author><style face="normal" font="default" size="100%">Ng, Kenney</style></author><author><style face="normal" font="default" size="100%">Lebo, Matthew</style></author><author><style face="normal" font="default" size="100%">Khera, Amit V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Association of Rare Pathogenic DNA Variants for Familial Hypercholesterolemia, Hereditary Breast and Ovarian Cancer Syndrome, and Lynch Syndrome With Disease Risk in Adults According to Family History.</style></title><secondary-title><style face="normal" font="default" size="100%">JAMA Netw Open</style></secondary-title><alt-title><style face="normal" font="default" size="100%">JAMA Netw Open</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Aged</style></keyword><keyword><style  face="normal" font="default" size="100%">Cohort Studies</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorectal Neoplasms, Hereditary Nonpolyposis</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Predisposition to Disease</style></keyword><keyword><style  face="normal" font="default" size="100%">Hereditary Breast and Ovarian Cancer Syndrome</style></keyword><keyword><style  face="normal" font="default" size="100%">Heterozygote</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Hyperlipoproteinemia Type II</style></keyword><keyword><style  face="normal" font="default" size="100%">Male</style></keyword><keyword><style  face="normal" font="default" size="100%">Middle Aged</style></keyword><keyword><style  face="normal" font="default" size="100%">Pedigree</style></keyword><keyword><style  face="normal" font="default" size="100%">Proportional Hazards Models</style></keyword><keyword><style  face="normal" font="default" size="100%">United Kingdom</style></keyword><keyword><style  face="normal" font="default" size="100%">Whole Exome Sequencing</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 04 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e203959</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;Importance: &lt;/b&gt;Pathogenic DNA variants associated with familial hypercholesterolemia, hereditary breast and ovarian cancer syndrome, and Lynch syndrome are widely recognized as clinically important and actionable when identified, leading some clinicians to recommend population-wide genomic screening.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Objectives: &lt;/b&gt;To assess the prevalence and clinical importance of pathogenic or likely pathogenic variants associated with each of 3 genomic conditions (familial hypercholesterolemia, hereditary breast and ovarian cancer syndrome, and Lynch syndrome) within the context of contemporary clinical care.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Design, Setting, and Participants: &lt;/b&gt;This cohort study used gene-sequencing data from 49 738 participants in the UK Biobank who were recruited from 22 sites across the UK between March 21, 2006, and October 1, 2010. Inpatient hospital data date back to 1977; cancer registry data, to 1957; and death registry data, to 2006. Statistical analysis was performed from July 22, 2019, to November 15, 2019.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Exposures: &lt;/b&gt;Pathogenic or likely pathogenic DNA variants classified by a clinical laboratory geneticist.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Main Outcomes and Measures: &lt;/b&gt;Composite end point specific to each genomic condition based on atherosclerotic cardiovascular disease events for familial hypercholesterolemia, breast or ovarian cancer for hereditary breast and ovarian cancer syndrome, and colorectal or uterine cancer for Lynch syndrome.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results: &lt;/b&gt;Among 49 738 participants (mean [SD] age, 57 [8] years; 27 144 female [55%]), 441 (0.9%) harbored a pathogenic or likely pathogenic variant associated with any of 3 genomic conditions, including 131 (0.3%) for familial hypercholesterolemia, 235 (0.5%) for hereditary breast and ovarian cancer syndrome, and 76 (0.2%) for Lynch syndrome. Presence of these variants was associated with increased risk of disease: for familial hypercholesterolemia, 28 of 131 carriers (21.4%) vs 4663 of 49 607 noncarriers (9.4%) developed atherosclerotic cardiovascular disease; for hereditary breast and ovarian cancer syndrome, 32 of 116 female carriers (27.6%) vs 2080 of 27 028 female noncarriers (7.7%) developed associated cancers; and for Lynch syndrome, 17 of 76 carriers (22.4%) vs 929 of 49 662 noncarriers (1.9%) developed colorectal or uterine cancer. The predicted probability of disease at age 75 years despite contemporary clinical care was 45.3% for carriers of familial hypercholesterolemia, 41.1% for hereditary breast and ovarian cancer syndrome, and 38.3% for Lynch syndrome. Across the 3 conditions, 39.7% (175 of 441) of the carriers reported a family history of disease vs 23.2% (34 517 of 148 772) of noncarriers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions and Relevance: &lt;/b&gt;The findings suggest that approximately 1% of the middle-aged adult population in the UK Biobank harbored a pathogenic variant associated with any of 3 genomic conditions. These variants were associated with an increased risk of disease despite contemporary clinical care and were not reliably detected by family history.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32347951?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%">Rusu, Victor</style></author><author><style face="normal" font="default" size="100%">Hoch, Eitan</style></author><author><style face="normal" font="default" size="100%">Mercader, Josep M</style></author><author><style face="normal" font="default" size="100%">Tenen, Danielle E</style></author><author><style face="normal" font="default" size="100%">Gymrek, Melissa</style></author><author><style face="normal" font="default" size="100%">Hartigan, Christina R</style></author><author><style face="normal" font="default" size="100%">DeRan, Michael</style></author><author><style face="normal" font="default" size="100%">von Grotthuss, Marcin</style></author><author><style face="normal" font="default" size="100%">Fontanillas, Pierre</style></author><author><style face="normal" font="default" size="100%">Spooner, Alexandra</style></author><author><style face="normal" font="default" size="100%">Guzman, Gaelen</style></author><author><style face="normal" font="default" size="100%">Deik, Amy A</style></author><author><style face="normal" font="default" size="100%">Pierce, Kerry A</style></author><author><style face="normal" font="default" size="100%">Dennis, Courtney</style></author><author><style face="normal" font="default" size="100%">Clish, Clary B</style></author><author><style face="normal" font="default" size="100%">Carr, Steven A</style></author><author><style face="normal" font="default" size="100%">Wagner, Bridget K</style></author><author><style face="normal" font="default" size="100%">Schenone, Monica</style></author><author><style face="normal" font="default" size="100%">Ng, Maggie C Y</style></author><author><style face="normal" font="default" size="100%">Chen, Brian H</style></author><author><style face="normal" font="default" size="100%">Centeno-Cruz, Federico</style></author><author><style face="normal" font="default" size="100%">Zerrweck, Carlos</style></author><author><style face="normal" font="default" size="100%">Orozco, Lorena</style></author><author><style face="normal" font="default" size="100%">Altshuler, David M</style></author><author><style face="normal" font="default" size="100%">Schreiber, Stuart L</style></author><author><style face="normal" font="default" size="100%">Florez, Jose C</style></author><author><style face="normal" font="default" size="100%">Jacobs, Suzanne B R</style></author><author><style face="normal" font="default" size="100%">Lander, Eric S</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">MEDIA Consortium</style></author><author><style face="normal" font="default" size="100%">SIGMA T2D Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Cell</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Cell</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Basigin</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Membrane</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosomes, Human, Pair 17</style></keyword><keyword><style  face="normal" font="default" size="100%">Diabetes Mellitus, Type 2</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Knockdown Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Haplotypes</style></keyword><keyword><style  face="normal" font="default" size="100%">Hepatocytes</style></keyword><keyword><style  face="normal" font="default" size="100%">Heterozygote</style></keyword><keyword><style  face="normal" font="default" size="100%">Histone Code</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Liver</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Monocarboxylic Acid Transporters</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Jun 29</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">170</style></volume><pages><style face="normal" font="default" size="100%">199-212.e20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Type 2 diabetes (T2D) affects Latinos at twice the rate seen in populations of European descent. We recently identified a risk haplotype spanning SLC16A11 that explains ∼20% of the increased T2D prevalence in Mexico. Here, through genetic fine-mapping, we define a set of tightly linked variants likely to contain the causal allele(s). We show that variants on the T2D-associated haplotype have two distinct effects: (1) decreasing SLC16A11 expression in liver and (2) disrupting a key interaction with basigin, thereby reducing cell-surface localization. Both independent mechanisms reduce SLC16A11 function and suggest SLC16A11 is the causal gene at this locus. To gain insight into how SLC16A11 disruption impacts T2D risk, we demonstrate that SLC16A11 is a proton-coupled monocarboxylate transporter and that genetic perturbation of SLC16A11 induces changes in fatty acid and lipid metabolism that are associated with increased T2D risk. Our findings suggest that increasing SLC16A11 function could be therapeutically beneficial for T2D. VIDEO ABSTRACT.&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/28666119?dopt=Abstract</style></custom1></record></records></xml>