NGI offers spatial transcriptomics through the 10X Genomics Visium method, a technique recently nominated as Method of the Year by Nature Methods. The technology combines histology with unbiased transcriptomics in a spatial context.
The Illumina NovaSeq 6000 system is the largest of the Illumina sequencing instruments, able to run two flow cells independently of each other and generate massive sequencing depth at competitive prices.
SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.
L Malcovati, M Karimi, E Papaemmanuil, I Ambaglio, M Jädersten, M Jansson, C Elena, A Gallì, G Walldin, MG Della Porta, K Raaschou-Jensen, E Travaglino, K Kallenbach, D Pietra, V Ljungström, S Conte, E Boveri, R Invernizzi, R Rosenquist, PJ Campbell, M Cazzola, E Hellström Lindberg
Blood, 126 (2) 1528-0020 (2015)
Refractory anemia with ring sideroblasts (RARS) is a myelodysplastic syndrome (MDS) characterized by isolated erythroid dysplasia and 15% or more bone marrow ring sideroblasts. Ring sideroblasts are found also in other MDS subtypes, such as refractory cytopenia with multilineage dysplasia and ring sideroblasts (RCMD-RS). A high prevalence of somatic mutations of SF3B1 was reported in these conditions. To identify mutation patterns that affect disease phenotype and clinical outcome, we performed a comprehensive mutation analysis in 293 patients with myeloid neoplasm and 1% or more ring sideroblasts. SF3B1 mutations were detected in 129 of 159 cases (81%) of RARS or RCMD-RS. Among other patients with ring sideroblasts, lower prevalence of SF3B1 mutations and higher prevalence of mutations in other splicing factor genes were observed (P < .001). In multivariable analyses, patients with SF3B1 mutations showed significantly better overall survival (hazard ratio [HR], .37; P = .003) and lower cumulative incidence of disease progression (HR = 0.31; P = .018) compared with SF3B1-unmutated cases. The independent prognostic value of SF3B1 mutation was retained in MDS without excess blasts, as well as in sideroblastic categories (RARS and RCMD-RS). Among SF3B1-mutated patients, coexisting mutations in DNA methylation genes were associated with multilineage dysplasia (P = .015) but had no effect on clinical outcome. TP53 mutations were frequently detected in patients without SF3B1 mutation, and were associated with poor outcome. Thus, SF3B1 mutation identifies a distinct MDS subtype that is unlikely to develop detrimental subclonal mutations and is characterized by indolent clinical course and favorable outcome.
Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.
L He, M Vanlandewijck, MA Mäe, J Andrae, K Ando, F Del Gaudio, K Nahar, T Lebouvier, B Laviña, L Gouveia, Y Sun, E Raschperger, Å Segerstolpe, J Liu, S Gustafsson, M Räsänen, Y Zarb, N Mochizuki, A Keller, U Lendahl, C Betsholtz
Sci Data, 5 (1) 2052-4463 (2018)
Vascular diseases are major causes of death, yet our understanding of the cellular constituents of blood vessels, including how differences in their gene expression profiles create diversity in vascular structure and function, is limited. In this paper, we describe a single-cell RNA sequencing (scRNA-seq) dataset that defines vascular and vessel-associated cell types and subtypes in mouse brain and lung. The dataset contains 3,436 single cell transcriptomes from mouse brain, which formed 15 distinct clusters corresponding to cell (sub)types, and another 1,504 single cell transcriptomes from mouse lung, which formed 17 cell clusters. In order to allow user-friendly access to our data, we constructed a searchable database (http://betsholtzlab.org/VascularSingleCells/database.html). Our dataset constitutes a comprehensive molecular atlas of vascular and vessel-associated cell types in the mouse brain and lung, and as such provides a strong foundation for future studies of vascular development and diseases.
The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis.
Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium, DI Swerdlow, MV Holmes, KB Kuchenbaecker, JE Engmann, T Shah, R Sofat, Y Guo, C Chung, A Peasey, R Pfister, SP Mooijaart, HA Ireland, M Leusink, C Langenberg, KW Li, J Palmen, P Howard, JA Cooper, F Drenos, J Hardy, MA Nalls, YR Li, G Lowe, M Stewart, SJ Bielinski, J Peto, NJ Timpson, J Gallacher, M Dunlop, R Houlston, I Tomlinson, I Tzoulaki, J Luan, JM Boer, NG Forouhi, NC Onland-Moret, YT van der Schouw, RB Schnabel, JA Hubacek, R Kubinova, M Baceviciene, A Tamosiunas, A Pajak, R Topor-Madry, S Malyutina, D Baldassarre, B Sennblad, E Tremoli, U de Faire, L Ferrucci, S Bandenelli, T Tanaka, JF Meschia, A Singleton, G Navis, I Mateo Leach, SJ Bakker, RT Gansevoort, I Ford, SE Epstein, MS Burnett, JM Devaney, JW Jukema, RG Westendorp, G Jan de Borst, Y van der Graaf, PA de Jong, AH Mailand-van der Zee, OH Klungel, A de Boer, PA Doevendans, JW Stephens, CB Eaton, JG Robinson, JE Manson, FG Fowkes, TM Frayling, JF Price, PH Whincup, RW Morris, DA Lawlor, GD Smith, Y Ben-Shlomo, S Redline, LA Lange, M Kumari, NJ Wareham, WM Verschuren, EJ Benjamin, JC Whittaker, A Hamsten, F Dudbridge, JA Delaney, A Wong, D Kuh, R Hardy, BA Castillo, JJ Connolly, P van der Harst, EJ Brunner, MG Marmot, CL Wassel, SE Humphries, PJ Talmud, M Kivimaki, FW Asselbergs, M Voevoda, M Bobak, H Pikhart, JG Wilson, H Hakonarson, AP Reiner, BJ Keating, N Sattar, AD Hingorani, JP Casas
Lancet, 379 (9822) 1474-547X (2012)
A high circulating concentration of interleukin 6 is associated with increased risk of coronary heart disease. Blockade of the interleukin-6 receptor (IL6R) with a monoclonal antibody (tocilizumab) licensed for treatment of rheumatoid arthritis reduces systemic and articular inflammation. However, whether IL6R blockade also reduces risk of coronary heart disease is unknown.
Applying the mendelian randomisation principle, we used single nucleotide polymorphisms (SNPs) in the gene IL6R to evaluate the likely efficacy and safety of IL6R inhibition for primary prevention of coronary heart disease. We compared genetic findings with the effects of tocilizumab reported in randomised trials in patients with rheumatoid arthritis.
In 40 studies including up to 133,449 individuals, an IL6R SNP (rs7529229) marking a non-synonymous IL6R variant (rs8192284; p.Asp358Ala) was associated with increased circulating log interleukin-6 concentration (increase per allele 9·45%, 95% CI 8·34-10·57) as well as reduced C-reactive protein (decrease per allele 8·35%, 95% CI 7·31-9·38) and fibrinogen concentrations (decrease per allele 0·85%, 95% CI 0·60-1·10). This pattern of effects was consistent with IL6R blockade from infusions of tocilizumab (4-8 mg/kg every 4 weeks) in patients with rheumatoid arthritis studied in randomised trials. In 25,458 coronary heart disease cases and 100,740 controls, the IL6R rs7529229 SNP was associated with a decreased odds of coronary heart disease events (per allele odds ratio 0·95, 95% CI 0·93-0·97, p=1·53×10(-5)).
On the basis of genetic evidence in human beings, IL6R signalling seems to have a causal role in development of coronary heart disease. IL6R blockade could provide a novel therapeutic approach to prevention of coronary heart disease that warrants testing in suitably powered randomised trials. Genetic studies in populations could be used more widely to help to validate and prioritise novel drug targets or to repurpose existing agents and targets for new therapeutic uses.
UK Medical Research Council; British Heart Foundation; Rosetrees Trust; US National Heart, Lung, and Blood Institute; Du Pont Pharma; Chest, Heart and Stroke Scotland; Wellcome Trust; Coronary Thrombosis Trust; Northwick Park Institute for Medical Research; UCLH/UCL Comprehensive Medical Research Centre; US National Institute on Aging; Academy of Finland; Netherlands Organisation for Health Research and Development; SANCO; Dutch Ministry of Public Health, Welfare and Sports; World Cancer Research Fund; Agentschap NL; European Commission; Swedish Heart-Lung Foundation; Swedish Research Council; Strategic Cardiovascular Programme of the Karolinska Institutet; Stockholm County Council; US National Institute of Neurological Disorders and Stroke; MedStar Health Research Institute; GlaxoSmithKline; Dutch Kidney Foundation; US National Institutes of Health; Netherlands Interuniversity Cardiology Institute of the Netherlands; Diabetes UK; European Union Seventh Framework Programme; National Institute for Healthy Ageing; Cancer Research UK; MacArthur Foundation.
Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions.
M Vass, AJ Székely, ES Lindström, S Langenheder
Sci Rep, 10 (1) 2045-2322 (2020)
Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).
F Sánchez-Barreiro, S Gopalakrishnan, J Ramos-Madrigal, MV Westbury, M de Manuel, A Margaryan, MM Ciucani, FG Vieira, Y Patramanis, DC Kalthoff, Z Timmons, T Sicheritz-Pontén, L Dalén, OA Ryder, G Zhang, T Marquès-Bonet, Y Moodley, MTP Gilbert
Mol. Ecol., 30 (23) 1365-294X (2021)
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.
E Gering, M Johnsson, P Willis, T Getty, D Wright
Mol. Ecol., 24 (9) 1365-294X (2015)
A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.
Standards recommendations for the Earth BioGenome Project.
MKN Lawniczak, R Durbin, P Flicek, K Lindblad-Toh, X Wei, JM Archibald, WJ Baker, K Belov, ML Blaxter, T Marques Bonet, AK Childers, JA Coddington, KA Crandall, AJ Crawford, RP Davey, F Di Palma, Q Fang, W Haerty, N Hall, KJ Hoff, K Howe, ED Jarvis, WE Johnson, RN Johnson, PJ Kersey, X Liu, JV Lopez, EW Myers, OV Pettersson, AM Phillippy, MF Poelchau, KD Pruitt, A Rhie, JC Castilla-Rubio, SK Sahu, NA Salmon, PS Soltis, D Swarbreck, F Thibaud-Nissen, S Wang, JL Wegrzyn, G Zhang, H Zhang, HA Lewin, S Richards
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
Necessary cookies are absolutely essential for the website to function properly. This category only includes cookies that ensures basic functionalities and security features of the website. These cookies do not store any personal information.
Any cookies that may not be particularly necessary for the website to function and is used specifically to collect user personal data via analytics, ads, other embedded contents are termed as non-necessary cookies. It is mandatory to procure user consent prior to running these cookies on your website.