Methods to detect and analyze copy number variations at the genome-wide and locus-specific levels

Lee, Jeung Hee; Jeon, Jin-Tae

doi:10.1159/000184725

Cited by 26 publications

(17 citation statements)

References 105 publications

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“…It has been named as the “method of choice” for CNV analyses in spite of the limitations [10]–[12]. The current real-time qPCR methods for C4 CNV determination use the TaqMan® probing [13]–[15].…”

Section: Introductionmentioning

confidence: 99%

Copy Number Analysis of Complement C4A, C4B and C4A Silencing Mutation by Real-Time Quantitative Polymerase Chain Reaction

Paakkanen

Vauhkonen

Eronen³

et al. 2012

PLoS ONE

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Low protein levels and copy number variation (CNV) of the fourth component of human complement (C4A and C4B) have been associated with various diseases. High-throughput methods for analysing C4 CNV are available, but they commonly do not detect the most common C4A mutation, a silencing CT insertion (CTins) leading to low protein levels. We developed a SYBR® Green labelled real-time quantitative polymerase chain reaction (qPCR) with a novel concentration range approach to address C4 CNV and deficiencies due to CTins. This method was validated in three sample sets and applied to over 1600 patient samples. CTins caused C4A deficiency in more than 70% (76/105) of the carriers. Twenty per cent (76/381) of patients with a C4A deficiency would have been erroneously recorded as having none, if the CTins had not been assessed. C4A deficiency was more common in patients than a healthy reference population, (OR = 1.60, 95%CI = 1.02–2.52, p = 0.039). The number of functional C4 genes can be straightforwardly analyzed by real-time qPCR, also with SYBR® Green labelling. Determination of CTins increases the frequency of C4A deficiency and thus helps to elucidate the genotypic versus phenotypic disease associations.

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Section: Introductionmentioning

confidence: 99%

Copy Number Analysis of Complement C4A, C4B and C4A Silencing Mutation by Real-Time Quantitative Polymerase Chain Reaction

Paakkanen

Vauhkonen

Eronen³

et al. 2012

PLoS ONE

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“…A quantitative oligonucleotide ligation assay (qOLA_CNV; Lee and Jeon, 2008) and a pyrosequencing method (Pyro_Splice; Pielberg et al, 2003) were applied to analyze KIT CNV. A genotype definition for each individual was performed using both grouping observations on a scatter plot and clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package (Seo et al, 2007).…”

Section: Analysis Of the Genotypes Of Kit And Mc1rmentioning

confidence: 99%

Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

et al. 2011

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The roan coat color is characterized by white hairs intermingled with colored hairs. Candidate genes based on comparative phenotypes in horses and cattle involve the KIT and KIT ligand (MGF) genes. Here, we report the result of the whole genome scanning to detect genomic regions responsible for the roan coat color, using a three-generation pedigree of 62 pigs in an intercross between Landrace and Korean native pig. These pigs were genotyped using the PorcineSNP 60 BeadChip (Illumina, USA). The whole genome scan indicated that three genomic regions, 35~36 Mb, 38~39 Mb, and 58~59 Mb on SSC8, were commonly and highly associated/linked with the roan phenotype in the case/control, sib-pair, and linkage test, respectively. The porcine KIT was selected as a candidate gene, because it is located in one of the three significant regions and its function is related to coat color formation. SNPs and Indels within coding sequence (CDS), promoter, and 3'-UTR of KIT were surveyed. Twenty-two SNPs in the CDS reported previously, as well as nine variations in promoter (2 SNPs) and 3'-UTR (5 SNPs and 2 Indels) were detected. Although no causative mutations were identified, these results will help to elucidate the genetic mechanisms involved in the expression of the roan phenotype and will aid in identifying key mutations responsible for the roan phenotype in further studies.

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“…This assay uses an array of probes where differentially labeled test and reference DNA are jointly hybridized to the array [36,37]. Detection of CNV is based on the intensity ratio of the labeled probes.…”

Section: Introductionmentioning

confidence: 99%

The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges

Hoh

Yusoff

2013

Mol Cytogenet

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The ultimate goal of human genetics is to understand the role of genome variation in elucidating human traits and diseases. Besides single nucleotide polymorphism (SNP), copy number variation (CNV), defined as gains or losses of a DNA segment larger than 1 kb, has recently emerged as an important tool in understanding heritable source of human genomic differences. It has been shown to contribute to genetic susceptibility of various common and complex diseases. Despite a handful of publications, its role in cardiovascular diseases remains largely unknown. Here, we deliberate on the currently available technologies for CNV detection. The possible utility and the potential roles of CNV in exploring the mechanisms of cardiac remodeling in hypertension will also be addressed. Finally, we discuss the challenges for investigations of CNV in cardiovascular diseases and its possible implications in diagnosis of hypertension-related left ventricular hypertrophy (LVH).

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Methods to detect and analyze copy number variations at the genome-wide and locus-specific levels

Cited by 26 publications

References 105 publications

Copy Number Analysis of Complement C4A, C4B and C4A Silencing Mutation by Real-Time Quantitative Polymerase Chain Reaction

Copy Number Analysis of Complement C4A, C4B and C4A Silencing Mutation by Real-Time Quantitative Polymerase Chain Reaction

Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges

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