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Citations per year

Number of citations per year for the bioinformatics software tool SISu
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Protocols

SISu specifications

Information


Unique identifier OMICS_16573
Name SISu
Alternative name Sequencing Initiative Suomi
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Version 4.1
Maintained Yes

Documentation


Maintainer


  • person_outline Hannele Laivuori

Publication for Sequencing Initiative Suomi

SISu citations

 (12)
library_books

Whole exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma

2018
PMCID: 5880256
PMID: 29602769
DOI: 10.1101/mcs.a002246

[…] ions included allele frequencies reported in 1000 Genomes (), the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP6500, unpublished; http://evs.gs.washington.edu/EVS/), SISu, and ExAC (). To select somatic variants, we discarded the variants that were also detected in the respective germline sample. The rest of the somatic variants were manually inspected to remove s […]

library_books

Mechanical stability of talin rod controls cell migration and substrate sensing

2017
Sci Rep
PMCID: 5472591
PMID: 28620171
DOI: 10.1038/s41598-017-03335-2

[…] Gromacs version 4.6.7. On Sisu supercomputer, CSC, Espoo, Finland was used for all MD and SMD simulations. All models were built with explicit TIP3P water model in 0.15 M KCl neutralized solution and placed into a 10 * 10 * 30 […]

call_split

Whole exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera

2017
Hum Genomics
PMCID: 5397753
PMID: 28427458
DOI: 10.1186/s40246-017-0102-x
call_split See protocol

[…] variants which were present in an in-house control set of 542 Finns [93 whole genome sequenced individuals from the 1000 Genomes Project, 402 whole-genome sequenced individuals from Kuusamo, Finland (Sequencing Initiative Suomi), and 47 uterine leiomyoma patients] were excluded. To exclude common variants, we further filtered the variant set against the Exome Aggregation Consortium (ExAC v.0.3: 3, […]

library_books

Pseudoexons provide a mechanism for allele specific expression of APC in familial adenomatous polyposis

2016
Oncotarget
PMCID: 5342583
PMID: 27683109
DOI: 10.18632/oncotarget.12206

[…] ny inheritance pattern was accepted in the index patients from FAP families 42 and 103 (sporadic cases, Table ). The identified variants were checked against ExAC (http://exac.broadinstitute.org) and SISu databases (www.sisuproject.fi) as well as Ensembl database (http://www.ensembl.org) to assess population frequencies. Sequence data was visualized using Integrative Genomics Viewer (IGV) browser […]

library_books

Investigation of rare and low frequency variants using high throughput sequencing with pooled DNA samples

2016
Sci Rep
PMCID: 5025741
PMID: 27633116
DOI: 10.1038/srep33256

[…] more than one pre-eclampsia pool, but in less than five scoliosis pools. Taking the scoliosis data as an external reference together with the population-based reference from 1000 Genomes project and SiSu project (www.sisuproject.fi), the ratio of MAFs in all pre-eclampsia samples to MAFs in the reference dataset >1.5 was employed as the filtering threshold. In addition, one nonsense variant and o […]

library_books

Exome sequencing in pooled DNA samples to identify maternal pre eclampsia risk variants

2016
Sci Rep
PMCID: 4935848
PMID: 27384325
DOI: 10.1038/srep29085

[…] The MAF estimation is based on an assumption that each sample is equally represented within a pool. The MAF estimates in the pre-eclampsia pools were compared to the MAFs in the reference data sets (SISu 2014, the 1000 Genomes European data APR2012 and the scoliosis exome sequencing data). By using three reference data sets we were able to obtain comprehensive picture of the variant frequencies i […]


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SISu institution(s)
Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
SISu funding source(s)
This work was supported by the following grants: the European Commission FP7 projects no. 201413 ENGAGE, project no. 242167 SynSys, Health-2010 -projects no. 261433 BioSHare and project no. 261123 gEUVADIS, the Academy of Finland grants no. 251704 and 263401, the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, NIH/RFA-HL-12-007, the European Commission Health-2010-project no. 261433 BioSHare, the Academy of Finland grants no 255847 and no 251217, the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, the Academy of Finland grant #139635, the Finnish Foundation for Cardiovascular Research, the Australian National Health and Medical Research Council Early Career Fellowship no. 637400, the Wellcome Trust Research Career Development Fellow 086596/Z/08/Z, GoT2D RC2-DK088389, GoT2D Wellcome Trust 090367, Wellcome Trust 098381, T2DGENES NIDDM U01-DK-085545, DK062370, DK085584, DK088389, Academy of Finland grants 141054, 265240, 263278, Academy of Finland grant 250422, the European Union's Seventh Framework Programme FP7/2007-2013 (HEALTH-F2-2011-278913, BiomarCaRE), the Targeted Financing from the Estonian Ministry of Science and Education SF0180142s08, the US National Institute of Health R01DK075787, the Development Fund of the University of Tartu grant SP1GVARENG, the European Regional Development Fund to the Centre of Excellence in Genomics (EXCEGEN) grant 3.2.0304.11-0312, and FP7 grant 313010.

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