PROBER: Oligonucleotide FISH probe design software

Nicholas Navin; Vladimir Grubor; Jim Hicks; Evan Leibu; Elizabeth Thomas; Jennifer Troge; Michael Riggs; Pär Lundin; Susanne Månér; Jonathan Sebat; Anders Zetterberg; Michael Wigler

doi:10.1093/bioinformatics/btl273

PROBER: Oligonucleotide FISH probe design software

Nicholas Navin, Vladimir Grubor, Jim Hicks, Evan Leibu, Elizabeth Thomas, Jennifer Troge, Michael Riggs, Pär Lundin, Susanne Månér, Jonathan Sebat, Anders Zetterberg, Michael Wigler

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.

Original language	English (US)
Pages (from-to)	2437-2438
Number of pages	2
Journal	Bioinformatics
Volume	22
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/btl273
State	Published - Oct 2006
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btl273

Cite this

@article{d68154bf937445b3afcde02f12812226,

title = "PROBER: Oligonucleotide FISH probe design software",

abstract = "PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.",

author = "Nicholas Navin and Vladimir Grubor and Jim Hicks and Evan Leibu and Elizabeth Thomas and Jennifer Troge and Michael Riggs and P{\"a}r Lundin and Susanne M{\aa}n{\'e}r and Jonathan Sebat and Anders Zetterberg and Michael Wigler",

note = "Funding Information: The authors thank John Healy, Lakshmi Muthuswamy, Joan Alexander, Eirny Tholsdorf and Kristin Anna for their help. This work was supported by a fellowship from the Lindsey-Goldberg Foundation to N.N. and grants to A.Z. from the Swedish Cancer Society (0046-B04-38XAC) and from the Stockholm Cancer Society (03:171 and 02:144). This work was also supported by grants to M.W. from the National Institutes of Health (5R01-CA078544-07), Dept. of the Army (W81XWH04-1-0477), (W81XWH-05-1-0068), (W81XWH-04-0905), The Simons Foundation, Miracle Foundation, Breast Cancer Research Foundation, Long Islanders Against Breast Cancer, West Islip Breast Cancer Foundation, Long Island Breast Cancer (1 in 9), Elizabeth McFarland Breast Cancer Research Grant, Breast Cancer Help Inc. M.W. is an American Cancer Society Research Professor. Funding to pay the Open Access publication charges was provided by The Simons Foundation.",

year = "2006",

month = oct,

doi = "10.1093/bioinformatics/btl273",

language = "English (US)",

volume = "22",

pages = "2437--2438",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "19",

}

TY - JOUR

T1 - PROBER

T2 - Oligonucleotide FISH probe design software

AU - Navin, Nicholas

AU - Grubor, Vladimir

AU - Hicks, Jim

AU - Leibu, Evan

AU - Thomas, Elizabeth

AU - Troge, Jennifer

AU - Riggs, Michael

AU - Lundin, Pär

AU - Månér, Susanne

AU - Sebat, Jonathan

AU - Zetterberg, Anders

AU - Wigler, Michael

N1 - Funding Information: The authors thank John Healy, Lakshmi Muthuswamy, Joan Alexander, Eirny Tholsdorf and Kristin Anna for their help. This work was supported by a fellowship from the Lindsey-Goldberg Foundation to N.N. and grants to A.Z. from the Swedish Cancer Society (0046-B04-38XAC) and from the Stockholm Cancer Society (03:171 and 02:144). This work was also supported by grants to M.W. from the National Institutes of Health (5R01-CA078544-07), Dept. of the Army (W81XWH04-1-0477), (W81XWH-05-1-0068), (W81XWH-04-0905), The Simons Foundation, Miracle Foundation, Breast Cancer Research Foundation, Long Islanders Against Breast Cancer, West Islip Breast Cancer Foundation, Long Island Breast Cancer (1 in 9), Elizabeth McFarland Breast Cancer Research Grant, Breast Cancer Help Inc. M.W. is an American Cancer Society Research Professor. Funding to pay the Open Access publication charges was provided by The Simons Foundation.

PY - 2006/10

Y1 - 2006/10

N2 - PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.

AB - PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.

UR - http://www.scopus.com/inward/record.url?scp=33750028062&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33750028062&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btl273

DO - 10.1093/bioinformatics/btl273

M3 - Article

C2 - 16740623

AN - SCOPUS:33750028062

SN - 1367-4803

VL - 22

SP - 2437

EP - 2438

JO - Bioinformatics

JF - Bioinformatics

IS - 19

ER -

PROBER: Oligonucleotide FISH probe design software

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this