Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses.
BACKGROUND
Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses.


METHODS
Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancer patients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls.


RESULTS
Matched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs.


CONCLUSIONS
No- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.
Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA. Electronic address: DLHertz@med.umich.edu.
Daniel L
DL
Hertz
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA. Electronic address: kidwell@umich.edu.
Kelley M
KM
Kidwell
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: jthibert@med.umich.edu.
Jacklyn N
JN
Thibert
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: clgersch@med.umich.edu.
Christina
C
Gersch
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. Electronic address: mregan@jimmy.harvard.edu.
Meredith M
MM
Regan
Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA. Electronic address: tskaar@iu.edu.
Todd C
TC
Skaar
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: norahh@med.umich.edu.
N Lynn
NL
Henry
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: hayesdf@med.umich.edu.
Daniel F
DF
Hayes
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: cvanpoz@med.umich.edu.
Catherine H
CH
Van Poznak
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: jimmyrae@med.umich.edu.
James M
JM
Rae
D001940:Breast / Q000378:metabolism / Q000473:pathology; D001943:Breast Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D004247:DNA / Q000097:blood / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D005557:Formaldehyde / Q000737:chemistry; D060005:Genotyping Techniques; D006801:Humans; D016612:Paraffin Embedding; D010597:Pharmacogenetics; D020641:Polymorphism, Single Nucleotide; D016707:Tissue Fixation
D005557:Formaldehyde; D004247:DNA
Cancer; FFPE; Formalin-fixed paraffin embedded; Germline genome; Pharmacogenetics; Somatic genome