-Omics method development


Our ability to perform large-scale studies of a number of the key molecular players such as DNA, RNA, protein and cellular metabolites has greatly advanced our ability to understand complex biological systems. Analysis of combinations of of DNA, RNA and protein data, ie multi-omics data, provide the basis of large-scale data driven biology and medicine. Recent rapid progress in data-driven science has been enabled through a combination of high-throughput large-scale laboratory methods and development of sophisticated bioinformatics analyses. In this project we aim to improve upon existing and develop new technology solutions which enable large-scale multi-omics analyses using next generation DNA sequencing (NGS).

Group members working in the project

  • Jessica Nordlund
  • Amanda Raine
  • Anders Lundmark
  • Sara Ekberg

Main collaborators

  • Ann-Christin Wiman, NGI/SNP&SEQ Technology Platform, SciLifeLab Genomics, Uppsala
  • Claudia Bergin, MSCG unit, SciLifeLab Genomics, Uppsala

Funding

  • SciLifeLab Uppsala Technology Development Project -2019
  • EATRIS-Plus
  • EASI-Genomics

Recent Publications

  • Han Y, Zheleznyakova G, Marincevic-Zuniga Y, Pahlevan M, Raine A, Needhamsen M, Jagodic M (2021) Comparison of EM-seq and PBAT methylome libraries for low-input DNA, in press,  Epigenetics
  • Raine A, Lundmark A, Annett A, Wiman AC, Cavalli M, Wadelius C, Bergin C, Nordlund J (2021) scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation. bioRxiv https://doi.org/10.1101/2021.10.14.464375  
  • Skaftason A, Qu Y, Abdulla M, Nordlund J, Berglund M, Ednersson SB, Andersson PO,Enblad G, Amini RM,Rosenquist R, Mansouri L (2021) Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology in press https://doi.org/10.1002/gcc.23002
  • Xiao W, Ren L, Chen Z, Fang LT … Nordlund J, Liljedahl U … Wang C, Shi L (2021) Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nat Biotechnol 39 (https://doi.org/10.1038/s41587-021-00994-5)
  • Raine A, Liljedahl U, Nordlund J (2018) Data quality of whole genome bisulfite sequencing on Illumina platforms. PLoS ONE 13(4) https://doi.org/10.1371/journal.pone.0195972
  • Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J (2017) SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acid Res 45(6), e36
Last modified: 2022-04-29
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