van Hal, Sebastiaan J. Willems, Rob J. L. Gouliouris, Theodore Ballard, Susan A. Coque, Teresa M. Hammerum, Anette M. Hegstad, Kristin Westh, Hendrik T. Howden, Benjamin P. Malhotra-Kumar, Surbhi
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Published in
Genome Medicine
BackgroundThe 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 poorly understood.MethodsA large, globally representative collection of short-read genomic data from the hospital-associated A1...
Yahara, Koji Ma, Kevin C. Mortimer, Tatum D. Shimuta, Ken Nakayama, Shu-ichi Hirabayashi, Aki Suzuki, Masato Jinnai, Michio Ohya, Hitomi Kuroki, Toshiro
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Published in
Genome Medicine
BackgroundAntimicrobial 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 cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and pr...
DeCristo, Daniela M. Milko, Laura V. O’Daniel, Julianne M. Foreman, Ann Katherine M. Mollison, Lonna F. Powell, Bradford C. Powell, Cynthia M. Berg, Jonathan S.
Published in
Genome Medicine
BackgroundNewborn 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 precision medicine, genomic sequencing has been introduced to this area with the hopes of detecting variants related to a vastly ex...
Han, Bin Jiang, Wei Cui, Pan Zheng, Kai Dang, Chun Wang, Junjie Li, He Chen, Lin Zhang, Rongxin Wang, Qing Mei
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Published in
Genome Medicine
BackgroundNeuroinflammation 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 expression in mitochondrial biogenesis, was found to be transiently upregulated in microglia after AIS. However, the role of micro...
Nicholas, Thomas J. Cormier, Michael J. Huang, Xiaomeng Qiao, Yi Marth, Gabor T. Quinlan, Aaron R.
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Genome Medicine
BackgroundDNA 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 progression of a tumor represents a significant challenge. Furthermore, prioritizing the subset of such mutations most likely to con...
Dong, Shan-Shan Zhang, Kun Guo, Yan Ding, Jing-Miao Rong, Yu Feng, Jun-Cheng Yao, Shi Hao, Ruo-Han Jiang, Feng Chen, Jia-Bin
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Published in
Genome Medicine
BackgroundChildhood 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 causal associations between childhood body mass index (BMI) and various adult traits/diseases using two-sample Mendelian randomizatio...
Li, Young Li, Kun Zhu, Lianbang Li, Bin Zong, Dandan Cai, Pengfei Jiang, Chen Du, Pengcheng Lin, Jun Qu, Kun
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Published in
Genome Medicine
BackgroundT 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 levels. However, the development of double-positive (DP) T cells, which comprise the majority of thymocytes, has not been well investig...
Shafighi, Shadi Darvish Kiełbasa, Szymon M. Sepúlveda-Yáñez, Julieta Monajemi, Ramin Cats, Davy Mei, Hailiang Menafra, Roberta Kloet, Susan Veelken, Hendrik van Bergen, Cornelis A.M.
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Published in
Genome Medicine
BackgroundDrawing 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 genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increa...
Stranneheim, Henrik Lagerstedt-Robinson, Kristina Magnusson, Måns Kvarnung, Malin Nilsson, Daniel Lesko, Nicole Engvall, Martin Anderlid, Britt-Marie Arnell, Henrik Johansson, Carolina Backman
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Published in
Genome Medicine
BackgroundWe 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 mid-2015. GMCK-RD represents a long-term collaborative initiative between Karolinska University Hospital and Science for Life Labora...
Callens, Céline Driouch, Keltouma Boulai, Anaïs Tariq, Zakia Comte, Aurélie Berger, Frédérique Belin, Lisa Bièche, Ivan Servois, Vincent Legoix, Patricia
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Published in
Genome Medicine
BackgroundPrognosis 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 the impact of metastatic subtyping during the initial metastatic event in a prospective study. The genomic landscape of metastatic b...