A comparison between SNaPshot, pyrosequencing, and biplex invader SNP genotyping methods: accuracy, cost, and throughput

Pati, Nirupma; Schowinsky, Valerie; Kokanovic, Obrad; Magnuson, Victoria L.; Ghosh, Soumitra

doi:10.1016/j.jbbm.2003.11.005

Cited by 63 publications

(40 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Samples with high missing genotype call rate (44%, n ¼ 401), high heterozygosity (430%, n ¼ 11) and gender inconsistencies (n ¼ 41), and those obtained from individuals who had developed any kind of cancer (n ¼ 101) were excluded from subsequent analyses along with related or identical individuals whose computed average pairwise identity-by-state (IBS) value was higher than that estimated from first-degree relatives of Korean sibpair samples (40.80, n ¼ 601). Samples whose genotype-inferred sex disagreed with clinical records were re-tested for sex confirmation using the SNaPshot Multiplex System (Applied Biosystems) 24 . The methods to estimate heterozygosity and IBS have been described elsewhere 3 .…”

Section: Methodsmentioning

confidence: 99%

A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits

et al. 2009

View full text Add to dashboard Cite

Section: Methodsmentioning

confidence: 99%

A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits

et al. 2009

View full text Add to dashboard Cite

“…False negative results can occur due to sparse amount of tumor tissue below the detection limit. Incorrectly detected genotypes are rare (<1%) with this method which produces rarely (<2%) different genotypes in separate runs (41). The method has numerous advantages; it is fast, sensitive-tolerating a mix of normal and small quantities of tumor tissue, and can be assessed on routine paraffin sections evading the need for frozen tumor specimens and microdissection.…”

Section: Pik3ca Mutation Detection Methodologymentioning

confidence: 99%

PIK3CA Mutations May Be Discordant between Primary and Corresponding Metastatic Disease in Breast Cancer

Jensen

Laenkholm

Knoop

et al. 2011

Clinical Cancer Research

178

106

View full text Add to dashboard Cite

Purpose: PIK3CA mutations are frequent in breast cancer and activate the PI3K/Akt pathway. Unexpectedly, PIK3CA mutation appears in general to be associated with better outcome. In a cohort of patients where both primary and metastatic lesions were available, the objective was to assess changes in PIK3CA mutations. We wished to discern whether selective pressures occur and the influence of PIK3CA mutation on time to recurrence.Experimental Design: Formalin-fixed paraffin-embedded tumor blocks were obtained from 104 patients with paired samples from primary tumors and corresponding asynchronous metastatic breast tumors. Samples were analyzed for PIK3CA mutations (exons 9 and 20) as well as immunohistochemical evaluation for PTEN, pAKT, Ki67, ER, and HER2.Results: PIK3CA mutation was detected in 45% of the primary tumors. Overall, there was a net gain in mutation in metastatic disease, to 53%; nonetheless, there were instances where metastases were wild type in patients with PIK3CA mutant primary tumors. Laser capture microdissection on a subset of cases revealed microheterogeneity for PIK3CA mutational status in the primary tumor. PIK3CA mutants overall showed a significantly longer time to first recurrence than wild type cases (P ¼ 0.03).Conclusion: PIK3CA mutations occur at high frequency in primary and metastatic breast cancer; these may not necessarily confer increased aggressiveness as mutants had a longer time to recurrence. Because PIK3CA status quite frequently changes between primary and metastatic disease, it emphasizes the necessity of assessing the PIK3CA status in the metastatic lesion for selection of PIK3CA inhibitor therapy. Clin Cancer Res; 17(4); 667-77. Ó2010 AACR.

show abstract

“…Here, we describe a method which is both precise and relatively cost-effective, based on the SNaPshot assay (Pati et al 2004). Our aim was to apply this assay to a range of Czech spring malting barleys to track relevant allele frequencies over time in the local malting barley breeding genepool.…”

Section: Introductionmentioning

confidence: 99%

Haplotyping barley bmy1 using the SNaPshot assay

et al. 2010

View full text Add to dashboard Cite

Abstract:The allelic status at bmy1, which encodes the enzyme β-amylase 1 in the barley grain, has an important influence over a cultivar's malting quality. Changes in the malting process have been responsible for the need to improve the thermostability of this enzyme. We have compared a published bmy1 haplotyping assay based on TDI-FRET (templatedirected dye-terminator incorporation fluorescence resonance energy transfer) with a SNaPshot protocol by jointly analysing a set of 21 cultivars of known haplotype. The two methods gave the same result, but the SNaPshot assay was easier to interpret. The SNaPshot assay was therefore used to haplotype the Czech malting barley core collection with respect to bmy1. The old Czech cultivar Kasticky was the only entry identified as carrying the high thermostability haplotype, with the remainder carrying either the intermediate or the low thermostability haplotypes. Older materials were the most variable in terms of bmy1 haplotype, but the majority carried the intermediate type. Most of the descendants of cv. Diamant carried the low thermostability haplotype. The most recently released cultivars recommended for the brewing of Czech beer tend to carry the intermediate allele.

show abstract

A comparison between SNaPshot, pyrosequencing, and biplex invader SNP genotyping methods: accuracy, cost, and throughput

Cited by 63 publications

References 29 publications

A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits

A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits

PIK3CA Mutations May Be Discordant between Primary and Corresponding Metastatic Disease in Breast Cancer

Haplotyping barley bmy1 using the SNaPshot assay

Contact Info

Product

Resources

About