Whole genome amplification in preimplantation genetic diagnosis

Zheng, Yi; Wang, Ning; Li, Lei; Jin, Fan

doi:10.1631/jzus.b1000196

Cited by 54 publications

(37 citation statements)

References 85 publications

(98 reference statements)

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“…In the WGA-treated cell, no restriction sites were found in the other three undetected variants. The reason for these missing amplifications as observed in other studies, may be related to the procedural difficulties in the use of the kit, or to the WGA procedure itself (29)(30)(31). Conversely, using our methodological approach, in WGA-untreated CTCs we identified the same 10 variants as in the SK-MEL-28 pellet.…”

Section: Discussionsupporting

confidence: 50%

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

Palmirotta

Lovero

Silvestris

et al. 2017

CGP

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Section: Discussionsupporting

confidence: 50%

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

Palmirotta

Lovero

Silvestris

et al. 2017

CGP

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“…Both preferential amplification and allele dropout are known problems accompanying whole genome amplification, 33 as all mutations have been verified on the original (unamplified) DNA, false-positive cases have been excluded. The lower-positive test rate can also be explained by the fact that a cardiac anomaly was the most common (60%) indication for testing in this study group.…”

Section: Discussionmentioning

confidence: 99%

Prenatal diagnostic testing of the Noonan syndrome genes in fetuses with abnormal ultrasound findings

et al. 2013

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In recent studies on prenatal testing for Noonan syndrome (NS) in fetuses with an increased nuchal translucency (NT) and a normal karyotype, mutations have been reported in 9-16% of cases. In this study, DNA of 75 fetuses with a normal karyotype and abnormal ultrasound findings was tested in a diagnostic setting for mutations in (a subset of) the four most commonly mutated NS genes. A de novo mutation in either PTPN11, KRAS or RAF1 was detected in 13 fetuses (17.3%). Ultrasound findings were increased NT, distended jugular lymphatic sacs (JLS), hydrothorax, renal anomalies, polyhydramnios, cystic hygroma, cardiac anomalies, hydrops fetalis and ascites. A second group, consisting of anonymized DNA of 60 other fetuses with sonographic abnormalities, was tested for mutations in 10 NS genes. In this group, five possible pathogenic mutations have been identified (in PTPN11 (n ¼ 2), RAF1, BRAF and MAP2K1 (each n ¼ 1)). We recommend prenatal testing of PTPN11, KRAS and RAF1 in pregnancies with an increased NT and at least one of the following additional features: polyhydramnios, hydrops fetalis, renal anomalies, distended JLS, hydrothorax, cardiac anomalies, cystic hygroma and ascites. If possible, mutation analysis of BRAF and MAP2K1 should be considered.

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“…It uses the same primer pairs and cycling parameters for both stages of the protocol [6,7,[16][17][18][19][20].…”

Section: Discussionmentioning

confidence: 99%

A Simple Two-Stage PCR Method for Quality Amplification of Degenerate DNA

O¹

2015

Int J Cancer Clin Res

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Formalin-fixed, paraffin-embedded (FFPE) tissue banks are invaluable to cancer genetics and biomarker discovery. However, FFPE tissue-derived DNA is degenerate. As such, any PCR technique which will give adequate amplification of such DNA to enable downstream applications is important to the characterization of genetic biomarkers and to personalized medicine. The aim of this article is to describe a two-stage PCR method which efficiently amplifies degenerate FFPE tissue-derived DNA. Ampliconenriched templates were produced by a first-stage multiplex PCR which used five or more primer pairs with similar annealing temperature. Subsequently, the enriched products were used as templates for a singleplex PCR which utilized the same PCR cycling parameters and primer pairs as in the multiplex PCR. We compared the amplification of FFPE-derived and cell line DNA by this new protocol and the conventional PCR using the percentage of samples that achieved amplification at a cycle threshold (ct) of 30 or less, the mean of ct values obtained at the end of PCR, as well as our devised amplification efficiency test. Furthermore we compared the amplification of FFPE DNA using this present protocol and the Quick Multiplex Consensus-PCR (QMC-PCR) protocol on the fast programme of the ABI 7500 Fast Real Time PCR instrument. The present two-stage protocol has better sensitivity and amplification efficiency than the conventional PCR in amplifying degenerate DNA templates; and it also amplifies DNA better than the QMC-PCR protocol in fast cycling Real Time PCR programmes.

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Whole genome amplification in preimplantation genetic diagnosis

Cited by 54 publications

References 85 publications

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

Prenatal diagnostic testing of the Noonan syndrome genes in fetuses with abnormal ultrasound findings

A Simple Two-Stage PCR Method for Quality Amplification of Degenerate DNA

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