A Robust Approach for Blind Detection of Balanced Chromosomal Rearrangements with Whole-Genome Low-Coverage Sequencing

Dong, Zirui; Jiang, Lupin; Yang, Chuanchun; Hu, Hua; Wang, Xiuhua; Chen, Haixiao; Choy, Kwong Wai; Hu, Huamei; Dong, Yaping; Hu, Bin; Xu, Jie; Yang, Lei; Cao, Sujie; Chen, Hui; Wang, Wenjing; Jiang, Hui; Xu, Fengping; Yao, Hong; Xu, Xun; Liang, Zhiqing

doi:10.1002/humu.22541

Cited by 74 publications

(125 citation statements)

References 29 publications

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“…Next-generation sequencing has been reported to detect Balanced chromosomal rearrangement (BCA)-associated breakpoints with the aid of karyotyping. More recently, research reports demonstrated that low-coverage whole-genome sequencing has been applied to characterize chromosome structural variations with a high resolution, using different sequencing platform [28-31]. Our study results proved low-coverage whole-genome sequencing possesses significant advantages over conventional cytogenetic techniques once again.…”

Section: Discussionsupporting

confidence: 57%

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Clinical and genomic evaluation of a Chinese patient with a novel deletion associated with Phelan-McDermid syndrome

Lei

Banerjee

et al. 2016

Oncotarget

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Phelan–McDermid syndrome is a neurodevelopmental disorder caused by the terminal deletion of chromosome 22 (22q13) followed by the loss of function of the SHANK3 gene. Various terminal deletions of chromosome 22q13 are associated with Phelan–McDermid with a spectrum of phenotypic severity. Here, we have done a clinical molecular study of a Chinese proband with Phelan–McDermid syndrome. Both the proband and her younger brother are associated with this syndrome while their parents are phenotypically normal. We used a karyotype in order to detect the genotype of the proband and her younger brother. We have also used whole genome low-coverage paired-end next generation sequencing to determine whether the parent is the carrier of translocation with terminal 22q13 deletions. We found that both proband and her younger brother are comprises of a novel deletion of 22q13.31q13.33, harboring genes were associated with several clinical phenotype such as severity of speech delay, neonatal hypotonia, delayed in age of walking, male genital anomalies, dysplastic toenails, large and fleshy hands, macrocephaly, short stature, facial asymmetry, and atypical reflexes. Probands and her younger brother inherited this translocation from their mother whereas their father is genotypically normal. In conclusion, our present study expands the deletion spectrum and report a novel deletion associated with Phelan–McDermid syndrome.

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Section: Discussionsupporting

confidence: 57%

“…DNA samples from the proband, proband's younger brother and their parents were tested using a whole genome low-coverage paired-end NGS as described previously [32, 33]. …”

Section: Methodsmentioning

confidence: 99%

Clinical and genomic evaluation of a Chinese patient with a novel deletion associated with Phelan-McDermid syndrome

Lei

Banerjee

et al. 2016

Oncotarget

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“…The library concentration was measured by quantitative PCR, and libraries with index tags were sequenced by Illumina HiSeq 2000 platform. Data analysis was performed through the following steps: (1) removal of the reads of adaptors and low-quality reads; (2) alignment of the reads to hg19 or GRCh37.1; and (3) translocation discovery, chimeric read-pair inputs for T-CHR (an in-house software [10]), analysis of clustering by locations, removal of PCR duplicates, and four steps of filtration [10]. …”

Section: Methodsmentioning

confidence: 99%

BMPR1Bmutation causes Pierre Robin sequence

et al. 2017

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BackgroundWe investigated a large family with Pierre Robin sequence (PRS).Aim of the studyThis study aims to determine the genetic cause of PRS.ResultsThe reciprocal translocation t(4;6)(q22;p21) was identified to be segregated with PRS in a three-generation family. Whole-genome sequencing and Sanger sequencing successfully detected breakpoints in the intragenic regions of BMRP1B and GRM4. We hypothesized that PRS in this family was caused by (i) haploinsufficiency for BMPR1B or (ii) a gain of function mechanism mediated by the BMPR1B-GRM4 fusion gene. In an unrelated family, we identified another BMPR1B-splicing mutation that co-segregated with PRS.ConclusionWe detected two BMPR1B mutations in two unrelated PRS families, suggesting that BMPR1B disruption is probably a cause of human PRS.MethodsGTG banding, comparative genomic hybridization, whole-genome sequencing, and Sanger sequencing were performed to identify the gene causing PRS.

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“…These are very low numbers compared with approximately 28 998 tests and 258 laboratories available in the United States. It is partly due to under-reporting as some laboratories in China such as the Shenzhen Birth Defect Screening Project Lab (Dong et al 2014) are not included on the list.…”

Section: Integrated Genetic/genomics Services In Hong Kong Taiwan Anmentioning

confidence: 99%

Genomics education in nursing in Hong Kong, Taiwan and Mainland China

Waye

Calzone

Chan

2019

International Nursing Review

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Aim: To identify issues and challenges of genomics education in Hong Kong, Taiwan and Mainland China. Background: The use of genetics/genomics in health care, such as genetic testing, pharmacogenomics and tumour profiling in the context of cancer, is increasing. The rapid application of genetics/genomics in clinical practice requires healthcare providers to be competent to practise genetics-related patient care. Sources of evidence: We reviewed current practices in genomics education in nursing in Hong Kong, Taiwan and Mainland China, including the opportunities for nurses to advance their knowledge and recommendations to incorporate genomics education in the nursing curriculum in these regions. Findings: While many citizens and health professionals recognize the importance of new and exciting research areas of genomics/genetics, there are still many gaps in the translation of genetic/genomic medicine into clinical practice. There is also a similar lack of genetics professionals in China. Conclusion: Hong Kong, Taiwan and Mainland China face challenges in promoting genetic education in nursing. A strategic approach in a coordinated effort ineffectively translating genomic knowledge into healthcare practice should be established in these three regions. Implications for nursing and policy: Nursing educators in Hong Kong, Taiwan and Mainland China should link with the international nursing community (e.g. Global Genomics Nursing Alliance) and form closer networks to improve education in the area of genetics and genomics. From a policy level, genomics education is suggested to be incorporated in nursing curriculum to enhance nurses’ competency in incorporating genetics/genomics service into patient care.

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A Robust Approach for Blind Detection of Balanced Chromosomal Rearrangements with Whole-Genome Low-Coverage Sequencing

Cited by 74 publications

References 29 publications

Clinical and genomic evaluation of a Chinese patient with a novel deletion associated with Phelan-McDermid syndrome

Clinical and genomic evaluation of a Chinese patient with a novel deletion associated with Phelan-McDermid syndrome

BMPR1Bmutation causes Pierre Robin sequence

Genomics education in nursing in Hong Kong, Taiwan and Mainland China

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