Efficient typing of copy number variations in a segmental duplication-mediated rearrangement hotspot using multiplex competitive amplification

Du, Renqian; Lu, Chuncheng; Jiang, Zhengwen; Li, Shilin; Ma, Ruixiao; An, Haijia; Xu, Miao; An, Yu; Xia, Yankai; Li, Jin; Wang, Xinru; Zhang, Feng

doi:10.1038/jhg.2012.66

Cited by 57 publications

(61 citation statements)

References 31 publications

(46 reference statements)

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“…The AccuCopy technique, a CNV genotyping method based on multiplex fluorescence competitive amplification, was recently developed by Genesky Biotechnologies (Shanghai, China), and is well described by Du et al (2012). We used this technology for quantitative analysis of copy numbers of all these eight gene families.…”

Section: Cnv Genotyping Using the Accucopy Methodsmentioning

confidence: 99%

“…The reference genome sequences were obtained from the UCSC Genome Browser (http://genome.ucsc.edu; genome assembly hg19). Additionally, three reference segments used for normalization were screened and chosen at three loci of POP1, RPP14 and TBX15 (Du et al, 2012). These three loci are housekeeping genes, and their copy numbers are stable across the population.…”

Section: Cnv Genotyping Using the Accucopy Methodsmentioning

confidence: 99%

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Gene copy number alterations in the azoospermia-associated AZFc region and their effect on spermatogenic impairment

Jiang

Zhang

et al. 2014

MHR: Basic Science of Reproductive Medicine

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abstract:The azoospermia factor c (AZFc) region in the long arm of human Y chromosome is characterized by massive palindromes. It harbors eight multi-copy gene families that are expressed exclusively or predominantly in testis. To assess systematically the role of the AZFc region and these eight gene families in spermatogenesis, we conducted a comprehensive molecular analysis (including Y chromosome haplogrouping, AZFc deletion typing and gene copy quantification) in 654 idiopathic infertile men and 781 healthy controls in a Han Chinese population. The b2/b3 partial deletion (including both deletion-only and deletion-duplication) was consistently associated with spermatogenic impairment. In the subjects without partial AZFc deletions, a notable finding was that the frequency of DAZ and/or BPY2 copy number alterations in the infertile group was significantly higher than in the controls. Combined patterns of DAZ and/or BPY2 copy number abnormality were associated with spermatogenic impairment when compared with the pattern of all AZFc genes with common level copies. In addition, in Y chromosome haplogroup O1 (Y-hg O1), the frequency of copy number alterations of all eight gene families was significantly higher in the case group than that in the control group. Our findings indicate that the DAZ, BPY2 genes may be prominent players in spermatogenesis, and genomic rearrangements may be enriched in individuals belonging to Y-hg O1. Our findings emphasize the necessity of routine molecular analysis of AZFc structural variation during the workup of azoospermia and/or oligozoospermia, which may diminish the genetic risk of assisted reproduction.

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Section: Cnv Genotyping Using the Accucopy Methodsmentioning

confidence: 99%

Section: Cnv Genotyping Using the Accucopy Methodsmentioning

confidence: 99%

Gene copy number alterations in the azoospermia-associated AZFc region and their effect on spermatogenic impairment

Jiang

Zhang

et al. 2014

MHR: Basic Science of Reproductive Medicine

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“…However, the sample size is relatively small and although the AccuCopy method used in the current study has been validated by a number of studies (25,38), accurately measuring CNV remains a technical challenge, which requires further investigation. …”

Section: Discussionmentioning

confidence: 99%

“…The sample/competitive (S/C) peak ratio was calculated for the two target segments and three reference segments. The reference segments were screened and selected at three loci of POLR2A, POP1, and RPP14 as described previously (25). The S/C ratio for each target fragment was first normalized based on three reference segments, respectively.…”

Section: Patientsmentioning

confidence: 99%

“…The primers for target segments were obtained from the GenBank database (www.ncbi.nlm.nih.gov/genbank) ( Table I). The copy numbers of FCGR3B were measured by a custom-by-design Multiplex AccuCopy kit (Genesky Biotech Co., Ltd., Shanghai, China) based on a multiplex fluorescence competitive polymerase chain reaction (PCR) principle as described previously (25). Data was produced according to the manufacturer's protocol.…”

Section: Patientsmentioning

confidence: 99%

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Low copy number of FCGR3B is associated with lupus nephritis in a Chinese population

Zheng

Gao

et al. 2017

Exp Ther Med

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Abstract. Lupus nephritis (LN) is a polygenic disease caused by an interaction between hereditary and environmental factors. Numerous gene copy number variations have been identified to contribute to this disease. Previously, immunoglobulin (Ig)G Fcγ receptor 3B (FCGR3B) copy number variation (CNV) was reported to be associated with LN in the Caucasian population. However, the effect of FCGR3B CNV on LN in the Chinese population remains unknown. The present study aimed to investigate whether CNVs of FCGR3B are associated with LN in the Henan Chinese population. FCGR3B CNVs were determined in 142 LN patients and 328 healthy controls. A modified methodology based on competitive polymerase chain reaction, a Multiplex AccuCopy™ kit was used to detect FCGR3B copy number. Clinical and laboratory data was collected retrospectively from medical records. To evaluate associations between FCGR3B CNVs and LN susceptibility, the present study calculated the odds ratios using a logistic regression analysis. The current study identified that the distribution of FCGR3B copy number was significantly different between LN and healthy controls (P=0.031). A low copy number (<2) of FCGR3B was significantly enriched in LN patients (P= 0.042), and was a risk factor for LN (odds ratio=2.059; 95% confidence interval, 1.081-3.921; P=0.028). However, a high copy number (>2) had no effect on LN. There were no associations between FCGR3B CNV and clinical phenotypes of LN. The results from the present study demonstrate that a low copy number of FCGR3B is a risk factor for LN in a Chinese population.

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16p11.2 deletion in patients with paroxysmal kinesigenic dyskinesia but without intellectual disability

Wang

et al. 2018

Brain and Behavior

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IntroductionMutations of the PRRT2 gene are the most common cause for paroxysmal kinesigenic dyskinesia. However, patients with negative PRRT2 mutations are not rare. The aim of this study is to determine whether copy number variant of PRRT2 gene is another potential pathogenic mechanism in the patients with paroxysmal kinesigenic dyskinesia with negative PRRT2 point and frameshift mutations.MethodsWe screened PRRT2 copy number variants using the AccuCopy™ method in 29 patients with paroxysmal kinesigenic dyskinesia with negative PRRT2 point and frameshift mutations. Next‐generation sequencing was used to determine the chromosomal deletion sites in patients with PRRT2 copy number variants, and to exclude mutations in other known causative genes for paroxysmal kinesigenic dyskinesia.ResultsTwo sporadic patients with negative PRRT2 point and frameshift mutations (6.9%) were identified to have de novo PRRT2 copy number deletions (591 and 832 Kb deletions located in 16p11.2). The two patients presented with pure paroxysmal kinesigenic dyskinesia and paroxysmal kinesigenic dyskinesia and benign infantile convulsions, respectively. They had normal intelligence and neuropsychiatric development, in contrast to those previously reported with 16p11.2 deletions complicated with neuropsychiatric disorders. No correlation between the deletion ranges and phenotypic variations was found.Conclusion16p11.2 deletions play causative roles in paroxysmal kinesigenic dyskinesia, especially for sporadic cases. Our findings extend the phenotype of 16p11.2 deletions to pure paroxysmal kinesigenic dyskinesia. Screening for 16p11.2 deletions should thus be included in genetic evaluations for patients with paroxysmal kinesigenic dyskinesia.

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Efficient typing of copy number variations in a segmental duplication-mediated rearrangement hotspot using multiplex competitive amplification

Cited by 57 publications

References 31 publications

Gene copy number alterations in the azoospermia-associated AZFc region and their effect on spermatogenic impairment

Gene copy number alterations in the azoospermia-associated AZFc region and their effect on spermatogenic impairment

Low copy number of FCGR3B is associated with lupus nephritis in a Chinese population

16p11.2 deletion in patients with paroxysmal kinesigenic dyskinesia but without intellectual disability

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