Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for Routine Clinical Use on Formalin-fixed Paraffin-embedded Tissues

Lyons‐Weiler, Maureen A.; Hagenkord, Jill; Sciulli, Christin; Dhir, Rajiv; Monzon, Federico A.

doi:10.1097/pdm.0b013e31815aca30

Cited by 38 publications

(38 citation statements)

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“…After tumor enrichment via manual microdissection, DNA was obtained from 10 lm paraffin sections as described previously, 15 and 250K Nsp Assay Kits (Affymetrix, Santa Clara, Calif) were used according to the manufacturer's protocol, except for increased starting genomic DNA. One microgram of genomic DNA was digested with Nsp restriction enzyme, ligated to adaptors, and amplified by polymerase chain reaction (PCR) using a universal primer.…”

Section: Single Nucleotide Polymorphism Arraymentioning

confidence: 99%

Assessment of HER2 gene status in breast carcinomas with polysomy of chromosome 17

Vranić

Teruya

Repertinger

et al. 2010

Cancer

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BACKGROUND:The current study was performed to determine the impact of polysomy 17 on the interpretation of HER2 testing of invasive breast carcinomas using fluorescent in situ hybridization methods. Current American Society of Clinical Oncology/College of American Pathologists guidelines define HER2-positive tumors as those with >6 HER2 genes per nucleus or those with HER2/CEP17 (chromosome 17) ratio >2.2. These guidelines are potentially contradictory in tumors with polysomy of chromosome 17. METHODS: Seventy-two breast carcinoma cases with reported polysomy of chromosome 17 (3 CEP17 signals on average) by fluorescent in situ hybridization were identified, and the corresponding HER2 immunohistochemistry was obtained. The HER2 status of the archived samples was reviewed, and the tumors were recategorized according to the 2007 American Society of Clinical Oncology/College of American Pathologists guidelines. RESULTS: The average CEP17 copy number for the group was 4.5 (range, 3.0-10.4). Thirty-three (45.8%) cases had >6 copies of HER2 per nucleus. Twenty-one cases (29.2%) qualified as HER2 gene amplified using the HER2/CEP17 ratio (>2.2) guideline. All these cases had >6 HER2 signals, which represented 63.6% of all cases with >6 HER2 signals. HER2 protein expression showed significant positive correlations with both HER2 gene copy number and HER2/CEP17 ratio (P < .01, r s ¼ 0.56 and 0.64, respectively). CONCLUSIONS: Increased CEP17 signals detected in invasive breast carcinomas may lead to discordant interpretation of gene amplification in a significant proportion of the cases, depending on which criterion (ratio vs absolute number) is used for interpretation. However, increased gene dosage (>6 HER2 genes or HER2/CEP17 ratio >2.2), regardless of the evaluation method, is positively correlated with HER2 protein expression. Cancer 2011;117:48-53.

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Section: Single Nucleotide Polymorphism Arraymentioning

confidence: 99%

Assessment of HER2 gene status in breast carcinomas with polysomy of chromosome 17

Vranić

Teruya

Repertinger

et al. 2010

Cancer

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“…Fingernail DNA was processed in a similar manner but with the two following modifications to adapt to the oligonucleotide microarray system [24]. Prolongation of digestion time from 120 minutes as the standard protocol to overnight; and increase of the PCR cycle number from 35 to 45 cycles.…”

Section: Snp Genotyping With Affymetrix 10k 20 Arraymentioning

confidence: 99%

Familial brain arteriovenous malformation maps to 5p13–q14, 15q11–q13 or 18p11: Linkage analysis with clipped fingernail DNA on high-density SNP array

Oikawa

Kuniba

Kondoh³

et al. 2010

European Journal of Medical Genetics

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Familial arteriovenous malformations (AVM) in the brain is a very rare disease. It is defined as its occurrence in two or more relatives (up to third-degree relatives) in a family without any associated disorders, such as hereditary hemorrhagic telangiectasia.We encountered a Japanese family with brain AVM in which four affected members in four successive generations were observed. One DNA sample extracted from leukocytes of the proband and ten DNA samples from clipped finger nails of other members were available. A genome-wide linkage analysis was performed on this pedigree using Affymetrix GeneCip 10K 2.0 Xba Array and MERLIN software. We obtained sufficient performance of SNP genotyping in the fingernail samples with the mean SNP call rate of 92.49%, and identified 18 regions with positive LOD scores.Haplotype and linkage analyses with microsatellite markers at these regions confirmed three possible disease-responsible regions, i.e., 5p13.2-q14.1, 15q11.2-q13.1 and 18p11.32-p11.22. Sequence analysis was conducted for ten selected candidate genes at 5p13.2-q14.1, such as MAP3K1, DAB2, OCLN, FGF10, ESM1, ITGA1, ITGA2, EGFLAM, ERBB2IP, and PIK3R1, but no causative genetic alteration was detected. This is the first experience of adoption of fingernail DNA to genome-wide, high-density SNP microarray analysis, showing candidate brain AVM susceptible regions.

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“…24 Four of these samples (one from each morphologic group) have been reported previously in the manuscript describing the SNP array assay utilized for this study. 25 Ten 10 mm slides and a corresponding hematoxilin and eosin stained slide were obtained for all samples. All cases were reviewed by two pathologists (FAM & AP) to verify the reported diagnosis.…”

Section: Tissue Samplesmentioning

confidence: 99%

“…25 DNA was quantitated on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). All samples processed for downstream analysis in this study had an OD 260/280 ratio higher than 1.8.…”

Section: Sample Preparation and Extractionmentioning

confidence: 99%

Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors

et al. 2008

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Renal tumors with complex or unusual morphology require extensive workup for accurate classification. Chromosomal aberrations that define subtypes of renal epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations and classify renal epithelial tumors. We analyzed 20 paraffin-embedded tissues representing clear cell, papillary renal and chromophobe renal cell carcinoma, as well as oncocytoma with Affymetrix GeneChip 10K 2.0 Mapping arrays. SNP array results were in concordance with known genetic aberrations for each renal tumor subtype. Additional chromosomal aberrations were detected in all renal cell tumor types. The unique patterns allowed 19 out of 20 tumors to be readily categorized by their chromosomal copy number aberrations. One papillary renal cell carcinoma type 2 did not show the characteristic 7/17 trisomies. Clustering using the median copy number of each chromosomal arm correlated with histological class when using a restricted set of chromosomes. In addition, three morphologically challenging tumors were analyzed to explore the potential clinical utility of this method. In these cases, the SNP array-based copy number evaluation yielded information with potential clinical value. These results show that SNP arrays can detect characteristic chromosomal aberrations in paraffin-embedded renal tumors, and thus offer a high-resolution, genome-wide method that can be used as an ancillary study for classification and potentially for prognostic stratification of these tumors.

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Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for Routine Clinical Use on Formalin-fixed Paraffin-embedded Tissues

Cited by 38 publications

References 0 publications

Assessment of HER2 gene status in breast carcinomas with polysomy of chromosome 17

Assessment of HER2 gene status in breast carcinomas with polysomy of chromosome 17

Familial brain arteriovenous malformation maps to 5p13–q14, 15q11–q13 or 18p11: Linkage analysis with clipped fingernail DNA on high-density SNP array

Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors

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