Supplementary Data - Bioinformatics

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Oct 1, 2013 (3 years and 9 months ago)

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© Oxford University Press 2011

1

SUPPLEMENTARY MATERIAL

Bioinformatics Challenges for Personalized Medicine

Guy Haskin Fernald
1
, Emidio Capriotti
2,3
, Roxana Daneshjou
4
, Konrad J. Karczewski
1,5
, and
Russ B. Altman
2,5,*

1
B
iomedical Informatics Training Program, Stanford University School of

Medicine, Stanford, CA, USA
.

2
Department of Bioengineering, Stanford University, Stanford, CA, USA.

3
Department of Mathematics and Computer Sciences, University of Balearic Islands, Palma de Mallorca, Spain
.

4
Stanford University School of Medicine, Stanfo
rd, CA, USA.

5
Department of Genetics, Stanford University, Stanford, CA, USA.




Database

Description

Web site

Ref
erence

1000Genomes

Human Genetic Variation

http://www.1000genomes.org/

(
Durbin, et al., 2010
)

COSMIC

Somatic Mutations in

Cancer

http://www.sanger.ac.uk/genetics/CGP/cosmic

(
Forbes, et al., 2010
)

dbSNP

SNP database at the NCBI

http://www.ncbi.nlm.nih.gov/projects/SNP

(Fernald, et al., 2011; Sherry, et al., 2001)

HapMap

Database of Human Haplotypes

http://www.hapmap.org

(
International HapMap Consortium, 200
3
)

HGMD

Human Genetic Mutation Database

http://www.hgmd.cf.ac.uk

(
Stenson, et al., 2009
)

OMIM

Online Mendelian Inheri
ted in Man

http://www.ncbi.nlm.nih.gov/omim

(
Amberger, et al.,

2009
)

PharmGKB

Pharmacogenomics resource

http://www.pharmgkb.org

(
Thorn, et al., 2010
)

SwissVar

Swiss
-
Prot diseases and variants

http://expasy.org/swissvar

(
Mottaz, et al., 2010
)

Supplemental
Table
1
.

SNP databases.


Database

D
escription

Web site

Reference

Is
-
rSNP

Effect of variants in regulatory r
e
gions.

http://www.genomics.csse.unimelb.edu.au/is
-
rSNP/

(Macintyre, et al., 2010)

PANTHER

Protein families HMM
-
based method.

http://www.pant
herdb.org/

(
Thomas, et al., 200
3
)

PhD
-
SNP

Sequence and profile
-
based SVM met
h
od.

http://gpcr.biocomp.unibo.it/PhD
-
SNP.htm

(
Capriotti, et al
., 2006
)

PolyPhen

Decision Tree
-
based method.

http://genetics.bwh.harvard.edu/pph

(
Ramensky, et al., 2002
)

LS
-
SNP

Protein structure
-
based SVM predictor

http://modbase.compbio.ucsf.edu/LS
-
SNP

(
Karchin, et al., 2005
)

MutPred

Random forest meta predictor

http://mutdb.org/mutpred

(
Li, et al., 2009
)

SIFT

Protein block alignment
-
based method

http://sift.jcvi.org

(
Ng and Henikoff, 2003
)

Skippy

Predicts variants affecting splicing sites

http://research.nhgri.nih.gov/skippy

(
Woo
lfe, et al., 2010
)

SNAP

Sequence profile
-
based neural network

http://rostlab.org/services/snap

(
Bromberg, et al., 2008
)

SNPEffect

Precalculated scores for mutation impact

http://snpeffect.vib.be

(
Reumers, et al., 2006
)

SNPs3D

Structure
-
based SVM predictor

http://www.snps3d.org

(
Yue, et al., 2006
)

SNPs&GO

Se
quence profile and functional
-
based SVM

ht
tp://snps
-
and
-
go.biocomp.unibo.it

(
Calabrese, et al., 2009
)

Supple
mental
Table 2.

Tools and resources for functional prediction of SNPs
.


GH. Fernald et

al.

2

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Capriotti,
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