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Curr Protoc Hum Genet. 2017 Jul 11;94:8.17.1-8.17.16. doi: 10.1002/cphg.43.

Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing.

Dong Z1,2,3, Xie W3,4, Chen H3,4, Xu J3,4, Wang H1,2,5, Li Y3,4, Wang J3,4, Chen F3,4, Choy KW1,2,6, Jiang H3,4.

Author information

1
Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.
2
Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
3
BGI-Shenzhen, Shenzhen, China.
4
China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.
5
Bao'an Maternal and Child Health Hospital, Shenzhen, China.
6
The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China.

Abstract

Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage and the lengthy turn-around time is not ideal for clinical implementation. In addition, the demand for computational resources also reduces the probability of clinical integration into each laboratory. Herein, a protocol providing CNV detection from low-pass, whole-genome sequencing (0.25×) in a clinical laboratory setting is described. The cost is reduced to less than $200 USD per sample and the turn-around time is within an acceptable clinically workable time-frame (7 days).

KEYWORDS:

copy-number variants; low-pass whole-genome sequencing

PMID:
28696555
DOI:
10.1002/cphg.43
[Indexed for MEDLINE]

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