About SISu

The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate the whole genome and the whole exome sequence data from Finnish samples and to provide summary data for researchers and clinicians. The SISu website offers a way to search for variants and examine their attributes and appearance in Finnish cohorts. In the current version users can search for summary data on single nucleotide variants and indels from exomes of over 10 000 individuals sequenced in disease-specific and population genetic studies. The first version of the SISu search engine was released in 2014.

Finland's gene pool has been molded by several bottlenecks in Finland's population history and small settler groups inhabitating remote areas in the large country. Therefore a specific reference dataset of sequence variants in Finns is needed, which is why SISu exists. It is an international collaboration between research groups aiming to build tools for genomic medicine. These groups are generating whole genome and whole exome sequence data from Finnish samples. They also provide data resources for the research community. Key groups of the project are from the Universities of Eastern Finland, Oulu and Helsinki; The Institute for Health and Welfare, Finland; Lund University; The Wellcome Trust Sanger Institute; University of Oxford; The Broad Institute of Harvard and MIT; Massachusetts General Hospital; University of Michigan; Washington University in St. Louis, and the University of California, Los Angeles (UCLA). The project is coordinated in the Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki.

Current release

SISu v4.1
2016/09/01
GRCh37
10490 Finnish samples
13 cohorts
1343601 sites
1230641 SNVs
130006 indels
More info

As you can see above, the new SISu release contains over 10 000 samples from multiple cohorts. Besides the new samples, the new release also brings along updated data from ExAC and ClinVar to be displayed alongside the SISu reference data. In this release, you are also provided a link directly to ExAC and ClinVar from the variant page, if one is available.

In addition, we have added a visualization based on Finrisk data which shows how a variant is spread throughout Finland and how common the variant is in each county. This visualization is different between common (>= 75 samples) and rare (< 75 samples) variants and more information about it can be found here.

Sequencing and QC

The samples in SISu have been exome sequenced in The Broad Institute of Harvard and MIT, Wellcome Trust Sanger Institute or Washington University in St. Louis. The sequencing has been done using four different platforms: Agilent 1.1 refseq plus 3 boosters, Agilent sureselect 50mb, Illumina coding v1, and Nimblegen SeqCap EZ VCRome. All cohorts have been jointly called at The Broad Institute of Harvard and MIT. After variant calling, a quality control has been performed at FIMM which is described in the image below.  

Citing and publications

Sequencing Initiative Suomi project (SISu), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland (URL: http://sisuproject.fi) [SISu v4.1, date (month, year) accessed]

To cite the SISu browser in your publications, please use the citation example above. For your interest, we have also listed below the publications where SISu has been used. If you want to add your publication to the list, you can send it to us on the contact page by using the feedback form or by contacting the SISu project coordinator.

Cousminer DL, Leinonen JT, Sarin AP, Chheda H, Surakka I, Wehkalampi K, Ellonen P, Ripatti S, Dunkel L, Palotie A, Widén E;
Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty
PLoS One. 2015 Jun 1;10(6):e0128524. doi: 10.1371/journal.pone.0128524. eCollection 2015.PMID:26030606.

Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A;
Sequencing Initiative Suomi (SISu) Project. Distribution and medical impact of loss-of-function variants in the Finnish founder population
PLoS Genet. 2014 Jul 31;10(7):e1004494. doi: 10.1371/journal.pgen.1004494. eCollection 2014 Jul. PubMed PMID: 25078778; PubMed Central PMCID: PMC4117444.

Contact person

Mervi Kinnunen, Research coordinator
Sequencing Initiative Suomi (SISu)

Institute for Molecular Medicine Finland FIMM
PL 20 (Tukholmankatu 8)
00014 University of Helsinki
mervi.kinnunen(at)helsinki.fi

SISu steering group

Aarno Palotie, Project leader
Institute for Molecular Medicine Finland, University of Helsinki, Finland Broad Institute of Harvard and MIT, Cambridge, and Massachusetts General Hospital, Boston, Massachusetts, USA

Samuli Ripatti
Institute for Molecular Medicine Finland, and Public Health, University of Helsinki, Helsinki, Finland

Veikko Salomaa
National Institute for Health and Welfare (THL), Helsinki, Finland.

Markus Perola
National Institute for Health and Welfare (THL),Institute for Molecular Medicine Finland, University of Helsinki, Finland The Estonian Genome Center, University of Tartu, Tartu, Estonia.

Jaakko Kaprio 
Institute for Molecular Medicine (FIMM), and Public Health, University of Helsinki, Helsinki, Finland National Institute for Health and Welfare, Helsinki, Finland.

Markku Laakso
University of Eastern Finland, Kuopio Campus and Kuopio University Hospital, Kuopio, Finland.

Jeff Barrett
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Michael Boehnke
University of Michigan, Ann Arbor, Michigan, USA.

Mark Daly
Broad Institute of Harvard and MIT, Cambridge, and Massachusetts General Hospital, Massachusetts, USA.

Nelson Freimer
UCLA, Los Angeles, California, USA.

Leif Groop
Lund University, Malmö, Sweden Finnish Institute for Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland.

Joel Hirschhorn
Broad Institute of Harvard and MIT, Cambridge, and Boston Children’s Hospital Hospital, Boston, Massachusetts, USA.

Daniel MacArthur
Broad Institute of Harvard and MIT, Cambridge, and Massachusetts General Hospital, Boston, Massachusetts, USA

Mark McCarthy
Wellcome Trust Centre for Human Genetics, University of Oxford and Churchill Hospital, Headington, Oxford, UK.

Benjamin Neale
Broad Institute of Harvard and MIT, Cambridge, and Massachusetts General Hospital, Boston, Massachusetts, USA