NGI Uppsala (SNP&SEQ Technology Platform)

National facility

SNPSEQ

The SNP&SEQ Technology Platform offers SNP genotyping and second-generation sequencing as a service to researchers in Sweden and abroad. The unit’s genotyping and sequencing procedures are accredited by SWEDAC according to ISO 17025 and the facility is CsPro-certified as a service provider using Illumina genotyping and sequencing technology.

SERVICES

  • Sequencing. Sequencing services include:
    • Next generation sequencing with Illumina HiSeq and MiSeq systems
    • Optimized library preparations for genomes, targeted genomic regions, transcriptomes and methylomes
    • Single read or paired-end sequencing
    • Delivery of sequence reads with quality information via SNIC-UPPMAX
    • Bioinformatics support
  • SNP genotyping. Genotyping services include:
    • High-density SNP genotyping on all scales
    • Analysis of copy number variation (CNV)
    • Genome-wide DNA methylation profiling
    • Custom designed SNP panels for any organism
  • Compiling materials and methods for publications.

EQUIPMENT

 

  • HiSeq X and HiSeq 2500 sequencers (Illumina).
  • MiSeq sequencer (Illumina).
  • iScan system (Illumina).
  • BeadExpress (Illumina).
  • GeniosPro (Tecan).

APPLICATIONS

  • Genome-wide disease association studies
  • Epigenetic and cancer studies
  • Evolutionary studies and population genetics

RECENT PROJECTS

Smoking is associated with mosaic loss of chromosome Y.
Dumanski JP, Rasi C, Lönn M, Davies H, Ingelsson M, Giedraitis V, Lannfelt L, Magnusson PKE, Lindgren CM, Morris AP, Cesarini D, Johannesson M, Tiensuu Janson E, Lind L, Pedersen NL, Ingelsson E, Forsberg LA.  Science 347(6217), 81-83 2015

Common genetic variants influence human subcortical brain structures.
Hibar DP, Stein JL, Renteria ME, Arias-Vasquez A, .... , Schumann G, Franke B, Thompson PM and Medland SE. Nature, 520(7546), 224-229 2015

Genetic studies of body mass index yield new insights for obesity biology.
Locke AE, Kahali B, Berndt SI, Justice AE, .... , Ingelsson E, Hirschhorn JN, Loos RJF and Speliotes EK. Nature 518(7538), 197-206 2015

Evolution of Darwin's finches and their beaks revealed by genome sequencing.
Lamichhaney S, Berglund J, Almen MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerova M, Rubin C-J, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L.  Nature 518(7539), 371-375  2015

Genetically Determined Height and Coronary Artery Disease.
Nelson CP, Hamby SE, Saleheen D, Hopewell JC, Zeng L, Assimes TL, Kanoni S, Willenborg C, Burgess S, Amouyel P, Anand S, Blankenberg S, Boehm BO, Clarke RJ, Collins R, Dedoussis G, Farrall M, Franks PW, Groop L, Hall AS, Hamsten A, Hengstenberg C, Hovingh GK, Ingelsson E, Kathiresan S, Kee F, König IR, Kooner J, Lehtimäki T, März W, McPherson R, Metspalu A, Nieminen MS, O'Donnell CJ, Palmer CNA, Peters A, Perola M, Reilly MP, Ripatti S, Roberts R, Salomaa V, Shah SH, Schreiber S, Siegbahn A, Thorsteinsdottir U, Veronesi G, Wareham N, Willer CJ, Zalloua PA, Erdmann J, Deloukas P, Watkins H, Schunkert H, Danesh J, Thompson JR, Samani N. N Engl J Med 372(17), 1608-1618  2015

Complex archaea that bridge the gap between prokaryotes and eukaryotes.
Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. Nature 521(7551), 173-179  2015

Directional dominance on stature and cognition in diverse human populations.
Joshi PK, Esko T, Mattsson H, Eklund N, .... , Hirschhorn JN, Perola M, Polašek O and Wilson JF. Nature 523(7561), 459-462  2015