Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel

Barker, David; Hansen, Mark; Faruqi, A. Fawad; Giannola, Diane; Irsula, Orlando R.; Lasken, Roger S.; Latterich, Martin; Makarov, Vladimir; Oliphant, Arnold; Pinter, Jonathon H.; Shen, Richard; Sleptsova, Irina; Ziehler, William A.; Lai, Eric

doi:10.1101/gr.1949704

Cited by 183 publications

(138 citation statements)

References 24 publications

(36 reference statements)

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“…Lastly, new technologies are emerging that may overcome limitations of the current methodology. For example, random hexamer priming and terminal transferase end-labeling 33,34 may enhance cDNA synthesis, a troublesome step in the current approach. It is reasonable to believe these approaches may improve cDNA synthesis over methods relying on traditional oligo-dT primer as polyA tracts seem particularly prone to formalin-mediated covalent modification.…”

Section: Discussionmentioning

confidence: 99%

RNA expression analysis of formalin-fixed paraffin-embedded tumors

Penland

Keku

Torrice

et al. 2007

Laboratory Investigation

145

120

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RNA expression analysis is an important tool in cancer research, but a limitation has been the requirement for high-quality RNA, generally derived from frozen samples. Such tumor sets are often small and lack clinical annotation, whereas formalin-fixed paraffin-embedded (FFPE) materials are abundant. Although RT-PCR-based methods from FFPE samples are finding clinical application, genome-wide microarray analysis has proven difficult. Here, we report expression profiling on RNA from 157 FFPE tumors. RNA was extracted from 2-to 8-year-old FFPE or frozen tumors of known and unknown histologies. Total RNA was analyzed, reverse-transcribed and used for the synthesis of labeled aRNA after two rounds of amplification. Labeled aRNA was hybridized to a 3 0 -based 22K spot oligonucleotide arrays, and compared to a labeled reference by two-color microarray analysis. After normalization, gene expression profiles were compared by unsupervised hierarchical clustering. Using this approach, at least 24% of unselected FFPE samples produced RNA of sufficient quality for microarray analysis. From our initial studies, we determined criteria based on spectrophotometric analyses and a novel TaqMan-based assay to predict which samples were of sufficient quality for microarray analysis before hybridization. These criteria were validated on an independent set of tumors with a 100% success rate (20 of 20). Unsupervised analysis of informative gene expression profiles distinguished tumor type and subtype, and identified tumor tissue of origin in three unclassified carcinomas. Although only a minority of FFPE blocks could be analyzed, we show that informative RNA expression analysis can be derived from selected FFPE samples.

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Section: Discussionmentioning

confidence: 99%

RNA expression analysis of formalin-fixed paraffin-embedded tumors

Penland

Keku

Torrice

et al. 2007

Laboratory Investigation

145

120

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“…Whole genome amplification of genomic DNA was performed before genotyping of the initial dataset using the GenomiPhi Amplification Kit (GE Healthcare, Little Chalfont, UK). 46 Single nucleotide polymorphisms with a genotype success rate o80% in the initial data set, MAFo0.05 or with unreliable genotype calling, were omitted, leaving 137 SNPs, in Hardy-Weinberg equilibrium, for statistical analyses. The average distance between the SNPs was 14 kb on the basis of the UCSC Genome Browser, May 2004 assembly (http://genome.ucsc.edu/).…”

Section: Genotypingmentioning

confidence: 99%

Reproducible association with type 1 diabetes in the extended class I region of the major histocompatibility complex

et al. 2009

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The high-risk human leukocyte antigen (HLA)-DRB1, DQA1 and DQB1 alleles cannot explain the entire type 1 diabetes (T1D) association observed within the extended major histocompatibility complex. We have earlier identified an association with D6S2223, located 2.3 Mb telomeric of HLA-A, on the DRB1*03-DQA1*0501-DQB1*0201 haplotype, and this study aimed to fine-map the associated region also on the DRB1*0401-DQA1*03-DQB1*0302 haplotype, characterized by less extensive linkage disequilibrium. To exclude associations secondary to DRB1-DQA1-DQB1 haplotypes, 205 families with at least one parent homozygous for these loci, were genotyped for 137 polymorphisms. We found novel associations on the DRB1*0401-DQA1*03-DQB1*0302 haplotypic background with eight single nucleotide polymorphisms (SNPs) located within or near the PRSS16 gene. In addition, association at the butyrophilin (BTN)-gene cluster, particularly the BTN3A2 gene, was observed by multilocus analyses. We replicated the associations with SNPs in the PRSS16 region and, albeit weaker, to the BTN3A2 region, in an independent material of 725 families obtained from the Type 1 Diabetes Genetics Consortium. It is important to note that these associations were independent of the HLA-DRB1-DQA1-DQB1 genes, as well as of associations observed at HLA-A, -B and -C. Taken together, our results identify PRSS16 and BTN3A2, two genes thought to play important roles in regulating the immune response, as potentially novel susceptibility genes for T1D.

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“…It has been used successfully by other groups, and has shown no detectable locus or allele bias. 21,22 We found that this method worked well for amplifying DNA from archival formalin-fixed, paraffin-embedded samples. Whole genome amplified DNA was purified using the Qiagen MinElute PCR purification kit (Qiagen), prior to LOH analysis.…”

Section: Whole Genome Amplificationmentioning

confidence: 99%

Molecular genetic evidence that endometriosis is a precursor of ovarian cancer

Prowse

Manek

Varma

et al. 2006

Intl Journal of Cancer

146

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Histopathology and epidemiology studies have consistently demonstrated a strong link between endometriosis and endometriosisassociated ovarian cancers (EAOCs)-in particular, the endometrioid and clear cell subtypes. However, it is still unclear whether endometriosis is a precursor to EAOCs, or whether there is an indirect link because similar factors predispose to both diseases. In order to search for evidence of clonal progression, we analyzed 10 EAOCs (endometrioid 5 4; clear cell 5 6) with coexisting endometriosis for common molecular genetic alterations in both the carcinoma and corresponding endometriosis. We used 82 microsatellite markers spanning the genome to examine loss of heterozygosity (LOH) in the coexisting carcinoma and endometriosis samples. A total of 63 LOH events were detected in the carcinoma samples; twenty two of these were also detected in the corresponding endometriosis samples. In each case, the same allele was lost in the endometriosis and cancer samples. Interestingly, no marker showed LOH in the endometriosis alone. These data provide evidence that endometriosis is a precursor to EAOCs. ' 2006 Wiley-Liss, Inc.

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Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel

Cited by 183 publications

References 24 publications

RNA expression analysis of formalin-fixed paraffin-embedded tumors

RNA expression analysis of formalin-fixed paraffin-embedded tumors

Reproducible association with type 1 diabetes in the extended class I region of the major histocompatibility complex

Molecular genetic evidence that endometriosis is a precursor of ovarian cancer

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