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.
NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.
Are you interested in developing solutions to optimize the flow of large-scale genotyping and sequencing data from our instruments to researchers? We are now recruiting two new members to join our team at NGI Uppsala (SNP&SEQ Technology Platform).
Would you like to work in a field with rapid development in technologies and applications? We are now recruiting a new member to join our team of project coordinators at NGI Uppsala (the SNP&SEQ Technology platform)
Want to stay in touch? Join our newsletter!
All the latest updates from NGI direct to your inbox!
Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris.
J Rodriguez-Algaba, S Walter, CK Sørensen, MS Hovmøller, AF Justesen
Fungal Genet. Biol., 70 1096-0937 (2014)
An isolate of the basidiomycete Puccinia striiformis, which causes yellow (stripe) rust on wheat, was selfed on the newly discovered alternate host, Berberis vulgaris. This allowed a study of the segregation of molecular markers and virulence in the progeny isolates, and of the development of fungal sexual structures and spore forms. Pycnia and aecia were obtained after inoculation of B. vulgaris with basidiospores resulting from germinating teliospores from infected wheat leaves. Subsequent inoculation of wheat with aeciospores from bulked aecia resulted in 16 progeny isolates of the S1 generation. Genotyping with 42 simple sequence repeat (SSR) markers confirmed a parental origin of progeny isolates. Of the 42 analyzed loci, 15 were heterozygous in the parental isolate and 14 revealed segregation in the progenies. This resulted in 11 new multilocus genotypes (MLGs), which confirmed segregation following sexual reproduction. Additionally, parental and progeny isolates were phenotyped using a genetic stock of wheat genotypes representing 21 resistance genes. All S1 progeny isolates had virulence for 14 out of 15 loci where the parental isolate was virulent. This was consistent with the hypothesis that virulence in plant pathogens is often recessive to avirulence, i.e., only expressed in a homozygous state. Furthermore, no segregation was observed for five out of six loci, for which the parental isolate had an avirulent phenotype. The results for one of the two segregating virulence/avirulence loci suggested that the parental isolate was heterozygous with Avr alleles resulting in different but clearly avirulent phenotypes. The other locus indicated that additional genes modifying the phenotypic expression of avirulence were involved.
Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.
OC Bedoya-Reina, W Li, M Arceo, M Plescher, P Bullova, H Pui, M Kaucka, P Kharchenko, T Martinsson, J Holmberg, I Adameyko, Q Deng, C Larsson, CC Juhlin, P Kogner, S Schlisio
Nat Commun, 12 (1) 2041-1723 (2021)
Childhood neuroblastoma has a remarkable variability in outcome. Age at diagnosis is one of the most important prognostic factors, with children less than 1 year old having favorable outcomes. Here we study single-cell and single-nuclei transcriptomes of neuroblastoma with different clinical risk groups and stages, including healthy adrenal gland. We compare tumor cell populations with embryonic mouse sympatho-adrenal derivatives, and post-natal human adrenal gland. We provide evidence that low and high-risk neuroblastoma have different cell identities, representing two disease entities. Low-risk neuroblastoma presents a transcriptome that resembles sympatho- and chromaffin cells, whereas malignant cells enriched in high-risk neuroblastoma resembles a subtype of TRKB+ cholinergic progenitor population identified in human post-natal gland. Analyses of these populations reveal different gene expression programs for worst and better survival in correlation with age at diagnosis. Our findings reveal two cellular identities and a composition of human neuroblastoma tumors reflecting clinical heterogeneity and outcome.
Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.
Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.
Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.
T James, M Lindén, H Morikawa, SJ Fernandes, S Ruhrmann, M Huss, M Brandi, F Piehl, M Jagodic, J Tegnér, M Khademi, T Olsson, D Gomez-Cabrero, I Kockum
Hum. Mol. Genet., 27 (5) 1460-2083 (2018)
Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as multiple sclerosis (MS). As a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk single nucleotide polymorphisms and 7 associated human leukocyte antigen variants. We identified 77 statistically significant eQTL associations, including pseudogenes and non-coding RNAs. Thirty-eight out of 40 testable eQTL effects were colocalized with the disease association signal. As many eQTLs are tissue specific, we aimed to detail their significance in different cell types. Approximately 70% of the eQTLs were replicated and characterized in at least one major peripheral blood mononuclear cell-derived cell type. Furthermore, 40% of eQTLs were found to be more pronounced in MS patients compared with non-inflammatory neurological diseases patients. In addition, we found two single nucleotide polymorphisms to be significantly associated with the proportions of three different cell types. Mapping to enhancer histone marks and predicted transcription factor binding sites added additional functional evidence for eight eQTL regions. As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. This study provides many novel and validated targets for future functional characterization of MS and other diseases.
Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.
SH Stephens, SM Hartz, NR Hoft, NL Saccone, RC Corley, JK Hewitt, CJ Hopfer, N Breslau, H Coon, X Chen, F Ducci, N Dueker, N Franceschini, J Frank, Y Han, NN Hansel, C Jiang, T Korhonen, PA Lind, J Liu, LP Lyytikäinen, M Michel, JR Shaffer, SE Short, J Sun, A Teumer, JR Thompson, N Vogelzangs, JM Vink, A Wenzlaff, W Wheeler, BZ Yang, SH Aggen, AJ Balmforth, SE Baumeister, TH Beaty, DJ Benjamin, AW Bergen, U Broms, D Cesarini, N Chatterjee, J Chen, YC Cheng, S Cichon, D Couper, F Cucca, D Dick, T Foroud, H Furberg, I Giegling, NA Gillespie, F Gu, AS Hall, J Hällfors, S Han, AM Hartmann, K Heikkilä, IB Hickie, JJ Hottenga, P Jousilahti, M Kaakinen, M Kähönen, PD Koellinger, S Kittner, B Konte, MT Landi, T Laatikainen, M Leppert, SM Levy, RA Mathias, DW McNeil, SE Medland, GW Montgomery, T Murray, M Nauck, KE North, PD Paré, M Pergadia, I Ruczinski, V Salomaa, J Viikari, G Willemsen, KC Barnes, E Boerwinkle, DI Boomsma, N Caporaso, HJ Edenberg, C Francks, J Gelernter, HJ Grabe, H Hops, MR Jarvelin, M Johannesson, KS Kendler, T Lehtimäki, PK Magnusson, ML Marazita, J Marchini, BD Mitchell, MM Nöthen, BW Penninx, O Raitakari, M Rietschel, D Rujescu, NJ Samani, AG Schwartz, S Shete, M Spitz, GE Swan, H Völzke, J Veijola, Q Wei, C Amos, DS Cannon, R Grucza, D Hatsukami, A Heath, EO Johnson, J Kaprio, P Madden, NG Martin, VL Stevens, RB Weiss, P Kraft, LJ Bierut, MA Ehringer
Genet. Epidemiol., 37 (8) 1098-2272 (2013)
Neuronal nicotinic acetylcholine receptor (nAChR) genes (CHRNA5/CHRNA3/CHRNB4) have been reproducibly associated with nicotine dependence, smoking behaviors, and lung cancer risk. Of the few reports that have focused on early smoking behaviors, association results have been mixed. This meta-analysis examines early smoking phenotypes and SNPs in the gene cluster to determine: (1) whether the most robust association signal in this region (rs16969968) for other smoking behaviors is also associated with early behaviors, and/or (2) if additional statistically independent signals are important in early smoking. We focused on two phenotypes: age of tobacco initiation (AOI) and age of first regular tobacco use (AOS). This study included 56,034 subjects (41 groups) spanning nine countries and evaluated five SNPs including rs1948, rs16969968, rs578776, rs588765, and rs684513. Each dataset was analyzed using a centrally generated script. Meta-analyses were conducted from summary statistics. AOS yielded significant associations with SNPs rs578776 (beta = 0.02, P = 0.004), rs1948 (beta = 0.023, P = 0.018), and rs684513 (beta = 0.032, P = 0.017), indicating protective effects. There were no significant associations for the AOI phenotype. Importantly, rs16969968, the most replicated signal in this region for nicotine dependence, cigarettes per day, and cotinine levels, was not associated with AOI (P = 0.59) or AOS (P = 0.92). These results provide important insight into the complexity of smoking behavior phenotypes, and suggest that association signals in the CHRNA5/A3/B4 gene cluster affecting early smoking behaviors may be different from those affecting the mature nicotine dependence phenotype.
Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.
J Bryois, NG Skene, TF Hansen, LJA Kogelman, HJ Watson, Z Liu, Eating Disorders Working Group of the Psychiatric Genomics Consortium, International Headache Genetics Consortium, 23andMe Research Team, L Brueggeman, G Breen, CM Bulik, E Arenas, J Hjerling-Leffler, PF Sullivan
Nat. Genet., 52 (5) 1546-1718 (2020)
Genome-wide association studies have discovered hundreds of loci associated with complex brain disorders, but it remains unclear in which cell types these loci are active. Here we integrate genome-wide association study results with single-cell transcriptomic data from the entire mouse nervous system to systematically identify cell types underlying brain complex traits. We show that psychiatric disorders are predominantly associated with projecting excitatory and inhibitory neurons. Neurological diseases were associated with different cell types, which is consistent with other lines of evidence. Notably, Parkinson's disease was genetically associated not only with cholinergic and monoaminergic neurons (which include dopaminergic neurons) but also with enteric neurons and oligodendrocytes. Using post-mortem brain transcriptomic data, we confirmed alterations in these cells, even at the earliest stages of disease progression. Our study provides an important framework for understanding the cellular basis of complex brain maladies, and reveals an unexpected role of oligodendrocytes in Parkinson's disease.
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
YOO Hu, N Ndegwa, J Alneberg, S Johansson, JB Logue, M Huss, M Käller, J Lundeberg, J Fagerberg, AF Andersson
NGI CollaborationSci Rep, 8 (1) 2045-2322 (2018)
Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.
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.