Computational and Digital Genomics
The Computational and Digital Genomics Lab develops computational tools to identify genetic and non-genetic risk factors associated with chronic diseases, using large biobank-scale datasets.
Lead
Professor of Computational Genomics
+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at
Team
About
We develop computational tools to identify genetic and non-genetic risk factors associated with chronic diseases, using large biobank-scale datasets. Our current focus is on complex gene regions, such as the LPA VNTR project, to analyze their contributions to missing heritability.
Previous examples include the Michigan Imputation Server, a backbone for the GWAS community worldwide, and the mtDNA classification tool Haplogrep, both developed in our lab. We are also engaged in numerous big data projects, providing reproducible solutions for thousands of samples and millions of data points.
Students
Bachelor Student Molecular Medicine
Medical Student
Master Student Molecular Medicine (Project Week Jan 25)
We are always seeking highly motivated students. If you’re interested in joining our team and contributing to innovative research, please reach out!
News
- October 2024: Sebastian will give a talk on the Michigan Imputation Server at the Nextflow Summit in Barcelona.
- July 2024: Big news: our latest work on VNTR has been published in Genome Biology and covered on the MUI website.
- May 2024: Silvia joins the Computational Group. Welcome!
- November 2023: We extended our UK Biobank project for another 3 years. Thanks to the financial support from the Medical Univeristy of Innsbruck!
Ongoing Projects
The Computational Genomics group maintains a close collaboration with the Genome Informatics team. These projects are listed in both groups.
- Contamination detection in mtDNA
- GWAS Nextflow pipeline
- Michigan Imputation Server
- Resolving intra-repeat variation in medically relevant VNTRs
- Variant calling in mtDNA
Genepi Investigators
Cooperations
- Eurac Research Bozen/Bolzano (Christian Fuchsberger)
- University of Michigan (Gonçalo Abecasis, Albert Smith, Michael Boehnke)
- Johns Hopkins University (Enis Afgan)
Consortia activities
- gnomAD, TOPMed, HRC, GenomeAsia, GCKD, ncRNAPain, nonHFE
Key Publications
Di Maio S, Zöscher P, Weissensteiner H, Forer L, Schachtl-Riess JF, Amstler S, Streiter G, Pfurtscheller C, Paulweber B, Kronenberg F, Coassin S, Schönherr S: Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model. Genome Biol. 25:167, 2024. PMID: 38926899 Journal Article
Weissensteiner H, Forer L, Kronenberg F, Schönherr S: mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res. 52:W102-W107, 2024. PMID: 38709886 Journal Article
Das S, Forer L, Schönherr S*, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C: Next-generation genotype imputation service and methods. Nat. Genet. 48:1284-1287, 2016. PMID: 27571263 Journal Article
McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R, Haplotype Reference Consortium: A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48:1279-1283, 2016. PMID: 27548312 Journal Article
Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, L Price A: Reference-based phasing using the Haplotype Reference Consortium panel. Nat. Genet. 48:1443-1448, 2016. PMID: 27694958 Journal Article
GenomeAsia100K Consortium: The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576:106-111, 2019. PMID: 31802016 Journal Article
Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S: Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31:309-316, 2021. PMID: 33452015 Journal Article