High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Persistent Link:
http://hdl.handle.net/10150/610039
Title:
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays
Author:
Wang, Yuker; Carlton, Victoria; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang; Richardson, Andrea; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia; Spellman, Paul; Gray, Joe; Mills, Gordon; Faham, Malek
Affiliation:
Affymetrix Inc. Santa Clara, CA, USA; MD Anderson Cancer Center, Houston, TX, USA; DF/BWH Cancer Center, Boston, MA, USA; University of California San Francisco, San Francisco, CA, USA; Cancer Research UK, London Research Institute, London, UK; Arizona Cancer Center, Tucson, AZ, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Issue Date:
2009
Publisher:
BioMed Central
Citation:
BMC Medical Genomics 2009, 2:8 doi:10.1186/1755-8794-2-8
Journal:
BMC Medical Genomics
Rights:
© 2009 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
EISSN:
1755-8794
DOI:
10.1186/1755-8794-2-8
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1755-8794/2/8

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Yukeren
dc.contributor.authorCarlton, Victoriaen
dc.contributor.authorKarlin-Neumann, Georgeen
dc.contributor.authorSapolsky, Ronalden
dc.contributor.authorZhang, Lien
dc.contributor.authorMoorhead, Martinen
dc.contributor.authorWang, Zhigangen
dc.contributor.authorRichardson, Andreaen
dc.contributor.authorWarren, Roberten
dc.contributor.authorWalther, Axelen
dc.contributor.authorBondy, Melissaen
dc.contributor.authorSahin, Aysegulen
dc.contributor.authorKrahe, Ralfen
dc.contributor.authorTuna, Musaffeen
dc.contributor.authorThompson, Patriciaen
dc.contributor.authorSpellman, Paulen
dc.contributor.authorGray, Joeen
dc.contributor.authorMills, Gordonen
dc.contributor.authorFaham, Maleken
dc.date.accessioned2016-05-20T08:57:09Z-
dc.date.available2016-05-20T08:57:09Z-
dc.date.issued2009en
dc.identifier.citationBMC Medical Genomics 2009, 2:8 doi:10.1186/1755-8794-2-8en
dc.identifier.doi10.1186/1755-8794-2-8en
dc.identifier.urihttp://hdl.handle.net/10150/610039-
dc.description.abstractBACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1755-8794/2/8en
dc.rights© 2009 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleHigh quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarraysen
dc.typeArticleen
dc.identifier.eissn1755-8794en
dc.contributor.departmentAffymetrix Inc. Santa Clara, CA, USAen
dc.contributor.departmentMD Anderson Cancer Center, Houston, TX, USAen
dc.contributor.departmentDF/BWH Cancer Center, Boston, MA, USAen
dc.contributor.departmentUniversity of California San Francisco, San Francisco, CA, USAen
dc.contributor.departmentCancer Research UK, London Research Institute, London, UKen
dc.contributor.departmentArizona Cancer Center, Tucson, AZ, USAen
dc.contributor.departmentLawrence Berkeley National Laboratory, Berkeley, CA, USAen
dc.identifier.journalBMC Medical Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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